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not annotated - annotated - LINNAEUS only
Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge.
A novel methane-producing archaeon, strain SMSP(T), was isolated from an anaerobic, propionate-degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket (UASB) reactor used to treat a beer brewery effluent. Cells were non-motile, blunt-ended, straight rods, 1.0-2.6 mum long by 0.5 mum wide; cells were sometimes up to 7 mum long. Asymmetrical cell division was observed in rod-shaped cells. Coccoid cells (0.5-1.0 mum in diameter) were also observed in mid- to late-exponential phase cultures. Growth was observed between 10 and 40 ^0C (optimum, 30-33 ^0C) and pH 7.0 and 7.6 (optimum, pH 7.4). The G+C content of the genomic DNA was 56.2 mol%. The strain utilized formate and hydrogen for growth and methane production. Based on comparative sequence analyses of the 16S rRNA and mcrA (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-producing pathway) genes, strain SMSP(T) was affiliated with group E1/E2 within the order Methanomicrobiales. The closest relative based on both 16S rRNA and mcrA gene sequences was Methanoregula boonei 6A8(T) (96.3 % 16S rRNA gene sequence similarity, 85.4 % deduced McrA amino acid sequence similarity). The percentage of 16S rRNA gene sequence similarity indicates that strain SMSP(T) and Methanoregula boonei 6A8(T) represent different species within the same genus. This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range. Based on these genetic and phenotypic properties, we propose that strain SMSP(T) represents a novel species of the genus Methanoregula, for which we propose the name Methanoregula formicica sp. nov., with the type strain SMSP(T) (=NBRC 105244(T) =DSM 22288(T)).
not annotated - annotated - LINNAEUS only
Characterizing the role of the microtubule binding protein Bim1 in Cryptococcus neoformans.
During sexual development the human fungal pathogen Cryptococcus neoformans undergoes a developmental transition from yeast-form growth to filamentous growth. This transition requires cellular restructuring to form a filamentous dikaryon. Dikaryotic growth also requires tightly controlled nuclear migration to ensure faithful replication and dissemination of genetic material to spore progeny. Although the gross morphological changes that take place during dikaryotic growth are largely known, the molecular underpinnings that control this process are uncharacterized. Here we identify and characterize a C. neoformans homolog of the Saccharomyces cerevisiae BIM1 gene, and establish the importance of BIM1 for proper filamentous growth of C. neoformans. Deletion of BIM1 leads to truncated sexual development filaments, a severe defect in diploid formation, and a block in monokaryotic fruiting. Our findings lead to a model consistent with a critical role for BIM1 in both filament integrity and nuclear congression that is mediated through the microtubule cytoskeleton.
not annotated - annotated - LINNAEUS only
Serinicoccus profundi sp. nov., an actinomycete isolated from deep-sea sediment, and emended description of the genus Serinicoccus.
A Gram-reaction-positive bacterial strain of the genus Serinicoccus, designated MCCC 1A05965(T), was isolated from a deep-sea (5368 m) sediment of the Indian Ocean. Comparison of 16S rRNA gene sequences revealed that the isolate shared 97.6 % sequence similarity with Serinicoccus marinus JC1078(T), the type strain of the only described species of the genus Serinicoccus. The DNA-DNA relatedness between these two strains was 46.2 % (standard deviation 1.86 %). The cell wall contained alanine, glycine, serine, l-ornithine and glutamic acid, which corresponds to the description of the genus Serinicoccus. The acyl type of the glycan chain of the peptidoglycan was glycolyl. Other characteristics of strain MCCC 1A05965(T) were consistent with those of the genus Serinicoccus. Cells were coccoid, moderately halophilic, oxidase-negative, catalase-positive and non-spore-forming. The major menaquinone was MK-8(H(4)). The predominant cellular fatty acids were iso-C(15 : 0) (34.7 %) and iso-C(16 : 0) (17.0 %). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glycolipid. The DNA G+C content was 72 mol%. Strain MCCC 1A05965(T) (=0714S6-1(T) =DSM 21363(T) =CGMCC 4.5582(T)) is assigned as the type strain of a novel species, for which the name Serinicoccus profundi sp. nov. is proposed.
not annotated - annotated - LINNAEUS only
Proposal of Mingxiaea gen. nov. for the anamorphic basidiomycetous yeast species in the Bulleribasidium clade (Tremellales) based on molecular phylogenetic analysis, with six new combinations and four novel species.
The distinction and monophyletic property of the basidiomycetous yeast species in the Bulleribasidium clade of the order Tremellales was resolved by molecular phylogenetic analysis based on the combined sequences of the 18S rRNA gene, internal transcribed spacer (ITS) region including 5.8S rRNA gene and 26S rRNA gene D1/D2 domain. The addition to the clade of new anamorphic species identified among ballistoconidium-forming yeasts isolated from China confirmed and strengthened the separation of this clade from other clades or lineages in the order Tremellales. A new anamorphic genus, Mingxiaea gen. nov. (type species Mingxiaea variabilis comb. nov.) is therefore proposed to accommodate the anamorphic species in the Bulleribasidium clade. Six new combinations are proposed for the described species of this clade which were formerly assigned to the genus Bullera. Four novel species in the new genus were identified among 16 ballistoconidium-forming yeast strains isolated from plant leaves collected in Hainan province, southern China, by D1/D2 and ITS sequence analyses. The novel species are described as Mingxiaea sanyaensis sp. nov. (type strain SY-3.23(T) =AS 2. 3623(T) =CBS 11408(T)), Mingxiaea hainanensis (type strain WZS-8.13(T) =AS 2.4161(T) =CBS 11409(T)), Mingxiaea foliicola (type strain WZS-8.14(T) =AS 2.3518(T) =CBS 11407(T)) and Mingxiaea wuzhishanensis (type strain WZS-29.8(T) =AS 2.4163(T) =CBS 11411(T)).
not annotated - annotated - LINNAEUS only
Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata.
Six strains of anaerobic, pleomorphic Gram-positive bacilli, isolated from the human oral cavity and an infected arm wound, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed that the isolates were most closely related to Scardovia inopinata CCUG 35729(T) (94.8-94.9 % 16S rRNA gene sequence similarity). The isolates were saccharolytic and produced acetic and lactic acids as end products of fermentation. The major fatty acids were C(16 : 0) (49.8 %) and C(18 : 1)omega9c (35.8 %). Polar lipid analysis revealed a variety of glycolipids, diphosphatidylglycerol, an unidentified phospholipid and an unidentified phosphoglycolipid. No respiratory quinones were detected. The peptidoglycan was of the type A4alpha L-Lys-Thr-Glu, with L-lysine partially replaced by L-ornithine. The DNA G+C content of one of the strains, C1A_55(T)(,) was 55 mol%. A novel species, Scardovia wiggsiae sp. nov., is proposed to accommodate the six isolates, with the type strain C1A_55(T) (=DSM 22547(T)=CCUG 58090(T)).
not annotated - annotated - LINNAEUS only
Flavobacterium ponti sp. nov., isolated from seawater.
A Gram-stain-negative, non-flagellated, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated GSW-R14(T), was isolated from seawater of Geoje Island in the South Sea, Korea. Strain GSW-R14(T) grew optimally at 25 ^0C, at pH 7.0-8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GSW-R14(T) belonged to the genus Flavobacterium, joining Flavobacterium gelidilacus LMG 21477(T) by a bootstrap resampling value of 100 %. Strain GSW-R14(T) exhibited 97.6 % 16S rRNA gene sequence similarity to F. gelidilacus LMG 21477(T) and similarities of 91.2-95.2 % to other members of the genus Flavobacterium. Strain GSW-R14(T) contained MK-6 as the predominant menaquinone. The fatty acid profile of strain GSW-R14(T) was similar to that of F. gelidilacus LMG 21477(T). The DNA G+C content of strain GSW-R14(T) was 31.4 mol% and its DNA-DNA relatedness with F. gelidilacus LMG 21477(T) was 31 %. Strain GSW-R14(T) could be distinguished from F. gelidilacus and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. On the basis of these data, strain GSW-R14(T) is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium ponti sp. nov. is proposed; the type strain is GSW-R14(T) (=KCTC 22802(T) =CCUG 58402(T)).
not annotated - annotated - LINNAEUS only
Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost.
A thermophilic, Gram-positive bacterium that formed a branched vegetative mycelium was isolated from compost. The strain, designated I3(T), grew at temperatures between 35 and 62 ^0C, with optimum growth at 50-55 ^0C. No growth was observed below 29 ^0C or above 65 ^0C. The pH range for growth was 5.7-10.0, the pH for optimum growth was 7.0 and no growth was observed below pH 5.6 or above pH 10.8. The DNA G+C content of strain I3(T) was 69.2 mol%. The major fatty acids found were C(15 : 0) iso (14.2 %), C(15 : 0) anteiso (12.1 %), C(17 : 0) iso (16.3 %) and C(17 : 0) anteiso (21.7 %). The major menaquinones were MK-9(H(4)), MK-10(H(4)) and MK-11(H(4)). The cell wall contained glutamic acid, glycine, alanine and ll-diaminopimelic acid in a molar ratio of 1.0 : 3.9 : 0.6 : 0.5. The polar lipids consisted of ninhydrin-positive phosphoglycolipids, phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The cell-wall sugars were rhamnose and arabinose. 16S rRNA gene sequence analysis assigned this actinomycete to the family Nocardioidaceae, but its 16S rRNA gene sequence shared no more than 95.5 % similarity with those of other members of the family. The chemotaxonomic and phenotypic characteristics of strain I3(T) differed in some respects from those of members of the genus Actinopolymorpha, the most closely related genus. Therefore, strain I3(T) represents a novel species in a new genus of the family Nocardioidaceae, for which the name Thermasporomyces composti gen. nov., sp. nov. is proposed. The type strain of the type species is I3(T) (=JCM 16421(T)=DSM 22891(T)).
not annotated - annotated - LINNAEUS only
Phycicoccus cremeus sp. nov., isolated from forest soil, and emended description of the genus Phycicoccus.
A bacterial strain, designated V2M29(T), was isolated from forest soil collected in the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M29(T) were Gram-positive, rod-shaped (0.5-0.8 mum in diameter and 1.5-2.0 mum in length), strictly aerobic and non-motile. Colonies produced on R2A agar plates were creamy, smooth, circular and 0.3-0.8 mm in diameter. Strain V2M29(T) grew at 14-35 ^0C (optimum, 29 ^0C), at pH 4.1-10.0 (optimum, pH 7.0-8.0) and in the presence of 0-7.0 % (w/v) NaCl (optimum, 0-2.0 %). Strain V2M29(T) contained MK-8(H(4)) as the major respiratory quinone and iso-C(15 : 0) (20.9 %), iso-C(16 : 0) (18.5 %), C(17 : 1)omega8c (16.7 %) and 10-methyl-C(17 : 0) (9.2 %) as the major cellular fatty acids. The cell-wall peptidoglycan type was based on meso-2,6-diaminopimelic acid and the acyl type of the muramic acid was acetyl. Diphosphatidylglycerol, phosphatidylinositol and six unknown glycolipids were the major polar lipids. The G+C content of the DNA was 72.0 mol% (T(m)). 16S rRNA gene sequence analysis indicated that strain V2M29(T) was phylogenetically related to members of the genus Phycicoccus, with sequence similarities ranging from 96.6-97.8 %. The DNA-DNA relatedness values of strain V2M29(T) to Phycicoccus dokdonensis DS-8(T) and Phycicoccus bigeumensis DSM 19264(T) were 32.5+/-3.3 % and 29.2+/-2.3 %, respectively. Based on these results, it is concluded that strain V2M29(T) represents a novel species of the genus Phycicoccus, for which the name Phycicoccus cremeus sp. nov. is proposed, with V2M29(T) (=CGMCC 1.6963(T) =NBRC 104261(T)) as the type strain.
not annotated - annotated - LINNAEUS only
Streptomyces hyderabadensis sp. nov., an actinomycete isolated from soil.
A novel actinomycete, designated strain OU-40(T), was isolated from farm soil collected from the Hyderabad region of Andhra Pradesh, southern India. The strain was found to have morphological and chemotaxonomic characteristics typical of species of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain OU-40(T) belonged to the genus Streptomyces, and was related most closely to Streptomyces pactum NBRC 13433(T) (99.0 % sequence similarity), Streptomyces olivaceus NBRC 12805(T) (99.0 %) and Streptomyces parvulus NBRC 13193(T) (98.8 %). Strain OU-40(T) could be distinguished from the type strains of its closest phylogenetic relatives based on levels of DNA-DNA relatedness and comparison of morphological and phenotypic data. It is therefore concluded that strain OU-40(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces hyderabadensis sp. nov. is proposed. The type strain is OU-40(T) (=CCTCC AA 209024(T) =PCM 2692(T)).
not annotated - annotated - LINNAEUS only
Gordonia humi sp. nov., isolated from soil.
A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301(T)) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301(T) was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6 % similarity), Gordonia terrae (97.5 %), Gordonia amarae (97.5 %) and Gordonia malaquae (97.4 %). The quinone system was determined to consist predominantly of menaquinone MK-9(H(2)), minor amounts of MK-8(H(2)) and MK-7(H(2)). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C(16 : 1) cis9, C(16 : 0), C(18 : 1) and tuberculostearic acid (10-methyl C(18 : 0)), supported the affiliation of strain CC-12301(T) to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301(T) from the most closely related Gordonia species. Strain CC-12301(T) therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301(T) (=DSM 45298(T) =CCM 7727(T)).
not annotated - annotated - LINNAEUS only
Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog.
A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8(T), was isolated from an acidic (pH 4.0-4.5) and ombrotrophic (rain-fed) bog located near Ithaca, NY, USA. Cultures were dimorphic, containing thin rods (0.2-0.3 mum in diameter and 0.8-3.0 mum long) and irregular cocci (0.2-0.8 mum in diameter). The culture utilized H(2)/CO(2) to produce methane but did not utilize formate, acetate, methanol, ethanol, 2-propanol, butanol or trimethylamine. Optimal growth conditions were near pH 5.1 and 35 ^0C. The culture grew in basal medium containing as little as 0.43 mM Na(+) and growth was inhibited completely by 50 mM NaCl. To our knowledge, strain 6A8(T) is one of the most acidiphilic (lowest pH optimum) and salt-sensitive methanogens in pure culture. Acetate, coenzyme M, vitamins and yeast extract were required for growth. It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov. The type strain of Methanoregula boonei is 6A8(T) (=DSM 21154(T) =JCM 14090(T)).
not annotated - annotated - LINNAEUS only
Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida).
A Gram-negative, aerobic bacterium, designated R-40509(T), was isolated from mucus of the reef builder coral (Mussismilia hispida) located in the Sao Sebastiao Channel, Sao Paulo, Brazil. The strain was oxidase-positive and catalase-negative, and required Na(+) for growth. Its phylogenetic position was in the genus Marinobacterium and the closest related species were Marinobacterium sediminicola, Marinobacterium maritimum and Marinobacterium stanieri; the isolate exhibited 16S rRNA gene sequence similarities of 97.5-98.0 % with the type strains of these species. 16S rRNA gene sequence similarities with other type strains of the genus Marinobacterium were below 96 %. DNA-DNA hybridizations between strain R-40509(T) and the type strains of the phylogenetically closest species of the genus Marinobacterium revealed less than 70 % DNA-DNA relatedness, supporting the novel species status of the strain. Phenotypic characterization revealed that the strain was able to grow at 15-42 ^0C and in medium containing up to 9 % NaCl. The isolate could be differentiated from phenotypically related species by several features, including its ability to utilize d-alanine, l-alanine, bromosuccinic acid, Beta-hydroxybutyric acid and alpha-ketovaleric acid, but not acetate or l-arabinose. It produced acetoin (Voges-Proskauer), but did not have esterase lipase (C8) or catalase activities. It possessed C(18 : 1)omega7c (35 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c; 25 %) and C(16 : 0) (22 %) as major cellular fatty acids. The DNA G+C content was 58.5 mol%. The name Marinobacterium coralli sp. nov. is proposed to accommodate this novel isolate; the type strain is R-40509(T) (=LMG 25435(T) =CAIM 1449(T)).
not annotated - annotated - LINNAEUS only
Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae.
A Gram-positive, non-motile bacterium, designated KSL51201-037(T), was isolated from Anyang stream, Republic of Korea, and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL51201-037(T) belonged to the family Microbacteriaceae of the class Actinobacteria and exhibited 96.9 % gene sequence similarity to Labedella gwakjiensis KSW2-17(T), 96.0 % to Leifsonia ginsengi wged11(T) and 95.9 % to Microterricola viridarii KV-677(T). The G+C content of the genomic DNA was 72.7 mol%. Strain KSL51201-037(T) had l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, MK-11 and MK-12 as the major menaquinones, anteiso-C(15 : 0) (47.8 %) and iso-C(16 : 0) (24.0 %) as the major fatty acids and phosphatidylglycerol and three unknown phospholipids as the major polar lipids. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, it is suggested that strain KSL51201-037(T) represents a novel species of a new genus in the family Microbacteriaceae for which the name Amnibacterium kyonggiense gen. nov., sp. nov. is proposed. The type strain of the type species is KSL51201-037(T) (=KEMC 51201-037(T)=JCM 16463(T)).
not annotated - annotated - LINNAEUS only
Miniimonas arenae gen. nov., sp. nov., an actinobacterium isolated from sea sand.
A Gram-positive, non-motile, coccoid- to rod-shaped, non-spore-forming bacterium, designated strain YM18-15(T), was isolated from sea sand and studied using a polyphasic taxonomic approach. Strain YM18-15(T) grew under both aerobic and anaerobic conditions. The cell-wall peptidoglycan type was A4Beta and ornithine was the diagnostic diamino acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown phospholipid, MK-8(H(4)) was the major menaquinone and the predominant fatty acids were anteiso-C(15 : 0) and C(16 : 0). The DNA G+C content was 74.2 mol%. High 16S rRNA gene sequence similarities (96.3-97.3 %) were found with the sequences of the type strains of the three genera of the family Beutenbergiaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YM18-15(T) formed a clade with Serinibacter salmoneus, Salana multivorans and Beutenbergia cavernae. Strain YM18-15(T) differed from these three type strains in chemotaxonomic characteristics and in 16S rRNA gene signature nucleotides. Based on genetic and chemotaxonomic evidence, it is suggested that strain YM18-15(T) represents a novel species of a new genus within the family Beutenbergiaceae, for which the name Miniimonas arenae gen. nov., sp. nov. is proposed. The type strain of the type species is YM18-15(T) (=NBRC 106267(T)=KCTC 19750(T)=MBIC 08348(T)).
not annotated - annotated - LINNAEUS only
Anoxybacillus tengchongensis sp. nov. and Anoxybacillus eryuanensis sp. nov., facultatively anaerobic, alkalitolerant bacteria from hot springs.
Two novel thermophilic, spore-forming bacterial strains, T-11(T) and E-112(T), were isolated from hot springs in Tengchong and Eryuan counties of Yunnan province in south-west China. The strains were Gram-stain-positive rods, occurring singly or in chains. Growth of strain T-11(T) was observed between 30 and 75 ^0C (optimum 50 ^0C) and at pH 7-11 (optimum pH 8.5), while the temperature range for strain E-112(T) was 35-70 ^0C (optimum 55 ^0C) and the pH range was 7.0-11.0 (optimum pH 8.0). The DNA G+C contents of strains T-11(T) and E-112(T) were 41.1 and 42.6 mol%, respectively. On the basis of 16S rRNA gene sequence similarity, the two strains were shown to be related most closely to Anoxybacillus species. The chemotaxonomic characteristics [predominant isoprenoid quinone menaquinone 7 (MK-7); major fatty acids iso-C(15 : 0) and iso-C(17 : 0)] also supported the affiliation of strains T-11(T) and E-112(T) to the genus Anoxybacillus. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains T-11(T) and E-112(T) from Anoxybacillus species with validly published names. Strains T-11(T) and E-112(T) therefore represent two novel species, for which the names Anoxybacillus tengchongensis sp. nov. (type strain T-11(T) =CCTCC AB209237(T) =KCTC 13721(T)) and Anoxybacillus eryuanensis sp. nov. (type strain E-112(T) =CCTCC AB209236(T) =KCTC 13720(T)) are proposed.
not annotated - annotated - LINNAEUS only
Neisseria wadsworthii sp. nov. and Neisseria shayeganii sp. nov., isolated from clinical specimens.
An analysis of 16S rRNA gene sequences from archived clinical reference specimens has identified two novel Neisseria species. For each species, two strains from independent sources were identified. Amongst species with validly published names, the closest species to the newly identified organisms were Neisseria canis, N. dentiae, N. zoodegmatis, N. animaloris and N. weaveri. DNA-DNA hybridization studies demonstrated that the newly identified isolates represent species that are distinct from these nearest neighbours. Analysis of partial 23S rRNA gene sequences for the newly identified strains and their nearest neighbours provided additional support for the species designation. Bayesian analysis of 16S rRNA gene sequences suggested that the newly identified isolates belong to distinct but related species of the genus Neisseria, and are members of a clade that includes N. dentiae, N. bacilliformis and N. canis. The predominant cellular fatty acids [16 : 0, summed feature 3 (16 : 1omega7c and/or iso-15 : 0 2-OH) and 18 : 1omega7c], as well as biochemical and morphological analyses further support the designation of Neisseria wadsworthii sp. nov. (type strain 9715(T) =DSM 22247(T) =CIP 109934(T)) and Neisseria shayeganii sp. nov. (type strain 871(T) =DSM 22246(T) =CIP 109933(T)).
not annotated - annotated - LINNAEUS only
Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring.
A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated P(T) was isolated from a sulfur 'Thiodendron' mat in a saline spring at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain P(T) exhibited a helical shape. The spirochaete required sulfide in the growth medium and was able to oxidize it non-enzymically to elemental sulfur via the interaction of H(2)O(2) with sulfide and deposit it in the periplasmic space. Growth occurred at 4-32 ^0C (optimum at 28-30 ^0C), pH 6.0-8.5 (optimum pH 7.0-7.5), and in 0.1-1 M NaCl (optimum 0.35 M). The isolate used several sugars and polysaccharides as carbon or energy sources but did not use peptides, amino acids, organic acids or alcohols. The products of glucose fermentation were formate, acetate, ethanol, pyruvate, CO(2) and H(2). The genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed that strain P(T) fell within a group of species in the genus Spirochaeta, including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with which it shared less then 89 % sequence similarity. On the basis of its morphology, physiology and other phenotypic properties, as well as its phylogenetic position, the new isolate is considered to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov. is proposed. The type strain is P(T) (=DSM 19205(T) =VKM B-2514(T)).
not annotated - annotated - LINNAEUS only
Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil-contaminated soil.
A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37(T), was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37(T) stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37(T) had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C(15 : 0) (41 %), iso-C(14 : 0) 3-OH and/or iso-C(15 : 0) dimethyl acetal (21.6 %), iso-C(13 : 0) (4.4 %), anteiso-C(15 : 0) (3.9 %) and iso-C(15 : 1) (2.8 %). Strain SOL3f37(T) grew between 20 and 48 ^0C (optimum 40 ^0C) and at pH 6.2-8.1 (optimum pH 6.9). Strain SOL3f37(T) required at least 0.5 NaCl l(-1) and grew in the presence of NaCl concentrations up to 150 g l(-1) (optimum 40 g l(-1)). Yeast extract (2 g l(-1)) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37(T) grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37(T) was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37(T) was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60(T), 91.8 % with Thermohalobacter berrensis CTT3(T) and 91.7 % with Caloranaerobacter azorensis MV1087(T). On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37(T) represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is proposed, with SOL3f37(T) (=DSM 21485(T) =JCM 15487(T)) as the type strain of Sporosalibacterium faouarense.
not annotated - annotated - LINNAEUS only
Streptomyces lacticiproducens sp. nov., a lactic acid-producing streptomycete isolated from the rhizosphere of tomato plants.
A novel actinomycete, designated strain GIMN4.001(T), was isolated from the rhizosphere of tomato plants grown in Guangzhou, China. The strain produced greyish white aerial mycelia, lactic acid and a large quantity of double diamond-shaped crystals on potato dextrose agar and yeast extract-malt extract agar. The colour of the substrate mycelium was not sensitive to pH. Microscopic observations revealed that strain GIMN4.001(T) produced verticillate chains of cylindrical spores. Chemotaxonomic data confirmed that strain GIMN4.001(T) belonged to the genus Streptomyces. Melanin pigments were not produced. No antibacterial activity was observed against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis or Candida albicans, but inhibitory activity was observed against Penicillium citrinum. 16S rRNA gene sequence analysis revealed that strain GIMN4.001(T) was related most closely to Streptomyces morookaense ATCC 19166(T) (98.9 % similarity) and Streptomyces lavenduligriseus ATCC 13306(T) (98.7 %). Levels of DNA-DNA relatedness between strain GIMN4.001(T) and the type strains of these species were low (14-20 %). Furthermore, strain GIMN4.001(T) could be differentiated from S. morookaense, S. lavenduligriseus and other closely related species of the genus Streptomyces based on morphological, physiological and biochemical characteristics. On the basis of its physiological and molecular properties, strain GIMN4.001(T) is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces lacticiproducens sp. nov. is proposed. The type strain is GIMN4.001(T) (=CCTCC M208214(T)=NRRL B-24800(T)).
not annotated - annotated - LINNAEUS only
An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria.
The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment. In the past two decades, the availability of sequences, such as those of the 16S rRNA, nif, cpc and rpoC1 genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment. Conserved indels (insertions/deletions) are present in all cyanobacterial RpoB (Beta subunit of RNA polymerase) sequences presently available in public databases. These indels are located in the Rpb2_6 domain of RpoB, which is involved in DNA binding and DNA-directed RNA polymerase activity. They are variable in length (6-44 aa) and sequence, and form part of what appears to be a longer signature sequence (43-81 aa). Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species. These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and/or to assess cyanobacterial biodiversity in space and time in natural ecosystems.
not annotated - annotated - LINNAEUS only
Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al. 2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae.
A Gram-reaction-positive, aerobic, catalase-positive, non-spore-forming, rod-shaped bacterium designated IMMIB L-1656(T) was isolated from an ear swab of a man and characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain IMMIB L-1656(T) is related to members of the family Micrococcaceae (<95.1 % sequence similarity). Anaylsis using different phylogenetic algorithms consistently grouped strain IMMIB L-1656(T) with members of the genus Yaniella. The organism posessed a cell-wall murein based on L-lysine (variation A4alpha, type L-Lys-Gly-L-Glu), MK-10 as the predominant menaquinone and long-chain cellular fatty acids of straight-chain and branched-chain saturated types (with iso-C(15 : 0) and anteiso-C(17 : 0) predominating). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol in addition to unknown glycolipids. The DNA G+C content was 59.7 mol%. Based on its distinctive genotypic and phenotypic characteristics, strain IMMIB L-1656(T) represents a novel species in a novel genus, for which the name Auritidibacter ignavus gen. nov., sp. nov. is proposed. We also propose that members of the family Yaniellaceae be transferred to the family Micrococcaceae with amendments to the description of the suborder Micrococcineae. The type strain of Auritidibacter ignavus is IMMIB L-1656(T) (=DSM 45359(T) =CCUG 57943(T)).
not annotated - annotated - LINNAEUS only
Flavobacterium beibuense sp. nov., isolated from marine sediment.
A taxonomic study was carried out on strain F44-8(T), which was isolated from a crude-oil-degrading consortium, enriched from marine sediment of the Beibu Gulf, PR China. The 16S rRNA gene sequence of strain F44-8(T) showed highest similarities to those of Flavobacterium frigoris LMG 21922(T) (93.3 %), Flavobacterium terrae R2A1-13(T) (93.3 %) and Flavobacterium gelidilacus LMG 21477(T) (93.1 %). Sequence similarities to other members of the genus Flavobacterium were <93.0 %. The dominant fatty acids of strain F44-8(T) were iso-C(15 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c), iso-C(15 : 1) G and iso-C(17 : 0) 3-OH. The DNA G+C content of strain F44-8(T) was 38.6 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. Strain F44-8(T) could, however, be readily distinguished from all known Flavobacterium species by a number of phenotypic features. Therefore, according to the phenotypic and 16S rRNA gene sequence data, strain F44-8(T) represents a novel species in the genus Flavobacterium, for which the name Flavobacterium beibuense sp. nov. is proposed (type strain F44-8(T) =CCTCC AB 209067(T) =LMG 25233(T) =MCCC 1A02877(T)).
not annotated - annotated - LINNAEUS only
Fungal secondary metabolites - strategies to activate silent gene clusters.
Filamentous fungi produce a multitude of low molecular weight bioactive compounds. The increasing number of fungal genome sequences impressively demonstrated that their biosynthetic potential is far from being exploited. In fungi, the genes required for the biosynthesis of a secondary metabolite are clustered. Many of these bioinformatically newly discovered secondary metabolism gene clusters are silent under standard laboratory conditions. Consequently, no product can be found. This review summarizes the current strategies that have been successfully applied during the last years to activate these silent gene clusters in filamentous fungi, especially in the genus Aspergillus. The techniques take advantage of genome mining, vary from the simple search for compounds with bioinformatically predicted physicochemical properties up to methods that exploit a probable interaction of microorganisms. Until now, the majority of successful approaches have been based on molecular biology like the generation of gene "knock outs", promoter exchange, overexpression of transcription factors or other pleiotropic regulators. Moreover, strategies based on epigenetics opened a new avenue for the elucidation of the regulation of secondary metabolite formation and will certainly continue to play a significant role for the elucidation of cryptic natural products. The conditions under which a given gene cluster is naturally expressed are largely unknown. One technique is to attempt to simulate the natural habitat by co-cultivation of microorganisms from the same ecosystem. This has already led to the activation of silent gene clusters and the identification of novel compounds in Aspergillus nidulans. These simulation strategies will help discover new natural products in the future, and may also provide fundamental new insights into microbial communication.
not annotated - annotated - LINNAEUS only
Compartmentalization and molecular traffic in secondary metabolism: a new understanding of established cellular processes.
Great progress has been made in understanding the regulation of expression of genes involved in secondary metabolism. Less is known about the mechanisms that govern the spatial distribution of the enzymes, cofactors, and substrates that mediate catalysis of secondary metabolites within the cell. Filamentous fungi in the genus Aspergillus synthesize an array of secondary metabolites and provide useful systems to analyze the mechanisms that mediate the temporal and spatial regulation of secondary metabolism in eukaryotes. For example, aflatoxin biosynthesis in Aspergillus parasiticus has been studied intensively because this mycotoxin is highly toxic, mutagenic, and carcinogenic in humans and animals. Using aflatoxin synthesis to illustrate key concepts, this review focuses on the mechanisms by which sub-cellular compartmentalization and intra-cellular molecular traffic contribute to the initiation and completion of secondary metabolism within the cell. We discuss the recent discovery of aflatoxisomes, specialized trafficking vesicles that participate in the compartmentalization of aflatoxin synthesis and export of the toxin to the cell exterior; this work provides a new and clearer understanding of how cells integrate secondary metabolism into basic cellular metabolism via the intra-cellular trafficking machinery.
not annotated - annotated - LINNAEUS only
The lipid language of plant-fungal interactions.
Lipid mediated cross-kingdom communication between hosts and pathogens is a rapidly emerging field in molecular plant-fungal interactions. Amidst our growing understanding of fungal and plant chemical cross-talk lies the distinct, yet little studied, role for a group of oxygenated lipids derived from polyunsaturated fatty acids, termed oxylipins. Endogenous fungal oxylipins are known for their roles in carrying out pathogenic strategies to successfully colonize their host, reproduce, and synthesize toxins. While plant oxylipins also have functions in reproduction and development, they are largely recognized as agents that facilitate resistance to pathogen attack. Here we review the composition and endogenous functions of oxylipins produced by both plants and fungi and introduce evidence which suggests that fungal pathogens exploit host oxylipins to facilitate their own virulence and pathogenic development. Specifically, we describe how fungi induce plant lipid metabolism to utilize plant oxylipins in order to promote G-protein-mediated regulation of sporulation and mycotoxin production in the fungus. The use of host-ligand mimicry (i.e. coronatine) to manipulate plant defense responses that benefit the fungus are also implicated.
not annotated - annotated - LINNAEUS only
Treatment non-adherence in teenage and young adult patients with cancer.
Adhering to treatment can be a significant issue for many patients diagnosed with chronic health conditions and this has been reported to be greater during the adolescent years. However, little is known about treatment adherence in teenage and young adult (TYA) patients with cancer. To increase awareness of the adherence challenges faced by these patients, we have reviewed the published work. The available evidence suggests that a substantial proportion of TYA patients with cancer do have difficulties, with reports that up to 63% of patients do not adhere to their treatment regimens. However, with inconsistent findings across studies, the true extent of non-adherence for these young patients is still unclear. Furthermore, it is apparent that there are many components of the cancer treatment regimen that have yet to be assessed in relation to patient adherence. Factors that have been shown to affect treatment adherence in TYA patients include patient emotional functioning (depression and self-esteem), patient health beliefs (perceived illness severity and vulnerability), and family environment (parental support and parent-child concordance). Strategies that foster greater patient adherence are also identified. These strategies are multifactorial, targeting not only the patient, but the health professional, family, and treatment regimen. This review highlights the lack of interventional studies addressing treatment adherence in TYA patients with cancer, with only one such intervention being identified: a video game intervention focusing on behavioural issues related to cancer treatment and care. Methodological issues in measuring adherence are addressed and suggestions for improving the design of future adherence studies highlighted, of which there is a great need.
not annotated - annotated - LINNAEUS only
Monovalent cations regulate expression and activity of the Hak1 potassium transporter in Debaryomyces hansenii.
Debaryomyces hansenii was able to grow in a medium containing residual amounts of K(+), indicating the activity of high affinity K(+) transporters. Transcriptional regulation analysis of the genes encoding the two potassium uptake systems in D. hansenii revealed that while DhTRK1 is not regulated at transcriptional level, expression of DhHAK1 required starvation in the absence of K(+) and Na(+) and was not affected by changes in membrane potential. Rb(+) transport in cells expressing DhHAK1 was activated by external Na(+) or acidic pH and inhibited by high pH. We propose a K(+)-H(+) symporter that, under certain conditions may work as a K(+)-Na(+) transporter, as the mechanism driving K(+) influx mediated by DhHak1p.
not annotated - annotated - LINNAEUS only
Isocitrate dehydrogenase-1 mutations: a fundamentally new understanding of diffuse glioma?
The discovery of somatic mutations in the gene encoding isocitrate dehydrogenase-1 (IDH1) in glioblastomas was remarkable because the enzyme was not previously identified with any known oncogenic pathway. IDH1 is mutated in up to 75% of grade II and grade III diffuse gliomas. Apart from acute myeloid leukaemia, other tumour types do not carry IDH1 mutations. Mutations in a homologous gene, IDH2, have also been identified, although they are much rarer. Although TP53 mutations and 1p/19q codeletions are mutually exclusive in gliomas, in both of these genotypes IDH1 mutations are common. IDH1 and IDH2 mutations are early events in the development of gliomas. Moreover, IDH1 and IDH2 mutations are a major prognostic marker for overall and progression-free survival in grade II-IV gliomas. Mutated IDH1 has an altered catalytic activity that results in the accumulation of 2-hydroxyglutarate. Molecularly, IDH1 and IDH2 mutations are heterozygous, affect only a single codon, and rarely occur together. Because IDH1 does not belong to a traditional oncogenic pathway and is specifically and commonly mutated in gliomas, the altered enzymatic activity of IDH1 may provide a fundamentally new understanding of diffuse glioma.
not annotated - annotated - LINNAEUS only
Characterization of the GPI-anchored endo Beta-1,3-glucanase Eng2 of Aspergillus fumigatus.
A GPI-anchored endo Beta-1,3-glucanase of Aspergillus fumigatus was characterized. The enzyme encoded by ENG2 (AFUA_2g14360) belongs to the glycoside hydrolase family 16 (GH16). The activity was characterized using a recombinant protein produced by Pichiapastoris. The recombinant enzyme preferentially acts on soluble Beta-1,3-glucans. Enzymatic analysis of the endoglucanase activity using Carboxymethyl-Curdlan-Remazol Brilliant Blue (CM-Curdlan-RBB) as a substrate revealed a wide temperature optimum of 24-40^0C, a pH optimum of 5.0-6.5 and a K(m) of 0.8 mg ml(-1). HPAEC analysis of the products formed by Eng2 when acting on different oligo-Beta-1,3-glucans confirmed the predicted endoglucanase activity and also revealed a transferase activity for oligosaccharides of a low degree of polymerization. The growth phenotype of the Afeng2 mutant was identical to that of the wt strain.
not annotated - annotated - LINNAEUS only
Measuring impact in the Millennium Development Goal era and beyond: a new approach to large-scale effectiveness evaluations.
Evaluation of large-scale programmes and initiatives aimed at improvement of health in countries of low and middle income needs a new approach. Traditional designs, which compare areas with and without a given programme, are no longer relevant at a time when many programmes are being scaled up in virtually every district in the world. We propose an evolution in evaluation design, a national platform approach that: uses the district as the unit of design and analysis; is based on continuous monitoring of different levels of indicators; gathers additional data before, during, and after the period to be assessed by multiple methods; uses several analytical techniques to deal with various data gaps and biases; and includes interim and summative evaluation analyses. This new approach will promote country ownership, transparency, and donor coordination while providing a rigorous comparison of the cost-effectiveness of different scale-up approaches.
not annotated - annotated - LINNAEUS only
UreA, the major urea/H+ symporter in Aspergillus nidulans.
We report here the characterization of UreA, a high-affinity urea/H+ symporter of Aspergillus nidulans. The deletion of the encoding gene abolishes urea transport at low substrate concentrations, suggesting that in these conditions UreA is the sole transport system specific for urea in A. nidulans. The ureA gene is not inducible by urea or its precursors, but responds to nitrogen metabolite repression, necessitating for its expression the AreA GATA factor. In contrast to what was observed for other transporters in A. nidulans, repression by ammonium is also operative during the isotropic growth phase. The activity of UreA is down-regulated post-translationally by ammonium-promoted endocytosis. A number of homologues of UreA have been identified in A. nidulans and other Aspergilli, which cluster in four groups, two of which contain the urea transporters characterized so far in fungi and plants. This phylogeny may have arisen by gene duplication events, giving place to putative transport proteins that could have acquired novel, still unidentified functions.
not annotated - annotated - LINNAEUS only
The Candida albicans Rgd1 is a RhoGAP protein involved in the control of filamentous growth.
Rho proteins are essential regulators of polarized growth in eukaryotic cells. These proteins are down-regulated in vivo by specific Rho GTPase Activating Proteins (RhoGAP). We investigated the role of Rgd1 RhoGAP, encoded by the Candida albicans RGD1 gene. We demonstrated that CaCdc42, CaRho3 and CaRho4 proteins had an intrinsic GTPase activity and that CaRgd1 stimulates in vitro GTP hydrolysis of these GTPases. Deletion of RGD1 in C. albicans results in sensitivity to low pH as already described for rgd1Delta in Saccharomyces cerevisiae. The role of Rgd1 in survival at low pH is conserved in the two yeast species as the CaRGD1 gene complements the Scrgd1Delta sensitivity. By tagging the RhoGAP with GFP, we found that CaRgd1 is localized at the tip and cortex of growing cells and during cytokinesis at the septation sites in yeast and filamentous forms. We investigated the effect of CaRgd1 on the control of the polarized growth. Removing CaRGD1 alleles increased filamentous growth and cells lacking CaRgd1 presented longer germ tubes. Conversely, RGD1 overexpression restricted hyphae growth. Our results demonstrate that Rgd1 is critical for filamentous formation in C. albicans especially for filamentous elongation.
not annotated - annotated - LINNAEUS only
Surface and flagella morphology of the motile form of Chromera velia revealed by field-emission scanning electron microscopy.
Chromera velia (Chromerida; Alveolata) is an autotrophic protist isolated from stony corals. Ch. velia possesses a chloroplast thought to be most closely related to the apicoplasts of non-photosynthetic apicomplexa. Phylogenetic analyses place Ch. velia as a close relative of parasitic apicomplexa and predatory colpodellids. We have used field-emission scanning electron microscopy of cells sputter-coated with gold or chromium and non-coated cells to characterise the surface ultrastructure of the motile form of Ch. velia. In overall morphology the biflagellated Ch. velia cells resemble the colpodellid Colpodella edax, but with some notable differences. The ventral side of the flagellated Ch. velia cell has two grooves extending from the anterior flagella insertion point with a ridge rising towards the anterior apex of the cell. The anterior flagellum is shorter than the posterior flagellum and possesses a distinct, small curved appendage. The insertion point of the anterior flagellum is partly enclosed by a flap extending from the cell. The posterior flagellum is approximately four times the length of the cell and possesses mastigonemes. The combination of coating techniques proved superior to the commonly used gold coating to determine fine surface ultrastructure. This new ultrastructural information for Ch. velia allowed us to emend its diagnosis.
not annotated - annotated - LINNAEUS only
Stress-induced pseudocyst formation--a newly identified mechanism of protection against organic solvents in acanthamoebae of the T4 genotype.
Differentiation into highly resistant double-walled cysts is a major mechanism allowing amphizoic acanthamoebae to survive under long-lasting, unfavourable environmental conditions. We found that relatively low concentrations of methanol, acetone or DMSO stimulate prompt Acanthamoeba differentiation into a rounded cyst-like stage with a single envelope. To address whether this rapid response differs from the encystment, time-dependent changes in cell surface characteristics and cyst-specific gene expression were monitored in encystating cells and cells differentiating under methanol treatment using microscopic, lectin-binding, PCR and resistance studies. In contrast to the encystment: (1) a single-layered amorphous mannose/glucose coat was the only envelope assembled on the surface of the solvent-treated cells, (2) the cyst-specific protein (CSP21) was not expressed, (3) the coat did not protect cells against acidic pH and (4) in solvent-free encystment medium, the coated cells did not assemble the double-layered wall, thus indicating that these cells were not immature cysts. These findings lead us to specify a terminal stage of rapid Acanthamoeba differentiation elicited by acute organic solvent stress as "pseudocyst", and to suggest that encystation and pseudocyst formation are distinct stress responses. Moreover, the possibility exists that pseudocysts might form in response to certain contact lens solutions thus increasing resistance of acanthamoebae to disinfecting agents.
not annotated - annotated - LINNAEUS only
Possible roles of phospholipase A(2) in the biological activities of Acanthamoeba castellanii (T4 Genotype).
Using phospholipases A(2)-specific spectrophotometric assays, it was shown that A. castellanii lysates and their conditioned medium exhibit phospholipase activities. The extracellular levels of PLA(2)detected were significantly reduced compared with the cell-associated enzyme (P<0.05). Sphinganine, a PLA(2)inhibitor showed robust amoebistatic properties but had no effect on the viability of A. castellanii. The potency of sphinganine was demonstrated effectively towards purified PLA(2)derived from porcine pancreas. Using sphinganine, it was observed that PLA(2)is involved in neither binding nor cytotoxicity of the human brain microvascular endothelial cells due to A. castellanii. Unlike as was the case for Dictyostelium amoebae, PLA(2) appeared to be involved in A. castellanii phagocytosis of the fluorescently-labelled polystyrene beads. Horseradish peroxidase was used as a tracer molecule to develop assays to study pinocytosis in A. castellanii. The findings revealed that sphinganine impedes phagocytosis but augments pinocytosis in A. castellanii suggesting distinct nature of processes. A complete understanding of the role of phospholipases in the biology and pathogenesis of A. castellanii infections will determine their potential as therapeutic targets.
not annotated - annotated - LINNAEUS only
The roles played by Aspergillus nidulans apoptosis-inducing factor (AIF)-like mitochondrial oxidoreductase (AifA) and NADH-ubiquinone oxidoreductases (NdeA-B and NdiA) in farnesol resistance.
Farnesol (FOH) is a nonsterol isoprenoid produced by dephosphorylation of farnesyl pyrophosphate, a catabolite of the cholesterol biosynthetic pathway. These isoprenoids inhibit proliferation and induce apoptosis. Here, we show that Aspergillus nidulans AifA encoding the apoptosis-inducing factor (AIF)-like mitochondrial oxidoreductase plays a role in the function of the mitochondrial Complex I. Additionally, we demonstrated that ndeA-B and ndiA encode external and internal alternative NADH dehydrogenases, respectively, that have a function in FOH resistance. When exposed to FOH, the DeltaaifA and DeltandeA strains have increased ROS production while DeltandeB, DeltandeA DeltandeB, and DeltandiA mutant strains showed the same ROS accumulation than in the absence of FOH. We observed several compensatory mechanisms affecting the differential survival of these mutants to FOH.
not annotated - annotated - LINNAEUS only
Regulation of secondary metabolism by chromatin structure and epigenetic codes.
Chromatin, composed of DNA wrapped around an octamer of histones, is the relevant substrate for all genetic processes in eukaryotic nuclei. Changes in chromatin structure are associated with the activation and silencing of gene transcription and reversible post-translational modifications of histones are now known to direct chromatin structure transitions. Recent studies in several fungal species have identified a chromatin-based regulation of secondary metabolism (SM) gene clusters representing an upper-hierarchical level for the coordinated control of large chromosomal elements. Regulation by chromatin transition processes provides a mechanistic model to explain how different SM clusters located at dispersed genomic regions can be simultaneously silenced during primary metabolism. Activation of SM clusters has been shown to be associated with increased acetylation of histones H3 and H4 and, consequently, inhibition of histone de-acetylase activities also leads to increased production of secondary metabolites. New findings suggest that SM clusters are silenced by heterochromatic histone marks and that the "closed" heterochromatic structures are reversed during SM activation. This process is mediated by the conserved activator of SM, LaeA. Despite the increase in knowledge about these processes, much remains to be learned from chromatin-level regulation of SM. For example, which proteins "position" the chromatin restructuring signal onto SM clusters or how exactly LaeA works to mediate the low level of heterochromatic marks inside different clusters remain open questions. Answers to these and other chromatin-related questions would certainly complete our understanding of SM gene regulation and signaling and, because for many predicted SM clusters corresponding products have not been identified so far, anti-silencing strategies would open new ways for the identification of novel bioactive substances.
not annotated - annotated - LINNAEUS only
Conservation of POPs, the plant organellar DNA polymerases, in eukaryotes.
POPs, plant organellar DNA polymerases, have been isolated from various photosynthetic eukaryotes. Previously, we purified the native POP of Cyanidioschyzon merolae (CmPOP) from whole cellular extracts and showed that CmPOP has DNA polymerase activity with a high processivity and a 3'-5' exonuclease activity, and its expression is related to cell proliferation. In rice, the recombinant protein of POP has activities found in CmPOP, and high fidelity of POP has also been demonstrated. These facts suggest that POPs are involved in the replication of organellar genomes. POPs are also conserved in most non-opisthokont eukaryotes, which lack DNA polymerase gamma (Polgamma), a mitochondrial replication enzyme in opisthokonts (fungi and animals). The ciliate Tetrahymena thermophila contains a single gene for a putative POP (TetPOP). Immunoblot analysis demonstrated that TetPOP is localized in mitochondria, and TetPOP has been purified from mitochondria through a column chromatography series. Sensitivity to phosphonoacetate and dideoxyTTP was examined in POPs (TetPOP and CmPOP) or POP-containing organelles (chloroplasts of Arabidopsis) and other polymerases (DNA polymerase I and mitochondria of rat liver, which contain Polgamma), and the results suggest that high sensitivity to phosphonoacetate is unique to POPs in Family-A DNA polymerases. Finally, we propose a model for the succession of organellar DNA polymerases.
not annotated - annotated - LINNAEUS only
Identification of a mastigoneme protein from Phytophthora nicotianae.
Tripartite tubular hairs (mastigonemes) on the anterior flagellum of protists in the stramenopile taxon are responsible for reversing the thrust of flagellar beat and for cell motility. Immunoprecipitation experiments using antibodies directed towards mastigonemes on the flagella of zoospores of Phytophthora nicotianae have facilitated the cloning of a gene encoding a mastigoneme shaft protein in this Oomycete. Expression of the gene, designated PnMas2, is up-regulated during asexual sporulation, a period during which many zoospore components are synthesized. Analysis of the sequence of the PnMas2 protein has revealed that, like other stramenopile mastigoneme proteins, PnMas2 has an N-terminal secretion signal and contains four cysteine-rich epidermal growth factor (EGF)-like domains. Evidence from non-denaturing gels indicates that PnMas2 forms large oligomeric complexes, most likely through disulphide bridging. Bioinformatic analysis has revealed that Phytophthora species typically contain three or four putative mastigoneme proteins containing the four EGF-like domains. These proteins are similar in sequence to mastigoneme proteins in other stramenopile protists including the algae Ochromonas danica, Aureococcus anophagefferens and Scytosiphon lomentaria and the diatoms Thalassiosira pseudonana and T. weissflogii.
not annotated - annotated - LINNAEUS only
Prasinoderma singularis sp. nov. (Prasinophyceae, Chlorophyta), a solitary coccoid Prasinophyte from the South-East Pacific Ocean.
During the BIOSOPE cruise in the South-East Pacific Ocean in 2004, several unidentified strains of prasinophytes were isolated into culture. Of these, nine strains composed a group for which the partial 18S rRNA gene sequence was related to Prasinoderma coloniale. The ultrastructure, morphology, division process, pigment composition, genome size and molecular genetic phylogeny of these nine strains were investigated, using P. coloniale as a reference. The 18S rRNA gene sequence of P. singularis sp. nov. shares only 96.9% of identity with that of P. coloniale and contains a conserved insertion of 567bp length not recorded in P. coloniale. When compared to P. coloniale, P. singularis sp. nov. is morphologically characterized by the absence of colonies, smaller cells with a thinner cell wall, and a second cell type with a different cell covering.
not annotated - annotated - LINNAEUS only
Dependence between volumes of protoplast and lorica in lugol-fixed tintinnid ciliates.
The relationship between the volume of tintinnid loricae and protoplasts was studied on the basis of bulk data derived from samples collected in a range of temperate environments: riverine, lacustrine, estuarine, and marine. All organisms were fixed with acid Lugol solution (0.5-1.0%). The dependence was described with the allometric equation: VL=2.74xVP(1.03), where VL and VP are volumes [mum(3)] of loricae and protoplasts, respectively. The dependence was highly significant (p<0.001, n=417, R(2)=0.85). On average, protoplasts occupied 31% of the lorica volume. One species, Helicostomella subulata,was omitted from the calculations and treated separately since this ciliate has a relatively large lorica. The relationship identified between lorica and protoplast volumes permits recalculating incomplete data if protoplasts are the only body part measured.
not annotated - annotated - LINNAEUS only
PRP8 intein in Ajellomycetaceae family pathogens: sequence analysis, splicing evaluation and homing endonuclease activity.
Inteins are intervening sequences that are transcribed and translated with flanking host protein sequences and then self-excised by protein splicing. Bi-functional inteins also contain a homing endonuclease responsible for their genetic mobility. The PRP8 intein, the most widespread among fungi, occurs in important pathogens such as Histoplasma capsulatum and Paracoccidioides brasiliensis, from the Ajellomycetaceae family. Herein, we describe the bi-functional PRP8 intein in two other Ajellomycetacean pathogens, Blastomyces dermatitidis and Emmonsia parva. Sequence analysis and experimental evidence suggest that the homing endonuclease from PbrPRP8 is inactive. The splicing activity of the PRP8 intein from the B. dermatitidis, E. parva and P. brasiliensis species complex was demonstrated in a non-native protein context in Escherichia coli. Since the PRP8 intein is located in a functionally essential nuclear protein, it can be considered a promising therapeutic target for anti-fungal drugs, because inhibition of intein splicing should inhibit proliferation of intein-containing pathogens.
not annotated - annotated - LINNAEUS only
Barcoding Tetrahymena: discriminating species and identifying unknowns using the cytochrome c oxidase subunit I (cox-1) barcode.
DNA barcoding using the mitochondrial cytochromecoxidase subunit I (cox-1) gene has recently gained popularity as a tool for species identification of a variety of taxa. The primary objective of our research was to explore the efficacy of using cox-1 barcoding for species identification within the genus Tetrahymena. We first increased intraspecific sampling for Tetrahymena canadensis, Tetrahymena hegewischi, Tetrahymena pyriformis, Tetrahymena rostrata, Tetrahymena thermophila, and Tetrahymena tropicalis. Increased sampling efforts show that intraspecific sequence divergence is typically less than 1%, though it may be more in some species. The barcoding also showed that some strains might be misidentified or mislabeled. We also used cox-1 barcodes to provide species identifications for 51 unidentified environmental isolates, with a success rate of 98%. Thus, cox-1 barcoding is an invaluable tool for protistologists, especially when used in conjunction with morphological studies.
not annotated - annotated - LINNAEUS only
Facing unknowns: living cultures (Pirum gemmata gen. nov., sp. nov., and Abeoforma whisleri, gen. nov., sp. nov.) from invertebrate digestive tracts represent an undescribed clade within the unicellular Opisthokont lineage ichthyosporea (Mesomycetozoea).
During a culture-based survey of opisthokonts living in marine invertebrate digestive tracts, we isolated two new eukaryotes that differed from described taxa by more than 10% in their small subunit ribosomal DNA sequences. Phylogenetic analysis showed that the two isolates represented a divergent clade of ichthyosporeans known previously only from environmental clone sequences. We used light and electron microscopy to describe the isolates as new genera and species Pirum gemmata and Abeoforma whisleri. A. whisleri had a complex life cycle that remains incompletely known but involved walled spherical cells, plasmodia and amoebae. Asexual reproduction occurred via dispersal amoebae, endospores, binary fission and budding. In contrast P. gemmata had a less complex life cycle with no amoeboid or plasmodial stages. Both species had membrane-bound tubular extensions of the cytoplasm embedded in the inner layers of their cell walls. By comparing P. gemmata and A. whisleri to other ichthyosporea we speculate on the characters that may have been present in the ancestral ichthyosporean. P. gemmata and A. whisleri illustrate the unique and diverse forms that can be found by capturing taxa belonging to divergent and uncultured lineages.
not annotated - annotated - LINNAEUS only
Does climate warming stimulate or inhibit soil protist communities? A test on testate amoebae in high-arctic tundra with free-air temperature increase.
Soil testate amoebae assemblages in a grassland area at Zackenberg (Northeast Greenland) were subjected to simulated climate-warming during the growing season using the Free-Air Temperature Increase technique. Samples were collected in upper (0 - 3cm) and deeper (3 - 6cm) soil horizons. Mean temperature elevations at 2.5 and 7.5 cm depth were 2.58 +/- SD 1.11 and 2.13+/-SD 0.77^0C, respectively, and did not differ significantly. Soil moisture in the top 11cm was not affected by the warming. During the manipulation, the densities of living amoebae and empty shells were higher in the experimental plots but only in the upper layer. Possibly, testate amoebae in the deeper layer were limited by other factors, suggesting that warming enhances the carrying capacity only in favourable conditions. Species richness, on the other hand, was only increased in the deeper horizon. Warming did not change the percentage of individuals belonging to small-sized species in any of the living assemblages, contrary to our expectation that those species would quickly increase their density. However, in the empty shell assemblages, the proportion of small-sized individuals in the experimental plots was higher in both layers, indicating a rapid, transient increase in small amoebae before the first sampling date. Changes in successional state of testate amoebae assemblages in response to future climate change might thus be ephemeral, whereas alterations in density and species richness might be more sustained.
not annotated - annotated - LINNAEUS only
Characterization of the Aspergillus nidulans biotin biosynthetic gene cluster and use of the bioDA gene as a new transformation marker.
The genes involved in the biosynthesis of biotin were identified in the hyphal fungus Aspergillus nidulans through homology searches and complementation of Escherichia coli biotin-auxotrophic mutants. Whereas the 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase are encoded by distinct genes in bacteria and the yeast Saccharomyces cerevisiae, both activities are performed in A. nidulans by a single enzyme, encoded by the bifunctional gene bioDA. Such a bifunctional bioDA gene is a genetic feature common to numerous members of the ascomycete filamentous fungi and basidiomycetes, as well as in plants and oomycota. However, unlike in other eukaryota, the three bio genes contributing to the four enzymatic steps from pimeloyl-CoA to biotin are organized in a gene cluster in pezizomycotina. The A. nidulans auxotrophic mutants biA1, biA2 and biA3 were all found to have mutations in the 7,8-diaminopelargonic acid synthase domain of the bioDA gene. Although biotin auxotrophy is an inconvenient marker in classical genetic manipulations due to cross-feeding of biotin, transformation of the biA1 mutant with the bioDA gene from either A. nidulans or Aspergillus fumigatus led to the recovery of well-defined biotin-prototrophic colonies. The usefulness of bioDA gene as a novel and robust transformation marker was demonstrated in co-transformation experiments with a green fluorescent protein reporter, and in the efficient deletion of the laccase (yA) gene via homologous recombination in a mutant lacking non-homologous end-joining activity.
not annotated - annotated - LINNAEUS only
Regulation of virulence factors, carbon utilization and virulence by SNF1 in Cryptococcus neoformans JEC21 and divergent actions of SNF1 between cryptococcal strains.
We describe here the functions of a Snf1/AMPK homolog in the human pathogenic yeast Cryptococcus neoformans, strain JEC21. We found that JEC21 SNF1 is a key regulator for the biosynthesis of the major virulence factors, stress resistance and alternative carbon source utilization. Disruption of JEC21 SNF1 results in defects of laccase activity and capsule production, sensitivity to cation stress. Especially, we found that JEC21 SNF1 is essential for growth at elevated temperature and for thermotolerance. To our knowledge, a role for Snf1 proteins in thermotolerance has not been reported. Furthermore, we observed a functional divergence between JEC21 SNF1 and its equivalent from serotype A strain H99. A high temperature is needed for H99 SNF1 to function in stress response and carbon source preference, but not for the JEC21 SNF1. Our results confirmed a critical role of JEC21 SNF1 in regulation of stress response and virulence. Revelation of divergent actions of SNF1 may help to understand the evolution of cryptococcal pathogenesis and provides insights into the strain-associated biosynthesis of virulence factors.
not annotated - annotated - LINNAEUS only
Gout therapeutics: new drugs for an old disease.
The approval of febuxostat, a non-purine-analogue inhibitor of xanthine oxidase, by the European Medicines Agency and the US Food and Drug Administration heralds a new era in the treatment of gout. The use of modified uricases to rapidly reduce serum urate concentrations in patients with otherwise untreatable gout is progressing. Additionally, advances in our understanding of the transport of uric acid in the renal proximal tubule and the inflammatory response to monosodium urate crystals are translating into potential new treatments. In this Review, we focus on the clinical trials of febuxostat. We also review results from studies of pegloticase, a pegylated uricase in development, and we summarise data for several other pipeline drugs for gout, such as the selective uricosuric drug RDEA594 and various interleukin-1 inhibitors. Finally, we issue a word of caution about the proper use of the new drugs and the already available drugs for gout. At a time of important advances, we need to recommit ourselves to a rational approach to the treatment of gout.
not annotated - annotated - LINNAEUS only
Carry-over effects as drivers of fitness differences in animals.
1. Carry-over effects occur when processes in one season influence the success of an individual in the following season. This phenomenon has the potential to explain a large amount of variation in individual fitness, but so far has only been described in a limited number of species. This is largely due to difficulties associated with tracking individuals between periods of the annual cycle, but also because of a lack of research specifically designed to examine hypotheses related to carry-over effects. 2. We review the known mechanisms that drive carry-over effects, most notably macronutrient supply, and highlight the types of life histories and ecological situations where we would expect them to most often occur. We also identify a number of other potential mechanisms that require investigation, including micronutrients such as antioxidants. 3. We propose a series of experiments designed to estimate the relative contributions of extrinsic and intrinsic quality effects in the pre-breeding season, which in turn will allow an accurate estimation of the magnitude of carry-over effects. To date this has proven immensely difficult, and we hope that the experimental frameworks described here will stimulate new avenues of research vital to advancing our understanding of how carry-over effects can shape animal life histories. 4. We also explore the potential of state-dependent modelling as a tool for investigating carry-over effects, most notably for its ability to calculate optimal rates of acquisition of a multitude of resources over the course of the annual cycle, and also because it allows us to vary the strength of density-dependent relationships which can alter the magnitude of carry-over effects in either a synergistic or agonistic fashion. 5. In conclusion carry-over effects are likely to be far more widespread than currently indicated, and they are likely to be driven by a multitude of factors including both macro- and micronutrients. For this reason they could feasibly be responsible for a large amount of the observed variation in performance among individuals, and consequently warrant a wealth of new research designed specifically to decompose components of variation in fitness attributes related to processes across and within seasons.
not annotated - annotated - LINNAEUS only
General factors important for the formation of structured biofilm-like yeast colonies.
The lifestyle of wild and laboratory yeast strains significantly differs. In contrast to the smooth colonies of laboratory strains, wild Saccharomyces cerevisiae strains form biofilm-like, strikingly structured colonies possessing distinctive traits enabling them to better survive in hostile environments in the wild. Here, comparing three sets of strains forming differently structured colonies (fluffy, semi-fluffy and smooth), each derived from ancestors with distinct genetic backgrounds isolated from natural settings (BR-88, BR-99 and BR-103), we specified the factors essential for the formation of structured colonies, i.e. for the lifestyle most likely to be preferred in the wild. The ability to form an abundant extracellular matrix (ECM) is one of the features typical for structured colonies. ECM influences colony architecture and many other physiological properties, such as the capability to retain water in a 2-fold surplus to wet cell biomass. ECM composition, however, differs among distinct strains, depending on their particular genetic background. We further show that the expression of certain genes (AQY1, FLO11) is also strictly related to the particular colony morphology, being highest in the most structured colonies. Flo11p adhesin, important for cell-cell and cell-surface adhesion, is essential for the formation of fluffy colonies and thus significantly contributes to the phenotype variability of wild yeast strains. On the other hand, surprisingly, neither the cell shape nor budding pattern nor the ability to form pseudohyphae directly influences the formation of three-dimensional fluffy colony architecture.
not annotated - annotated - LINNAEUS only
Parallel evolution of cytochrome b mediated bifenazate resistance in the citrus red mite Panonychus citri.
Bifenazate is a recently developed acaricide that is mainly used to control spider mites on a variety of crops. Although first thought to be a neurotoxin, genetic evidence obtained from bifenazate resistant Tetranychus urticae strains suggested an alternative mode of action as a Qo pocket inhibitor of the mitochondrial complex III. In this study, we reveal how bifenazate resistance in strains of Panonychus citri is maternally inherited and can confer cross-resistance to the known Qo inhibitor acequinocyl. The mitochondrial genome of P. citri was sequenced and Qo pocket mutations were shown to be linked with the resistant trait. Parallel evolution of cytochrome b mediated bifenazate resistance corroborates the alternative mode of action and yet again illustrates that care should be taken when employing Qo inhibitors as crop protection compounds.
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Wildlife diseases: from individuals to ecosystems.
1. We review our ecological understanding of wildlife infectious diseases from the individual host to the ecosystem scale, highlighting where conceptual thinking lacks verification, discussing difficulties and challenges, and offering potential future research directions. 2. New molecular approaches hold potential to increase our understanding of parasite interactions within hosts. Also, advances in our knowledge of immune systems makes immunological parameters viable measures of parasite exposure, and useful tools for improving our understanding of causal mechanisms. 3. Studies of transmission dynamics have revealed the importance of heterogeneity in host behaviour and physiology, and of contact processes operating at different spatial and temporal scales. An important future challenge is to determine the key transmission mechanisms maintaining the persistence of different types of diseases in the wild. 4. Regulation of host populations is too complex to consider parasite effects in isolation from other factors. One solution is to seek a unified understanding of the conditions under which (and the ecological rules determining when) population scale impacts of parasites can occur. 5. Good evidence now shows that both direct effects of parasites, and trait mediated indirect effects, frequently mediate the success of invasive species and their impacts on recipient communities. A wider exploration of these effects is now needed. 6. At the ecosystem scale, research is needed to characterize the circumstances and conditions under which both fluxes in parasite biomass, and trait mediated effects, are significant in ecosystem processes, and to demonstrate that parasites do indeed increase 'ecosystem health'. 7. There is a general need for more empirical testing of predictions and subsequent development of theory in the classic research cycle. Experimental field studies, meta-analyses, the collection and analysis of long-term data sets, and data constrained modelling, will all be key to advancing our understanding. 8. Finally, we are only now beginning to understand the importance of cross-scale interactions associated with parasitism. Such interactions may offer key insights into bigger picture questions such as when and how different regulatory factors are important, when disease can cause species extinctions, and what characteristics are indicative of functionally resilient ecosystems.
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Can we predict indirect interactions from quantitative food webs?--an experimental approach.
1. Shared enemies may link the dynamics of their prey. Recently, quantitative food webs have been used to infer that herbivorous insect species attacked by the same major parasitoid species will affect each other negatively through apparent competition. Nonetheless, theoretical work predicts several alternative outcomes, including positive effects. 2. In this paper, we use an experimental approach to link food web patterns to realized population dynamics. First, we construct a quantitative food web for three dominant leaf miner species on the oak Quercus robur. We then measure short- and long-term indirect effects by increasing leaf miner densities on individual trees. Finally, we test whether experimental results are consistent with natural leaf miner dynamics on unmanipulated trees. 3. The quantitative food web shows that all leaf miner species share a minimum of four parasitoid species. While only a small fraction of the parasitoid pool is shared among Tischeria ekebladella and each of two Phyllonorycter species, the parasitoid communities of the congeneric Phyllonorycter species overlap substantially. 4. Based on the structure of the food web, we predict strong short- and long-term indirect interactions between the Phyllonorycter species, and limited interactions between them and T. ekebladella. As T. ekebladella is the main source of its own parasitoids, we expect to find intraspecific density-dependent parasitism in this species. 5. Consistent with these predictions, parasitism in T. ekebladella was high on trees with high densities of conspecifics in the previous generation. Among leaf miner species sharing more parasitoids, we found positive rather than negative interactions among years. No short-term indirect interactions (i.e. indirect interactions within a single generation) were detected. 6. Overall, this study is the first to experimentally demonstrate that herbivores with overlapping parasitoid communities may exhibit independent population dynamics - or even apparent mutualism. Hence, it proves the potential for versatile indirect interactions in nature, and suggests that the link between patterns in food web structure and realized population dynamics should be verified by rigorous experiments.
not annotated - annotated - LINNAEUS only
Comparison of transcriptional and translational changes caused by long-term menadione exposure in Aspergillus nidulans.
Under long-term oxidative stress caused by menadione sodium bisulfite, genome-wide transcriptional and proteome-wide translational changes were compared in Aspergillus nidulans vegetative cells. The comparison of proteomic and DNA microarray expression data demonstrated that global gene expression changes recorded with either flip-flop or dendrimer cDNA labeling techniques supported proteome changes moderately with 40% and 34% coincidence coefficients, respectively. Enzyme levels in the glycolytic pathway were alternating, which was a direct consequence of fluctuating gene expression patterns. Surprisingly, enzymes in the vitamin B2 and B6 biosynthetic pathways were repressed concomitantly with the repression of some protein folding chaperones and nuclear transport elements. Under long-term oxidative stress, the peroxide-detoxifying peroxiredoxins and cytochrome c peroxidase were replaced by thioredoxin reductase, a nitroreductase and a flavohemoprotein, and protein degradation became predominant to eliminate damaged proteins.
not annotated - annotated - LINNAEUS only
Contrasting impacts of climate-driven flowering phenology on changes in alien and native plant species distributions.
* Plant phenology is particularly sensitive to climate and a key indicator of environmental change. Globally, first flowering dates (FFDs) have advanced by several days per decade in response to recent climate warming, but, while earlier flowering should allow plant distributions to increase, a link between FFD and range changes has not been observed. * Here I show for 347 species that the extent to which FFD has responded to climate warming is linked to the degree to which their relative distributions have changed over 30 yr across the British Isles. * Native plant species whose phenology did not track climate change declined in distribution, whereas species that became more widespread all exhibited earlier flowering. In contrast, alien neophytes showed both a stronger phenological response to warming and a more marked increase in distribution, but no link between the two. * These trends were consistent both for relative changes in the national distribution and for local abundance. At the national scale, the more recently an alien species became established in Britain, the more likely it was to increase in distribution irrespective of FFD, suggesting that recent changes in alien species distributions are decoupled from climate and driven by other factors.
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A root is a root is a root? Water uptake rates of Citrus root orders.
Knowledge about the physiological function of root orders is scant. In this study, a system to monitor the water flux among root orders was developed using miniaturized chambers. Different root orders of 4-year-old Citrus volkameriana trees were analysed with respect to root morphology and water flux. The eight root orders showed a broad overlap in diameter, but differences in tissue densities and specific root area (SRA) were clearly distinguishable. Thirty per cent of the root branch biomass but 50% of the surface area (SA) was possessed by the first root order, while the fifth accounted for 5% of the SA (20% biomass). The root order was identified as a determinant of water flux. First-order roots showed a significantly higher rate of water uptake than the second and third root orders, whereas the fourth and fifth root orders showed water excess. The water excess suggested the occurrence of hydraulic redistribution (HR) as a result of differences in osmotic potentials. We suggest that plants may utilize hydraulic redistribution to prevent coarse root desiccation and/or to increase nutrient acquisition. Our study showed that the novel 'miniature depletion chamber' method enabled direct measurement of water fluxes per root order and can be a major tool for future studies on root order traits.
not annotated - annotated - LINNAEUS only
Increased intracellular H2O2 availability preferentially drives glutathione accumulation in vacuoles and chloroplasts.
One biochemical response to increased H2O2 availability is the accumulation of glutathione disulphide (GSSG), the disulphide form of the key redox buffer glutathione. It remains unclear how this potentially important oxidative stress response impacts on the different sub-cellular glutathione pools. We addressed this question by using two independent in situ glutathione labelling techniques in Arabidopsis wild type (Col-0) and the GSSG-accumulating cat2 mutant. A comparison of in situ labelling with monochlorobimane (MCB) and in vitro labelling with monobromobimane (MBB) revealed that, whereas in situ labelling of Col-0 leaf glutathione was complete within 2 h incubation, about 50% of leaf glutathione remained inaccessible to MCB in cat2. High-performance liquid chromatography (HPLC) and enzymatic assays showed that this correlated tightly with the glutathione redox state, pointing to significant in vivo pools of GSSG in cat2 that were unavailable for MCB labelling. Immunogold labelling of leaf sections to estimate sub-cellular glutathione distribution showed that the accumulated GSSG in cat2 was associated with only a minor increase in cytosolic glutathione but with a 3- and 10-fold increase in plastid and vacuolar pools, respectively. The data are used to estimate compartment-specific glutathione concentrations under optimal and oxidative stress conditions, and the implications for redox homeostasis and signalling are discussed.
not annotated - annotated - LINNAEUS only
Fungal secondary metabolites as modulators of interactions with insects and other arthropods.
Fungi share a diverse co-evolutionary history with animals, especially arthropods. In this review, we focus on the role of secondary metabolism in driving antagonistic arthropod-fungus interactions, i.e., where fungi serve as a food source to fungal grazers, compete with saprophagous insects, and attack insects as hosts for growth and reproduction. Although a wealth of studies on animal-fungus interactions point to a crucial role of secondary metabolites in deterring animal feeding and resisting immune defense strategies, causal evidence often remains to be provided. Moreover, it still remains an unresolved puzzle as to what extent the tight regulatory control of secondary metabolite formation in some model fungi represents an evolved chemical defense system favored by selective pressure through animal antagonists. Given these gaps in knowledge, we highlight some co-evolutionary aspects of secondary metabolism, such as induced response, volatile signaling, and experimental evolution, which may help in deciphering the ecological importance and evolutionary history of secondary metabolite production in fungi.
not annotated - annotated - LINNAEUS only
A multispecies perspective on ecological impacts of climatic forcing.
1. In the prevailing context of concerns over climate change and its potential impacts on ecosystems, evaluating ecological consequences of climatic forcing has become a critical issue. 2. Historical data on the abundance of organisms have been extensively used to characterize the ecological effects of climatic forcing through specific weather and/or climatic variables, with most of the studies confined to single population models. 3. However, population responses to environmental fluctuations typically depend upon positive and negative feedbacks induced by interactions with other species. It is therefore important to integrate the insights gained from single population approaches into a multispecies perspective. 4. Here we combine the hierarchical Bayesian modelling approach with the state-space formulation to extend the scope of previously proposed models of population dynamics under climatic forcing to multi-species systems. 5. We use our model to analyse long-term macro-moth (Lepidoptera) community data from the Rothamsted Insect Survey network in the UK, using winter rainfall and winter temperature as environmental covariates. 6. The effects of the two weather variables were consistent across species, being negative for winter rainfall and positive for winter temperature. The two weather variables jointly explained 15-40% of the total environmental variation affecting the dynamics of individual species, and could explain up to 90% of covariances in species dynamics. 7. The contribution of interspecific interactions to community-level variation was found to be weak compared to the contributions of environmental forcing and intraspecific interactions.
not annotated - annotated - LINNAEUS only
Cross-talk between light and glucose regulation controls toxin production and morphogenesis in Aspergillus nidulans.
Light is a major environmental stimulus that has a broad effect on organisms, triggering a cellular response that results in an optimal adaptation enhancing fitness and survival. In fungi, light affects growth, and causes diverse morphological changes such as those leading to reproduction. Light can also affect fungal metabolism, including the biosynthesis of natural products. In this study we show that in Aspergillus nidulans the effect of light on the production of the sterigmatocystin (ST) toxin depends on the glucose concentration. In cultures grown with 1% glucose and exposed to light, ST production was lower than when grown in the dark. This lower ST production coincided with an elevated rate of cellular damage with partial loss of nuclear integrity and vacuolated cytoplasm. However, in cultures grown with 2% glucose these effects were reversed and light enhanced ST production. Glucose abundance also affected the light-dependent subcellular localization of the VeA (velvet) protein, a key regulator necessary for normal light-dependent morphogenesis and secondary metabolism in Aspergilli and other fungal genera. The role of other VeA-associated proteins, particularly the blue-light-sensing proteins LreA and LreB (WC-1 and WC-2 orthologs), on conidiation could also be modified by the abundance of glucose. We also show that LreA and LreB, as well as the phytochrome FphA, modulate not only the synthesis of sterigmatocystin, but also the production of the antibiotic penicillin.
not annotated - annotated - LINNAEUS only
Characterization of the developmental regulator FlbE in Aspergillus fumigatus and Aspergillus nidulans.
Several upstream developmental activators control asexual development (conidiation) in Aspergillus. In this study, we characterize one of such activators called flbE in Aspergillus fumigatus and Aspergillus nidulans. The predicted FlbE protein is composed of 222 and 201 aa in A. fumigatus and A. nidulans, respectively. While flbE is transiently expressed during early phase of growth in A. nidulans, it is somewhat constitutively expressed during the lifecycle of A. fumigatus. The deletion of flbE causes reduced conidiation and delayed expression of brlA and vosA in both species. Moreover, FlbE is necessary for salt-induced development in liquid submerged culture in A. fumigatus. The A. nidulans flbE null mutation is fully complemented by A. fumigatus flbE, indicating a functional conservancy of FlbE in Aspergillus. Both the deletion and overexpression of flbE in A. nidulans result in developmental defects, enhanced autolysis, precocious cell death, and delayed expression of brlA/vosA, suggesting that balanced activity of FlbE is crucial for proper growth and development. Importantly, the N-terminal portion of FlbE exhibits the trans-activation ability in yeast, whereas the C-terminal half negatively affects its activity. Site-directed mutagenesis of certain conserved N-terminal amino acids abolishes the ability of trans-activation, overexpression-induced autolysis, and complementing the null mutation. Finally, overexpression of flbD, but not flbB or flbC, restores conidiation in A. nidulans DeltaflbE, generally supporting the current genetic model for developmental regulation.
not annotated - annotated - LINNAEUS only
Dinoflagellates associated with freshwater sponges from the ancient lake baikal.
Dinoflagellates are a diverse group of protists that are common in both marine and freshwater environments. While the biology of marine dinoflagellates has been the focus of several recent studies, their freshwater relatives remain little-investigated. In the present study we explore the diversity of dinoflagellates in Lake Baikal by identifying and analyzing dinoflagellate sequences for 18S rDNA and ITS-2 from total DNA extracted from three species of endemic Baikalian sponges (Baikalospongia intermedia, Baikalospongia recta and Lubomirskia incrustans). Phylogenetic analyses of these sequences revealed extensive dinoflagellate diversity in Lake Baikal. We found two groups of sequences clustering within the order Suessiales, known for its symbiotic relationships with various invertebrates. Thus they may be regarded as potential symbionts of Baikalian sponges. In addition,Gyrodinium helveticum, representatives from the genus Gymnodinium, dinoflagellates close to the family Pfiesteriaceae, and a few dinoflagellates without definite affiliation were detected. No pronounced difference in the distribution of dinoflagellates among the studied sponges was found, except for the absence of the Piscinoodinium-like dinoflagellates in L. incrustans. To the best of our knowledge, this is the first study of the diversity of dinoflagellates in freshwater sponges, the first systematic investigation of dinoflagellate molecular diversity in Lake Baikal and the first finding of members of the order Suessiales as symbionts of freshwater invertebrates.
not annotated - annotated - LINNAEUS only
Transcription factors BmPOUM2 and BmBetaFTZ-F1 are involved in regulation of the expression of the wing cuticle protein gene BmWCP4 in the silkworm, Bombyx mori.
In Bombyx mori, the wing cuticle protein gene BmWCP4 is expressed specifically in the epidermis at the onset and mid-stage of pupation and is responsible for the formation of the pupal cuticle during the larval-pupal metamorphosis. The gene consists of four exons and three introns and is present as a single copy in the genome. Its expression was up-regulated by 20-hydroxyecdysone (20E) and the 20E-induced expression was suppressed by juvenile hormone (JH) III. The upstream regulatory sequence region of the BmWCP4 gene was cloned and the regulatory elements responsible for 20E induction were identified. Two cis-regulatory elements (CREs) bound by the transcription factors BmPOUM2 and BmBetaFTZ-F1 were identified that mediated 20E-regulated expression of this gene. An electrophoretic mobility shift assay detected two nuclear proteins isolated from the epidermis and the BmN cell line that specifically bound to the POU and BetaFTZ-F1 CREs, respectively. BmPOUM2 recombinant protein explicitly bound to the POU CRE. Developmental and 20E-induced expression of the BmWCP4, BmPOUM2 and BmBetaFTZ-F1 genes showed that BmPOUM2 and BmBetaFTZ-F1 were initially expressed, followed by BmWCP4. These data suggest that the 20E-induced expression of BmWCP4 is mediated by the transcription factors BmPOUM2 and BmBetaFTZ-F1 binding to their CREs in the regulatory sequence region of the BmWCP4 gene.
not annotated - annotated - LINNAEUS only
Drought limitation of photosynthesis differs between C3and C4grass species in a comparative experiment.
Phylogenetic analyses show that C4 grasses typically occupy drier habitats than their C3 relatives, but recent experiments comparing the physiology of closely related C3 and C4 species have shown that advantages of C4 photosynthesis can be lost under drought. We tested the generality of these paradoxical findings in grass species representing the known evolutionary diversity of C4 NADP-me and C3 photosynthetic types. Our experiment investigated the effects of drought on leaf photosynthesis, water potential, nitrogen, chlorophyll content and mortality. C4 grasses in control treatments were characterized by higher CO2 assimilation rates and water potential, but lower stomatal conductance and nitrogen content. Under drought, stomatal conductance declined more dramatically in C3 than C4 species, and photosynthetic water-use and nitrogen-use efficiency advantages held by C4 species under control conditions were each diminished by 40%. Leaf mortality was slightly higher in C4 than C3 grasses, but leaf condition under drought otherwise showed no dependence on photosynthetic-type. This phylogenetically controlled experiment suggested that a drought-induced reduction in the photosynthetic performance advantages of C4 NADP-me relative to C3 grasses is a general phenomenon.
not annotated - annotated - LINNAEUS only
OsRAN2, essential for mitosis, enhances cold tolerance in rice by promoting export of intranuclear tubulin and maintaining cell division under cold stress.
With global climate change, abnormally low temperatures have affected the world's rice production. Many genes have been shown to be essential for molecular improvement of rice cold-tolerance traits. However, less is known about the molecular cellular mechanism of their response to cold stress. Here, we investigated OsRAN2 involved in regulation of cell division during cold stress in rice. Expression of OsRAN2 was increased under cold treatment, but not during salt and drought stress. The mean root mitotic index was closely related to the expression level of OsRAN2. Knockdown transgenic rice lines showed an aberrant organization of spindles during mitosis and stunted growth during development. Overexpression of OsRAN2 enhanced cold tolerance in rice. The transgenic rice overexpressing OsRAN2 showed maintained cell division, decreased proportion of cells with intranuclear tubulin and formation of a normal nuclear envelope under the cold condition. Our study suggests a mechanism for OsRAN2 in regulating cold resistance in rice by maintaining cell division through promoting the normal export of intranuclear tubulin at the end of mitosis. This insight could help improve the cold-tolerance trait in rice.
not annotated - annotated - LINNAEUS only
Drought increases freezing tolerance of both leaves and xylem of Larrea tridentata.
Drought and freezing are both known to limit desert plant distributions, but the interaction of these stressors is poorly understood. Drought may increase freezing tolerance in leaves while decreasing it in the xylem, potentially creating a mismatch between water supply and demand. To test this hypothesis, we subjected Larrea tridentata juveniles grown in a greenhouse under well-watered or drought conditions to minimum temperatures ranging from -8 to -24 ^0C. We measured survival, leaf retention, gas exchange, cell death, freezing point depression and leaf-specific xylem hydraulic conductance (k1). Drought-exposed plants exhibited smaller decreases in gas exchange after exposure to -8 ^0C compared to well-watered plants. Drought also conferred a significant positive effect on leaf, xylem and whole-plant function following exposure to -15 ^0C; drought-exposed plants exhibited less cell death, greater leaf retention, higher k1 and higher rates of gas exchange than well-watered plants. Both drought-exposed and well-watered plants experienced 100% mortality following exposure to -24 ^0C. By documenting the combined effects of drought and freezing stress, our data provide insight into the mechanisms determining plant survival and performance following freezing and the potential for shifts in L. tridentata abundance and range in the face of changing temperature and precipitation regimes.
not annotated - annotated - LINNAEUS only
Nitrogen source interacts with ROP signalling in root hair tip-growth.
Root hairs elongate in a highly polarized manner known as tip growth. Overexpression of constitutively active Rho of Plant (ROP)/RAC GTPases mutants induces swelling of root hairs. Here, we demonstrate that Atrop11(CA)-induced swelling of root hairs depends on the composition of the growth medium. Depletion of ammonium allowed normal root hair elongation in Atrop11(CA) plants, induced the development of longer root hairs in wild-type plants and suppressed the effect of Atrop11(CA) expression on actin organization and reactive oxygen species distribution, whereas membrane localization of the protein was not affected. Ammonium at concentrations higher than 1 mM and the presence of nitrate were required for induction of swelling. Oscillations in wall and cytoplasmic pH are known to accompany tip growth in root hairs, and buffering of the growth medium decreased Atrop11(CA)-induced swelling. Fluorescence ratio imaging experiments revealed that in wild-type root hairs, the addition of NH4NO3 to the growth medium induced an increase in the amplitude of extracellular and intracellular pH oscillations and an overall decrease in cytoplasmic pH at the cell apex. Based on these results, we suggest a model in which ROP GTPases and nitrogen-dependent pH oscillations function in parallel pathways, creating a positive feedback loop during root hair growth.
not annotated - annotated - LINNAEUS only
Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin.
Most photosynthetic dinoflagellates possess plastids containing chlorophyllsa+c,but species belonging to the genus Lepidodinium are unique in bearing non-canonical plastids containing chlorophyllsa+b. According to the pioneering works on pigment composition data, it has been proposed that Lepidodinium plastids were derived from a prasinophyte species, though this hypothesis was not supported by a recent phylogenetic analysis based on an alignment comprised of eight plastid proteins (Takishita et al. 2008, Gene 410: 26-26). This "8-protein" analysis however was insufficient to clarify the origin of Lepidodinium plastids for two major reasons: First, the alignment lacked sufficient evolutionary information to resolve the precise origin of Lepidodinium plastids. Second, the taxa considered did not well represent the diversity of Chlorophyta. Particularly, prasinophytes were poorly sampled in the alignment. In this study, we sequenced plastid-encoded genes from L. chlorophorum, one pedinophyte species, one ulvophyte species, and six prasinophyte species. The 85 sequences newly determined in this study and recent progress in plastid genome sequencing enabled us to prepare an alignment comprised of 11 plastid proteins from green algal taxa that appropriately cover the diversity of Chlorophyta. All the analyses of the 11-protein data set robustly grouped L. chlorophorum with members of the "core chlorophytes." Thus, we here propose that Lepidodinium plastids are of core chlorophyte origin.
not annotated - annotated - LINNAEUS only
Floret initiation, tissue expansion and carbon availability at the meristem of the sunflower capitulum as affected by water or light deficits.
* The co-ordination between floret initiation and meristem expansion, and their relationships with carbon availability, were studied and quantified in sunflower (Helianthus annuus) plants subjected to light or water shortages. * Meristem size, number of floret primordia, primordium size, rate of plant biomass accumulation, leaf area, photosynthetic rate, and soluble sugar content in the capitulum were measured until completion of floret initiation. * Although treatments differentially affected tissue expansion and biomass acquisition, a common relationship between the final number of florets and the rate and duration of meristem expansion was conserved. In the absence of water deficit, changes in relative expansion rate in the meristem paralleled changes in soluble sugar content. Water deficit reduced tissue expansion both in leaves and in the capitulum, and induced the accumulation of soluble sugars in the meristem. Use of these sugars at re-watering was associated with increased meristem growth and higher floret numbers compared with control plants. * Floret initiation and meristem tissue expansion remained strongly co-ordinated under all studied circumstances, and both depended on local carbon availability when water supply was unlimited. Transient water deficits favoured reproductive meristem growth and floret production. Equations accounting for these results constitute a framework for phenotyping the response to drought.
not annotated - annotated - LINNAEUS only
A hydraulic explanation for size-specific plant shrinkage: developmental hydraulic sectoriality.
* While great attention has been paid to the mechanisms controlling plant growth, much less is known about why and how plants shrink. The modular design of plants may facilitate the independence of modules if the xylem vasculature is hydraulically sectored. We examined the hydraulic connectivity of modules comprising juveniles and adults of the aridland chamaephyte Cryptantha flava (Boraginaceae), motivated by the observation that rosette mortality is spatially aggregated in adults, but not in juveniles. * We explored spatial patterns of leaf wilting after clipping a single lateral root, tracked physiological dyes taken up by a single root, and measured within-plant variation in leaf water potentials after watering a portion of the root system. We then measured xylem anatomical features related to hydraulic connectivity. * Our approaches revealed hydraulic integration in juveniles but hydraulic sectoriality in adults. We attribute such developmental changes to increasing distances between xylem bundles, and larger xylem lumen and heartwood areas as plants age. * We have demonstrated functional sectoriality in a desert chamaephyte, and report the mechanism by which sectoriality occurs, offering a hydraulic explanation for the death of whole plant portions resulting in shrinkage of large plants, and for the high occurrence of this design in deserts.
not annotated - annotated - LINNAEUS only
Bird community specialization, bird conservation and disturbance: the role of wildfires.
1. Although niche theory predicts that disturbance should favour generalist species, the community-level implications of this pattern have been sparsely analysed. Here, we test the hypothesis that disturbance favours generalist species within communities, analysing effects of wildfires in bird communities in a Mediterranean climate area as a case study. 2. We use bird occurrence data in more than 500 1 x 1 km squares forming a gradient running from forest to completely burnt areas. The level of specialization of bird communities was estimated by means of three complementary species specialization indices, calculated for different landscape gradients and averaged at the community level (i.e. 1 x 1 km squares), and mean species rarity. 3. We also calculated mean habitat preferences along landscape gradients, as well as an index of conservation value and total species richness. 4. Different estimators of bird community specialization varied in contrasting fashion along the wildfire disturbance gradient, and thus we conclude that it is not justified to expect unique community responses to the sharp variations in habitat characteristics brought by wildfire disturbances. 5. Burnt areas tended to have rarer and urban-avoider bird species, whereas unburnt forests tended to have larger proportions of forest specialist species. 6. The mean conservation value of communities clearly increased towards the burnt extreme of the wildfire disturbance gradient, while this had a negligible effect on species richness. 7. Wildfires seem to play an important role for the maintenance of open-habitat, urban-avoider bird populations in Mediterranean landscapes and also to benefit a set of bird species of unfavourable European conservation status. 8. In this context, it cannot be unambiguously concluded that fire disturbance, even in a context in which fires are greatly favoured by human-related activities, leads to more functionally simplified communities dominated by generalist species.
not annotated - annotated - LINNAEUS only
Contrasting patterns of individual specialization and trophic coupling in two marine apex predators.
1. Apex predators are often assumed to be dietary generalists and, by feeding on prey from multiple basal nutrient sources, serve to couple discrete food webs. But there is increasing evidence that individual level dietary specialization may be common in many species, and this has not been investigated for many marine apex predators. 2. Because of their position at or near the top of many marine food webs, and the possibility that they can affect populations of their prey and induce trophic cascades, it is important to understand patterns of dietary specialization in shark populations. 3. Stable isotope values from body tissues with different turnover rates were used to quantify patterns of individual specialization in two species of 'generalist' sharks (bull sharks, Carcharhinus leucas, and tiger sharks, Galeocerdo cuvier). 4. Despite wide population-level isotopic niche breadths in both species, isotopic values of individual tiger sharks varied across tissues with different turnover rates. The population niche breadth was explained mostly by variation within individuals suggesting tiger sharks are true generalists. In contrast, isotope values of individual bull sharks were stable through time and their wide population level niche breadth was explained by variation among specialist individuals. 5. Relative resource abundance and spatial variation in food-predation risk tradeoffs may explain the differences in patterns of specialization between shark species. 6. The differences in individual dietary specialization between tiger sharks and bull sharks results in different functional roles in coupling or compartmentalizing distinct food webs. 7. Individual specialization may be an important feature of trophic dynamics of highly mobile marine top predators and should be explicitly considered in studies of marine food webs and the ecological role of top predators.
not annotated - annotated - LINNAEUS only
Genetic mapping of 14 avirulence genes in an EU-B04 x 1639 progeny of Venturia inaequalis.
Durable resistance to apple scab (Venturia inaequalis (Cke) Wint; anamorph Spilocaea pomi Fries) is one of the major goals of apple (Malus) breeding programs. Since current scab resistance breeding is heavily reliant on genes with gene-for-gene relationships, a good understanding of the genetic basis of host-pathogen interactions needs to be developed for this strategy to be successful. While the genomic organization of apple scab resistance genes has been studied extensively, little is known about the avirulence genes in the pathogen. The progeny of a cross of European V. inaequalis race (1) isolate EU-B04 and race (1,2,8,9) isolate 1639 was used to generate a genetic map based on microsatellite and AFLP markers, and investigated for inheritance of avirulence traits on 20 Malus accessions representing 17 scab resistance genes. The accessions comprised scab differential hosts (0), (1), (2), (8), and (9), and hosts carrying known as well as not previously reported secondary resistance genes, including some identified in crosses that have resistant accessions 'Geneva', 'Dolgo', Malus baccata jackii, M. micromalus, or 'Antonovka' in their pedigree. The latter genes appear to be narrow spectrum genes that showed gene-for-gene relationships as a segregation ratio of Avr:avr=1:1 was observed on 12 accessions, while a ratio of 3:1 was observed on five accessions and a ratio of 7:1 on one host. All progenies were shown to be pathogenic, as all of them were able to infect hosts (0) and (1). A genetic map consisting of 15 major linkage groups (LGs) and spanning 972cM was generated with the aid of 156 markers. The map position of 12 avirulence traits was determined: eight avirulence genes mapped into two separate clusters (1: AvrVdg2, AvrVv1, AvrVu1, AvrVrjrd; and 2: AvrVu2, AvrVh3.2, AvrVs1, AvrVu4), while four avirulence genes (AvrRvi8, AvrVv2, AvrVt57 and AvrVsv) mapped to different LGs. AvrRvi2 and AvrRvi9 also are genetically linked, but showed an interaction with AvrRvi8, the nature of which is unclear. While AvrRvi8 segregated at 1:1 ratio, the other two Avrs segregated at 3:1 ratios. However, all progeny avirulent on hosts (2) and (9) were also avirulent on host (8) and further research is required to determine the avirulence gene relationships. A further two independently segregating loci, AvrRvi1 and AvrRvi6, identified in previous studies, were mapped by inference based on their known linkage to SSR markers. The clustering of avirulence genes in V. inaequalis reflecting the clustering of resistance genes in Malus suggests this pathosystem is a classical example of an "arms race" between host and pathogen. This also seems to apply to the narrow spectrum scab resistance genes, which may imply a larger role in plant defense for these genes than has been assumed to date.
not annotated - annotated - LINNAEUS only
Functional characterization of Arabidopsis thaliana isopropylmalate dehydrogenases reveals their important roles in gametophyte development.
* Isopropylmalate dehydrogenases (IPMDHs) catalyze the oxidative decarboxylation of 3-isopropylmalate (3-IPM) in leucine biosynthesis in microorganisms. The Arabidopsis thaliana genome contains three putative IPMDH genes. * IPMDH2 and IPMDH3 proteins exhibited significantly higher activity toward 3-IPM than IPMDH1, which is indicative of a pivotal role in leucine biosynthesis. Single mutants of IPMDH2 or IPMDH3 lacked a discernible phenotype. Genetic analysis showed that ipmdh2 ipmdh3 was lethal in male gametophytes and had reduced transmission through female gametophytes. The aborted pollen grains were small, abnormal in cellular structure, and arrested in germination. In addition, half of the double mutant embryo sacs exhibited slowed development. * The IPMDH2/ipmdh2 ipmdh3/ipmdh3 genotype exhibited abnormal vegetative phenotypes, suggesting haplo-insufficiency of IPMDH2 in the ipmdh3 background. This mutant and a triple mutant containing one allele of IPMDH2 or IPMDH3 had decreased leucine biosynthetic enzyme activities and lower free leucine concentrations. The latter mutant showed changes in glucosinolate profiles different from those in the ipmdh1 mutant. * The results demonstrate that IPMDH2 and IPMDH3 primarily function in leucine biosynthesis, are essential for pollen development and are needed for proper embryo sac development.
not annotated - annotated - LINNAEUS only
OsHMA3, a P1B-type of ATPase affects root-to-shoot cadmium translocation in rice by mediating efflux into vacuoles.
* The cadmium (Cd) over-accumulating rice (Oryza sativa) cv Cho-Ko-Koku was previously shown to have an enhanced rate of root-to-shoot Cd translocation. This trait is controlled by a single recessive allele located at qCdT7. * In this study, using positional cloning and transgenic strategies, heavy metal ATPase 3 (OsHMA3) was identified as the gene that controls root-to-shoot Cd translocation rates. The subcellular localization and Cd-transporting activity of the gene products were also investigated. * The allele of OsHMA3 that confers high root-to-shoot Cd translocation rates (OsHMA3mc) encodes a defective P(1B) -ATPase transporter. OsHMA3 fused to green fluorescent protein was localized to vacuolar membranes in plants and yeast. An OsHMA3 transgene complemented Cd sensitivity in a yeast mutant that lacks the ability to transport Cd into vacuoles. By contrast, OsHMA3mc did not complement the Cd sensitivity of this yeast mutant, indicating that the OsHMA3mc transport function was lost. * We propose that the root cell cytoplasm of Cd-overaccumulating rice plants has more Cd available for loading into the xylem as a result of the lack of OsHMA3-mediated transportation of Cd to the vacuoles. This defect results in Cd translocation to the shoots in higher concentrations. These data demonstrate the importance of vacuolar sequestration for Cd accumulation in rice.
not annotated - annotated - LINNAEUS only
Spatial distribution of arsenic and temporal variation of its concentration in rice.
* In order to gain insights into the transport and distribution of arsenic (As) in intact rice (Oryza sativa) plants and its unloading into the rice grain, we investigated the spatial distribution of As and the temporal variation of As concentration in whole rice plants at different growth stages. To the best of our knowledge, this is the first time that such a study has been performed. * Inductively coupled plasma mass spectroscopy (ICP-MS) and high-performance liquid chromatography (HPLC)-ICP-MS were used to analyze total As concentration and speciation. Moreover, synchrotron-based X-ray fluorescence (SXRF) was used to investigate in situ As distribution in the leaf, internode, node and grain. * Total As concentrations of vegetative tissues increased during the 2 wk after flowering. The concentration of dimethylarsinic acid (DMA) in the caryopsis decreased progressively with its development, whereas inorganic As concentration remained stable. The ratios of As content between neighboring leaves or between neighboring internodes were c. 0.6. SXRF revealed As accumulation in the center of the caryopsis during its early development and then in the ovular vascular trace. * These results indicate that there are different controls on the unloading of inorganic As and DMA; the latter accumulated mainly in the caryopsis before flowering, whereas inorganic As was mainly transported into the caryopsis during grain filling. Moreover, nodes appeared to serve as a check-point in As distribution in rice shoots.
not annotated - annotated - LINNAEUS only
Reduced predator species richness drives the body gigantism of a frog species on the Zhoushan Archipelago in China.
1. Shifts in the body size of insular vertebrates have been an interesting theme in ecological and evolutionary studies. Four primary factors, including predation pressures, resource availability, inter-species competition and immigrant selection, have been proposed to explain the trend in insular body size. Life-history theory predicts that body size, average age, the proportion of old-aged members and the density of insular populations are negatively correlated with predator species richness, and that body size and population density are positively related to resource availability. The niche expansion hypothesis argues that a positive relationship is expected to exist between insular body size and prey size, which varies in response to extinction due to small or large competitors. The immigrant hypothesis predicts that insular body size is positively correlated with distance to the mainland. 2. We tested these hypotheses by using populations of rice frogs Rana limnocharis on 20 islands in the Zhoushan Archipelago and two sites of nearby mainland China. 3. The body size (snout-vent length) of rice frogs on half of the islands was larger before and after the variable of age was controlled for; rice frog density and prey availability was higher and prey size was larger on most of the islands as compared to the two mainland sites. On the islands, the body size and other features [e.g. average age, the proportion of old-aged frogs (ages 3 and 4) and density] of the rice frogs were negatively associated with predator species richness; female body size and other features were positively associated with prey availability. The inference of multivariate linear models based on corrected Akaike Information Criterion (AIC(c) ) showed that the relative importance of predator species richness on body size and each of the other features was larger than that of prey availability, prey size and distance to the mainland. In addition, the parameters for predator species richness were all negative. 4. The results provided strong support for the life-history theory of predation pressures, but weak evidence for the life-history theory of prey availability, the niche expansion or the immigrant hypothesis. The reduced predator species richness was a dominant factor contributing to the body gigantism of rice frogs on the islands.
not annotated - annotated - LINNAEUS only
Contrasted demographic responses facing future climate change in Southern Ocean seabirds.
1. Recent climate change has affected a wide range of species, but predicting population responses to projected climate change using population dynamics theory and models remains challenging, and very few attempts have been made. The Southern Ocean sea surface temperature and sea ice extent are projected to warm and shrink as concentrations of atmospheric greenhouse gases increase, and several top predator species are affected by fluctuations in these oceanographic variables. 2. We compared and projected the population responses of three seabird species living in sub-tropical, sub-Antarctic and Antarctic biomes to predicted climate change over the next 50 years. Using stochastic population models we combined long-term demographic datasets and projections of sea surface temperature and sea ice extent for three different IPCC emission scenarios (from most to least severe: A1B, A2, B1) from general circulation models of Earth's climate. 3. We found that climate mostly affected the probability to breed successfully, and in one case adult survival. Interestingly, frequent nonlinear relationships in demographic responses to climate were detected. Models forced by future predicted climatic change provided contrasted population responses depending on the species considered. The northernmost distributed species was predicted to be little affected by a future warming of the Southern Ocean, whereas steep declines were projected for the more southerly distributed species due to sea surface temperature warming and decrease in sea ice extent. For the most southerly distributed species, the A1B and B1 emission scenarios were respectively the most and less damaging. For the two other species, population responses were similar for all emission scenarios. 4. This is among the first attempts to study the demographic responses for several populations with contrasted environmental conditions, which illustrates that investigating the effects of climate change on core population dynamics is feasible for different populations using a common methodological framework. Our approach was limited to single populations and have neglected population settlement in new favourable habitats or changes in inter-specific relations as a potential response to future climate change. Predictions may be enhanced by merging demographic population models and climatic envelope models.
not annotated - annotated - LINNAEUS only
The role of abscisic acid and water stress in root herbivore-induced leaf resistance.
* Herbivore-induced systemic resistance occurs in many plants and is commonly assumed to be adaptive. The mechanisms triggered by leaf-herbivores that lead to systemic resistance are largely understood, but it remains unknown how and why root herbivory also increases resistance in leaves. * To resolve this, we investigated the mechanism by which the root herbivore Diabrotica virgifera induces resistance against lepidopteran herbivores in the leaves of Zea mays. * Diabrotica virgifera infested plants suffered less aboveground herbivory in the field and showed reduced growth of Spodoptera littoralis caterpillars in the laboratory. Root herbivory did not lead to a jasmonate-dependent response in the leaves, but specifically triggered water loss and abscisic acid (ABA) accumulation. The induction of ABA by itself was partly responsible for the induction of leaf defenses, but not for the resistance against S. littoralis. Root-herbivore induced hydraulic changes in the leaves, however, were crucial for the increase in insect resistance. * We conclude that the induced leaf resistance after root feeding is the result of hydraulic changes, which reduce the quality of the leaves for chewing herbivores. This finding calls into question whether root-herbivore induced leaf-resistance is an evolved response.
not annotated - annotated - LINNAEUS only
Do quantitative vessel and pit characters account for ion-mediated changes in the hydraulic conductance of angiosperm xylem?
* The hydraulic conductance of angiosperm xylem has been suggested to vary with changes in sap solute concentrations because of intervessel pit properties. * The magnitude of the 'ionic effect' was linked with vessel and pit dimensions in 20 angiosperm species covering 13 families including six Lauraceae species. * A positive correlation was found between ionic effect and vessel grouping parameters, especially the portion of vessel walls in contact with neighbouring vessels. Species with intervessel contact fraction (F(C)) values < 0.1 showed an ionic effect between 2% and 17%, while species with F(C) values > 0.1 exhibited a response between 10% and 32%. The ionic effect increased linearly with the mean fraction of the total vessel wall area occupied by intervessel pits as well as with the intervessel contact length. However, no significant correlation occurred between the ionic effect and total intervessel pit membrane area per vessel, vessel diameter, vessel length, vessel wall area, and intervessel pit membrane thickness. * Quantitative vessel and pit characters are suggested to contribute to interspecific variation of the ionic effect, whereas chemical properties of intervessel pit membranes are likely to play an additional role.
not annotated - annotated - LINNAEUS only
Identification and characterization of genes responsible for biosynthesis of kojic acid, an industrially important compound from Aspergillus oryzae.
Kojic acid is produced in large amounts by Aspergillus oryzae as a secondary metabolite and is widely used in the cosmetic industry. Glucose can be converted to kojic acid, perhaps by only a few steps, but no genes for the conversion have thus far been revealed. Using a DNA microarray, gene expression profiles under three pairs of conditions significantly affecting kojic acid production were compared. All genes were ranked using an index parameter reflecting both high amounts of transcription and a high induction ratio under producing conditions. After disruption of nine candidate genes selected from the top of the list, two genes of unknown function were found to be responsible for kojic acid biosynthesis, one having an oxidoreductase motif and the other a transporter motif. These two genes are closely associated in the genome, showing typical characteristics of genes involved in secondary metabolism.
not annotated - annotated - LINNAEUS only
Identification of the structural proteins of VP1 and VP2 of a novel mud crab dicistrovirus.
Mud crab dicistrovirus (MCDV), a newly identified single-stranded positive RNA virus, is an important pathogen that causes serious economic losses to mud crab aquaculture. In this study, MCDV was purified, and three structural proteins of MCDV were separated by SDS-PAGE. The N-terminal 15 amino acids were sequenced and aligned with the main structural proteins of other dicistrovirus. The three structural proteins were named VP1, VP2 and VP3. Monoclonal antibodies (MAbs) against the two main structural proteins, VP1 and VP2, were prepared, and the two structural proteins were then identified using these MAbs. The results of Western blot analyses demonstrated that five MAbs recognised VP1 and two recognised VP2. The results of immunogold transmission electron microscopy (IEM) revealed that the epitopes of the two structural proteins recognised by the MAbs were located at the outer surface of the virions, which suggested that the two structural proteins are MCDV capsid proteins. The identification of the two structural proteins of MCDV is useful for studying their functions, as well as the mechanism of infection and the pathogenesis of MCDV.
not annotated - annotated - LINNAEUS only
SGT1 contributes to coronatine signaling and Pseudomonas syringae pv. tomato disease symptom development in tomato and Arabidopsis.
* Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) causes an economically important bacterial speck disease on tomato and produces symptoms with necrotic lesions surrounded by chlorosis. The chlorosis is mainly attributed to a jasmonic acid (JA)-isoleucine analogue, coronatine (COR), produced by Pst DC3000. However, the molecular processes underlying lesion development and COR-induced chlorosis are poorly understood. * In this study, we took advantage of a chlorotic phenotype elicited by COR on Nicotiana benthamiana leaves and virus-induced gene silencing (VIGS) as a rapid reverse genetic screening tool and identified a role for SGT1 (suppressor of G2 allele of skp1) in COR-induced chlorosis. * Silencing of SGT1 in tomato resulted in reduction of disease-associated symptoms (cell death and chlorosis), suggesting a molecular connection between COR-induced chlorosis and cell death. In Arabidopsis, AtSGT1b but not AtSGT1a was required for COR responses, including root growth inhibition and Pst DC3000 symptom (water soaked lesion) development. Notably, overexpression of AtSGT1b did not alter Pst DC3000 symptoms or sensitivity to COR. * Taken together, our results demonstrate that SGT1/SGT1b is required for COR-induced chlorosis and subsequent necrotic disease development in tomato and Arabidopsis. SGT1 is therefore a component of the COR/JA-mediated signal transduction pathway.
not annotated - annotated - LINNAEUS only
Growth-mediated stress escape: convergence of signal transduction pathways activated upon exposure to two different environmental stresses.
* Plants can escape from specific environmental stresses through active growth strategies. Here, we compared two such stress-escape syndromes to investigate whether plants use conserved signal transduction pathways to escape from different stresses. * Full submergence is a threat to terrestrial plants as it cuts off their access to oxygen and CO(2). Proximate neighbors, in contrast, take away resources such as light. Both submergence and shade can be escaped through rapid shoot elongation. We analysed the precise kinetics and physiological control of petiole elongation responses to shade and submergence in the flood-tolerant species Rumex palustris. * We found that petiole elongation induced by submergence and that induced by shade occurred with similar kinetics, both involving cell expansion. These responses were induced by two different signals, elevated ethylene and a reduced red : far-red light ratio (R : FR), respectively. A downstream target for ethylene was abscisic acid, but low R : FR appeared to act independently of this hormone. Gibberellin, however, appeared to be essential to both ethylene- and low R : FR-induced petiole elongation. * We propose that gibberellin and expansins, a family of cell wall-loosening proteins, represent elements of a conserved growth machinery that is activated by stress-specific signaling events to regulate escape from stress.
not annotated - annotated - LINNAEUS only
PsOr1, a potential target for RNA interference-based pest management.
Insect pests cause billions of dollars in agricultural losses, and attempts to kill them have resulted in growing threats from insecticide resistance, dietary pesticide pollution and environmental destruction. New approaches to control refractory insect pests are therefore needed. The host-plant preferences of insect pests rely on olfaction and are mediated via a seven transmembrane-domain odorant receptor (Or) family. The present study reports the cloning and characterization of PsOr1, the first candidate member of the Or gene family from Phyllotreta striolata, a devastating beetle pest that causes damage worldwide. PsOr1 is remarkably well conserved with respect to other insect orthologues, including DmOr83b from Drosophila melanogaster. These insect orthologues form an essential non-conventional Or sub-family and may play an important and generalized role in insect olfaction. We designed double-stranded (ds) RNA directly against the PsOr1 gene and exploited RNA interference (RNAi) to control P. striolata. The chemotactic behavioural measurements showed that adult beetles were unable to sense the attractant or repellent odour stimulus after microinjection of dsRNA against PsOr1. Reverse Transcription (RT)-PCR analysis showed specific down-regulation of mRNA transcript levels for this gene. Furthermore, host-plant preference experiments confirmed that silencing PsOr1 by RNAi treatment impaired the host-plant preferences of P. striolata for cruciferous vegetables. These results demonstrate that this insect control approach of using RNAi to target PsOr1 and its orthologues might be effective in blocking host-plant-seeking behaviours in diverse insect pests. The results also support the theory that this unique receptor type plays an essential general role in insect olfaction.
not annotated - annotated - LINNAEUS only
Expression of diverse midgut serine proteinases in the sericigenous Lepidoptera Antheraea assamensis (Helfer) is influenced by choice of host plant species.
Antheraea assamensis is reared on various species of the Lauraceae family from north-east India for its distinctive cocoon silk. We demonstrate differential expression of digestive trypsin and chymotrypsins in larvae feeding on a primary host, Persea bombycina Kosterm., in comparison to larvae feeding on Litsea monopetala Roxb. using in vitro proteolytic assays, zymogram analyses with proteinase inhibitors, restriction digestion of RNA-PCR amplicons and quantitative real-time PCR (RT-PCR). Eight novel members of the serine proteinase gene family were identified, including an intron-spliced trypsin (AaPb4) and seven putative chymotrypsins (AaPb2, AaPb4, AaPb12, AaLm4, AaLm6, AaLm19 and AaLm29). Midgut transcript levels of the putative trypsin were higher in larvae fed P. bombycina whereas levels of transcripts encoding putative chymotrypsins were higher in larvae reared on L. monopetala. Complex, differential expression of sequence divergent midgut serine proteinases may reflect the ability of lepidopteran larvae to feed on different species of host plants. Possible implications of host plant choice on the digestive physiology of A. assamensis are discussed.
not annotated - annotated - LINNAEUS only
Functional test of the influence of Wolbachia genes on cytoplasmic incompatibility expression in Drosophila melanogaster.
Wolbachia are inherited intracellular bacteria that infect a broad range of invertebrate hosts. They commonly manipulate host reproduction in a variety of ways and thereby favour their invasion into host populations. While the biology of Wolbachia has been extensively studied at the ecological and phenotypic level, little is known about the molecular mechanisms underlying the interaction between Wolbachia and their hosts. Recent comparative genomics studies of Wolbachia strains have revealed putative candidate genes involved in the expression of cytoplasmic incompatibility (CI) in insects. However the functional testing of these genes is hindered by the lack of available genetic tools in Wolbachia. To circumvent this problem we generated transgenic Drosophila lines expressing various Wolbachia CI candidate genes under the control of the GAL4/UAS system in order to evaluate their possible role in Wolbachia-related phenotypes in Drosophila. The expression of a number of these genes in Drosophila melanogaster failed to mimic or alter CI phenotypes across a range of Wolbachia backgrounds or in the absence of Wolbachia.
not annotated - annotated - LINNAEUS only
Differential transcription of two highly divergent gut-expressed Bm86 antigen gene homologues in the tick Rhipicephalus appendiculatus (Acari: Ixodida).
The transcriptional control of gene expression is not well documented in the Arthropoda. We describe transcriptional analysis of two exceptionally divergent homologues (Ra86) of the Bm86 gut antigen from Rhipicephalus appendiculatus. Bm86 forms the basis of a commercial vaccine for the control of Rhipicephalus (Boophilus) microplus. The R. appendiculatus Ra86 proteins contain 654 and 693 amino acids, with only 80% amino acid sequence identity. Reverse-transcription PCR of gut cDNA showed transcription of only one genotype in individual female ticks. PCR amplification of 3' untranslated sequences from genomic DNA indicated that both variants could be encoded within a single genome. When both variants were present, one of the two Ra86 genotypes was transcriptionally dominant.
not annotated - annotated - LINNAEUS only
Detection and quantitation of infectious human adenoviruses and JC polyomaviruses in water by immunofluorescence assay.
Human adenoviruses (HAdV) and JC polyomaviruses (JCPyV) have been proposed as markers of fecal/urine contamination of human origin. An indirect immunofluorescence assay has been developed to quantify infectious human adenoviruses types 2human adenoviruses types 2 and 41 and JC polyomaviruses strain Mad-4 in water samples. The immunofluorescence assay was compared with other quantitative techniques used commonly such as plaque assay, tissue culture infectious dose-50 and quantitative PCR (qPCR). The immunofluorescence assays showed to be specific for the detection of infectious viruses, obtaining negative results when UV or heat-inactivated viruses were analyzed. The assays required less time and showed higher sensitivity for the detection of infectious viral particles than other cell culture techniques (1 log(10) more) evaluated. River water samples spiked previously with human adenoviruses and raw sewage samples were also analyzed using the proposed immunofluorescence assay as well as by qPCR. The results show quantitations with 2 log(10) reduction in the numbers of infectious viruses compared with the number of genome copies detected by qPCR. The immunofluorescence assay developed is fast, sensitive, specific, and a standardizable technique for the quantitation and detection of infectious viruses in water samples.
not annotated - annotated - LINNAEUS only
Expression of the C-terminal ORF2 protein of duck astrovirus for application in a serological test.
Duck astrovirus (DAstV) is an important pathogen causing duck viral hepatitis (DVH), a highly contagious and fatal disease in young ducklings. To provide an antigen for a diagnostic serum test, the C-terminus of DAstV ORF2 protein was expressed in Escherichia coli. Four positive and 30 negative sera were used to validate the purified ORF2 protein by developing an indirect enzyme-linked immunosorbent assay (ELISA). No cross-reactions were found against other duck pathogens, including duck hepatitis A virus, duck plague herpesvirus, duck reovirus, Newcastle disease virus, and Riemerella anatipestifer 12/19Riemerella anatipestifer 12/19 (63.2%) and 26/51 (51%) sera samples from two flocks of ducks that survived DAstV infections in commercial duck farms were positive for DAstV by this method, respectively. Interestingly, DAstV-specific antibodies were also detected in 12 (28.6%) of 42 sera samples from a different flock without DVH, indicating a wide distribution of subclinical infections caused by DAstV.
not annotated - annotated - LINNAEUS only
A fundamental, eco-hydrological basis for niche segregation in plant communities.
* Ecologists still puzzle over how plant species manage to coexist with one another while competing for the same essential resources. The classic answer for animal communities is that species occupy different niches, but how plants do this is more difficult to determine. We previously found niche segregation along fine-scale hydrological gradients in European wet meadows and proposed that the mechanism might be a general one, especially in communities that experience seasonal saturation. * We quantified the hydrological niches of 96 species from eight fynbos communities in the biodiversity hotspot of the Cape Floristic Region, South Africa and 99 species from 18 lowland wet meadow communities in the UK. Niche overlap was computed for all combinations of species. * Despite the extreme functional and phylogenetic differences between the fynbos and wet meadow communities, an identical trade-off (i.e. specialization of species towards tolerance of aeration and/or drying stress) was found to cause segregation along fine-scale hydrological gradients. * This study not only confirms the predicted generality of hydrological niche segregation, but also emphasizes its importance for structuring plant communities. Eco-hydrological niche segregation will have implications for conservation in habitats that face changing hydrology caused by water abstraction and climate change.
not annotated - annotated - LINNAEUS only
Role of lupeol synthase in Lotus japonicus nodule formation.
* Triterpenes are plant secondary metabolites, derived from the cyclization of 2,3-oxidosqualene by oxidosqualene cyclases (OSCs). Here, we investigated the role of lupeol synthase, encoded by OSC3, and its product, lupeol, in developing roots and nodules of the model legume Lotus japonicus. * The expression patterns of OSC3 in different developmental stages of uninfected roots and in roots infected with Mesorhizobium loti were determined. The tissue specificity of OSC3 expression was analysed by in situ hybridization. Functional analysis, in which transgenic L. japonicus roots silenced for OSC3 were generated, was performed. The absence of lupeol in the silenced plant lines was determined by GC-MS. * The expression of ENOD40, a marker gene for nodule primordia initiation, was increased significantly in the OSC3-silenced plant lines, suggesting that lupeol influences nodule formation. Silenced plants also showed a more rapid nodulation phenotype, consistent with this. Exogenous application of lupeol to M. loti-infected wild-type plants provided further evidence for a negative regulatory effect of lupeol on the expression of ENOD40. * The synthesis of lupeol in L. japonicus roots and nodules can be solely attributed to OSC3. Taken together, our data suggest a role for lupeol biosynthesis in nodule formation through the regulation of ENOD40 gene expression.
not annotated - annotated - LINNAEUS only
Drug interactions in childhood cancer.
Children with cancer are increasingly benefiting from new treatment strategies and advances in supportive care, as shown by improvements in both survival and quality-of-life. However, the continuous emergence of new cancer drugs and supportive-care drugs has increased the possibility of harmful drug interactions; health-care providers need to be very cautious when combining drugs. We discuss the most common interactions between chemotherapeutic drugs and supportive-care drugs-such as anticonvulsants, antiemetics, uric-acid-lowering compounds, acid suppressants, antimicrobials, and pain-management medications in paediatric patients. We also review the interactions between chemotherapy drugs and food and herbal supplements, and provide recommendations to avoid unwanted and potentially fatal interactions in children with cancer. Because of the constant release of new drugs, health-care providers need to check the most recent references before making recommendations about drug interactions.
not annotated - annotated - LINNAEUS only
Mutational analysis of the transmembrane helix 2-HAMP domain connection in the Escherichia coli aspartate chemoreceptor tar.
Transmembrane helix 2 (TM2) of the Tar chemoreceptor undergoes an inward piston-like displacement of 1 to 3 A upon binding aspartate. This signal is transmitted to the kinase-control module via the HAMP domain. Within Tar, the HAMP domain forms a parallel four-helix bundle consisting of a dimer of two amphipathic helices connected by a flexible linker. In the nuclear magnetic resonance structure of an archaeal HAMP domain, residues corresponding to the MLLT sequence between Arg-214 at the end of TM2 and Pro-219 of Tar are an N-terminal helical extension of AS1. We modified this region to test whether it behaves as a continuous helical connection between TM2 and HAMP. First, one to four Gly residues were inserted between Thr-218 and Pro-219. Second, the MLLT sequence was replaced with one to nine Gly residues. Third, the sequence was shortened or extended with residues compatible with helix formation. Cells expressing receptors in which the MLLT sequence was shortened to MLL or in which the MLLT sequence was replaced by four Gly residues performed good aspartate chemotaxis. Other mutant receptors supported diminished aspartate taxis. Most mutant receptors had biased signal outputs and/or abnormal patterns of adaptive methylation. We interpret these results to indicate that a strong, permanent helical connection between TM2 and the HAMP domain is not necessary for normal transmembrane signaling.
not annotated - annotated - LINNAEUS only
Dissection of the phytohormonal regulation of trichome formation and biosynthesis of the antimalarial compound artemisinin in Artemisia annua plants.
* Biosynthesis of the sesquiterpene lactone and potent antimalarial drug artemisinin occurs in glandular trichomes of Artemisia annua plants and is subjected to a strict network of developmental and other regulatory cues. * The effects of three hormones, jasmonate, gibberellin and cytokinin, were studied at the structural and molecular levels in two different A. annua chemotypes by microscopic analysis of gland development, and by targeted metabolite and transcript profiling. Furthermore, a genome-wide cDNA-amplified fragment length polymorphism (AFLP)-based transcriptome profiling was carried out of jasmonate-elicited leaves at different developmental stages. * Although cytokinin and gibberellin positively affected at least one aspect of gland formation, these two hormones did not stimulate artemisinin biosynthesis. Only jasmonate simultaneously promoted gland formation and coordinated transcriptional activation of biosynthetic gene expression, which ultimately led to increased sesquiterpenoid accumulation with chemotype-dependent effects on the distinct pathway branches. Transcriptome profiling revealed a trichome-specific fatty acyl- coenzyme A reductase, trichome-specific fatty acyl-CoA reductase 1 (TFAR1), the expression of which correlates with trichome development and sesquiterpenoid biosynthesis. * TFAR1 is potentially involved in cuticular wax formation during glandular trichome expansion in leaves and flowers of A. annua plants. Analysis of phytohormone-modulated transcriptional regulons provides clues to dissect the concerted regulation of metabolism and development of plant trichomes.
not annotated - annotated - LINNAEUS only
Climate effects on population fluctuations of the white-throated dipper Cinclus cinclus.
1. Climate change may have profound consequences for many organisms. We have studied fluctuations in a population of the white-throated dipper Cinclus cinclus during 31 years (1978-2008) in a river system in southern Norway in relation to both large-scale and local weather conditions occurring during the non-breeding season. 2. Multiple regression and partial least squares regression were used to model the growth rate of the population, accounting for population size in the previous year. 3. Population growth was influenced by North Atlantic Oscillation (NAO), mean winter temperature, precipitation and timing of ice formation on the main lake in the river system in autumn. These variables explained 84% of the variation in population growth over the 31-year study period. 4. Local winter conditions played a prominent role in explaining the population fluctuations, which is plausible because the dipper depends on open water for foraging. In the study area, winters can be harsh and rivers and lakes may freeze and severely affect the subsequent population size of the dipper in spring. 5. The breeding population of the dipper does not seem yet to have reached a level where all possible territories in the area have been occupied, even after mild winters, and the estimated carrying capacity is also decidedly lower (66 breeding pairs) than the number of available territories. If the trend of milder winters continues, the population might increase in the future. However, strong climate variation is expected to continue in the future, and hence periods of rapid growth of the dipper population will probably be followed by severe declines.
not annotated - annotated - LINNAEUS only
Interference from long-tailed finches constrains reproduction in the endangered Gouldian finch.
1. Interspecific interference competition for nest-sites among cavity-nesting birds can have important effects on reproductive fitness and the distribution of competing species. 2. We observed interference at nest-sites in free-living populations of the endangered Gouldian finch (Erythrura gouldiae) and sympatric long-tailed finch (Poephila acuticauda), and also experimentally tested the relative strength and effect of interference at nest-sites in captive populations. 3. Levels of competitive interference at nest-sites in the wild were high for Gouldian, but not long-tailed finches, and interference frequency was inversely related to Gouldian finch reproductive success. High levels of interference conferred reduced fledging success but did not affect offspring condition. 4. Captive experiments corroborated the field data, also demonstrating fitness costs of interspecific competition, and that long-tailed finches dominated resources under standardized conditions. 5. Such asymmetrical competition dynamics are likely to constrain reproduction in Gouldian finch populations, potentially affecting recruitment and hindering the recovery of remaining populations of this endangered species.
not annotated - annotated - LINNAEUS only
Predation is associated with variation in colour pattern, but not body shape or colour reflectance, in a rainbowfish (Melanotaenia australis).
1. In freshwater fishes, inter-population variation in male phenotype is often associated with differences in predation intensity, but these effects can be difficult to disentangle from environmental influences. 2. The western rainbowfish Melanotaenia australis exhibits marked sexual dimorphism - females are plain with a slender body, while males have striking coloration and are deeper in the body. Male traits differ in expression among populations, but this has not been described or explored in the literature. 3. This paper describes a study designed to test for geographic structuring of male phenotype in M. australis and to determine whether between-population variation in male phenotype is attributable to variation in predation regime, after accounting for environment. 4. We collected data describing habitat, and the size, activity and abundance of predators at sites containing M. australis populations. We then used photography, spectrometry and geometric morphometrics to describe colour pattern, spectral reflectance and body shape in males from these populations. Finally, we used permutation-based multivariate statistics to partition variance in these traits according to environment and predation regime. 5. Downstream environments posed higher predation risk to M. australis. Furthermore, males from these sites consistently exhibited larger cheek spots and fewer coloured lateral stripes than those from upstream sites. Variation in predation regime accounted for a significant proportion of the total variance in these traits (30*9%), after controlling for the effects of environment. 6. Variation in predation regime did not explain variation in reflectance or shape. Environmental variation, however, explained a significant portion of the total variance in reflectance (74*9%), and there was a strong trend towards it explaining a portion of the total variance in body shape (34*9%). 7. We conclude that natural selection by predators may be an important determinant of the evolution of colour pattern variation in M. australis, but not of that of body shape or colour reflectance. 8. Further study of M. australis will complement existing models, which show complex relationships between predation regime, environment and phenotype. Understanding these relationships is prerequisite to predicting the evolution of phenotypic variation in natural systems.
not annotated - annotated - LINNAEUS only
Adult predation risk drives shifts in parental care strategies: a long-term study.
1. Grouping provides antipredatory benefits, and therefore aggregation tendencies increase under heightened predation risk. In socially breeding groups, however, conflicts over reproductive shares or safety tend to disintegrate groups. Group formation thereby involves a balance between the antipredatory benefits of aggregation and the destabilizing effect of reproductive conflict. 2. We study the grouping behaviour of a facultatively social precocial sea duck with uniparental female care, the eider (Somateria mollissima Linnaeus). Females tend their young solitarily or in groups of 2-5 females. Here, we focus on the effect predation on adults has on group-formation decisions of brood-caring females. 3. By modifying an existing bidding game over care, we model the effects of predation risk on the width of the window of selfishness, which delimits the reproductive sharing allowing cooperation within brood-rearing coalitions, and generate predictions about the relative frequencies of solitary versus cooperative parental care modes. Furthermore, we model the dilution effect as a function of female group size and predation risk. 4. The window of selfishness widens with increasing predation risk, and the dilution of predation risk increases with both female group size and increasing predation risk, yielding the following predictions: (i) cooperative brood care becomes more prevalent and, conversely, solitary brood care less prevalent under heightened predation risk and (ii) group sizes increase concomitantly. 5. We tested these predictions using 13 years of data on female grouping decisions and annual predation rates, while controlling for the potentially confounding effect of female body condition. 6. Our data supported both predictions, where heightened predation risk of nesting females, but not changes in their condition, increased the relative frequency of cooperative brood care. Increased female nesting mortality also resulted in larger groups of cooperative females. 7. The predation risk of incubating females has long-term implications for later parental care decisions. We discuss the potential consequences of predation-induced shifts in group size on per capita fitness and population-wide productivity.
not annotated - annotated - LINNAEUS only
Evidence for functional divergence in arbuscular mycorrhizal fungi from contrasting climatic origins.
A considerable amount of phenotypic, genetic and symbiotic functional variability has been documented in arbuscular mycorrhizal fungi (AMF). However, little is known about whether distinct AMF ecotypes have evolved within their geographic range. We tested the hypothesis that AMF growing at temperatures closer to those prevalent within their origin would benefit their host and grow more than isolates distant from their native conditions. For each of six AMF species, we chose pairs of isolates that originated from distant areas with contrasting climates. Each isolate was grown in association with two grass species of different thermal optima at two temperature settings. Thus, we also tested whether AMF from different climatic origins were dependent on the thermal adaptation of the host plant species or to temperature per se. Although fungal growth was not directly affected by temperature, we found that AMF isolates originating from contrasting climates consistently and differentially altered plant growth. Our results suggest that AMF from contrasting climates have altered symbiotic function, thus linking an abiotic factor to ecotypic differentiation of putatively important symbionts.
not annotated - annotated - LINNAEUS only
A new, vapour-phase mechanism for stomatal responses to humidity and temperature.
A new mechanism for stomatal responses to humidity and temperature is proposed. Unlike previously-proposed mechanisms, which rely on liquid water transport to create water potential gradients within the leaf, the new mechanism assumes that water transport to the guard cells is primarily through the vapour phase. Under steady-state conditions, guard cells are assumed to be in near-equilibrium with the water vapour in the air near the bottom of the stomatal pore. As the water potential of this air varies with changing air humidity and leaf temperature, the resultant changes in guard cell water potential produce stomatal movements. A simple, closed-form, mathematical model based on this idea is derived. The new model is parameterized for a previously published set of data and is shown to fit the data as well as or better than existing models. The model contains mathematical elements that are consistent with previously-proposed mechanistic models based on liquid flow as well as empirical models based on relative humidity. As such, it provides a mechanistic explanation for the realm of validity for each of these approaches.
not annotated - annotated - LINNAEUS only
Cadmium uptake and sequestration kinetics in individual leaf cell protoplasts of the Cd/Zn hyperaccumulator Thlaspi caerulescens.
Hyperaccumulators store accumulated metals in the vacuoles of large leaf epidermal cells (storage cells). For investigating cadmium uptake, we incubated protoplasts obtained from leaves of Thlaspi caerulescens (Ganges ecotype) with a Cd-specific fluorescent dye. A fluorescence kinetic microscope was used for selectively measuring Cd-uptake and photosynthesis in different cell types, so that physical separation of cell types was not necessary. Few minutes after its addition, cadmium accumulated in the cytoplasm before its transport into the vacuole. This demonstrated that vacuolar sequestration is the rate-limiting step in cadmium uptake into protoplasts of all leaf cell types. During accumulation in the cytoplasm, Cd-rich vesicle-like structures were observed. Cd uptake rates into epidermal storage cells were higher than into standard-sized epidermal cells and mesophyll cells. This shows that the preferential heavy metal accumulation in epidermal storage cells, previously observed for several metals in intact leaves of various hyperaccumulator species, is due to differences in active metal transport and not differences in passive mechanisms like transpiration stream transport or cell wall adhesion. Combining this with previous studies, it seems likely that the transport steps over the plasma and tonoplast membranes of leaf epidermal storage cells are driving forces behind the hyperaccumulation phenotype.
not annotated - annotated - LINNAEUS only
Factors required for the high CO2 specificity of the anaerobically induced maize GapC4 promoter in transgenic tobacco.
Flooding, a natural cause of anaerobiosis, is often accompanied by high CO(2) concentrations in the flood water. Plants need to respond to these environmental conditions. Strong anaerobic reporter gene activity in tobacco (Nicotiana tabacum) controlled by the glycolytic glyceraldehyde-3-phosphate dehydrogenase (GapC4) promoter from maize (Zea mays) depends on the presence of CO(2) and light. To identify factors required for CO(2) regulated gene expression, promoter deletions fused to the Beta-glucuronidase reporter gene were studied in transgenic tobacco. Deletion of a 40 bp fragment directly upstream of the TATA box leads to increased anaerobic reporter gene activity both, in the presence and absence of CO(2). This deletion does not affect light specific anaerobic expression. A positive correlation between increasing CO(2) concentrations and gene activity is observed. Electrophoretic mobility shift experiments indicate that tobacco nuclear extracts harbour proteins that bind to part of the 40 bp fragment. Database assisted as well as experimental analysis reveal a role for AP2/EREBP transcription factors for conferring the high CO(2) specificity to the GapC4 promoter in tobacco leaves. This work highlights the importance for plants to respond to high environmental CO(2) concentrations under anaerobic conditions.
not annotated - annotated - LINNAEUS only
Arabidopsis thaliana populations show clinal variation in a climatic gradient associated with altitude.
* Understanding the adaptive basis of life history variation is a central goal in evolutionary ecology. The use of model species enables the combination of molecular mechanistic knowledge with ecological and evolutionary questions, but the study of life history variation in natural environments is required to merge these disciplines. * Here, we tested for clinal variation in life history and associated traits along an environmental and altitudinal gradient in the model species Arabidopsis thaliana. Seventeen natural populations of A. thaliana were geo-referenced in north-eastern Spain on a gradient in which precipitation increases but maximum spring temperature and minimum winter temperature decrease with altitude. * One hundred and eighty-nine genotypes from the 17 populations were grown under uniform controlled conditions. Variations in traits related to biomass allocation, fecundity, phenology and vegetative growth were tested for relationships with the altitude and climatic variables associated with the home sites. Above-ground mass, number of rosette leaves at bolting, developmental time and seed weight increased with the home site's altitude. Root allocation, vegetative growth during winter and number of seeds decreased with altitude. * We suggest that the differences among home sites provide clues to the variation in adaptive strategies associated with the climatic gradient. We compared these results with adaptations and clinal relationships reported for other species and with molecular mechanisms described in Arabidopsis.
not annotated - annotated - LINNAEUS only
Recovery of ectomycorrhiza after 'nitrogen saturation' of a conifer forest.
Trees reduce their carbon (C) allocation to roots and mycorrhizal fungi in response to high nitrogen (N) additions, which should reduce the N retention capacity of forests. The time needed for recovery of mycorrhizas after termination of N loading remains unknown. Here, we report the long-term impact of N loading and the recovery of ectomycorrhiza after high N loading on a Pinus sylvestris forest. We analysed the N% and abundance of the stable isotope (15) N in tree needles and soil, soil microbial fatty acid biomarkers and fungal DNA. Needles in N-loaded plots became enriched in (15) N, reflecting decreased N retention by mycorrhizal fungi and isotopic discrimination against (15) N during loss of N. Meanwhile, needles in N-limited (control) plots became depleted in (15) N, reflecting high retention of (15) N by mycorrhizal fungi. N loading was terminated after 20yr. The delta(15) N and N% of the needles decreased 6yr after N loading had been terminated, and approached values in control plots after 15yr. This decrease, and the larger contributions compared with N-loaded plots of a fungal fatty acid biomarker and ectomycorrhizal sequences, suggest recovery of ectomycorrhiza. High N loading rapidly decreased the functional role of ectomycorrhiza in the forest N cycle, but significant recovery occurred within 6-15yr after termination of N loading.
not annotated - annotated - LINNAEUS only
Structural and hydraulic correlates of heterophylly in Ginkgo biloba.
This study investigates the functional significance of heterophylly in Ginkgo biloba, where leaves borne on short shoots are ontogenetically distinct from those on long shoots. Short shoots are compact, with minimal internodal elongation; their leaves are supplied with water through mature branches. Long shoots extend the canopy and have significant internodal elongation; their expanding leaves receive water from a shoot that is itself maturing. Morphology, stomatal traits, hydraulic architecture, Huber values, water transport efficiency, in situ gas exchange and laboratory-based steady-state hydraulic conductance were examined for each leaf type. Both structure and physiology differed markedly between the two leaf types. Short-shoot leaves were thinner and had higher vein density, lower stomatal pore index, smaller bundle sheath extensions and lower hydraulic conductance than long-shoot leaves. Long shoots had lower xylem area:leaf area ratios than short shoots during leaf expansion, but this ratio was reversed at shoot maturity. Long-shoot leaves had higher rates of photosynthesis, stomatal conductance and transpiration than short-shoot leaves. We propose that structural differences between the two G. biloba leaf types reflect greater hydraulic limitation of long-shoot leaves during expansion. In turn, differences in physiological performance of short- and long-shoot leaves correspond to their distinct ontogeny and architecture.
not annotated - annotated - LINNAEUS only
Symbiotic Chlorella vulgaris of the ciliate Paramecium bursaria plays an important role in maintaining perialgal vacuole membrane functions.
Treatment of symbiotic alga-bearing Paramecium bursaria cells with a protein synthesis inhibitor, cycloheximide, induces synchronous swelling of all perialgal vacuoles at about 24h after treatment under a constant light condition. Subsequently, the vacuoles detach from the host cell cortex. The algae in the vacuoles are digested by the host's lysosomal fusion to the vacuoles. To elucidate the timing of algal degeneration, P. bursaria cells were treated with cycloheximide under a constant light condition. Then the cells were observed using transmission electron microscopy. Results show that algal chloroplasts and nuclei degenerated within 9h after treatment, but before the synchronous swelling of the perialgal vacuole and appearance of acid phosphatase activity in the perialgal vacuole by lysosomal fusion. Treatment with cycloheximide under a constant dark condition and treatment with chloramphenicol under a constant light condition induced neither synchronous swelling of the vacuoles nor digestion of the algae inside the vacuoles. These results demonstrate that algal proteins synthesized during photosynthesis are necessary to maintain chloroplastic and nuclear structures, and that inhibition of protein synthesis induces rapid lysis of these organelles, after which synchronous swelling of the perialgal vacuole and fusion occur with the host lysosomes.
not annotated - annotated - LINNAEUS only
Rapid and sensitive detection of infectious hypodermal and hematopoietic necrosis virus by loop-mediated isothermal amplification combined with a lateral flow dipstick.
Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is an important shrimp pathogen that causes mortality in Penaeus stylirostris and stunting (called runt deformity syndrome or RDS) in Penaeus vannamei. Loop-mediated isothermal amplification (LAMP) allows rapid amplification of nucleic acids under isothermal conditions. It can be combined with a chromatographic lateral flow dipstick (LFD) for highly specific, rapid and simple visual detection of IHHNV-specific amplicons. Using this protocol, a 30-min amplification followed by 5 min hybridization with an FITC-labeled DNA probe and 5 min LFD resulted in visualization of DNA amplicons trapped at the LFD test line. Thus, 10 min for rapid DNA extraction followed by LAMP combined with LFD detection resulted in a total assay time of approximately 50 min. Detection sensitivity was comparable to other methods used commonly for nested PCR detection of IHHNV but had the additional advantages of reduced assay time, confirmation of amplicon identity by hybridization and elimination of electrophoresis with carcinogenic ethidium bromide.
not annotated - annotated - LINNAEUS only
The FvMK1 mitogen-activated protein kinase gene regulates conidiation, pathogenesis, and fumonisin production in Fusarium verticillioides.
Fusarium verticillioides is one of the most important fungal pathogens to cause destructive diseases of maize worldwide. Fumonisins produced by the fungus are harmful to human and animal health. To date, our understanding of the molecular mechanisms associated with pathogenicity and fumonisin biosynthesis in F. verticillioides is limited. Because MAP kinase pathways have been implicated in regulating diverse processes important for plant infection in phytopathogenic fungi, in this study we identified and functionally characterized the FvMK1 gene in F. verticillioides. FvMK1 is orthologous to FMK1 in F. oxysporum and GPMK1 in F. graminearum. The Fvmk1 deletion mutant was reduced in vegetative growth and production of microconidia. However, it was normal in sexual reproduction and increased in the production of macroconidia. In infection assays with developing corn kernels, the Fvmk1 mutant was non-pathogenic and failed to colonize through wounding sites. It also failed to cause stalk rot symptoms beyond the inoculation sites on corn stalks, indicating that FvMK1 is essential for plant infection. Furthermore, the Fvmk1 mutant was significantly reduced in fumonisin production and expression levels of FUM1 and FUM8, two genes involved in fumonisin biosynthesis. The defects of the Fvmk1 mutant were fully complemented by re-introducing the wild type FvMK1 allele. These results demonstrate that FvMK1 plays critical roles in the regulation of vegetative growth, asexual reproduction, fumonisin biosynthesis, and pathogenicity.
not annotated - annotated - LINNAEUS only
Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic.
True morels (Morchella, Ascomycota) are arguably the most highly-prized of the estimated 1.5 million fungi that inhabit our planet. Field guides treat these epicurean macrofungi as belonging to a few species with cosmopolitan distributions, but this hypothesis has not been tested. Prompted by the results of a growing number of molecular studies, which have shown many microbes exhibit strong biogeographic structure and cryptic speciation, we constructed a 4-gene dataset for 177 members of the Morchellaceae to elucidate their origin, evolutionary diversification and historical biogeography. Diversification time estimates place the origin of the Morchellaceae in the middle Triassic 243.63 (95% highest posterior density [HPD] interval: 169.35-319.89) million years ago (Mya) and the divergence of Morchella from its closest relatives in the early Cretaceous 129.61 (95% HPD interval: 90.26-173.16) Mya, both within western North America. Phylogenetic analyses identified three lineages within Morchella: a basal monotypic lineage represented by Morchella rufobrunnea, and two sister clades comprising the black morels (Elata Clade, 26 species) and yellow morels (Esculenta Clade, 16 species). Morchella possesses a Laurasian distribution with 37/41 species restricted to the Holarctic. All 33 Holarctic species represented by multiple collections exhibited continental endemism. Moreover, 16/18 North American and 13/15 Eurasian species appeared to exhibit provincialism. Although morel fruit bodies produce thousands of explosively discharged spores that are well suited to aerial dispersal, our results suggest that they are poorly adapted at invading novel niches. Morels also appear to have retained the ancestral fruit body plan, which has remained remarkably static since the Cretaceous.
not annotated - annotated - LINNAEUS only
A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme.
A novel approach is presented to map avirulence gene Avr1 in the basidiomycete Cronartium quercuum f.sp. fusiforme, the causal agent of fusiform rust disease in pines. DNA markers tightly linked to resistance gene Fr1 in loblolly pine tree 10-5 were used to classify 10-5 seedling progeny as either resistant or susceptible. A single dikaryotic isolate (P2) heterozygous at the corresponding Avr1 gene was developed by crossing Fr1 avirulent isolate SC20-21 with Fr1 virulent isolate NC2-40. Bulk basidiospore inoculum derived from isolate P2 was used to challenge the pine progeny. The ability to unambiguously marker classify 10-5 progeny as resistant (selecting for virulence) or susceptible (non-selecting) permitted the genetic mapping of the corresponding Avr1 gene by bulked segregant analysis. Using this approach, 14 genetic markers significantly linked to Avr1 were identified and placed within the context of a genome-wide linkage map produced for isolate P2 using samples from susceptible seedlings.
not annotated - annotated - LINNAEUS only
Universal primers for rapid detection of hytrosaviruses.
Hytrosaviridae is a proposed virus family encompassing viruses that cause salivary gland hypertrophy (SGH) syndrome in infected insects and reduce the fertility in their dipteran insect hosts. They contain a large, double stranded DNA genome of 120-190 kbp. To date, these viruses have been detected only in adult Diptera. These include hytrosaviruses detected in various tsetse fly species (Glossina spp.), the narcissus bulb fly Merodon equestris and the house fly Musca domestica. The limited number of hytrosaviruses reported to date may be a reflection of the frequent absence of external symptoms in infected adult flies and the fact that the virus does not cause rapid mortality. Based on the complete genome sequence of Glossinia pallidipes (GpSGHV) and Musca domestica (MdSGHV) salivary gland hypertrophy viruses, a PCR based methodology was developed to detect the viruses in these species. To be able to detect hytrosaviruses in other Diptera, five degenerate primer pairs were designed and tested on GpSGHV and MdSGHV DNA using gradient PCR with annealing temperatures from 37 to 61^0C. Two pairs of primers were selected from p74, two pairs from PIF-1 and one pair from ODV-e66 homologous proteins. Four primer pairs generated a virus specific PCR product on both MdSGHV and GpSGHV at all tested annealing temperatures, while the ODV-e66 based primers did not generate a virus specific product with annealing temperatures higher that 47^0C. No non-specific PCR product was found when using genomic DNA of infected flies as template DNA. These results offer new sets of primers that could be used to detect hytrosaviruses in other insects.
not annotated - annotated - LINNAEUS only
Simultaneous virus-specific detection of the two cassava brown streak-associated viruses by RT-PCR reveals wide distribution in East Africa, mixed infections, and infections in Manihot glaziovii.
The expanding cassava brown streak disease (CBSD) epidemic in East Africa is caused by two ipomoviruses (genus Ipomovirus; Potyviridae), namely, Cassava brown streak virus (CBSV), and Ugandan cassava brown streak virus (UCBSV) that was described recently. A reverse transcription polymerase chain reaction (RT-PCR) based diagnostic method was developed in this study for simultaneous virus-specific detection of the two viruses. Results showed that CBSV and UCBSV are distributed widely in the highlands (> 1000 m above the sea level) of the Lake Victoria zone in Uganda and Tanzania and also in the Indian Ocean costal lowlands of Tanzania. Isolates of UCBSV from the Lake Victoria zone were placed to two phylogenetic clusters in accordance with their origin in Uganda or Tanzania, respectively. Mixed infections with CBSV and UCBSV were detected in many cassava plants in the areas surveyed. CBSV was also detected in the perennial species Manihot glaziovii (DNA-barcoded in this study) in Tanzania, which revealed the first virus reservoir other than cassava. The method for detection of CBSV and UCBSV described in this study has important applications for plant quarantine, resistance breeding of cassava, and studies on epidemiology and control of CBSD in East Africa.
not annotated - annotated - LINNAEUS only
Development of a blocking ELISA for detection of serum neutralizing antibodies against porcine circovirus type 2.
A monoclonal antibody (Mab)-based blocking ELISA was developed for the detection of serum neutralizing antibodies to porcine circovirus type 2 (PCV2). The Mab with neutralizing activity, which was produced by immunizing a recombinant capsid protein of PCV2 expressed in insect cells, was used as the detector antibody. The assay was evaluated in comparison with a serum neutralization assay, and its sensitivity and specificity were determined to be 98.8% and 88.5%, respectively. A significant positive correlation was found between results of the blocking ELISA and the serum neutralization assay (r=0.9381). The assay was verified by testing experimental and commercial pig sera. A longitudinal antibody profile showed that serum neutralizing antibodies were detected 2 weeks after vaccination and that the detection rate reached 100% at 4 weeks. The serum neutralizing antibody profile showed a decrease from the age of 4 to 13 weeks, and seroconversion after 13 weeks in pigs from a commercial pig farm. Additionally, the positive detection rate in 703 sera collected from nine commercial pig farms was 73%. This report demonstrates that the assay is a simple, specific, sensitive and convenient method for epidemiological surveys and evaluations of serum neutralizing antibodies against PCV2.
not annotated - annotated - LINNAEUS only
Oramoeba fumarolia gen. nov., sp. nov., a new marine heterolobosean amoeboflagellate growing at 54 ^0C.
An amoeba strain was isolated from marine sediment taken from the beach near a fumarole in Italy. The trophozoites of this new marine species transforms into flagellates with variable numbers of flagella, from 2 to 10. The strain forms round to oval cysts. This thermophilic amoeboflagellate grows at temperatures up to 54^0C. Molecular phylogenetic analysis of the small subunit ribosomal DNA (SSU rDNA) places the amoeboflagellate in the Heterolobosea. The closest relatives are Stachyamoeba sp. ATCC50324, a strain isolated from an ocean sample, and Vrihiamoeba italica, a recent isolate from a rice field. Like some other heterolobosean species, this new isolate has a group I intron in the SSU rDNA. Because of the unique place in the molecular phylogenetic tree, and because there is no species found in the literature with similar morphological and physiological characteristics, this isolate is considered to be a new genus and a new species, Oramoeba fumarolia gen. nov., sp. nov.
not annotated - annotated - LINNAEUS only
Monoclonal antibody-based triple antibody sandwich-enzyme-linked immunosorbent assay and immunocapture reverse transcription-polymerase chain reaction for Odontoglossum ringspot virus detection.
Odontoglossum ringspot virus (ORSV) infects numerous commercially important orchids and causes significant losses worldwide. The coat protein (CP) gene of ORSV was cloned and expressed in Escherichia coli by using the pET-32a expression vector, and the expression of recombinant protein was confirmed by Western blotting using anti-ORSV antibodies. The recombinant protein was purified using Ni-NTA agarose, and the purified protein was used as an immunogen to produce monoclonal antibodies (MAbs) and polyclonal antibodies (PAbs). Five murine MAbs against ORSV CP were obtained. Among them, two MAbs (6B4 and 1D1) also reacted with TMV CP. The triple antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) and immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) methods using the MAb (8A5) were then developed for sensitive, specific, and rapid detection of ORSV. TAS-ELISA and IC-RT-PCR could detect ORSV in the infected leaf saps with dilutions of 1:10,240 and 1:81,920 (w/v, g mL(-1)), respectively. TAS-ELISA and IC-RT-PCR detections indicated that ORSV was prevalent in orchids in the Zhejiang Province of China.
not annotated - annotated - LINNAEUS only
Detection and discrimination of members of the family Luteoviridae by real-time PCR and SYBR(R) GreenER(TM) melting curve analysis.
This study investigated the suitability of a two step real-time RT-PCR melting curve analysis as a tool for the detection and discrimination of nine species in the plant virus family Luteoviridae, being Soybean dwarf virus [SbDV], Bean leafroll virus [BLRV], Beet chlorosis virus [BChV], Beet mild yellowing virus [BMYV], Beet western yellows virus [BWYV], Cereal yellow dwarf virus-RPV [CYDV-RPV], Cucurbit aphid-borne yellows virus [CABYV], Potato leafroll virus [PLRV] and Turnip yellows virus [TuYV]. Melting temperature and shape of the melting peak were analysed for 68 bp and 148 bp coat protein gene amplicons using SYBR(R) GreenER(TM) fluorescent dye. Specific melting peaks with unique melting temperature were observed for the various species of the family Luteoviridae using the 68 bp amplicon, but not with the 148 bp amplicon. Due to the high variability of sequences for some members of this family, different melting temperatures were also observed between different isolates of the species CYDV-RPV and TuYV. Nevertheless, discrimination between species was achieved for SbDV, BLRV, BChV, BMYV, CABYV and either PLRV or BWYV. Melting curve analysis, in this study, is a faster and more discriminatory alternative to gel electrophoresis of end-point PCR products for the detection of Luteoviridae infection.
not annotated - annotated - LINNAEUS only
Detection and differentiation of tick-borne encephalitis virus subtypes by a reverse transcription quantitative real-time PCR and pyrosequencing.
Tick-borne encephalitis (TBE) virus causes one of the most important flaviviral infections of the human central nervous system in Europe and Asia. In recent years the rate of TBE infection has been raising and the virus has been spreading to new areas. Currently, the diagnosis of TBE is based on detection of specific antibodies in patients' sera which appear as late as about 2 weeks post-infection. For a timely diagnosis of TBE virus infections and epidemiological studies, a TBE virus-specific reverse transcription quantitative real-time PCR (RT-qPCR) followed by pyrosequencing was developed. The assay is based on one degenerated primer pair detecting all three human-pathogenic TBE virus subtypes with a detection limit of 10 copies. Even though primers and probe are highly degenerated, the assay is specific for TBE virus species and detects all subtypes with a comparable sensitivity. Furthermore, TBE virus RT-qPCR could be carried out as one-step or two-step assay. RT-qPCR can be followed by pyrosequencing which allows a rapid subtyping of TBE viruses. For detection purposes an internal control to monitor RNA extraction, cDNA synthesis and amplification is included. In summary, the method is sensitive, highly specific and easy-to-handle tool for the detection and differentiation of TBE virus in the early phase of illness or in TBE host animal species and ticks.
not annotated - annotated - LINNAEUS only
Adaptation of a Madin-Darby canine kidney cell line to suspension growth in serum-free media and comparison of its ability to produce avian influenza virus to Vero and BHK21 cell lines.
Madin-Darby canine kidney (MDCK) cells are currently considered for influenza vaccine manufacturing. A drawback of these cells is their anchorage dependent growth, which greatly complicates process scale-up. In this paper a novel MDCK cell line (MDCK-SFS) is described that grows efficiently in suspension and retained high expression levels of both alpha-2,6 and alpha-2,3 sialic acid receptors, which bind preferably to human and avian influenza viruses, respectively. The production of avian influenza virus by BHK21, Vero and MDCK-SFS cell lines was compared. Although BHK21 cells consisted of two populations, one of which lacks the alpha-2,3 receptor, they supported the replication of two influenza strains to high titres. However, BHK21 cells are generally not applicable for influenza production since they supported the replication of six further strains poorly. MDCK-SFS cells yielded the highest infectious virus titres and virus genome equivalent concentration for five of the eight influenza strains analyzed and the highest hemagglutination activity for all eight virus strains. Taken together with their suitability for suspension growth this makes the MDCK-SFS cell line potentially useful for large scale influenza virus production.
not annotated - annotated - LINNAEUS only
Cyanobacterial endosymbionts in the benthic dinoflagellate Sinophysis canaliculata (Dinophysiales, Dinophyceae).
Photosynthetic dinoflagellates possess a great diversity of plastids that have been acquired through successful serial endosymbiosis. The peridinin-containing plastid in dinoflagellates is canonical, but many other types are known within this group. Within the Dinophysiales, several species of Dinophysis contain plastids, derived from cryptophytes or haptophytes. In this work, the presence of numerous intracellular cyanobacteria-like microorganisms compartmentalized by a separate membrane is reported for the first time within the benthic dinophysoid dinoflagellate Sinophysis canaliculata Quod et al., a species from a genus morphologically close to Dinophysis. Although the contribution of these cyanobacterial endosymbionts to S. canaliculata is still unknown, this finding suggests a possible undergoing primary endosymbiosis in a dinoflagellate.
not annotated - annotated - LINNAEUS only
Roles of vaccinia virus genes E3L and K3L and host genes PKR and RNase L during intratracheal infection of C57BL/6 mice.
The importance of the 2'-5' oligoadenylate synthetase (OAS)/RNase L and double-stranded RNA (dsRNA)-dependent protein kinase (PKR) pathways in host interferon induction resulting from virus infection in response to dsRNA has been well documented. In poxvirus infections, the interactions between the vaccinia virus (VV) genes E3L and K3L, which target RNase L and PKR, respectively, serve to prevent the induction of the dsRNA-dependent induced interferon response in cell culture. To determine the importance of these host genes in controlling VV infections, mouse single-gene knockouts of RNase L and PKR and double-knockout mice were studied following intratracheal infection with VV, VVDeltaK3L, or VVDeltaE3L. VV caused lethal disease in all mouse strains. The single-knockout animals were more susceptible than wild-type animals, while the RNase L(-/-) PKR(-/-) mice were the most susceptible. VVDeltaE3L infections of wild-type mice were asymptomatic, demonstrating that E3L plays a critical role in controlling the host immune response. RNase L(-/-) mice showed no disease, whereas 20% of the PKR(-/-) mice succumbed at a dose of 10(8) PFU. Lethal disease was routinely observed in RNase L(-/-) PKR(-/-) mice inoculated with 10(8) PFU of VVDeltaE3L, with a distinct pathology. VVDeltaK3L infections exhibited no differences in virulence among any of the mouse constructs, suggesting that PKR is not the exclusive target of K3L. Surprisingly, VVDeltaK3L did not disseminate to other tissues from the lung. Hence, the cause of death in this model is respiratory disease. These results also suggest that an unanticipated role of the K3L gene is to facilitate virus dissemination.
not annotated - annotated - LINNAEUS only
Host plant secondary metabolite profiling shows a complex, strain-dependent response of maize to plant growth-promoting rhizobacteria of the genus Azospirillum.
Most Azospirillum plant growth-promoting rhizobacteria (PGPR) benefit plant growth through source effects related to free nitrogen fixation and/or phytohormone production, but little is known about their potential effects on plant physiology. These effects were assessed by comparing the early impacts of three Azospirillum inoculant strains on secondary metabolite profiles of two different maize (Zea mays) cultivars. After 10d of growth in nonsterile soil, maize methanolic extracts were analyzed by reverse-phase high-performance liquid chromatography (RP-HPLC) and secondary metabolites identified by liquid chromatography/mass spectrometry (LC/MS) and nuclear magnetic resonance (NMR). Seed inoculation resulted in increased shoot biomass (and also root biomass with one strain) of hybrid PR37Y15 but had no stimulatory effect on hybrid DK315. In parallel, Azospirillum inoculation led to major qualitative and quantitative modifications of the contents of secondary metabolites, especially benzoxazinoids, in the maize plants. These modifications depended on the PGPR strainxplant cultivar combination. Thus, Azospirillum inoculation resulted in early, strain-dependent modifications in the biosynthetic pathways of benzoxazine derivatives in maize in compatible interactions. This is the first study documenting a PGPR effect on plant secondary metabolite profiles, and suggests the establishment of complex interactions between Azospirillum PGPR and maize.
not annotated - annotated - LINNAEUS only
A seed high-lysine trait is negatively associated with the TCA cycle and slows down Arabidopsis seed germination.
* Lysine is a nutritionally important essential amino acid, but significant elevation of its levels in Arabidopsis seeds, by enhancing its synthesis and blocking its catabolism, causes a retardation of germination. Here, we hypothesized that this negative effect is associated with changes in primary metabolism and gene expression programs that are essential for early germination. * Seeds at different stages of germination sensu stricto of the seed-high-lysine genotype were subjected to detailed analysis of primary metabolism, using GC-MS, as well as microarray analysis and two-dimensional, isoelectric focusing, sodium dodecylsulfate polyacrylamide gel electrophoresis, to detect storage protein mobilization. * Our results exposed a major negative effect of the seed-specific increased lysine synthesis and knockout of its catabolism on the levels of a number of TCA cycle metabolites. This metabolic alteration also influences significantly the transcriptome, primarily attenuating the boost of specific transcriptional programs that are essential for seedling establishment, such as the onset of photosynthesis, as well as the turnover of specific transcriptional programs associated with seed embryonic traits. * Our results indicate that catabolism of the aspartic acid family of amino acids is an important contributor to the energy status of plants, and hence to the onset of autotrophic growth-associated processes during germination.
not annotated - annotated - LINNAEUS only
Functional characterization of pheromone receptors in the tobacco budworm Heliothis virescens.
Functional analyses of candidate Heliothis virescens pheromone odorant receptors (HvORs) were conducted using heterologous expression in Xenopus oocytes. HvOR6 was found to be highly tuned to Z9-14:Ald, while HvOR13, HvOR14 and HvOR16 showed specificity for Z11-16:Ald, Z11-16:OAc and Z11-16:OH, respectively. HvOR15, which had been considered a candidate receptor for Z9-14:Ald did not respond to any of the pheromone compounds tested, nor to 50 other general odorants. Thus, while HvOR15 is specifically expressed in H. virescens male antennae, its role in pheromone reception remains unknown. Based on our results and previous research we can now assign pheromone receptors in H. virescens males to each of the critical H. virescens agonistic pheromone compounds and two antagonistic compounds produced by heterospecific females.
not annotated - annotated - LINNAEUS only
Glycinebetaine protects plants against abiotic stress: mechanisms and biotechnological applications.
Various compatible solutes enable plants to tolerate abiotic stress, and glycinebetaine (GB) is one of the most-studied among such solutes. Early research on GB focused on the maintenance of cellular osmotic potential in plant cells. Subsequent genetically engineered synthesis of GB-biosynthetic enzymes and studies of transgenic plants demonstrated that accumulation of GB increases tolerance of plants to various abiotic stresses at all stages of their life cycle. Such GB-accumulating plants exhibit various advantageous traits, such as enlarged fruits and flowers and/or increased seed number under non-stress conditions. However, levels of GB in transgenic GB-accumulating plants are relatively low being, generally, in the millimolar range. Nonetheless, these low levels of GB confer considerable tolerance to various stresses, without necessarily contributing significantly to cellular osmotic potential. Moreover, low levels of GB, applied exogenously or generated by transgenes for GB biosynthesis, can induce the expression of certain stress-responsive genes, including those for enzymes that scavenge reactive oxygen species. Thus, transgenic approaches that increase tolerance to abiotic stress have enhanced our understanding of mechanisms that protect plants against such stress.
not annotated - annotated - LINNAEUS only
Evaluation of an immunoglobulin M-specific capture enzyme-linked immunosorbent assay for rapid diagnosis of dengue infection.
Various assays have been developed to diagnose dengue virus infection, relying on techniques from the fields of serology and molecular biology. Many of these assays have been successful, but there is still an urgent need for accurate, simple and rapid diagnostic assays to diagnose dengue virus infection and to assist in patient management. Using a panel of well-characterized sera and a collection of retrospective samples obtained during the dengue epidemics that occurred in Belem, Brazil, between 2002 and 2009, a modified immunoglobulin M-specific capture enzyme-linked immunosorbent assay (Rapid-MAC-ELISA) was evaluated and compared with the "gold standard" MAC-ELISA, in order to assess the specificity, sensitivity, stability, reproducibility and cost-effectiveness of this new assay. These results demonstrated that the Rapid-MAC-ELISA is comparable to the MAC-ELISA in terms of sensitivity and specificity and is highly reproducible; additionally, it is easily performed, less expensive than other available formats and can be completed within three hours. Furthermore, the Rapid-MAC-ELISA can be used for the diagnosis of dengue virus infections in resource-limited areas where dengue is endemic.
not annotated - annotated - LINNAEUS only
Rapid detection of Newcastle disease virus replication in embryonated chicken eggs using quantitative real time polymerase chain reaction.
Newcastle disease virus (NDV), an avian paramyxovirus, is an economically important disease of poultry globally. Rapid methods to detect and differentiate the virus are important to curtail the spread of this virus. Nucleic acid based detection methods are routinely employed for diagnosis that suffer from the disadvantage of failure to discriminate viable virus and non-infectious genome. However, virus isolation remains the gold standard for diagnosis of field outbreaks. The sensitivity of virus isolation was combined with nucleic acid based detection methods so that the time taken for confirmatory diagnosis could be considerably reduced while increasing sensitivity. Quantitative real time reverse transcription polymerase chain reaction (qRT-PCR) and conventional RT-PCR techniques were compared for the detection of NDV genome replication in 9-11-day-old embryonated chicken eggs (ECE) using the nucleoprotein (NP) gene of the virus as a target. The results suggest that at least two to fourfold increase in cycle threshold (C(t)) values over the baseline C(t) value of samples lacking infectious virus, would indicate live NDV replication. The limit of detection of NDV replication using qRT-PCR was 1x10(4.0) mean embryo infective doses (EID(50)). The earliest time point when live virus replication was detectable by qRT-PCR or RT-PCR was 30h post-inoculation in ECE.
not annotated - annotated - LINNAEUS only
Development of a polyprobe to detect six viroids of pome and stone fruit trees.
A simple and sensitive dot blot hybridization assay using a digoxigenin-labeled cRNA polyprobe was developed for the simultaneous detection of six viroids that infect pome and stone fruit trees. The polyprobe was constructed by cloning sequentially partial sequences of each viroid into a single vector, with run-off transcription driven by the T7 promoter. All six viroids were detectable within a dilution range of 5(-3) to 5(-4) in total nucleic acid extracts from infected trees. Individual trees were co-inoculated to create mixed infections and all four pome fruit viroids and both stone fruit viroids could be detected in pear and peach trees, respectively, using the polyprobe. The results of the assays using the polyprobe were comparable to those using single probes. The methods were validated by testing geographically diverse isolates of viroids, as well as field samples from several collections in the US. The assay offers a rapid, reliable and cost-effective approach to the simultaneous detection of six fruit trees viroids and has the potential for routine use in quarantine, certification, and plant genebank programs where many samples are tested and distributed worldwide.
not annotated - annotated - LINNAEUS only
Development and validation of a lateral flow immunoassay using colloidal gold for the identification of serotype-specific foot-and-mouth disease virus O, A and Asia 1.
A lateral flow immunoassay (LFI) was developed to identify and diagnose foot-and-mouth disease virus (FMDV) serotypes Ofoot-and-mouth disease virus (FMDV) serotypesfoot-and-mouth disease virus (FMDV) serotypes O, A and Asia 1. Antibodies obtained from rabbits and guinea pigs immunized with cell-culture-adapted virus strains (O/CHA/99, A/GS/LX/66, Asia 1/CHN/05) and suckling-mouse adapted virus strains (O/AV99(L), A/AV88(L), Asia 1/YNBS/58) were used as capture antibodies. The diagnostic kit included three immunochromatographic strips of types O, A and Asia 1, and the type-specific results were confirmed by color on the test lines of the three strips. The LFI was evaluated using epithelial and vesicular samples (n=396) prepared from current and historical field samples (provide by the National Foot-and-Mouth Disease Reference Laboratory of China at Lanzhou Veterinary Research Institute). Negative samples (n=95) were collected from healthy animals. The diagnostic sensitivity of the LFI for FMDV serotypes OFMDV serotypesFMDV serotypes O, A and Asia 1 was 88.3% compared to 89.7% obtained by the reference method of indirect-sandwich ELISA. The sensitivity of the LFI for FMDV type Asia 1 was higher at 92.1% compared to 90.5% for the ELISA. The specificity of the LFI was 97.1% compared with 97.4%.
not annotated - annotated - LINNAEUS only
Implementation and validation of a sensitive PCR detection method in the eradication campaign against Aleutian mink disease virus.
Aleutian mink disease virus (AMDV) is a severe progressive disease causing multiple different clinical syndromes in mink. In Denmark, the disease is notifiable and under official control. The control programme, based on serological screening, has confined successfully AMDV to the northern part of Denmark. However, re-infections and new introductions of virus into farms require a confirmatory virological test to verify the positive test results of single animals and ultimately to investigate disease transmission. A one step PCR amplifying a 374-base fragment of the NS1 gene of AMDV was compared to the counter-current immune electrophoresis (CIE) routinely used in the serological screening programme. Mink organs (n=299) obtained from 55 recently infected farms and 8 non-infected farms from 2008 to 2010 were tested by PCR, and the results were found to have a high correlation with the serological status of the mink. The relative diagnostic sensitivity of the PCR was 94.7%, and the relative diagnostic specificity was 97.9% when read in parallel with the CIE. PCR positive samples were sequenced and phylogenetic analysis revealed high similarity within the analysed AMDV strains and to AMDV strains described previously.
not annotated - annotated - LINNAEUS only
A new method for detection of pandemic influenza virus using High Resolution Melting analysis of the neuraminidase gene.
Diagnostic methods based upon exclusive detection of haemagglutinin do not detect sequence variation in other gene segments of the Influenza A virus. A complementary approach is described based upon high-resolution melting curve analysis of the neuraminidase gene, an approach with the potential ability to detect small changes in the neuraminidase sequence without the need for specific probes.
not annotated - annotated - LINNAEUS only
Physiological and morphological adaptations in relation to water use efficiency in Mediterranean accessions of Solanum lycopersicum.
The physiological traits underlying the apparent drought resistance of 'Tomatiga de Ramellet' (TR) cultivars, a population of Mediterranean tomato cultivars with delayed fruit deterioration (DFD) phenotype and typically grown under non-irrigation conditions, are evaluated. Eight different tomato accessions were selected and included six TR accessions, one Mediterranean non-TR accession (NTR(M)) and a processing cultivar (NTR(O)). Among the TR accessions two leaf morphology types, normal divided leaves and potato-leaf, were selected. Plants were field grown under well-watered (WW) and water-stressed (WS) treatments, with 30 and 10% of soil water capacity, respectively. Accessions were clustered according to the leaf type and TR phenotype under WW and WS, respectively. Correlation among parameters under the different water treatments suggested that potential improvements in the intrinsic water-use efficiency (A(N)/g(s)) are possible without negative impacts on yield. Under WS TR accessions displayed higher A(N)/g(s), which was not due to differences in Rubisco-related parameters, but correlated with the ratio between the leaf mesophyll and stomatal conductances (g(m)/g(s)). The results confirm the existence of differential traits in the response to drought stress in Mediterranean accessions of tomato, and demonstrate that increases in the g(m)/g(s) ratio would allow improvements in A(N)/g(s) in horticultural crops.
not annotated - annotated - LINNAEUS only
A new filter that accurately mimics the solar UV-B spectrum using standard UV lamps: the photochemical properties, stabilization and use of the urate anion liquid filter.
The physiological effects unique to solar ultraviolet (UV)-B exposure (280-315 nm) are difficult to accurately replicate in the laboratory. This study evaluates the effectiveness of the sodium urate anion in a liquid filter that yields a spectrum nearly indistinguishable from the solar UV-B spectrum while filtering the emissions of widely used UV-B lamps. The photochemical properties and stability of this filter are examined and weighed against a typical spectrum of ground-level solar UV-B radiation. To test the effectiveness of this filter, light-saturated photosynthetic oxygen evolution rates were measured following exposure to UV-B filtered either by this urate filter or the widely used cellulose acetate (CA) filter. The ubiquitous marine Chlorophyte alga Dunaliella tertiolecta was tested under identical UV-B flux densities coupled with ecologically realistic fluxes of UV-A and visible radiation for 6 and 12 h exposures. These results indicate that the urate-filtered UV-B radiation yields minor photosynthetic inhibition when compared with exposures lacking in UV-B. This is in agreement with published experiments using solar radiation. In sharp contrast, radiation filtered by CA filters produced large inhibition of photosynthesis.
not annotated - annotated - LINNAEUS only
The 13C/12C isotopic signal of day-respired CO2 in variegated leaves of Pelargonium x hortorum.
In leaves, although it is accepted that CO(2) evolved by dark respiration after illumination is naturally (13) C-enriched compared to organic matter or substrate sucrose, much uncertainty remains on whether day respiration produces (13) C-depleted or (13) C-enriched CO(2). Here, we applied equations described previously for mesocosm CO(2) exchange to investigate the carbon isotope composition of CO(2) respired by autotrophic and heterotrophic tissues of Pelargonium x hortorum leaves, taking advantage of leaf variegation. Day-respired CO(2) was slightly (13) C-depleted compared to organic matter both under 21% O(2) and 2% O(2). Furthermore, most, if not all CO(2) molecules evolved in the light came from carbon atoms that had been fixed previously before the experiments, in both variegated and green leaves. We conclude that the usual definition of day respiratory fractionation, that assumes carbon fixed by current net photosynthesis is the respiratory substrate, is not valid in Pelargonium leaves under our conditions. In variegated leaves, total organic matter was slightly (13) C-depleted in white areas and so were most primary metabolites. This small isotopic difference between white and green areas probably came from the small contribution of photosynthetic CO(2) refixation and the specific nitrogen metabolism in white leaf areas.
not annotated - annotated - LINNAEUS only
Auxin depletion in barley plants under high-temperature conditions represses DNA proliferation in organelles and nuclei via transcriptional alterations.
Many plant species are susceptible to high-temperature (HT) injury during reproductive development. We recently demonstrated that HT represses the expression of YUCCA auxin biosynthesis genes and reduces endogenous auxin in the developing anthers of barley and Arabidopsis. Here, we show that DNA proliferation in mitochondria, chloroplasts and nuclei of developing panicles is inhibited with increasing temperatures in barley. Following DNA proliferation suppression, terminal abnormalities were observed in the organelles of anther wall cells, including mitochondrial swelling and overdevelopment of chloroplasts. Comprehensive transcriptome analyses using both reproductive organs and vegetative tissues showed high and positive pairwise correlations between the expression profiles of auxin-induced genes, DNA replication-related genes and mitochondrial-related genes. In contrast, the expression profiles of auxin-repressed protein genes and photosynthesis-/chloroplast-related genes were negatively correlated with those of the previously mentioned genes. Under HT conditions, the former was repressed and the latter was up-regulated in the developing panicles. Furthermore, application of exogenous auxin promoted the expression of DNA replication-related genes under HT conditions, inducing anther cell proliferation. These suggest that compromised auxin biosynthesis/IAA level under HT condition results in nuclear and organellar DNA proliferation arrest due to co-transcriptional alterations.
not annotated - annotated - LINNAEUS only
Minimum hydraulic safety leads to maximum water-use efficiency in a forage grass.
Understanding how water-use regulation relates to biomass accumulation is imperative for improving crop production in water-limited environments. Here, we examine how the vulnerability of xylem to water stress-induced cavitation and the coordination between water transport capacity and assimilation (A) influences diurnal water-use efficiency (WUE) and dry-matter production in Lolium perenne L. - a commercial forage grass. Plants were exposed to a range of water stresses, causing up to 90% leaf death, by withholding water and then rewatering to observe the recovery process. Leaf hydraulic conductance (K(leaf) ) declined to 50% of maximum at a leaf water potential (psi(leaf) ) of -1 MPa, whereas complete stomatal closure occurred well after this point, at -2.35 MPa, providing no protection against hydraulic dysfunction. Instantaneous A remained maximal until >70% of hydraulic conductivity had been lost. Post-stress rewatering showed that 95% loss of K(leaf) could be incurred before the recovery of gas exchange exceeded 1 d, with a rapid transition to leaf death after this point. Plants exposed to sustained soil water deficits through restricted nightly watering regimes did not suffer cumulative losses in K(leaf) ; instead, psi(leaf) and gas exchange recovered diurnally. The effect was improved WUE during the day and optimal psi(leaf) during the night for the maintenance of growth.
not annotated - annotated - LINNAEUS only
Novel mutations reveal two important regions in Aspergillus nidulans transcriptional activator MetR.
Expression of the sulfur assimilation pathway in Aspergillus nidulans is under control of sulfur metabolite repression, which is composed of scon genes encoding subunits of ubiquitin ligase and the metR gene coding for a transcriptional activator. In this paper we report three dominant suppressors of methionine requirement isolated from a metB3 diploid strain. All three mutations lead to the substitution of phenylalanine 48 by serine or leucine in the conserved N-terminal region of the MetR protein. Strains carrying the dominant suppressor mutations exhibit increased activities of homocysteine synthase and sulfur assimilation enzymes as well as elevated levels of the corresponding transcripts. These changes are observed even under conditions of methionine repression, which suggests that the mutated MetR protein may be resistant to inactivation or degradation mediated by sulfur metabolite repression. We also found that a mutant impaired in sulfite reductase activity, known until now as sG8, has a frameshift which changes 41 C-terminal amino acids. Therefore, it is now designated metR18. This mutant has elevated levels of MetR-regulated transcripts and of activities of sulfur assimilation enzymes (except sulfite reductase), which can be repressed to the wild type level by exogenous methionine. Thus, metR18 and the three dominant suppressors represent new types of mutations affecting different parts of the A. nidulans MetR protein.
not annotated - annotated - LINNAEUS only
Paralogous cyp51 genes in Fusarium graminearum mediate differential sensitivity to sterol demethylation inhibitors.
Analysis of the genome sequence of Fusarium graminearum revealed three paralogous cyp51 genes (designated cyp51A, -B, and -C) encoding 14-alpha demethylases in this fungus. Targeted gene disruption showed that the cyp51A, -B or -C disruption mutants were morphologically indistinguishable from the parent isolate on potato dextrose agar medium, which indicates that none of these genes is essential for mycelial growth. The sensitivity of cyp51A deletion mutants to seven sterol demethylation inhibitor (DMI) fungicides increased significantly compared to the parent strain, while sensitivity of cyp51C deletion mutants increased to some but not all DMIs. No change in DMI sensitivity was observed for cyp51B deletion mutants. The parental phenotypes of cyp51A and cyp51C deletion mutants were completely restored by genetic complementation with the wild-type cyp51A and cyp51C genes, respectively. The sensitivity of F. graminearum isolates increased significantly when subjected in vitro to a mixture of DMI fungicides triadimefon and tebuconazole as compared to the individual components. These results indicate that different DMI fungicides target different CYP51 proteins in F. graminearum and that a mixture of DMI fungicides can result in synergistic effects. Our findings have directly implications on chemical management strategies of plant diseases caused by Fusarium species.
not annotated - annotated - LINNAEUS only
Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution.
The two fungal pathogens Blumeria graminis f. sp. triticiBlumeria graminis f. sp. tritici (B.g. tritici) and hordei (B.g. hordei) cause powdery mildew specifically in wheat or barley. They have the same life cycle, but their growth is restricted to the respective host. Here, we compared the sequences of two loci in both cereal mildews to determine their divergence time and their relationship with the evolution of their hosts. We sequenced a total of 273.3kb derived from B.g. tritici BAC sequences and compared them with the orthologous regions in the B.g. hordei genome. Protein-coding genes were colinear and well conserved. In contrast, the intergenic regions showed very low conservation mostly due to different integration patterns of transposable elements. To estimate the divergence time of B.g. tritici and B.g. hordei, we used conserved intergenic sequences including orthologous transposable elements. This revealed that B.g. tritici and B.g. hordei have diverged about 10 million years ago (MYA), two million years after wheat and barley (12 MYA). These data suggest that B.g. tritici and B.g. hordei have co-evolved with their hosts during most of their evolutionary history after host divergence, possibly after a short phase of host expansion when the same pathogen could still grow on the two diverged hosts.
not annotated - annotated - LINNAEUS only
Can we predict carbon stocks in tropical ecosystems from tree diversity? Comparing species and functional diversity in a plantation and a natural forest.
* Linking tree diversity to carbon storage can provide further motivation to conserve tropical forests and to design carbon-enriched plantations. Here, we examine the role of tree diversity and functional traits in determining carbon storage in a mixed-species plantation and in a natural tropical forest in Panama. * We used species richness, functional trait diversity, species dominance and functional trait dominance to predict tree carbon storage across these two forests. Then we compared the species ranking based on wood density, maximum diameter, maximum height, and leaf mass per area (LMA) between sites to reveal how these values changed between different forests. * Increased species richness, a higher proportion of nitrogen fixers and species with low LMA increased carbon storage in the mixed-species plantation, while a higher proportion of large trees and species with high LMA increased tree carbon storage in the natural forest. Furthermore, we found that tree species varied greatly in their absolute and relative values between study sites. * Different results in different forests mean that we cannot easily predict carbon storage capacity in natural forests using data from experimental plantations. Managers should be cautious when applying functional traits measured in natural populations in the design of carbon-enriched plantations.
not annotated - annotated - LINNAEUS only
Profile of the mosaic element BTMR1 in the genome of the bumble bee Bombus terrestris (Hymenoptera: Apidae).
Co-evolution involving a mariner transposon, Botmar1 and the other repeats contained in the Bombus terrestris genome was investigated. We found that the 5'-region of Botmar1 forms one of the components of a mosaic element, known as B. terrestris mosaic repeat 1 (BTMR1), which is also composed of inner segments originating from two different retrotransposons and a pseudogene corresponding to an RNA methyltransferase cDNA. The fact that BTMR1 is interspersed within chromosomes and the differences in its abundance in different species indicate that it is very probably a mobile element. Nevertheless, the absences of direct or inverted repeats at its ends and of target site duplication indicate that its mobility is not ensured by a cardinal transposable element, but putatively by a Crypton-like element.
not annotated - annotated - LINNAEUS only
The RNA-Seq approach to studying the expression of mosquito mitochondrial genes.
In this study, we used extensive expressed sequence tag evidence obtained through 454 and Solexa next-generation sequencing to explore mtDNA transcription in male and female first instar larvae of Aedes aegypti and adults of Aedes aegypti, Anopheles gambiae, and Anopheles quadrimaculatus. Relative abundances of individual transcripts differed considerably within each sample, consistent with the differential stability of messenger RNA species. Large differences were also observed between species and between larval and adult stages; however, the male and female larval samples were remarkably similar. Quantitative PCR analysis of selected genes, cox1, l-rRNA and nd5, in larvae and adults of Ae. aegypti and in An. gambiae adults was consistent with the RNA-Seq-based quantification of expression. Finally, the absence of a conserved mtDNA region involved in transcriptional control in other dipterans suggests that mosquitoes have evolved a distinct mechanism of regulation of gene expression in the mitochondrion.
not annotated - annotated - LINNAEUS only
Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum.
* The genome of Tuber melanosporum has recently been sequenced. Here, we used this information to identify genes involved in the reproductive processes of this edible fungus. The sequenced strain (Mel28) possesses only one of the two master genes required for mating, that is, the gene that codes for the high mobility group (HMG) transcription factor (MAT1-2-1), whereas it lacks the gene that codes for the protein containing the alpha-box- domain (MAT1-1-1), suggesting that this fungus is heterothallic. * A PCR-based approach was initially employed to screen truffles for the presence of the MAT1-2-1 gene and amplify the conserved regions flanking the mating type (MAT) locus. The MAT1-1-1 gene was finally identified using primers designed from the conserved regions of strains that lack the MAT1-2-1 gene. * Mating type-specific primer pairs were developed to screen asci and gleba from truffles of different origins and to genotype single ascospores within the asci. These analyses provided definitive evidence that T. melanosporum is a heterothallic species with a MAT locus that is organized similarly to those of ancient fungal lineages. * A greater understanding of the reproductive mechanisms that exist in Tuber spp. allows for optimization of truffle plantation management strategies.
not annotated - annotated - LINNAEUS only
Updated hypothesis on the evolution of oligotrichid ciliates (Ciliophora, Spirotricha, Oligotrichida) based on somatic ciliary patterns and ontogenetic data.
The two recently established genera Apostrombidium Xu et al., 2009 and Varistrombidium Xu et al., 2009 and the analysis of ontogenetic data in Strombidium constrictum, S. montagnesi, S. wilberti, Omegastrombidium elegans, and Paratontonia gracillima necessitated a revision of the hypothesis about the somatic ciliary pattern evolution in oligotrichid ciliates. As a consequence, the species-rich genus Strombidium was split, establishing two genera for species with a horizontal girdle kinety posterior to the oral primordium: Opisthostrombidium nov. gen. with the extrusome attachment sites along the anterior margin of the girdle kinety and posterior to the oral primordium and Foissneridium nov. gen. with the extrusome attachment sites distinctly apart from the girdle kinety and anterior to the oral primordium. The ontogenetic data revealed that the Omega-shaped girdle kinety pattern evolved convergently from the Pseudotontonia pattern with its horizontal girdle kinety in the tailed genus Paratontonia and from the Novistrombidium pattern with its dextrally spiralled girdle kinety in the tailless genus Omegastrombidium. The somatic ciliary pattern of the latter genus probably gave rise to the patterns of Apostrombidium and Varistrombidium.
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Neutralizing antibody-resistant hepatitis C virus cell-to-cell transmission.
Hepatitis C virus (HCV) can initiate infection by cell-free particle and cell-cell contact-dependent transmission. In this study we use a novel infectious coculture system to examine these alternative modes of infection. Cell-to-cell transmission is relatively resistant to anti-HCV glycoprotein monoclonal antibodies and polyclonal immunoglobulin isolated from infected individuals, providing an effective strategy for escaping host humoral immune responses. Chimeric viruses expressing the structural proteins representing the seven major HCV genotypes demonstrate neutralizing antibody-resistant cell-to-cell transmission. HCV entry is a multistep process involving numerous receptors. In this study we demonstrate that, in contrast to earlier reports, CD81 and the tight-junction components claudin-1 and occludin are all essential for both cell-free and cell-to-cell viral transmission. However, scavenger receptor BI (SR-BI) has a more prominent role in cell-to-cell transmission of the virus, with SR-BI-specific antibodies and small-molecule inhibitors showing preferential inhibition of this infection route. These observations highlight the importance of targeting host cell receptors, in particular SR-BI, to control viral infection and spread in the liver.
not annotated - annotated - LINNAEUS only
Chikungunya virus induces IPS-1-dependent innate immune activation and protein kinase R-independent translational shutoff.
Chikungunya virus (CHIKV) is an arthritogenic mosquito-transmitted alphavirus that is undergoing reemergence in areas around the Indian Ocean. Despite the current and potential danger posed by this virus, we know surprisingly little about the induction and evasion of CHIKV-associated antiviral immune responses. With this in mind we investigated innate immune reactions to CHIKV in human fibroblasts, a demonstrable in vivo target of virus replication and spread. We show that CHIKV infection leads to activation of the transcription factor interferon regulatory factor 3 (IRF3) and subsequent transcription of IRF3-dependent antiviral genes, including beta interferon (IFN-Beta). IRF3 activation occurs by way of a virus-induced innate immune signaling pathway that includes the adaptor molecule interferon promoter stimulator 1 (IPS-1). Despite strong transcriptional upregulation of these genes, however, translation of the corresponding proteins is not observed. We further demonstrate that translation of cellular (but not viral) genes is blocked during infection and that although CHIKV is found to trigger inactivation of the translational molecule eukaryotic initiation factor subunit 2alpha by way of the double-stranded RNA sensor protein kinase R, this response is not required for the block to protein synthesis. Furthermore, overall diminution of cellular RNA synthesis is also observed in the presence of CHIKV and transcription of IRF3-dependent antiviral genes appears specifically blocked late in infection. We hypothesize that the observed absence of IFN-Beta and antiviral proteins during infection results from an evasion mechanism exhibited by CHIKV that is dependent on widespread shutoff of cellular protein synthesis and a targeted block to late synthesis of antiviral mRNA transcripts.
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Blood myeloid dendritic cells from HIV-1-infected individuals display a proapoptotic profile characterized by decreased Bcl-2 levels and by caspase-3+ frequencies that are associated with levels of plasma viremia and T cell activation in an exploratory study.
Reduced frequencies of myeloid and plasmacytoid dendritic cell (DC) subsets (mDCs and pDCs, respectively) have been observed in the peripheral blood of HIV-1-infected individuals throughout the course of disease. Accumulation of DCs in lymph nodes (LNs) may partly account for the decreased numbers observed in blood, but increased DC death may also be a contributing factor. We used multiparameter flow cytometry to evaluate pro- and antiapoptotic markers in blood mDCs and pDCs from untreated HIV-1-infected donors, from a subset of infected donors before and after receiving antiretroviral therapy (ART), and from uninfected control donors. Blood mDCs, but not pDCs, from untreated HIV-1-infected donors expressed lower levels of antiapoptotic Bcl-2 than DCs from uninfected donors. A subset of HIV-1-infected donors had elevated frequencies of proapoptotic caspase-3(+) blood mDCs, and positive correlations were observed between caspase-3(+) mDC frequencies and plasma viral load and CD8(+) T-cell activation levels. Caspase-3(+) mDC frequencies, but not mDC Bcl-2 expression, were reduced with viral suppression on ART. Apoptosis markers on DCs in blood and LN samples from a cohort of untreated, HIV-1-infected donors with chronic disease were also evaluated. LN mDCs displayed higher levels of Bcl-2 and lower caspase-3(+) frequencies than did matched blood mDCs. Conversely, LN pDCs expressed lower Bcl-2 levels than their blood counterparts. In summary, blood mDCs from untreated HIV-1-infected subjects displayed a proapoptotic profile that was partially reversed with viral suppression, suggesting that DC death may be a factor contributing to blood DC depletion in the setting of chronic, untreated HIV disease.
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Identification of binary interactions between human cytomegalovirus virion proteins.
Human cytomegalovirus (HCMV) virions are composed of a DNA-containing nucleocapsid surrounded by a tegument layer and host-derived lipid envelope studded with virally encoded glycoproteins. These complex virions are estimated to be composed of more than 50 viral proteins. Assembly of HCMV virions is poorly understood, especially with respect to acquisition of the tegument; however, it is thought to involve the stepwise addition of virion components through protein-protein interactions. We sought to identify interactions among HCMV virion proteins using yeast two-hybrid analysis. Using 33 known capsid and tegument proteins, we tested 1,089 pairwise combinations for binary interaction in the two-hybrid assay. We identified 24 interactions among HCMV virion proteins, including 13 novel interactions among tegument proteins and one novel interaction between capsid proteins. Several of these novel interactions were confirmed by coimmunoprecipitation of protein complexes from transfected cells. In addition, we demonstrate three of these interactions in the context of HCMV infection. This study reveals several new protein-protein interactions among HCMV tegument proteins, some of which are likely important for HCMV replication and pathogenesis.
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Modifications in the polymerase genes of a swine-like triple-reassortant influenza virus to generate live attenuated vaccines against 2009 pandemic H1N1 viruses.
On 11 June 2009, the World Health Organization (WHO) declared that the outbreaks caused by novel swine-origin influenza A (H1N1) virus had reached pandemic proportions. The pandemic H1N1 (H1N1pdm) virus is the predominant influenza virus strain in the human population. It has also crossed the species barriers and infected turkeys and swine in several countries. Thus, the development of a vaccine that is effective in multiple animal species is urgently needed. We have previously demonstrated that the introduction of temperature-sensitive mutations into the PB2 and PB1 genes of an avian H9N2 virus, combined with the insertion of a hemagglutinin (HA) tag in PB1, resulted in an attenuated (att) vaccine backbone for both chickens and mice. Because the new pandemic strain is a triple-reassortant (TR) virus, we chose to introduce the double attenuating modifications into a swine-like TR virus isolate, A/turkey/OH/313053/04 (H3N2) (ty/04), with the goal of producing live attenuated influenza vaccines (LAIV). This genetically modified backbone had impaired polymerase activity and restricted virus growth at elevated temperatures. In vivo characterization of two H1N1 vaccine candidates generated using the ty/04 att backbone demonstrated that this vaccine is highly attenuated in mice, as indicated by the absence of signs of disease, limited replication, and minimum histopathological alterations in the respiratory tract. A single immunization with the ty/04 att-based vaccines conferred complete protection against a lethal H1N1pdm virus infection in mice. More importantly, vaccination of pigs with a ty/04 att-H1N1 vaccine candidate resulted in sterilizing immunity upon an aggressive intratracheal challenge with the 2009 H1N1 pandemic virus. Our studies highlight the safety of the ty/04 att vaccine platform and its potential as a master donor strain for the generation of live attenuated vaccines for humans and livestock.
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Novel F141L pre-S2 mutation in hepatitis B virus increases the risk of hepatocellular carcinoma in patients with chronic genotype C infections.
Several lines of evidence have suggested that some naturally occurring mutations of hepatitis B virus (HBV) play a critical role in hepatocellular carcinoma (HCC). Here, we describe a novel HCC-related pre-S2 mutation, F141L. To prove the relationship between the F141L mutation and HCC, molecular epidemiology studies using MboII PCR restriction analysis (PRA) were performed, and the molecular mechanism was investigated through construction of a stable hepatocyte cell line expressing the large surface HB protein (LHB) with the F141L mutation (F141L-LHB). Application of MboII PRA to samples from 241 Korean patients with chronic liver diseases of different clinical stages confirmed that F141L mutants were significantly related to HCC, even in comparison to liver cirrhosis (HCC, 26.3% of patients, or 26/99; liver cirrhosis, 3.8% of patients, or 2/52; P = 0.001). By studying stable cell lines, we found that F141L-LHBs could induce cell cycle progression by downregulating the p53 and p21 pathways and upregulating CDK4 and cyclin A. Furthermore, we found that in a colony-forming assay, the colony-forming rates in cell lines expressing F141L-LHBs were about twice as high as those of the wild type. In conclusion, our results suggest that F141L-LHBs may contribute importantly to the pathogenesis of HCC by inducing cell proliferation and transformation. So, the F141L mutation examined in this study could serve as a diagnostic marker for the prognosis of HCC.
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Poliovirus-mediated disruption of cytoplasmic processing bodies.
Metazoan cells form cytoplasmic mRNA granules such as stress granules (SG) and processing bodies (P bodies) that are proposed to be sites of aggregated, translationally silenced mRNAs and mRNA degradation. Poliovirus (PV) is a plus-strand RNA virus containing a genome that is a functional mRNA; thus, we investigated if PV antagonizes the processes that lead to formation of these structures. We have previously shown that PV infection inhibits the ability of cells to form stress granules by cleaving RasGAP-SH3-binding protein (G3BP). Here, we show that P bodies are also disrupted during PV infection in cells by 4 h postinfection. The disruption of P bodies is more rapid and more complete than disruption of stress granules. The kinetics of P body disruption correlated with production of viral proteinases and required substantial viral gene product expression. The organizing mechanism that forms P body foci in cells is unknown; however, potential scaffolding, aggregating, or other regulatory proteins found in P bodies were investigated for degradation. Two factors involved in 5'-end mRNA decapping and degradation, Xrn1 and Dcp1a, and the 3' deadenylase complex component Pan3 underwent accelerated degradation during infection, and Dcp1a may be a direct substrate of PV 3C proteinase. Several other key factors proposed to be essential for P body formation, GW182, Edc3, and Edc4, were unaffected by poliovirus infection. Since deadenylation has been reported to be required for P body formation, viral inhibition of deadenylation, through Pan3 degradation, is a potential mechanism of P body disruption.
not annotated - annotated - LINNAEUS only
The magnitude of local immunity in the lungs of mice induced by live attenuated influenza vaccines is determined by local viral replication and induction of cytokines.
While live attenuated influenza vaccines (LAIVs) have been shown to be efficacious and have been licensed for human use, the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA) have to be updated for optimal protective efficacy. Little is known about the effect of different HA and NA proteins on the immunogenicity of LAIVs developed using the same backbone. A panel of LAIVs that share the internal protein genes, with unique HA and NA gene segments from different influenza subtypes, was rescued by reverse genetics, and a comparative study of immune responses induced by these vaccines was conducted in mice. The results suggest that the magnitude of lung immunity, including pulmonary IgA antibody and memory CD8(+) T lymphocytes, induced by the vaccines depends on the replication efficiency of the LAIVs, as well as the induction of cytokines/chemokines in the lungs. However, these factors are not important in determining systemic immunity such as serum antibody titers and memory CD8(+) T cells in the spleen. A qualitative analysis of immune responses induced by a single dose of an H5N1 LAIV revealed that the vaccine induced robust systemic and mucosal immunity in mice. In addition, antibodies and memory lymphocytes established in the lungs following vaccination were required for protection against lethal challenge with homologous and heterologous H5N1 viruses. Our results highlight the different requirements for inducing systemic and lung immunity that can be explored for the development of pulmonary immunity for protection against respiratory pathogens.
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Multiple innate immune pathways contribute to the immunogenicity of recombinant adenovirus vaccine vectors.
The innate immune pathways that contribute to the potent immunogenicity of recombinant adenovirus (rAd) vaccine vectors remain largely undefined. Previous studies assessing innate immunity triggered by vaccine vectors have largely focused on in vitro studies involving antigen-presenting cells and on early in vivo inflammatory responses. Here, we systematically explore the Toll-like receptor (TLR) signaling requirements for the generation of cellular immune responses by intramuscular immunization with common and alternative serotype rAd vectors in mice. Antigen-specific CD8(+) T-lymphocyte responses elicited by these rAd vectors were significantly diminished in MyD88(-/-) mice but not in TRIF(-/-) or TLR3(-/-) mice, suggesting the importance of MyD88-dependent TLR signaling. However, the absence of each individual TLR resulted in minimal to no effect on vaccine-elicited cellular immune responses. Moreover, responses were not diminished in IL-1R(-/-) or IL-18R(-/-) mice. These data suggest that rAd vectors engage multiple MyD88-dependent signaling pathways, none of which are individually critical; rather, they are integrated to contribute to the potent immunogenicity of rAd vectors. Stimulation of multiple innate immune mechanisms may prove a generalizable property of potent vaccines, and this strategy could be harnessed in the development of next-generation vaccine vectors and adjuvants.
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Marek's disease virus type 1 microRNA miR-M3 suppresses cisplatin-induced apoptosis by targeting Smad2 of the transforming growth factor beta signal pathway.
Viruses cause about 15% of the cancers that are still the leading causes of human mortality. The discovery of viral oncogenes has enhanced our understanding of viral oncogenesis. However, the underlying molecular mechanisms of virus-induced cancers are complex and require further investigation. The present study has attempted to investigate the effects of the microRNAs (miRNAs) encoded by Marek's disease virus 1 (MDV1), a chicken herpesvirus causing acute T-cell lymphomas and solid visceral tumors in chickens, on anti-cancer drug-induced apoptosis and identify the targets of the miRNAs. The results showed that of the total 14 miRNAs encoded by MDV1, MDV1-miR-M3 significantly promoted cell survival under treatment with cisplatin, a widely used chemotherapy drug. MDV1-miR-M3 suppressed cisplatin-induced apoptosis by directly downregulating expression at the protein but not the mRNA level of Smad2, a critical component in the transforming growth factor Beta signal pathway. Our data suggest that latent/oncogenic viruses may encode miRNAs to directly target cellular factors involved in antiviral processes including apoptosis, thus proactively creating a cellular environment beneficial to viral latency and oncogenesis. Furthermore, the knowledge of the apoptosis resistance conferred by viral miRNAs has great practical implications for improving the efficacy of chemotherapies for treating cancers, especially those induced by oncogenic viruses.
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Macaque long-term nonprogressors resist superinfection with multiple CD8+ T cell escape variants of simian immunodeficiency virus.
Human immunodeficiency virus (HIV)-positive individuals can be superinfected with different virus strains. Individuals who control an initial HIV infection are therefore still at risk for subsequent infection with divergent viruses, but the barriers to such superinfection remain unclear. Here we tested long-term nonprogressors' (LTNPs') susceptibility to superinfection using Indian rhesus macaques that express the major histocompatibility complex class I (MHC-I) allele Mamu-B 17, which is associated with control of the pathogenic AIDS virus SIVmac239. The Mamu-B 17-restricted CD8(+) T cell repertoire is focused almost entirely on 5 epitopes. We engineered a series of SIVmac239 variants bearing mutations in 3, 4, or all 5 of these epitopes and used them to serially challenge 2 Mamu-B 17-positive LTNPs. None of the escape variants caused breakthrough replication in LTNPs, although they readily infected Mamu-B 17-negative naive macaques. In vitro competing coculture assays and examination of viral evolution in hosts lacking Mamu-B 17 suggested that the mutant viruses had negligible defects in replicative fitness. Both LTNPs maintained robust immune responses, including simian immunodeficiency virus (SIV)-specific CD8(+) and CD4(+) T cells and neutralizing antibodies. Our results suggest that escape mutations in epitopes bound by "protective" MHC-I molecules may not be sufficient to establish superinfection in LTNPs.
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Induction of type I interferon secretion through recombinant Newcastle disease virus expressing measles virus hemagglutinin stimulates antibody secretion in the presence of maternal antibodies.
Measles virus (MV) vaccine effectively protects seronegative individuals against infection. However, inhibition of vaccine-induced seroconversion by maternal antibodies after vaccination remains a problem, as it leaves infants susceptible to MV infection. In cotton rats, passive transfer of MV-specific IgG mimics maternal antibodies and inhibits vaccine-induced seroconversion. Here, we report that immunization in the presence of passively transferred IgG inhibits the secretion of neutralizing antibodies but not the generation of MV-specific B cells. This finding suggested that MV-specific B cells require an additional stimulus to mature into antibody-secreting plasma cells. In order to provide such a stimulus, we generated a recombinant Newcastle disease virus (NDV) expressing the MV hemagglutinin (NDV-H). In contrast to MV, NDV-H induced high levels of type I interferon in plasmacytoid dendritic cells and in lung tissue. In cotton rats immunized with NDV-H, neutralizing antibodies were also generated in the presence of passively transferred antibodies. In the latter case, however, the level and kinetics of antibody generation were reduced. In vitro, alpha interferon stimulated the activation of MV-specific B cells from MV-immune spleen cells. NDV infection (which induces alpha interferon) had the same effect, and stimulation could be abrogated by antibodies neutralizing alpha interferon, but not interleukin 6 (IL-6). In vivo, coapplication of UV-inactivated MV with NDV led to increased MV-specific antibody production in the presence and absence of passively transferred antibodies. These data indicate that MV-specific B cells are being generated after immunization in the presence of maternal antibodies and that the provision of alpha interferon as an additional signal leads to antibody secretion.
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Human pluripotent stem cells produce natural killer cells that mediate anti-HIV-1 activity by utilizing diverse cellular mechanisms.
Cell-based therapies against HIV/AIDS have been gaining increased interest. Natural killer (NK) cells are a key component of the innate immune system with the ability to kill diverse tumor cells and virus-infected cells. While NK cells have been shown to play an important role in the control of HIV-1 replication, their functional activities are often compromised in HIV-1-infected individuals. We have previously demonstrated the derivation of NK cells from human embryonic stem cells (hESCs) with the ability to potently kill multiple types of tumor cells both in vitro and in vivo. We now demonstrate the derivation of functional NK cells from human induced pluripotent stem cells (iPSCs). More importantly, both hESC- and iPSC-derived NK cells are able to inhibit HIV-1 NL4-3 infection of CEM-GFP cells. Additional studies using HIV-1-infected human primary CD4(+) T cells illustrated that hESC- and iPSC-derived NK cells suppress HIV-1 infection by at least three distinct cellular mechanisms: killing of infected targets through direct lysis, antibody-dependent cellular cytotoxicity, and production of chemokines and cytokines. Our results establish the potential to utilize hESC- and iPSC-derived NK cells to better understand anti-HIV-1 immunity and provide a novel cellular immunotherapeutic approach to treat HIV/AIDS.
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Yeast-elicited cross-reactive antibodies to HIV Env glycans efficiently neutralize virions expressing exclusively high-mannose N-linked glycans.
The HIV envelope (Env) protein uses a dense coat of glycans to mask conserved domains and evade host humoral immune responses. The broadly neutralizing antibody 2G12, which binds a specific cluster of high-mannose glycans on HIV Env, shows that the glycan shield can also serve as a target for neutralizing antibodies. We have described a triple mutant Saccharomyces cerevisiae strain that expresses high-mannose glycoproteins that bind to 2G12. When used to immunize rabbits, this yeast elicits antibodies that bind to gp120-associated glycans but fail to neutralize virus. Here we sought to determine the reason for these discordant results. Affinity purification of sera over columns conjugated with three 2G12-reactive yeast glycoproteins showed that these proteins could adsorb 80% of the antibodies that bind to gp120 glycans. Despite binding to monomeric gp120, these mannose-specific antibodies failed to bind cell surface-expressed trimeric Env. However, when Env was expressed in the presence of the mannosidase inhibitor kifunensine to force retention of high-mannose glycans at all sites, the purified antibodies gained the abilities to bind trimeric Env and to strongly and broadly neutralize viruses produced under these conditions. Combined, these data show that the triple mutant yeast strain elicits antibodies that bind to high-mannose glycans presented on the HIV envelope, but only when they are displayed in a manner not found on native Env trimers. This implies that the underlying structure of the protein scaffold used to present the high-mannose glycans may be critical to allow elicitation of antibodies that recognize trimeric Env and neutralize virus.
not annotated - annotated - LINNAEUS only
Role of RNase MRP in viral RNA degradation and RNA recombination.
RNA degradation, together with RNA synthesis, controls the steady-state level of viral RNAs in infected cells. The endoribonucleolytic cleavage of viral RNA is important not only for viral RNA degradation but for RNA recombination as well, due to the participation of some RNA degradation products in the RNA recombination process. To identify host endoribonucleases involved in degradation of Tomato bushy stunt virus (TBSV) in a Saccharomyces cerevisiae model host, we tested eight known endoribonucleases. Here we report that downregulation of SNM1, encoding a component of the RNase MRP, and a temperature-sensitive mutation in the NME1 gene, coding for the RNA component of RNase MRP, lead to reduced production of the endoribonucleolytically cleaved TBSV RNA in yeast. We also show that the highly purified yeast RNase MRP cleaves the TBSV RNA in vitro, resulting in TBSV RNA degradation products similar in size to those observed in yeast cells. Knocking down the NME1 homolog in Nicotiana benthamiana also led to decreased production of the cleaved TBSV RNA, suggesting that in plants, RNase MRP is involved in TBSV RNA degradation. Altogether, this work suggests a role for the host endoribonuclease RNase MRP in viral RNA degradation and recombination.
not annotated - annotated - LINNAEUS only
Identification and structural characterization of the ALIX-binding late domains of simian immunodeficiency virus SIVmac239 and SIVagmTan-1.
Retroviral Gag proteins contain short late-domain motifs that recruit cellular ESCRT pathway proteins to facilitate virus budding. ALIX-binding late domains often contain the core consensus sequence YPX(n)L (where X(n) can vary in sequence and length). However, some simian immunodeficiency virus (SIV) Gag proteins lack this consensus sequence, yet still bind ALIX. We mapped divergent, ALIX-binding late domains within the p6(Gag) proteins of SIV(mac239) ((40)SREKPYKEVTEDLLHLNSLF(59)) and SIV(agmTan-1) ((24)AAGAYDPARKLLEQYAKK(41)). Crystal structures revealed that anchoring tyrosines (in lightface) and nearby hydrophobic residues (underlined) contact the ALIX V domain, revealing how lentiviruses employ a diverse family of late-domain sequences to bind ALIX and promote virus budding.
not annotated - annotated - LINNAEUS only
Variola and monkeypox viruses utilize conserved mechanisms of virion motility and release that depend on abl and SRC family tyrosine kinases.
Vaccinia virus (VacV) enters mammalian cells, replicates extranuclearly, and produces virions that move to the cell surface along microtubules, fuse with the plasma membrane, and move from infected cells toward apposing cells on actin-filled membranous protrusions or actin tails. To form actin tails, cell-associated enveloped virions (CEV) require Abl and Src family tyrosine kinases. Furthermore, release of CEV from the cell requires Abl but not Src family tyrosine kinases and is blocked by imatinib mesylate (STI-571; Gleevec), an Abl family kinase inhibitor used to treat chronic myelogenous leukemia in humans. Here we demonstrate that the Poxviridae family members monkeypox virus (MPX) and variola virus (VarV) use conserved mechanisms for actin motility and extracellular enveloped virion (EEV) release. Furthermore, we show that imatinib mesylate is effective in a mouse model of infection with VacV, whether delivered prophylactically or postinfection, and restricts spread of virions from the site of inoculation. While inhibitors of both Src and Abl family kinases, such as dasatinib (BMS-354825; Sprycel), are effective in limiting dissemination of VacV, VarV, and MPX in vitro, members of this class of drugs appear to have immunosuppressive effects in vivo that preclude their use as anti-infectives. Together, these data suggest a possible utility for imatinib mesylate in treating smallpox or MPX infections or complications associated with vaccination.
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Replicative and transcriptional activities of hepatitis B virus in patients coinfected with hepatitis B and hepatitis delta virusesviruses.
Hepatitis B virus (HBV) and hepatitis delta virus (HDV) interplay was investigated by examining liver and serum samples from 21 coinfected and 22 HBV-monoinfected patients with chronic liver disease. Different real-time PCR assays were applied to evaluate intrahepatic amounts of HBV DNA, covalently closed circular DNA (cccDNA), pregenomic RNA (pgRNA), pre-S/S RNAs, and HDV RNA. Besides HBV DNA and HDV RNA levels, HBsAg concentrations in the sera were also determined. HDV-coinfected cases showed significantly lower median levels of serum HBV DNA (-5 log), intrahepatic relaxed-circular DNA (-2 log), and cccDNA (-2 log) than those of HBV-monoinfected cases. Interestingly, pgRNA and pre-S/S RNA amounts were significantly lower (both -1 log) in HDV-positive patients, whereas serum HBsAg concentrations were comparable between the two patient groups. Pre-S/S RNA and HBsAg amounts per cccDNA molecule were higher in HDV-positive patients (3-fold and 1 log, respectively), showing that HBV replication was reduced, whereas synthesis of envelope proteins was not specifically decreased. The ratios of cccDNA to intracellular total HBV DNA showed a larger proportion of cccDNA molecules in HDV-positive cases. For these patients, both intrahepatic and serum HDV RNA amounts were associated with cccDNA but not with HBsAg or HBV DNA levels. Finally, HBV genomes with large deletions in the basal core promoter/precore region were detected in 5/21 HDV-positive patients but in no HDV-negative patients and were associated with lower viremia levels. These findings provide significant information about the interference exerted by HDV on HBV replication and transcription activities in the human liver.
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Dynamics of two separate but linked HIV-1 CRF01_AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland.
Detailed phylogenetic analyses were performed to characterize an HIV-1 outbreak among injection drug users (IDUs) in Stockholm, Sweden, in 2006. This study investigated the source and dynamics of HIV-1 spread during the outbreak as well as associated demographic and clinical factors. Seventy Swedish IDUs diagnosed during 2004 to 2007 were studied. Demographic, clinical, and laboratory data were collected, and the V3 region of the HIV-1 envelope gene was sequenced to allow detailed phylogenetic analyses. The results showed that the Stockholm outbreak was caused by a CRF01_AE variant imported from Helsinki, Finland, around 2003, which was quiescent until the outbreak started in 2006. Local Swedish subtype B variants continued to spread at a lower rate. The number of new CRF01_AE cases over a rooted phylogenetic tree accurately reflected the transmission dynamics and showed a temporary increase, by a factor of 12, in HIV incidence during the outbreak. Virus levels were similar in CRF01_AE and subtype B infections, arguing against differences in contagiousness. Similarly, there were no major differences in other baseline characteristics. Instead, the outbreak in Stockholm (and Helsinki) was best explained by an introduction of HIV into a standing network of previously uninfected IDUs. The combination of phylogenetics and epidemiological data creates a powerful tool for investigating outbreaks of HIV and other infectious diseases that could improve surveillance and prevention.
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Thermally contingent plasticity: temperature alters expression of predator-induced colour and morphology in a Neotropical treefrog tadpole.
1. Behavioural, morphological and coloration plasticity are common responses of prey to predation risk. Theory predicts that prey should respond to the relative magnitude of risk, rather than a single level of response to any risk level. In addition to conspecific and predator densities, prey growth and differentiation rates affect the duration of vulnerability to size- and stage-limited predators and therefore the relative value of defences. 2. We reared tadpoles of the Neotropical treefrog Dendropsophus ebraccatus with or without cues from a predator (Belostoma sp.) in ecologically relevant warm or cool temperatures. To track phenotypic changes, we measured morphology, tail coloration and developmental stage at three points during the larval period. 3. Cues from predators interacted with growth conditions causing tadpoles to alter their phenotype, changing only tail colour in response to predators in warm water, but both morphology and colour in cool growth conditions. Tadpoles with predators in warm water altered coloration early but converged on the morphology of predator-free controls. Water temperature alone had no effect on tadpole phenotype. 4. We demonstrate that seemingly small variation in abiotic environmental conditions can alter the expression of phenotypic plasticity, consistent with predictions about how growth rate affects risk. Predator-induced tadpole phenotypes depended on temperature, with strong expression only in temperatures that slow development. Thermal modulation of plastic responses to predators may be broadly relevant to poikilotherm development. It is important to include a range of realistic growth conditions in experiments to more fully understand the ecological and evolutionary significance of plasticity.
not annotated - annotated - LINNAEUS only
Contrasting covariation of above- and belowground invertebrate species across plant genotypes.
1. Invertebrate species generally do not respond independently to genotypic variation in plants, giving rise to clusters of species that naturally associate with or avoid certain genotypes. This covariation causes coevolution to be diffuse rather than pairwise. Studies on this topic, however, have never considered the belowground invertebrate community, leaving a critical gap in our understanding. 2. We investigated the covariation among naturally colonising above- and belowground invertebrate species across six genetically distinct populations of the dune grass Ammophila arenaria. After having grown from seed in a common garden, plants were randomised in a single field site to exclude all but broad-sense genetic variation. 3. Strong positive covariation across genotypes among both above- and belowground invertebrates was detected, while correlations between these two groups were negative. This clustering of above- and belowground species matched well with order level taxonomy. Host range, trophic level and food type on the other hand did not correspond well with the clusters. Within the cluster of aboveground fauna, subsequent groupings were not related to any phylogenetic or ecological characteristic, although correlations within these subgroups were very high. We furthermore demonstrated significant differences in multiple invertebrate species occurrence between plant genotypes, in general as well as at the above- and belowground level. 4. The observed strong covariation suggests diffuse coevolution between A. arenaria and its associated invertebrate species. The trade-off between root and shoot invertebrates could however hamper directional selection on resistance to either group. 5. Our results clearly demonstrate the need for studies of plant-animal interactions to include the belowground fauna, as this might drastically alter our general conception of how plants and their associated animal communities interact and how these interactions shape the process of evolution.
not annotated - annotated - LINNAEUS only
Density-dependent population dynamics and dispersal in heterogeneous metapopulations.
1. Metapopulation microcosms were constructed to test the effect of four different types of habitat heterogeneity on the dynamics and dispersal in spatially extended systems; homogeneity, spatial heterogeneity, temporal heterogeneity and spatio-temporal heterogeneity. Resources were distributed across discrete habitat patches in bruchid beetle (Callosobruchus maculatus) metapopulations, and long-term time series were recorded. 2. Mathematical models were fitted to the long-term time series from the experimental systems using a maximum likelihood approach. Models were composed of separate birth, death, emigration and immigration terms all of which incorporated stochasticity drawn from different probability distributions. Models with density-dependent and density-independent birth, death and emigration terms were investigated and, in each case, the model that best described the empirical data was identified. 3. At the local scale, population sizes differed between patches depending on the type of heterogeneity. Larger populations were associated with higher resource availabilities. As a result of this, the variation between local population sizes was greatest when there was spatial heterogeneity in which mean resource abundance varied from patch to patch. Variation in population sizes within patches was largest when there was temporal heterogeneity. 4. Density-dependent processes leading to the regulation of local population dynamics in our experimental systems were strongest in homogeneity or temporal heterogeneity treatments. Associated with this, we found that these systems were best described using mathematical models with density dependence acting on mortality. In contrast, spatial and spatio-temporal time series were adequately described using density-independent population processes. 5. Experimental metapopulations showed varying degrees of density-dependent dispersal. Local net dispersal each week was primarily driven by the local population size and secondarily affected by neighbourhood population density. Mathematical population models illustrated the importance of explicit description of density-dependent dispersal in all systems except the homogeneous metapopulations.
not annotated - annotated - LINNAEUS only
Tuber melanosporum: mating type distribution in a natural plantation and dynamics of strains of different mating types on the roots of nursery-inoculated host plants.
* In light of the recent finding that Tuber melanosporum, the ectomycorrhizal ascomycete that produces the most highly prized black truffles, is a heterothallic species, we monitored the spatial distribution of strains with opposite mating types (MAT) in a natural truffle ground and followed strain dynamics in artificially inoculated host plants grown under controlled conditions. * In a natural truffle ground, ectomycorrhizas (ECMs), soil samples and fruit bodies were sampled and genotyped to determine mating types. Simple sequence repeat (SSR) markers were also used to fingerprint ECMs and fruit bodies. The ECMs from nursery-inoculated host plants were analysed for mating type at 6 months and 19 months post-inoculation. * In open-field conditions, all ECMs from the same sampling site showed an identical mating type and an identical haploid genotype, based on SSR analysis. Interestingly, the gleba of fruit bodies always demonstrated the same genotype as the surrounding ECMs. Although root tips from nursery-grown plants initially developed ECMs of both mating types, a dominance of ECMs of the same MAT were found after several months. * The present study deepens our understanding of the vegetative and sexual propagation modes of T. melanosporum. These results are highly relevant for truffle cultivation.
not annotated - annotated - LINNAEUS only
Jasmonate biosynthesis in legume and actinorhizal nodules.
Jasmonic acid (JA) is a plant signalling compound that has been implicated in the regulation of mutualistic symbioses. In order to understand the spatial distribution of JA biosynthetic capacity in nodules of two actinorhizal species, Casaurina glauca and Datisca glomerata, and one legume, Medicago truncatula, we determined the localization of allene oxide cyclase (AOC) which catalyses a committed step in JA biosynthesis. In all nodule types analysed, AOC was detected exclusively in uninfected cells. The levels of JA were compared in the roots and nodules of the three plant species. The nodules and noninoculated roots of the two actinorhizal species, and the root systems of M. truncatula, noninoculated or nodulated with wild-type Sinorhizobium meliloti or with mutants unable to fix nitrogen, did not show significant differences in JA levels. However, JA levels in all plant organs examined increased significantly on mechanical disturbance. To study whether JA played a regulatory role in the nodules of M. truncatula, composite plants containing roots expressing an MtAOC1-sense or MtAOC1-RNAi construct were inoculated with S. meliloti. Neither an increase nor reduction in AOC levels resulted in altered nodule formation. These data suggest that jasmonates are not involved in the development and function of root nodules.
not annotated - annotated - LINNAEUS only
Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers.
The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexa-nucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system.
not annotated - annotated - LINNAEUS only
Proteotyping to establish the lineage of type A H1N1 and type B human influenza virus.
The ability to establish the lineage of type A H1N1 and type B human influenza virus strains using a new proteotyping approach is demonstrated. Lineage-specific signature peptides have been determined for the hemagglutinin antigen of type A H1N1 and type B influenza viruses. The detection of these peptides alone within the high resolution mass spectra of whole antigen digests enables the lineage of the strain to be rapidly and unequivocally assigned. This proteotyping approach complements conventional PCR approaches and should aid in the monitoring of the evolution of the influenza virus in both humans and animals.
not annotated - annotated - LINNAEUS only
Development of an IgM-capture ELISA for Coxsackievirus A16 infection.
Diagnosis of Coxsackievirus A16 (CA16) infection in China relies mainly on reverse transcription-polymerase chain reaction (RT-PCR) that require expensive equipment and special trained personnel, thus making its wide application in health care settings unlikely. In this study, a novel IgM anti-CA16 assay was developed for the detection of IgM antibodies to CA16 in serum. The responses and diagnostic value of IgM for the CA16 infection were assessed by testing 1970 serum samples. The results showed that sensitivity of IgM test was 84.6% (259/306, 95% CI: 80.1-88.5), and specificity in control subjects and patients with CA16 HFMD was 99.2% (1508/1520, 95% CI: 98.6-99.6) and 90.3% (14/144, 95% CI: 84.2-94.6), respectively. The IgM positive rate reached 56.3% in the sera collected within the first day after onset, increased continuously to 95.3% at day 5 to day 7 after onset, and then reached 100% after more than 8 days. The cross-reaction rate in patients infected with other non-CA16 enteroviruses was 9.7% (14/144). These results suggest that the IgM anti-CA16 assay offers a rapid, convenient, and reliable method to detect acute CA16 infections.
not annotated - annotated - LINNAEUS only
A study of conflict between molecular phylogeny and taxonomy in the Desmidiaceae (Streptophyta, Viridiplantae): analyses of 291 rbcL sequences.
Molecular phylogenetic analyses of 93 new and 198 non-redundant GenBank rbcL sequences of the family Desmidiaceae (Zygnematophyceae, Streptophyta) established 22 mostly highly supported clades, in addition to four non-supported lineages and eight single-taxon branches within the family. Nine novel clades and single-taxon branches were identified, suggesting that current taxon sampling has not reached saturation in the family. The highly polyphyletic nature of most desmid genera corroborated in this study using a large taxon set, calls for re-evaluation of the genus concept in the family Desmidiaceae that traditionally relied on features of cell morphology. Molecular phylogenetic data have shown that these morphological characters are highly homoplastic or plesiomorphic and thus cannot be used to delineate genera. The dramatic discrepancy between the currently practised systematic treatment of the family and the composition of the clades based on sequence comparisons requires emendation of almost all existing genera and description of a larger number of novel genera. The clades identified during this study provide a framework for the future emendation/description of genera in the Desmidiaceae.
not annotated - annotated - LINNAEUS only
Ste50 adaptor protein governs sexual differentiation of Cryptococcus neoformans via the pheromone-response MAPK signaling pathway.
The mitogen-activated protein kinase (MAPK) pathways control diverse cellular functions in pathogenic fungi, including sexual differentiation, stress response, and maintenance of cell wall integrity. Here we characterized a Cryptococcus neoformans gene, which is homologous to the yeast Ste50 that is known to play an important role in mating pheromone response and stress response as an adaptor protein to the Ste11 MAPK kinase kinase in Saccharomyces cerevisiae. The C. neoformans Ste50 was not involved in any of the stress responses or virulence factor production (capsule and melanin) that are controlled by the HOG and Ras/cAMP signaling pathways. However, Ste50 was required for mating in both serotype A and serotype D C. neoformans strains. The ste50Delta mutant was completely defective in cell-cell fusion and mating pheromone production. Double mutation of the STE50 gene blocked increased production of pheromone and the hyper-filamentation phenotype of cells deleted of the CRG1 gene, which encodes the RGS protein that negatively regulates pheromone responsive G-protein signaling via the MAPK pathway. Regardless of the presence of the basidiomycota-specific SH3 domains of Ste50 that are known to be required for full virulence of Ustilago maydis, Ste50 was dispensable for virulence of C. neoformans in a murine model of cryptococcosis. In conclusion, the Ste50 adaptor protein controls sexual differentiation of C. neoformans via the pheromone-responsive MAPK pathway but is not required for virulence.
not annotated - annotated - LINNAEUS only
Nucleotide parasitism by Simkania negevensis (Chlamydiae).
Intracellular bacteria live in an environment rich in most essential metabolites but need special mechanisms to access these substrates. Nucleotide transport proteins (NTTs) catalyze the import of ATP and other nucleotides from the eukaryotic host into the bacterial cell and render de novo synthesis of these compounds dispensable. The draft genome sequence of Simkania negevensis strain Z, a chlamydial organism considered a newly emerging pathogen, revealed four genes encoding putative nucleotide transport proteins (SnNTT1 to SnNTT4), all of which are transcribed during growth of S. negevensis in Acanthamoeba host cells, as confirmed by reverse transcription-PCR. Using heterologous expression in Escherichia coli, we could show that SnNTT1 functions as an ATP/ADP antiporter, SnNTT2 as a guanine nucleotide/ATP/H(+) symporter driven by the membrane potential, and SnNTT3 as a nucleotide triphosphate antiporter. In addition, SnNTT3 is able to transport dCTP, which has not been shown for a prokaryotic transport protein before. No substrate could be identified for SnNTT4. Taking these data together, S. negevensis employs a set of nucleotide transport proteins to efficiently tap its host's energy and nucleotide pools. Although similar to other chlamydiae, these transporters show distinct and unique adaptations with respect to substrate specificities and mode of transport.
not annotated - annotated - LINNAEUS only
Insights into the extracytoplasmic stress response of Xanthomonas campestris pv. campestris: role and regulation of {sigma}E-dependent activity.
Xanthomonas campestris pv. campestris is an epiphytic bacterium that can become a vascular pathogen responsible for black rot disease of crucifers. To adapt gene expression in response to ever-changing habitats, phytopathogenic bacteria have evolved signal transduction regulatory pathways, such as extracytoplasmic function (ECF) sigma factors. The alternative sigma factor sigma(E), encoded by rpoE, is crucial for envelope stress response and plays a role in the pathogenicity of many bacterial species. Here, we combine different approaches to investigate the role and mechanism of sigma(E)-dependent activation in X. campestris pv. campestris. We show that the rpoE gene is organized as a single transcription unit with the anti-sigma gene rseA and the protease gene mucD and that rpoE transcription is autoregulated. rseA and mucD transcription is also controlled by a highly conserved sigma(E)-dependent promoter within the sigma(E) gene sequence. The sigma(E)-mediated stress response is required for stationary-phase survival, resistance to cadmium, and adaptation to membrane-perturbing stresses (elevated temperature and ethanol). Using microarray technology, we started to define the sigma(E) regulon of X. campestris pv. campestris. These genes encode proteins belonging to different classes, including periplasmic or membrane proteins, biosynthetic enzymes, classical heat shock proteins, and the heat stress sigma factor sigma(H). The consensus sequence for the predicted sigma(E)-regulated promoter elements is GGAACTN(15-17)GTCNNA. Determination of the rpoH transcription start site revealed that rpoH was directly regulated by sigma(E) under both normal and heat stress conditions. Finally, sigma(E) activity is regulated by the putative regulated intramembrane proteolysis (RIP) proteases RseP and DegS, as previously described in many other bacteria. However, our data suggest that RseP and DegS are not only dedicated to RseA cleavage and that the proteolytic cascade of RseA could involve other proteases.
not annotated - annotated - LINNAEUS only
Regulation and function of Escherichia coli sugar efflux transporter A (SetA) during glucose-phosphate stress.
Accumulation of certain nonmetabolizable sugar-phosphates (including alpha-methyl glucoside-6-phosphate) in Escherichia coli is growth inhibitory and elicits the glucose-phosphate stress response. The transcription factor SgrR activates transcription of the small RNA SgrS under stress conditions. SgrS represses translation of mRNAs encoding sugar transporters. The sgrR and sgrS genes are located directly upstream of setA, and this gene organization is conserved in numerous enteric species, prompting the hypothesis that SetA contributes to the glucose-phosphate stress response. SetA is a proton motive force-driven efflux pump capable of transporting various sugars and sugar analogs in vitro. This study demonstrates that setA expression is induced in response to glucose-phosphate stress, and this requires SgrR. Under stress conditions, setA is cotranscribed with sgrS from the sgrS promoter. A setA mutant exhibits a growth defect under stress conditions that can be complemented by setA in trans, suggesting that SetA contributes to the optimal cellular recovery from stress. Despite previous in vitro evidence that SetA can promote efflux of the stress-causing glucose analog alpha-methyl glucoside, in vivo data in this study indicate that SetA is not the major efflux pump responsible for removal of alpha-methyl glucoside under stress conditions.
not annotated - annotated - LINNAEUS only
Mapping of the Neisseria meningitidis NadA cell-binding site: relevance of predicted {alpha}-helices in the NH2-terminal and dimeric coiled-coil regions.
NadA is a trimeric autotransporter protein of Neisseria meningitidis belonging to the group of oligomeric coiled-coil adhesins. It is implicated in the colonization of the human upper respiratory tract by hypervirulent serogroup B N. meningitidis strains and is part of a multiantigen anti-serogroup B vaccine. Structure prediction indicates that NadA is made by a COOH-terminal membrane anchor (also necessary for autotranslocation to the bacterial surface), an intermediate elongated coiled-coil-rich stalk, and an NH(2)-terminal region involved in cell interaction. Electron microscopy analysis and structure prediction suggest that the apical region of NadA forms a compact and globular domain. Deletion studies proved that the NH(2)-terminal sequence (residues 24 to 87) is necessary for cell adhesion. In this study, to better define the NadA cell binding site, we exploited (i) a panel of NadA mutants lacking sequences along the coiled-coil stalk and (ii) several oligoclonal rabbit antibodies, and their relative Fab fragments, directed to linear epitopes distributed along the NadA ectodomain. We identified two critical regions for the NadA-cell receptor interaction with Chang cells: the NH(2) globular head domain and the NH(2) dimeric intrachain coiled-coil alpha-helices stemming from the stalk. This raises the importance of different modules within the predicted NadA structure. The identification of linear epitopes involved in receptor binding that are able to induce interfering antibodies reinforces the importance of NadA as a vaccine antigen.
not annotated - annotated - LINNAEUS only
The Burkholderia cenocepacia LysR-type transcriptional regulator ShvR influences expression of quorum-sensing, protease, type II secretion, and afc genes.
Burkholderia cenocepacia is a significant opportunistic pathogen in individuals with cystic fibrosis. ShvR, a LysR-type transcriptional regulator, has previously been shown to influence colony morphology, biofilm formation, virulence in plant and animal infection models, and some quorum-sensing-dependent phenotypes. In the present study, it was shown that ShvR negatively regulates its own expression, as is typical for LysR-type regulators. The production of quorum-sensing signal molecules was detected earlier in growth in the shvR mutant than in the wild type, and ShvR repressed expression of the quorum-sensing regulatory genes cepIR and cciIR. Microarray analysis and transcriptional fusions revealed that ShvR regulated over 1,000 genes, including the zinc metalloproteases zmpA and zmpB. The shvR mutant displayed increased gene expression of the type II secretion system and significantly increased protease and lipase activities. Both ShvR and CepR influence expression of a 24-kb genomic region adjacent to shvR that includes the afcA and afcC operons, required for the production of an antifungal agent; however, the reduction in expression was substantially greater in the shvR mutant than in the cepR mutant. Only the shvR mutation resulted in reduced antifungal activity against Rhizoctonia solani. ShvR, but not CepR, was shown to directly regulate expression of the afcA and afcC promoters. In summary, ShvR was determined to have a significant influence on the expression of quorum-sensing, protease, lipase, type II secretion, and afc genes.
not annotated - annotated - LINNAEUS only
Functional analysis of molybdopterin biosynthesis in mycobacteria identifies a fused molybdopterin synthase in Mycobacterium tuberculosis.
Most mycobacterial species possess a full complement of genes for the biosynthesis of molybdenum cofactor (MoCo). However, a distinguishing feature of members of the Mycobacterium tuberculosis complex is their possession of multiple homologs associated with the first two steps of the MoCo biosynthetic pathway. A mutant of M. tuberculosis lacking the moaA1-moaD1 gene cluster and a derivative in which moaD2 was also deleted were significantly impaired for growth in media containing nitrate as a sole nitrogen source, indicating a reduced availability of MoCo to support the assimilatory function of the MoCo-dependent nitrate reductase, NarGHI. However, the double mutant displayed residual respiratory nitrate reductase activity, suggesting that it retains the capacity to produce MoCo. The M. tuberculosis moaD and moaE homologs were further analyzed by expressing these genes in mutant strains of M. smegmatis that lacked one or both of the sole molybdopterin (MPT) synthase-encoding genes, moaD2 and moaE2, and were unable to grow on nitrate, presumably as a result of the loss of MoCo-dependent nitrate assimilatory activity. Expression of M. tuberculosis moaD2 in the M. smegmatis moaD2 mutant and of M. tuberculosis moaE1 or moaE2 in the M. smegmatis moaE2 mutant restored nitrate assimilation, confirming the functionality of these genes in MPT synthesis. Expression of M. tuberculosis moaX also restored MoCo biosynthesis in M. smegmatis mutants lacking moaD2, moaE2, or both, thus identifying MoaX as a fused MPT synthase. By implicating multiple synthase-encoding homologs in MoCo biosynthesis, these results suggest that important cellular functions may be served by their expansion in M. tuberculosis.
not annotated - annotated - LINNAEUS only
Plantazolicin, a novel microcin B17/streptolysin S-like natural product from Bacillus amyloliquefaciens FZB42.
Here we report on a novel thiazole/oxazole-modified microcin (TOMM) from Bacillus amyloliquefaciens FZB42, a Gram-positive soil bacterium. This organism is well known for stimulating plant growth and biosynthesizing complex small molecules that suppress the growth of bacterial and fungal plant pathogens. Like microcin B17 and streptolysin S, the TOMM from B. amyloliquefaciens FZB42 undergoes extensive posttranslational modification to become a bioactive natural product. Our data show that the modified peptide bears a molecular mass of 1,335 Da and displays antibacterial activity toward closely related Gram-positive bacteria. A cluster of 12 genes that covers -10 kb is essential for the production, modification, export, and self-immunity of this natural product. We have named this compound plantazolicin (PZN), based on the association of several producing organisms with plants and the incorporation of azole heterocycles, which derive from Cys, Ser, and Thr residues of the precursor peptide.
not annotated - annotated - LINNAEUS only
Mismatch repair modulation of MutY activity drives Bacillus subtilis stationary-phase mutagenesis.
Stress-promoted mutations that occur in nondividing cells (adaptive mutations) have been implicated strongly in causing genetic variability as well as in species survival and evolutionary processes. Oxidative stress-induced DNA damage has been associated with generation of adaptive His(+) and Met(+) but not Leu(+) revertants in strain Bacillus subtilis YB955 (hisC952 metB5 leuC427). Here we report that an interplay between MutY and MutSL (mismatch repair system [MMR]) plays a pivotal role in the production of adaptive Leu(+) revertants. Essentially, the genetic disruption of MutY dramatically reduced the reversion frequency to the leu allele in this model system. Moreover, the increased rate of adaptive Leu(+) revertants produced by a MutSL knockout strain was significantly diminished following mutY disruption. Interestingly, although the expression of mutY took place during growth and stationary phase and was not under the control of RecA, PerR, or sigma(B), a null mutation in the mutSL operon increased the expression of mutY several times. Thus, in starved cells, saturation of the MMR system may induce the expression of mutY, disturbing the balance between MutY and MMR proteins and aiding in the production of types of mutations detected by reversion to leucine prototrophy. In conclusion, our results support the idea that MMR regulation of the mutagenic/antimutagenic properties of MutY promotes stationary-phase mutagenesis in B. subtilis cells.
not annotated - annotated - LINNAEUS only
Mapping interactions between germinants and Clostridium difficile spores.
Germination of Clostridium difficile spores is the first required step in establishing C. difficile-associated disease (CDAD). Taurocholate (a bile salt) and glycine (an amino acid) have been shown to be important germinants of C. difficile spores. In the present study, we tested a series of glycine and taurocholate analogs for the ability to induce or inhibit C. difficile spore germination. Testing of glycine analogs revealed that both the carboxy and amino groups are important epitopes for recognition and that the glycine binding site can accommodate compounds with more widely separated termini. The C. difficile germination machinery also recognizes other hydrophobic amino acids. In general, linear alkyl side chains are better activators of spore germination than their branched analogs. However, L-phenylalanine and L-arginine are also good germinants and are probably recognized by distinct binding sites. Testing of taurocholate analogs revealed that the 12-hydroxyl group of taurocholate is necessary, but not sufficient, to activate spore germination. In contrast, the 6- and 7-hydroxyl groups are required for inhibition of C. difficile spore germination. Similarly, C. difficile spores are able to detect taurocholate analogs with shorter, but not longer, alkyl amino sulfonic acid side chains. Furthermore, the sulfonic acid group can be partially substituted with other acidic groups. Finally, a taurocholate analog with an m-aminobenzenesulfonic acid side chain is a strong inhibitor of C. difficile spore germination. In conclusion, C. difficile spores recognize both amino acids and taurocholate through multiple interactions that are required to bind the germinants and/or activate the germination machinery.
not annotated - annotated - LINNAEUS only
In vitro studies of peptidoglycan binding and hydrolysis by the Bacillus anthracis germination-specific lytic enzyme SleB.
The Bacillus anthracis endospore loses resistance properties during germination when its cortex peptidoglycan is degraded by germination-specific lytic enzymes (GSLEs). Although this event normally employs several GSLEs for complete cortex removal, the SleB protein alone can facilitate enough cortex hydrolysis to produce vulnerable spores. As a means to better understand its enzymatic function, SleB was overexpressed, purified, and tested in vitro for depolymerization of cortex by measurement of optical density loss and the solubilization of substrate. Its ability to bind peptidoglycan was also investigated. SleB functions independently as a lytic transglycosylase on both intact and fragmented cortex. Most of the muropeptide products that SleB generates are large and are potential substrates for other GSLEs present in the spore. Study of a truncated protein revealed that SleB has two domains. The N-terminal domain is required for stable peptidoglycan binding, while the C-terminal domain is the region of peptidoglycan hydrolytic activity. The C-terminal domain also exhibits dependence on cortex containing muramic-delta-lactam in order to carry out hydrolysis. As the conditions and limitations for SleB activity are further elucidated, they will enable the development of treatments that stimulate premature germination of B. anthracis spores, greatly simplifying decontamination measures.
not annotated - annotated - LINNAEUS only
Glucose-dependent activation of Bacillus anthracis toxin gene expression and virulence requires the carbon catabolite protein CcpA.
Sensing environmental conditions is an essential aspect of bacterial physiology and virulence. In Bacillus anthracis, the causative agent of anthrax, transcription of the two major virulence factors, toxin and capsule, is triggered by bicarbonate, a major compound in the mammalian body. Here it is shown that glucose is an additional signaling molecule recognized by B. anthracis for toxin synthesis. The presence of glucose increased the expression of the protective antigen toxin component-encoding gene (pagA) by stimulating induction of transcription of the AtxA virulence transcription factor. Induction of atxA transcription by glucose required the carbon catabolite protein CcpA via an indirect mechanism. CcpA did not bind specifically to any region of the extended atxA promoter. The virulence of a B. anthracis strain from which the ccpA gene was deleted was significantly attenuated in a mouse model of infection. The data demonstrated that glucose is an important host environment-derived signaling molecule and that CcpA is a molecular link between environmental sensing and B. anthracis pathogenesis.
not annotated - annotated - LINNAEUS only
Structural and functional analysis of the type III secretion system from Pseudomonas fluorescens Q8r1-96.
Pseudomonas fluorescens Q8r1-96 represents a group of rhizosphere strains responsible for the suppressiveness of agricultural soils to take-all disease of wheat. It produces the antibiotic 2,4-diacetylphloroglucinol and aggressively colonizes the roots of cereal crops. In this study, we analyzed the genome of Q8r1-96 and identified a type III protein secretion system (T3SS) gene cluster that has overall organization similar to that of the T3SS gene cluster of the plant pathogen Pseudomonas syringae. We also screened a collection of 30 closely related P. fluorescens strains and detected the T3SS genes in all but one of them. The Q8r1-96 genome contained ropAA and ropM type III effector genes, which are orthologs of the P. syringae effector genes hopAA1-1 and hopM1, as well as a novel type III effector gene designated ropB. These type III effector genes encoded proteins that were secreted in culture and injected into plant cells by both P. syringae and Q8r1-96 T3SSs. The Q8r1-96 T3SS was expressed in the rhizosphere, but mutants lacking a functional T3SS were not altered in their rhizosphere competence. The Q8r1-96 type III effectors RopAA, RopB, and RopM were capable of suppressing the hypersensitive response and production of reactive oxygen species, two plant immune responses.
not annotated - annotated - LINNAEUS only
C-terminal domain residues important for secretion and attachment of RgpB in Porphyromonas gingivalis.
Porphyromonas gingivalis, a periodontal pathogen, expresses a group of surface proteins with a common C-terminal domain (CTD) that are exported by a novel secretion system to the surface, where they are covalently attached. Using RgpB as a model CTD protein, we have produced a series of site-directed mutations in the CTD sequence at conserved residues and at residues that may be modified and, hence, surface attached. The mutant RgpB proteins were expressed in a P. gingivalis host lacking functional RgpB and RgpA Arg-specific proteases. The RgpB mutants produced were Y674F, Y674F Y718F, T675Q S679Q T682Q T684Q, T693Q, F695A, D696A, N698A, G699P, G716P, T724Q, T728Q T730Q, and K732Q and a protein with a deletion of residues 692 to 702 (Delta692-702). The mutants were characterized for cell-associated Arg-specific protease activity and for cellular distribution using anti-Rgp antibodies and Western blotting of culture fractions. All the mutants exhibited cell-associated Arg-specific activity similar to that of the positive control except for the D696A and Delta692-702 mutants. For all mutants, except D696A and Delta692-702, the RgpB proteins were found modified and attached to the cell surface, which was the same profile found in the positive-control strain. Only trace amounts of the precursor form of the Delta692-702 mutant were detected in the outer membrane, with none detected in the periplasm or culture fluid although cell transcript levels were normal. The results suggest that residues 692 to 702 of the CTD, in particular, residue D696, have an important role in the attachment of RgpB at the cell surface and that without attachment secretion does not occur.
not annotated - annotated - LINNAEUS only
Effects of deficiency and overdose of group 2 sigma factors in triple inactivation strains of Synechocystis sp. strain PCC 6803.
Acclimation of cyanobacteria to environmental changes includes major changes in the gene expression patterns partly orchestrated by the replacement of a particular sigma subunit with another in the RNA polymerase holoenzyme. The cyanobacterium Synechocystis sp. strain PCC 6803 encodes nine sigma factors, all belonging to the sigma(70) family. Cyanobacteria typically encode many group 2 sigma factors that closely resemble the principal sigma factor. We inactivated three out of the four group 2 sigma factors of Synechocystis simultaneously in all possible combinations and found that all triple inactivation strains grow well under standard conditions. Unlike the other strains, the DeltasigBCD strain, which contains SigE as the only functional group 2 sigma factor, did not grow faster under mixotrophic than under autotrophic conditions. The SigB and SigD factors were important in low-temperature acclimation, especially under diurnal light rhythm. The DeltasigBCD, DeltasigBCE, and DeltasigBDE strains were sensitive to high-light-induced photoinhibition, indicating a central role of the SigB factor in high-light tolerance. Furthermore, the DeltasigBCE strain (SigD is the only functional group 2 sigma factor) appeared to be locked in the high-fluorescence state (state 1) and grew slowly in blue but not in orange or white light. Our results suggest that features of the triple inactivation strains can be categorized as (i) direct consequences of the inactivation of a particular sigma factor(s) and (ii) effects resulting from the higher probability that the remaining group 2 sigma factors associate with the RNA polymerase core.
not annotated - annotated - LINNAEUS only
A combined method for rescue of modified enteroviruses by mutagenic primers, long PCR and T7 RNA polymerase-driven in vivo transcription.
The current methods for manipulation of enteroviral RNA genomes and production of modified virus particles include stepwise subcloning procedures and in vitro transcription and RNA transfection steps that are both time-consuming and inefficient. Several enteroviral cDNA clones with 5'-terminal T7 promoter and coxsackievirus A9 (CAV9) PCR product with the T7 promoter were transfected successfully into target cells expressing T7 RNA polymerase for the rescue of virus particles. This demonstrated the overall feasibility of the in vivo transcription method. Furthermore, a rapid method using high-fidelity DNA polymerase, Phusion(TM), for amplification and mutagenesis of CAV9 cDNA was generated. A long PCR method was employed together with mutagenic primers for direct introduction of a unique restriction enzyme site into the VP1-2A junction of the CAV9 cDNA clone during the PCR amplification process. Enhanced green fluorescent protein was subcloned to that site, and CAV9-eGFP cDNA was transfected to the target cells for in vivo transcription and successful rescue of CAV9-eGFP particles. The method allowed a straightforward mutagenesis and in vivo production of infectious enteroviral particles, and may be applicable routinely for rapid production of the modified picornaviruses over the use of the traditional subcloning protocols.
not annotated - annotated - LINNAEUS only
A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)(n) microsatellites.
The movement of miniature inverted repeat transposable elements (MITEs) modifies genome structure and function. We describe the microsatellite-associated interspersed nuclear element 2 (MINE-2), that integrates at consensus WTTTT target sites, creates dinucleotide TT target site duplications (TSDs), and forms predicted MITE-like secondary structures; a 5' subterminal inverted repeat (SIR; AGGGTTCCGTAG) that is partially complementary to a 5' inverted repeat (IR; ACGAAGCCCT) and 3'-SIRs (TTACGGAACCCT). A (GTCY)(n) microsatellite is hitchhiking downstream of conserved 5'MINE-2 secondary structures, causing flanking sequence similarity amongst mobile microsatellite loci. Transfection of insect cell lines indicates that MITE-like secondary structures are sufficient to mediate genome integration, and provides insight into the transposition mechanism used by MINE-2s.
not annotated - annotated - LINNAEUS only
DNA modifications and genome rearrangements during the development and sex differentiation of the bumble bee Bombus terrestris.
Bombus terrestris is a bumble bee that, like most hymenopteran species, exhibits ploidy-specific sex determination controlled by a single sex gene. Depending on their ploidy and the queen pheromone repression, the imagoes differentiate into three castes: males, workers and queens. Here, we focus on the differences of genome organization that occur during development and sex differentiation. We found that cytosine methylation is a significant epigenetic factor with profiles that can be correlated with both processes. We also showed that two kinds of genomic rearrangement occur. The first consists of important DNA amplifications that have sequence profiles that differ in the different developmental instars and sexes. In the second kind, DNA losses also occur, at least involving the mosaic transposable element B. terrestris mosaic repeat 1 (BTMR1).
not annotated - annotated - LINNAEUS only
A vaccinia virus deletion mutant reveals the presence of additional inhibitors of NF-kappaB.
The classical nuclear factor kappa B (NF-kappaB) signaling pathway is an important regulator of inflammation and innate immunity that is activated by a wide variety of stimuli, including virus infection, tumor necrosis factor alpha (TNF-alpha), and interleukin 1Beta (IL-1Beta). Poxviruses, including vaccinia virus (VV) and ectromelia virus, encode multiple proteins that function in immune evasion. Recently, a growing number of genes encoded by poxviruses have been shown to target and disrupt the NF-kappaB signaling pathway. To determine if additional gene products that interfere with NF-kappaB signaling existed, we used a vaccinia virus deletion mutant, VV811, which is missing 55 open reading frames lacking all known inhibitors of TNF-alpha-induced NF-kappaB activation. Immunofluorescence analysis of HeLa cells treated with TNF-alpha and IL-1Beta revealed that NF-kappaB translocation to the nucleus was inhibited in VV811-infected cells. This was further confirmed through Western blotting of cytoplasmic and nuclear extracts for NF-kappaB. Additionally, VV811 infection inhibited TNF-alpha-induced IkappaBalpha degradation. In contrast to vaccinia virus strain Copenhagen (VVCop)-infected cells, VV811 infection resulted in the dramatic accumulation of phosphorylated IkappaBalpha. Correspondingly, coimmunoprecipitation assays demonstrated that the NF-kappaB-inhibitory IkappaBalpha-p65-p50 complex was intact in VV811-infected cells. Significantly, cells treated with 1-Beta-d-arabinofuranosylcytosine, an inhibitor of poxvirus late gene expression, demonstrated that an additional vaccinia virus late gene was involved in the stabilization of IkappaBalpha. Overall, this work indicates that unidentified inhibitors of NF-kappaB exist in vaccinia virus. The complex inhibition of NF-kappaB by vaccinia virus illustrates the importance of NF-kappaB activation in the antiviral response.
not annotated - annotated - LINNAEUS only
Template recognition mechanisms by replicase proteins differ between bipartite positive-strand genomic RNAs of a plant virus.
Recognition of RNA templates by viral replicase proteins is one of the key steps in the replication process of all RNA viruses. However, the mechanisms underlying this phenomenon, including primary RNA elements that are recognized by the viral replicase proteins, are not well understood. Here, we used aptamer pulldown assays with membrane fractionation and protein-RNA coimmunoprecipitation in a cell-free viral translation/replication system to investigate how viral replicase proteins recognize the bipartite genomic RNAs of the Red clover necrotic mosaic virus (RCNMV). RCNMV replicase proteins bound specifically to a Y-shaped RNA element (YRE) located in the 3' untranslated region (UTR) of RNA2, which also interacted with the 480-kDa replicase complexes that contain viral and host proteins. The replicase-YRE interaction recruited RNA2 to the membrane fraction. Conversely, RNA1 fragments failed to interact with the replicase proteins supplied in trans. The results of protein-RNA coimmunoprecipitation assays suggest that RNA1 interacts with the replicase proteins coupled with their translation. Thus, the initial template recognition mechanisms employed by the replicase differ between RCNMV bipartite genomic RNAs and RNA elements are primary determinants of the differential replication mechanism.
not annotated - annotated - LINNAEUS only
Poliovirus RNA is released from the capsid near a twofold symmetry axis.
After recognizing and binding to its host cell, poliovirus (like other nonenveloped viruses) faces the challenge of translocating its genome across a cellular membrane and into the cytoplasm. To avoid entanglement with the capsid, the RNA must exit via a single site on the virion surface. However, the mechanism by which a single site is selected (from among 60 equivalents) is unknown; and until now, even its location on the virion surface has been controversial. To help to elucidate the mechanism of infection, we have used single-particle cryo-electron microscopy and tomography to reconstruct conformationally altered intermediates that are formed by the poliovirion at various stages of the poliovirus infection process. Recently, we reported icosahedrally symmetric structures for two forms of the end-state 80S empty capsid particle. Surprisingly, RNA was frequently visible near the capsid; and in a subset of the virions, RNA was seen on both the inside and outside of the capsid, caught in the act of exiting. To visualize RNA exiting, we have now determined asymmetric reconstructions from that subset, using both single-particle cryo-electron microscopy and cryo-electron tomographic methods, producing independent reconstructions at -50-A resolution. Contrary to predictions in the literature, the footprint of RNA on the capsid surface is located close to a viral 2-fold axis, covering a slot-shaped area of reduced density that is present in both of the symmetrized 80S reconstructions and which extends by about 20 A away from the 2-fold axis toward each neighboring 5-fold axis.
not annotated - annotated - LINNAEUS only
Differential regulation of human papillomavirus type 8 by interferon regulatory factors 3 and 7.
The genus Beta human papillomavirus (HPV) type 8 is associated with nonmelanoma skin cancer in patients with epidermodysplasia verruciformis, and evidence for its protumorigenic potential in the general population increases. To date, strategies to suppress genus Beta HPV infections are limited. Interferon regulatory factors IRF-3 and IRF-7 play key roles in the activation of the innate immune response to viral infections. In this study, we show for the first time that both IRF-3 and IRF-7 regulate transcription of a papillomavirus, but with opposing effects. IRF-7, expressed in the suprabasal layers of human epidermis, increased HPV8 late promoter activity via direct binding to viral DNA. UV-B light-induced activation of the HPV8 promoter involved IRF-7 as a downstream effector. In contrast, IRF-3, expressed in all layers of human epidermis, induced strong HPV8 suppression in primary keratinocytes. IRF-3-mediated suppression prevailed over IRF-7-induced HPV8 transcription. Unlike the E6 oncoprotein of the mucosal high-risk HPV16, the HPV8 E6 protein did not bind to IRF-3 and only weakly antagonized its activity. Strong antiviral activity was also observed, when keratinocytes were treated with potent IRF-3 activators, poly(I:C) or RNA bearing 5' phosphates. In conclusion, we show that IRF-3 activation induces a state of cell-autonomous immunity against HPV in primary human keratinocytes. Our study suggests that local application of IRF-3-activating compounds might constitute an attractive novel therapeutic strategy against HPV8-associated diseases, particularly in epidermodysplasia verruciformis patients.
not annotated - annotated - LINNAEUS only
Cytomegalovirus microRNA expression is tissue specific and is associated with persistence.
MicroRNAs (miRNAs) are a class of small noncoding RNAs involved in posttranscriptional regulation. miRNAs are utilized in organisms ranging from plants to higher mammals, and data have shown that DNA viruses also use this method for host and viral gene regulation. Here, we report the sequencing of the small RNAs in rat cytomegalovirus (RCMV)-infected fibroblasts and persistently infected salivary glands. We identified 24 unique miRNAs that mapped to hairpin structures found within the viral genome. While most miRNAs were detected in both samples, four were detected exclusively in the infected fibroblasts and two were specific for the infected salivary glands. The RCMV miRNAs are distributed across the viral genome on both the positive and negative strands, with clusters of miRNAs at a number of locations, including near viral genes r1 and r111. The RCMV miRNAs have a genomic positional orientation similar to that of the miRNAs described for mouse cytomegalovirus, but they do not share any substantial sequence conservation. Similar to other reported miRNAs, the RCMV miRNAs had considerable variation at their 3' and 5' ends. Interestingly, we found a number of specific examples of differential isoform usage between the fibroblast and salivary gland samples. We determined by real-time PCR that expression of the RCMV miRNA miR-r111.1-2 is highly expressed in the salivary glands and that miR-R87-1 is expressed in most tissues during the acute infection phase. Our study identified the miRNAs expressed by RCMV in vitro and in vivo and demonstrated that expression is tissue specific and associated with a stage of viral infection.
not annotated - annotated - LINNAEUS only
Adenovirus membrane penetration activates the NLRP3 inflammasome.
Adenovirus type 5 (Ad5) infection of macrophages results in rapid secretion of interleukin-1Beta (IL-1Beta) and is dependent on the inflammasome components NLRP3 and ASC and the catalytic activity of caspase-1. Using lentivirus-expressed short hairpin RNA (shRNA) and competitive inhibitors, we show that Ad-induced IL-1Beta release is dependent upon Toll-like receptor 9 (TLR9) sensing of the Ad5 double-stranded DNA (dsDNA) genome in human cell lines and primary monocyte-derived macrophages but not in mouse macrophages. Additionally, a temperature-sensitive mutant of Ad5 unable to penetrate endosomal membranes, ts1, is unable to induce IL-1Beta release in TLR2-primed THP-1 cells, suggesting that penetration of endosomal membranes is required for IL-1Beta release. Disruption of lysosomal membranes and the release of cathepsin B into the cytoplasm are required for Ad-induced NLRP3 activation. Ad5 cell entry also induces reactive oxygen species (ROS) production, and inhibitors of ROS prevent Ad-induced IL-1Beta release. Ad5 activation of NLRP3 also induces necrotic cell death, resulting in the release of the proinflammatory molecule HMGB1. This work further defines the mechanisms of virally induced inflammasome activation.
not annotated - annotated - LINNAEUS only
Function of the small hydrophobic protein of J paramyxovirus.
At 18,954 nucleotides, the J paramyxovirus (JPV) genome is one of the largest in the family Paramyxoviridae, consisting of eight genes in the order 3'-N-P/V/C-M-F-SH-TM-G-L-5'. To study the function of novel paramyxovirus genes in JPV, a plasmid containing a full-length cDNA clone of the genome of JPV was constructed. In this study, the function of the small hydrophobic (SH) protein of JPV was examined by generating a recombinant JPV lacking the coding sequence of the SH protein (rJPVDeltaSH). rJPVDeltaSH was viable and had no growth defect in tissue culture cells. However, more tumor necrosis factor alpha (TNF-alpha) was produced during rJPVDeltaSH infection, suggesting that SH plays a role in inhibiting TNF-alpha production. rJPVDeltaSH induced more apoptosis in tissue culture cells than rJPV. Virus-induced apoptosis was inhibited by neutralizing antibody against TNF-alpha, suggesting that TNF-alpha contributes to JPV-induced apoptosis in vitro. The expression of JPV SH protein inhibited TNF-alpha-induced NF-kappaB activation in a reporter gene assay, suggesting that JPV SH protein can inhibit TNF-alpha signaling in vitro. Furthermore, infection of mice with rJPVDeltaSH induced more TNF-alpha expression, indicating that SH plays a role in blocking TNF-alpha expression in vivo.
not annotated - annotated - LINNAEUS only
Successful vaccination strategies that protect aged mice from lethal challenge from influenza virus and heterologous severe acute respiratory syndrome coronavirus.
Newly emerging viruses often circulate as a heterogeneous swarm in wild animal reservoirs prior to their emergence in humans, and their antigenic identities are often unknown until an outbreak situation. The newly emerging severe acute respiratory syndrome coronavirus (SARS-CoV) and reemerging influenza virus cause disproportionate disease in the aged, who are also notoriously difficult to successfully vaccinate, likely due to immunosenescence. To protect against future emerging strains, vaccine platforms should induce broad cross-reactive immunity that is sufficient to protect from homologous and heterologous challenge in all ages. From initial studies, we hypothesized that attenuated Venezuelan equine encephalitis virus (VEE) replicon particle (VRP) vaccine glycoproteins mediated vaccine failure in the aged. We then compared the efficacies of vaccines bearing attenuated (VRP(3014)) or wild-type VEE glycoproteins (VRP(3000)) in young and aged mice within novel models of severe SARS-CoV pathogenesis. Aged animals receiving VRP(3000)-based vaccines were protected from SARS-CoV disease, while animals receiving the VRP(3014)-based vaccines were not. The superior protection for the aged observed with VRP(3000)-based vaccines was confirmed in a lethal influenza virus challenge model. While the VRP(3000) vaccine's immune responses in the aged were sufficient to protect against lethal homologous and heterologous challenge, our data suggest that innate defects within the VRP(3014) platform mediate vaccine failure. Exploration into the mechanism(s) of successful vaccination in the immunosenescent should aid in the development of successful vaccine strategies for other viral diseases disproportionately affecting the elderly, like West Nile virus, influenza virus, norovirus, or other emerging viruses of the future.
not annotated - annotated - LINNAEUS only
Reovirus infection or ectopic expression of outer capsid protein micro1 induces apoptosis independently of the cellular proapoptotic proteins Bax and Bak.
Mammalian orthoreoviruses induce apoptosis in vivo and in vitro; however, the specific mechanism by which apoptosis is induced is not fully understood. Recent studies have indicated that the reovirus outer capsid protein mu1 is the primary determinant of reovirus-induced apoptosis. Ectopically expressed mu1 induces apoptosis and localizes to intracellular membranes. Here we report that ectopic expression of mu1 activated both the extrinsic and intrinsic apoptotic pathways with activation of initiator caspases-8 and -9 and downstream effector caspase-3. Activation of both pathways was required for mu1-induced apoptosis, as specific inhibition of either caspase-8 or caspase-9 abolished downstream effector caspase-3 activation. Similar to reovirus infection, ectopic expression of mu1 caused release into the cytosol of cytochrome c and smac/DIABLO from the mitochondrial intermembrane space. Pancaspase inhibitors did not prevent cytochrome c release from cells expressing mu1, indicating that caspases were not required. Additionally, mu1- or reovirus-induced release of cytochrome c occurred efficiently in Bax(-/-)Bak(-/-) mouse embryonic fibroblasts (MEFs). Finally, we found that reovirus-induced apoptosis occurred in Bax(-/-)Bak(-/-) MEFs, indicating that reovirus-induced apoptosis occurs independently of the proapoptotic Bcl-2 family members Bax and Bak.
not annotated - annotated - LINNAEUS only
Assembly and immunological properties of Newcastle disease virus-like particles containing the respiratory syncytial virus F and G proteins.
Human respiratory syncytial virus (RSV) is a serious respiratory pathogen in infants and young children as well as elderly and immunocompromised populations. However, no RSV vaccines are available. We have explored the potential of virus-like particles (VLPs) as an RSV vaccine candidate. VLPs composed entirely of RSV proteins were produced at levels inadequate for their preparation as immunogens. However, VLPs composed of the Newcastle disease virus (NDV) nucleocapsid and membrane proteins and chimera proteins containing the ectodomains of RSV F and G proteins fused to the transmembrane and cytoplasmic domains of NDV F and HN proteins, respectively, were quantitatively prepared from avian cells. Immunization of mice with these VLPs, without adjuvant, stimulated robust, anti-RSV F and G protein antibody responses. IgG2a/IgG1 ratios were very high, suggesting predominantly T(H)1 responses. In contrast to infectious RSV immunization, neutralization antibody titers were robust and stable for 4 months. Immunization with a single dose of VLPs resulted in the complete protection of mice from RSV replication in lungs. Upon RSV intranasal challenge of VLP-immunized mice, no enhanced lung pathology was observed, in contrast to the pathology observed in mice immunized with formalin-inactivated RSV. These results suggest that these VLPs are effective RSV vaccines in mice, in contrast to other nonreplicating RSV vaccine candidates.
not annotated - annotated - LINNAEUS only
Domain structure of Lassa virus L protein.
The 200-kDa L protein of arenaviruses plays a central role in viral genome replication and transcription. This study aimed at providing evidence for the domain structure of L protein by combining bioinformatics with a stepwise mutagenesis approach using the Lassa virus minireplicon system. Potential interdomain linkers were predicted using various algorithms. The prediction was challenged by insertion of flexible sequences into the predicted linkers. Insertion of 5 or 10 amino acid residues was tolerated at seven sites (S407, G446, G467, G774, G939, S1952, and V2074 in Lassa virus AV). At two of these sites, G467 and G939, L protein could be split into an N-terminal and a C-terminal part, which were able to trans-complement each other and reconstitute a functional complex upon coexpression. Coimmunoprecipitation studies revealed physical interaction between the N- and C-terminal domains, irrespective of whether L protein was split at G467 or G939. In confocal immunofluorescence microscopy, the N-terminal domains showed a dot-like, sometimes perinuclear, cytoplasmic distribution similar to that of full-length L protein, while the C-terminal domains were homogenously distributed in cytoplasm. The latter were redistributed into the dot-like structures upon coexpression with the corresponding N-terminal domain. In conclusion, this study demonstrates two interdomain linkers in Lassa virus L protein, at G467 and G939, suggesting that L protein is composed of at least three structural domains spanning residues 1 to 467, 467 to 939, and 939 to 2220. The first domain seems to mediate accumulation of L protein into cytoplasmic dot-like structures.
not annotated - annotated - LINNAEUS only
Reverse genetics generation of chimeric infectious Junin/Lassa virus is dependent on interaction of homologous glycoprotein stable signal peptide and G2 cytoplasmic domains.
The Arenaviridae are a diverse and globally distributed collection of viruses that are maintained primarily by rodent reservoirs. Junin virus (JUNV) and Lassa virus (LASV) can both cause significant outbreaks of severe and often fatal human disease throughout their respective areas of endemicity. In an effort to improve upon the existing live attenuated JUNV Candid1 vaccine, we generated a genetically homogenous stock of this virus from cDNA copies of the virus S and L segments by using a reverse genetics system. Further, these cDNAs were used in combination with LASV cDNAs to successfully generate two recombinant Candid1 JUNV/LASV chimeric viruses (via envelope glycoprotein [GPC] exchange). It was found that while the GPC extravirion domains were readily exchangeable, homologous stable signal peptide (SSP) and G2 transmembrane and cytoplasmic tail domains were essential for correct GPC maturation and production of infectious chimeric viruses. The switching of the JUNV and LASV G1/G2 ectodomains within the Candid1 vaccine background did not alter the attenuated phenotype of the vaccine strain in a lethal mouse model. These recombinant chimeric viruses shed light on the fundamental requirements of arenavirus GPC maturation and may serve as a strategy for the development of bivalent JUNV and LASV vaccine candidates.
not annotated - annotated - LINNAEUS only
B7-mediated costimulation of CD4 T cells constrains cytomegalovirus persistence.
Cytomegalovirus (CMV) utilizes multiple strategies to modulate immunity and promote lifelong, persistent/latent infection, including suppressing T cell activation pathways. Here we examined the role of B7 costimulatory ligands in establishing immune detente from both the host and virus perspectives. Mice lacking both B7.1 and B7.2 showed reduced early expansion of CMV-specific CD4 T cells, consequently allowing for enhanced levels of persistent virus replication. In turn, a CMV mutant lacking expression of the m138 and m147.5 gene products, which restrict B7.1 and B7.2 expression in infected antigen-presenting cells, induced a more robust CD4 T cell response and showed decreased persistence. Together, these data reveal a requirement for B7-mediated signaling in regulating the CMV-specific CD4 T cell response and establishing host-virus equilibrium.
not annotated - annotated - LINNAEUS only
Upregulation of CXCL10 in human dorsal root ganglia during experimental and natural varicella-zoster virus infection.
Varicella-zoster virus (VZV) reactivation causes herpes zoster, which is accompanied by an influx of lymphocytes into affected ganglia, but the stimulus for this infiltrate is not known. We report that VZV infection of ganglia leads to increased CXCL10 production in vitro, in an explant ganglion model and in naturally infected dorsal root ganglia (DRG) during herpes zoster. Lymphocytes expressing the receptor for CXCL10, CXCR3, were also observed throughout naturally infected ganglia during herpes zoster, including immediately adjacent to neurons. This study identifies VZV-induced CXCL10 as a potential driver of T lymphocyte recruitment into DRG during herpes zoster.
not annotated - annotated - LINNAEUS only
Persistent Friend virus replication and disease in Apobec3-deficient mice expressing functional B-cell-activating factor receptor.
Rfv3 is an autosomal dominant gene that influences the recovery of resistant mice from Friend retrovirus (FV) infection by limiting viremia and promoting a more potent neutralizing antibody response. We previously reported that Rfv3 is encoded by Apobec3, an innate retrovirus restriction factor. However, it was recently suggested that the Rfv3 susceptible phenotype of high viremia at 28 days postinfection (dpi) was more dominantly controlled by the B-cell-activating factor receptor (BAFF-R), a gene that is linked to but located outside the genetically mapped region containing Rfv3. Although one prototypical Rfv3 susceptible mouse strain, A/WySn, indeed contains a dysfunctional BAFF-R, two other Rfv3 susceptible strains, BALB/c and A.BY, express functional BAFF-R genes, determined on the basis of genotyping and B-cell immunophenotyping. Furthermore, transcomplementation studies in (C57BL/6 [B6] x BALB/c)F(1) and (B6 x A.BY)F(1) mice revealed that the B6 Apobec3 gene significantly influences recovery from FV viremia, cellular infection, and disease at 28 dpi. Finally, the Rfv3 phenotypes of prototypic B6, A.BY, A/WySn, and BALB/c mouse strains correlate with reported Apobec3 mRNA expression levels. Overall, these findings argue against the generality of BAFF-R polymorphisms as a dominant mechanism to explain the Rfv3 recovery phenotype and further strengthen the evidence that Apobec3 encodes Rfv3.
not annotated - annotated - LINNAEUS only
Characterization of cross-reactive CD8+ T-cell recognition of HLA-A2-restricted HIV-Gag (SLYNTVATL) and HCV-NS5b (ALYDVVSKL) epitopes in individuals infected with human immunodeficiency and hepatitis C viruses.
The immunologic mechanisms underlying the faster progression of hepatitis C virus (HCV) disease in the presence of human immunodeficiency virus (HIV) coinfection are not clearly understood. T-cell cross-reactivity between HCV and influenza virus-specific epitopes has been associated with rapid progression of HCV disease (S. Urbani, B. Amadei, P. Fisicaro, M. Pilli, G. Missale, A. Bertoletti, and C. Ferrari, J. Exp. Med. 201:675-680, 2005). We asked whether T-cell cross-reactivity between HCV and HIV could exist during HCV/HIV coinfection and affect pathogenesis. Our search for amino acid sequence homology between the HCV and HIV proteomes revealed two similar HLA-A2-restricted epitopes, HIV-Gag (SLYNTVATL [HIV-SL9]) and HCV-NS5b (ALYDVVSKL [HCV-AL9]). We found that 4 out of 20 HLA-A2-positive (HLA-A2(+)) HIV-infected individuals had CD8(+) T cells that recognized both the HIV-SL9 and HCV-AL9 epitopes. However, the AL9 epitope was generally shown to be a weak agonist. Although HCV-monoinfected individuals in our study did not show AL9-specific responses, we found that about half of HCV/HIV-coinfected individuals had dual responses to both epitopes. High dual T-cell recognition among coinfected subjects was usually due to separate T-cell populations targeting each epitope, as determined by pentamer staining. The one individual demonstrating cross-reactive T cells to both epitopes showed the most advanced degree of liver disease. In coinfected individuals, we observed a positive correlation between the magnitudes of T-cell responses to both the SL9 and the AL9 epitopes, which was also positively associated with the clinical parameter of liver damage. Thus, we find that HIV infection induces T cells that can cross-react to heterologous viruses or prime for T cells that are closely related in sequence. However, the induction of cross-reactive T cells may not be associated with control of disease caused by the heterologous virus. This demonstrates that degeneracy of HIV-specific T cells may play a role in the immunopathology of HCV/HIV coinfection.
not annotated - annotated - LINNAEUS only
T cell-mediated protection against lethal 2009 pandemic H1N1 influenza virus infection in a mouse model.
Genetic mutation and reassortment of influenza virus gene segments, in particular those of hemagglutinin (HA) and neuraminidase (NA), that lead to antigenic drift and shift are the major strategies for influenza virus to escape preexisting immunity. The most recent example of such phenomena is the first pandemic of H1N1 influenza of the 21st century, which started in 2009. Cross-reactive antibodies raised against H1N1 viruses circulating before 1930 show protective activity against the 2009 pandemic virus. Cross-reactive T-cell responses can also contribute to protection, but in vivo support of this view is lacking. To explore the protection mechanisms in vivo, we primed mice with H1 and H3 influenza virus isolates and rechallenged them with a virus derived from the 2009 H1N1 A/CA/04/09 virus, named CA/E3/09. We found that priming with influenza viruses of both H1 and H3 homo- and heterosubtypes protected against lethal CA/E3/09 virus challenge. Convalescent-phase sera from these primed mice conferred no neutralization activity in vitro and no protection in vivo. However, T-cell depletion studies suggested that both CD4 and CD8 T cells contributed to the protection. Taken together, these results indicate that cross-reactive T cells established after initial priming with distally related viruses can be a vital component for prevention of disease and control of pandemic H1N1 influenza virus infection. Our results highlight the importance of establishing cross-reactive T-cell responses for protecting against existing or newly emerging pandemic influenza viruses.
not annotated - annotated - LINNAEUS only
Association of TRIM22 with the type 1 interferon response and viral control during primary HIV-1 infection.
Type 1 interferons (IFNs) induce the expression of the tripartite interaction motif (TRIM) family of E3 ligases, but the contribution of these antiviral factors to HIV pathogenesis is not completely understood. We hypothesized that the increased expression of select type 1 IFN and TRIM isoforms is associated with a significantly lower likelihood of HIV-1 acquisition and viral control during primary HIV-1 infection. We measured IFN-alpha, IFN-Beta, myxovirus resistance protein A (MxA), human TRIM5alpha (huTRIM5alpha), and TRIM22 mRNA levels in peripheral blood mononuclear cells (PBMCs) of high-risk, HIV-1-uninfected participants and HIV-1-positive study participants. Samples were available for 32 uninfected subjects and 28 infected persons, all within 1 year of infection. HIV-1-positive participants had higher levels of IFN-Beta (P = 0.0005), MxA (P = 0.007), and TRIM22 (P = 0.01) and lower levels of huTRIM5alpha (P < 0.001) than did HIV-1-negative participants. TRIM22 but not huTRIM5alpha correlated positively with type 1 IFN (IFN-alpha, IFN-Beta, and MxA) (all P < 0.0001). In a multivariate model, increased MxA expression showed a significant positive association with viral load (P = 0.0418). Furthermore, TRIM22 but not huTRIM5alpha, IFN-alpha, IFN-Beta, or MxA showed a negative correlation with plasma viral load (P = 0.0307) and a positive correlation with CD4(+) T-cell counts (P = 0.0281). In vitro studies revealed that HIV infection induced TRIM22 expression in PBMCs obtained from HIV-negative donors. Stable TRIM22 knockdown resulted in increased HIV-1 particle release and replication in Jurkat reporter cells. Collectively, these data suggest concordance between type 1 IFN and TRIM22 but not huTRIM5alpha expression in PBMCs and that TRIM22 likely acts as an antiviral effector in vivo.
not annotated - annotated - LINNAEUS only
Determinants that specify the integration pattern of retrotransposon Tf1 in the fbp1 promoter of Schizosaccharomyces pombe.
Long terminal repeat (LTR) retrotransposons are closely related to retroviruses and, as such, are important models for the study of viral integration and target site selection. The transposon Tf1 of Schizosaccharomyces pombe integrates with a strong preference for the promoters of polymerase II (Pol II)-transcribed genes. Previous work in vivo with plasmid-based targets revealed that the patterns of insertion were promoter specific and highly reproducible. To determine which features of promoters are recognized by Tf1, we studied integration in a promoter that has been characterized. The promoter of fbp1 has two upstream activating sequences, UAS1 and UAS2. We found that integration was targeted to two windows, one 180 nucleotides (nt) upstream and the other 30 to 40 nt downstream of UAS1. A series of deletions in the promoter showed that the integration activities of these two regions functioned autonomously. Integration assays of UAS2 and of a synthetic promoter demonstrated that strong promoter activity alone was not sufficient to direct integration. The factors that modulate the transcription activities of UAS1 and UAS2 include the activators Atf1p, Pcr1p, and Rst2p as well as the repressors Tup11p, Tup12p, and Pka1p. Strains lacking each of these proteins revealed that Atf1p alone mediated the sites of integration. These data indicate that Atf1p plays a direct and specific role in targeting integration in the promoter of fbp1.
not annotated - annotated - LINNAEUS only
Phylloplane location of glucosinolates in Barbarea spp. (Brassicaceae) and misleading assessment of host suitability by a specialist herbivore.
Glucosinolates are plant secondary metabolites used in host plant recognition by insects specialized on Brassicaceae, such as the diamondback moth (DBM), Plutella xylostella. Their perception as oviposition cues by females would seem to require their occurrence on the leaf surface, yet previous studies have reached opposite conclusions about whether glucosinolates are actually present on the surface of crucifer leaves. DBM oviposits extensively on Barbarea vulgaris, despite its larvae not being able to survive on this plant because of its content of feeding-deterrent saponins. Glucosinolates and saponins in plant tissue and mechanically removed surface waxes from leaves of Barbarea spp. were analyzed with high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS). Surface waxes from leaves of Barbarea spp. contained glucosinolates, but not feeding-deterrent saponins. Our research is the first to show that glucosinolates are present on the leaf surface of Barbarea spp., but not in other crucifers investigated, resolving some conflicting results from previous studies. Our research is also the first to quantify glucosinolates on the leaf surface of a crucifer, and to show that the concentrations of glucosinolates found on the leaf surface of Barbarea spp. are sufficient to be perceived by ovipositing DBM.
not annotated - annotated - LINNAEUS only
Improved nitrogen nutrition enhances root uptake, root-to-shoot translocation and remobilization of zinc ((65) Zn) in wheat.
This study focussed on the effect of increasing nitrogen (N) supply on root uptake and root-to-shoot translocation of zinc (Zn) as well as retranslocation of foliar-applied Zn in durum wheat (Triticum durum). Nutrient solution experiments were conducted to examine the root uptake and root-to-shoot translocation of (65) Zn in seedlings precultured with different N supplies. In additional experiments, the effect of varied N nutrition on retranslocation of foliar-applied (65) Zn was tested at both the vegetative and generative stages. When N supply was increased, the (65) Zn uptake by roots was enhanced by up to threefold and the (65) Zn translocation from roots to shoots increased by up to eightfold, while plant growth was affected to a much smaller degree. Retranslocation of (65) Zn from old into young leaves and from flag leaves to grains also showed marked positive responses to increasing N supply. The results demonstrate that the N-nutritional status of wheat affects major steps in the route of Zn from the growth medium to the grain, including its uptake, xylem transport and remobilization via phloem. Thus, N is a critical player in the uptake and accumulation of Zn in plants, which deserves special attention in biofortification of food crops with Zn.
not annotated - annotated - LINNAEUS only
Dynamic changes of canopy-scale mesophyll conductance to CO2 diffusion of flower as affected by CO2 concentration and abscisic acid.
Leaf-level measurements have shown that mesophyll conductance (g(m)) can vary rapidly in response to CO2 and other environmental factors, but similar studies at the canopy-scale are missing. Here, we report the effect of short-term variation of CO2 concentration on canopy-scale g(m) and other CO2 exchange parameters of sunflower (Helianthus annuus L.) stands in the presence and absence of abscisic acid (ABA) in their nutrient solution. g(m) was estimated from gas exchange and on-line carbon isotope discrimination (Delta(obs)) in a ^1^3CO2/^1^2CO2) gas exchange mesocosm. The isotopic contribution of (photo)respiration to stand-scale Delta(obs) was determined with the experimental approach of Tcherkez et al. Without ABA, short-term exposures to different CO2 concentrations (C(a) 100 to 900 mumol mol-^1) had little effect on canopy-scale g(m) . But, addition of ABA strongly altered the CO2-response: g(m) was high (approx. 0.5 mol CO2 m-^2 s-^1) at C(a) <200 mumol mol-^1 and decreased to <0.1 mol CO2 m-^2 s-^1 at C(a) >400 mumol mol-^1. In the absence of ABA, the contribution of (photo)respiration to stand-scale Delta(obs) was high at low C(a) (7.2 %) and decreased to <2 % at C(a) > 400 mumol mol-^1. Treatment with ABA halved this effect at all C(a) .
not annotated - annotated - LINNAEUS only
Hormone receptor-like in 96 and Broad-Complex modulate phenobarbital induced transcription of cytochrome P450 CYP6D1 in Drosophila S2 cells.
Phenobarbital (PB) is a prototypical inducer for studies of xenobiotic responses in animals. In mammals, the nuclear receptors constitutive androstane receptor (CAR) and pregnane X receptor (PXR) have been identified as key transcription factors regulating PB induced transcription of xenobiotic responsive genes. In insects, much less is known about the transcription factors involved in regulating PB induced transcription, although CAR and PXR have a single orthologue hormone receptor-like in 96 (HR96) in Drosophila melanogaster. Using dual luciferase reporter assays in Drosophila Schneider (S2) cells, constructs containing variable lengths of the promoter of the PB inducible cytochrome P450 CYP6D1 were evaluated in the presence and absence of PB. The promoter region between -330 and -280 (relative to the position of transcription start site, +1) was found to be critical for PB induction. Putative binding sites for Drosophila Broad-Complex (BR-C) and deformed (Dfd) were identified within this promoter region using TFsearch. RNA interference (RNAi) treatment of S2 cells in conjunction with CYP6D1 promoter assays showed that suppression of Drosophila HR96 and BR-C transcription in S2 cells resulted in a significant decrease and increase, respectively, of PB induction. Effects of HR96 and BR-C in mediating PB induction were PB specific and PB dependent. This represents new functional evidence that Drosophila HR96 and BR-C can act as an activator and repressor, respectively, in regulating PB induced transcription in insects.
not annotated - annotated - LINNAEUS only
Double-antigen sandwich ELISA for the detection of anti-hepatitis C virus antibodies.
A double-antigen sandwich ELISA was developed a detection of HCV antibodies by a recombinant multi-epitope HCV antigen and a biotin-streptavidin amplification system. Three plasma specimens from 1708 individuals who were suspected previously to be HCV-positive using an HCV antibody diagnostic kit (Chuangxin, Xiamen, China) displayed negative results when using the ELISA. These results were validated by a recombinant immunoblotting assay (two were negative, and one was indeterminate). Among 889 blood specimens donated for clinical evaluation, 246 were positive and 630 were negative using the ELISA. The sensitivity and specificity of the ELISA were 98.7% and 100%, respectively. In 43 donors and 14 patients with chronic hepatitis C, the detectable rates for HCV IgM by both ELISA and the HCV anti-IgM detection reagents (Huimin, Shenyang, China) were 100%, and the detectable rate for HCV IgG using an indirect HCV-antibody detection kit (GWK, Beijing, China) was 98.3%. Thus, the double-antigen sandwich ELISA exhibits strong specificity and sensitivity and has been approved by the China State Food and Drug Administration (SFDA). The performance of the double-antigen sandwich ELISA was similar to the Ortho ELISA 3.0. It did not give false-negative results otherwise IgM was undetectable using an indirect HCV-antibody detection kit. This ELISA provides another method for the detection of HCV antibodies.
not annotated - annotated - LINNAEUS only
Detection of infectious myonecrosis virus using monoclonal antibody specific to N and C fragments of the capsid protein expressed heterologously.
The gene encoding the capsid protein in ORF1 of the genome of infectious myonecrosis virus (IMNV) (GenBank AY570982) was amplified into three parts named CP-N (nucleotides 2248-3045), CP-I (nucleotides 3046-3954) and CP-C (nucleotides 3955-4953). The CP-N fragment was inserted into expression vector pTYB1 while CP-I and CP-C were each inserted into expression vector pGEX-6P-1 for transformation of BL21 E. coli strain. After induction, intein-CP-N (84 kDa), glutathione-S-transferase (GST)-CP-I (60 kDa) and GST-CP-C (62 kDa) fusion proteins were produced. They were separated by SDS-PAGE and electroeluted before immunization of Swiss mice for monoclonal antibody (MAb) production. Two MAbs specific to CP-N and one MAb specific to CP-C were selected for use for detection of natural IMNV infections in Penaeus vannamei by dot blotting, Western blotting and immunohistochemistry. There was no cross-reaction with shrimp tissues or common shrimp viruses including white spot syndrome virus (WSSV), yellow head virus (YHV), Taura syndrome virus (TSV), Penaeus monodon nucleopolyhedrovirus (PemoNPV), Penaeus stylirostris densovirus (PstDNV) and Penaeus monodon densovirus (PmDNV). The detection sensitivities of the MAbs were approximately 6 fmol/spot of purified recombinant intein-CP-N protein and 8 fmol/spot of GST-CP-C as determined by dot blotting. A combination of all three MAbs resulted in a twofold increase in sensitivity over use of any single MAb. However, this sensitivity was approximately 10 times lower than that of one-step RT-PCR using the same sample. Immunohistochemical analysis using MAbs specific to CP-N and CP-C in IMNV-infected shrimp revealed intense staining patterns in muscles, the lymphoid organ, gills, the heart, hemocytes and connective tissue.
not annotated - annotated - LINNAEUS only
Real time PCR method for simultaneous detection, quantitation and differentiation of capripoxviruses.
The genus Capripoxvirus (CaPV) comprises three members namely, sheep poxvirus (SPPV), goat poxvirus (GTPV) and lumpy skin disease virus (LSDV) affecting sheep, goats and cattle, respectively. CaPV infections produce similar symptoms in sheep and goats, and the three viruses cannot be distinguished serologically. Since there are conflicting opinions regarding the host specificity of CaPVs, particularly for goatpox and sheeppox viruses, the development of rapid genotyping tools will facilitate more accurate disease diagnosis and surveillance for better management of capripox outbreaks. This paper describes a species-specific, real time polymerase chain reaction (PCR), based on unique molecular markers that were found in the G-protein-coupled chemokine receptor (GPCR) gene sequences of CaPVs, that uses dual hybridization probes for their simultaneous detection, quantitation and genotyping. The assay can differentiate between CaPV strains based on differences in the melting point temperature (Tm) obtained after fluorescence melting curve analysis (FMCA). It is highly sensitive and presents low intra- and inter-run variation. This real time PCR assay will make a significant contribution to CaPV diagnosis and to the better understanding of the epidemiology of CaPVs by enabling rapid genotyping and gene-based classification of viral strains and unequivocal identification of isolates.
not annotated - annotated - LINNAEUS only
Multiplex PCR for rapid detection of serotype A foot-and-mouth disease virus variants with amino acid deletion at position 59 of the capsid protein VP3.
In India, there has been co-circulation, extinction and emergence of genotypes/lineages within serotype A foot-and-mouth disease (FMD) virus. At present an antigenically heterogeneous, unique lineage within genotype VII dominates the field outbreaks. This genetic cluster has amino acid deletion at position 59 of VP3 (VP3(59)-deletion group), considered to be critical antigenically. The emergence of this group warrants rapid and accurate detection to facilitate early planning and implementation of an effective control policy. A rapid multiplex PCR assay was developed for detection of the dominating VP3(59)-deletion group with 100% sensitivity and specificity, even before generating sequence data and confirmatory phylogenetic analysis. This development is important for surveillance of FMD in India.
not annotated - annotated - LINNAEUS only
Multiplex RT-PCR for rapid detection and differentiation of class I and class II Newcastle disease viruses.
A multiplex RT-PCR was developed for detection and differentiation of class I and class II strains of Newcastle disease virus (NDV). The method was shown to have high specificity and sensitivity. The results obtained from the multiplex RT-PCR for a total of 67 NDV field isolates obtained in 2009 were consistent with those obtained by nucleotide sequencing and phylogenetic analysis. A phylogenetic tree based on the partial sequences of the F gene revealed that the 67 field isolates of NDV could be divided into two classes. Twenty-seven NDV isolates were grouped into class I, and two genotypes were identified. Most of the class I isolates were determined to be of genotype 3, with the exception of isolate NDV09-034, which belonged to genotype 2. Forty class II NDV isolates were divided into three genotypes, namely genotype VII (27 isolates), genotype I (2 isolates) and genotype II (11 isolates). Isolates of genotypes I and II in class II were shown to be related to commercial vaccine strains used commonly in China. All isolates of genotype VII were predicted to be virulent, on the basis of the sequence motif at the cleavage site of the F gene. This genotype has become predominantly responsible for most outbreaks of ND in China in recent years. In conclusion, this multiplex RT-PCR provides a new assay for rapid detection and differentiation of both classes of NDV isolates.
not annotated - annotated - LINNAEUS only
Detection of Tomato black ring virus by real-time one-step RT-PCR.
A TaqMan-based real-time one-step RT-PCR assay was developed for the rapid detection of Tomato black ring virus (TBRV), a significant plant pathogen which infects a wide range of economically important crops. Primers and a probe were designed against existing genomic sequences to amplify a 72 bp fragment from RNA-2. The assay amplified all isolates of TBRV tested, but no amplification was observed from the RNA of other nepovirus species or healthy host plants. The detection limit of the assay was estimated to be around nine copies of the TBRV target region in total RNA. A comparison with conventional RT-PCR and ELISA, indicated that ELISA, the current standard test method, lacked specificity and reacted to all nepovirus species tested, while conventional RT-PCR was approximately ten-fold less sensitive than the real-time RT-PCR assay. Finally, the real-time RT-PCR assay was tested using five different RT-PCR reagent kits and was found to be robust and reliable, with no significant differences in sensitivity being found. The development of this rapid assay should aid in quarantine and post-border surveys for regulatory agencies.
not annotated - annotated - LINNAEUS only
Cross-genotypic polyclonal anti-HCV antibodies from human ascitic fluid.
Many anti-HCV antibodies are available, but more are needed for research and clinical applications. This study examines whether ascitic fluid from cirrhotic patients could be a source of reagent-grade antibodies. Ascitic fluid from 29 HCV patients was screened by ELISA for anti-HCV antibodies against three viral proteins: core, NS4B, and NS5A. Significant patient-to-patient variability in anti-HCV antibody titers was observed. Total ascitic fluid IgG purified by Protein-A chromatography reacted with HCV proteins in immunoblots, cell extracts, and replicon-expressing cells. Affinity-purification using synthetic peptides as bait allowed the preparation of cross-genotypic antibodies directed against pre-selected regions of HCV core, NS4B, and NS5A proteins. The performance of the polyclonal antibodies was comparable to that of monoclonal antibodies. Anti-NS4B antibody preparations reacted with genotype 1a, 1b, and 2a NS4B proteins in immunoblots and allowed NS4B to be localized in replicon-expressing cells. Ascitic fluid is an abundant source of human polyclonal cross-genotypic antibodies that can be used as an alternative to blood. This study shows the utility of selectively purifying human polyclonal antibodies from ascitic fluid. Affinity purification allows antibodies to be selected that are comparable to monoclonal antibodies in their ability to react with targeted regions of viral proteins.
not annotated - annotated - LINNAEUS only
A versatile vector for the production of pseudotyped viruses expressing gp120 antigens from different clades of primary HIV-1 isolates.
A novel HIV-1 Env expression vector (SF162-Z) was developed by introducing two new cloning sites on the backbone of an existing vector that produces a full length Env from HIV-1 SF162 isolate. These sites facilitate the swapping of the gp120 portion of the SF162 Env with matching gp120 antigens from HIV-1 isolates of different genetic clades. Final production of functional pseudotyped viruses will express chimeric Env antigens, including gp41 of the parental SF162 and gp120 from other primary isolates. This system is useful for testing the neutralizing sensitivity of partial env gene products frequently identified in viral quasi species in patients infected with HIV or when only partial gp120 gene products are available.
not annotated - annotated - LINNAEUS only
Catabolite control protein A controls hydrogen peroxide production and cell death in Streptococcus sanguinis.
Streptococcus sanguinis is a commensal oral bacterium producing hydrogen peroxide (H2O2) that is dependent on pyruvate oxidase (Spx) activity. In addition to its well-known role in bacterial antagonism during interspecies competition, H2O2 causes cell death in about 10% of the S. sanguinis population. As a consequence of H2O2-induced cell death, largely intact chromosomal DNA is released into the environment. This extracellular DNA (eDNA) contributes to the self-aggregation phenotype under aerobic conditions. To further investigate the regulation of spx gene expression, we assessed the role of catabolite control protein A (CcpA) in spx expression control. We report here that CcpA represses spx expression. An isogenic DeltaccpA mutant showed elevated spx expression, increased Spx abundance, and H2O2 production, whereas the wild type did not respond with altered spx expression in the presence of glucose and other carbohydrates. Since H2O2 is directly involved in the release of eDNA and bacterial cell death, the presented data suggest that CcpA is a central control element in this important developmental process in S. sanguinis.
not annotated - annotated - LINNAEUS only
Genome sequence of strain HTCC2083, a novel member of the marine clade Roseobacter.
Strain HTCC2083 was isolated from Oregon seawater using dilution-to-extinction culturing and represents a novel member of the Roseobacter clade. The draft genome sequence of HTCC2083 is presented here. The genome is predicted to contain genes for aerobic anoxygenic phototrophy, sulfite-oxidizing chemolithotrophy, anapleurotic CO(2) fixation, carbon monoxide oxidation, and dimethylsulfoniopropionate (DMSP) utilization.
not annotated - annotated - LINNAEUS only
Cadherin domains in the polysaccharide-degrading marine bacterium Saccharophagus degradans 2-40 are carbohydrate-binding modules.
The complex polysaccharide-degrading marine bacterium Saccharophagus degradans strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium.
not annotated - annotated - LINNAEUS only
Distinct roles of multiple NDH-1 complexes in the cyanobacterial electron transport network as revealed by kinetic analysis of P700+ reduction in various Ndh-deficient mutants of Synechocystis sp. strain PCC6803.
While methyl viologen had only a small effect on P700(+) rereduction kinetics after far-red pulses in KCN-treated wild-type Synechocystis sp. strain PCC6803 and an NdhF3/NdhF4 (NdhF3/F4)-defective mutant, it involved a rather slow P700(+) rereduction in an NdhF1-defective mutant. This strongly indicates that (i) active electron flow from metabolites to plastoquinone is suppressed upon deletion of ndhF1 and (ii) photosystem 1-mediated cyclic electron transport is dependent on NdhF3/F4-type NDH-1 complexes.
not annotated - annotated - LINNAEUS only
Adhesive activity of the haemophilus cryptic genospecies cha autotransporter is modulated by variation in tandem Peptide repeats.
The Haemophilus cryptic genospecies is an important cause of maternal genital tract and neonatal systemic infections and initiates infection by colonizing the genital or respiratory epithelium. In recent work, we identified a unique Haemophilus cryptic genospecies protein called Cha, which mediates efficient adherence to genital and respiratory epithelia. The Cha adhesin belongs to the trimeric autotransporter family and contains an N-terminal signal peptide, an internal passenger domain that harbors adhesive activity, and a C-terminal membrane anchor domain. The passenger domain in Cha contains clusters of YadA-like head domains and neck motifs as well as a series of tandem 28-amino-acid peptide repeats. In the current study, we report that variation in peptide repeat number gradually modulates Cha adhesive activity, associated with a direct effect on the length of Cha fibers on the bacterial cell surface. The N-terminal 404 residues of the Cha passenger domain mediate binding to host cells and also facilitate bacterial aggregation through intermolecular Cha-Cha binding. As the tandem peptide repeats expand, the Cha fiber becomes longer and Cha adherence activity decreases. The expansion and contraction of peptide repeats represent a novel mechanism for modulating adhesive capacity, potentially balancing the need of the organism to colonize the genital and respiratory tracts with the ability to attach to alternative substrates, disperse within the host, or evade the host immune system.
not annotated - annotated - LINNAEUS only
Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order Parvularculales in the class Alphaproteobacteria.
The order Parvularculales represents the seventh order in the class Alphaproteobacteria. Parvularcula bermudensis, the type species of the order, was isolated from the Sargasso Sea using dilution-to-extinction culturing. We present here the complete genome sequence of Parvularcula bermudensis HTCC2503(T), which contains genes for carotenoid biosynthesis, dimethylsulfoniopropionate demethylase, and transduction-like gene transfer agents.
not annotated - annotated - LINNAEUS only
Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis.
This work reports the completion and annotation of the genome sequence of Corynebacterium pseudotuberculosis I19, isolated from an Israeli dairy cow with severe clinical mastitis. To present the whole-genome sequence, a de novo assembly approach using 33 million short (25-bp) mate-paired SOLiD reads only was applied. Furthermore, the automatic, functional, and manual annotations were attained with the use of several algorithms in a multistep process.
not annotated - annotated - LINNAEUS only
X-ray structure and site-directed mutagenesis analysis of the Escherichia coli colicin M immunity protein.
Colicin M (ColM), which is produced by some Escherichia coli strains to kill competitor strains from the same or related species, was recently shown to inhibit cell wall peptidoglycan biosynthesis through enzymatic degradation of its lipid II precursor. ColM-producing strains are protected from the toxin that they produce by coexpression of a specific immunity protein, named Cmi, whose mode of action still remains to be identified. We report here the resolution of the crystal structure of Cmi, which is composed of four Beta strands and four alpha helices. This rather compact structure revealed a disulfide bond between residues Cys31 and Cys107. Interestingly, these two cysteines and several other residues appeared to be conserved in the sequences of several proteins of unknown function belonging to the YebF family which exhibit 25 to 35% overall sequence similarity with Cmi. Site-directed mutagenesis was performed to assess the role of these residues in the ColM immunity-conferring activity of Cmi, which showed that the disulfide bond and residues from the C-terminal extremity of the protein were functionally essential. The involvement of DsbA oxidase in the formation of the Cmi disulfide bond is also demonstrated.
not annotated - annotated - LINNAEUS only
Complete genome sequence of Bifidobacterium bifidum S17.
Here, we report on the first completely annotated genome sequence of a Bifidobacterium bifidum strain. B. bifidum S17, isolated from feces of a breast-fed infant, was shown to strongly adhere to intestinal epithelial cells and has potent anti-inflammatory activity in vitro and in vivo. The genome sequence will provide new insights into the biology of this potential probiotic organism and allow for the characterization of the molecular mechanisms underlying its beneficial properties.
not annotated - annotated - LINNAEUS only
Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae.
Strain HTCC2170 was isolated from surface waters off the Oregon coast using dilution-to-extinction culturing. Here, we present the finished genome sequence of a marine bacterium, Maribacter sp. strain HTCC2170. Strain sp. HTCC2170 is predicted to be a facultatively aerobic chemoorganotroph that, based on genomic sequence analysis, is capable of macromolecule degradation and anaerobic respiration.
not annotated - annotated - LINNAEUS only
Characterization of the Bacteroides CTnDOT regulatory protein RteC.
Excision of the Bacteroides conjugative transposon CTnDOT is stimulated by tetracycline. It was shown previously that a gene, rteC, is necessary for tetracycline-stimulated transcriptional regulation of the orf2c operon, which contains the excision genes. The protein encoded by this gene, RteC, did not have primary amino acid sequence homology to any known proteins in the databases. Accordingly, we sought structural homologs of RteC. A three-dimensional structure prediction by Robetta suggested that RteC might have two domains and that the C-terminal domain might have a winged helix motif. Based on the Robetta prediction, the human transcriptional factors E2F-4 and DP2 were identified as the most likely structural homologs of RteC. We made alanine substitutions within the putative DNA binding helix 3 region of RteC. Assays of orf2c::uidA activation by alanine mutants indicated that residues 174, 175, 178, 180, and 184 in helix 3 might contact the upstream region of P(E). The upstream region of orf2c contained two inverted-repeat half sites. Mutational analysis of these half sites showed that both half sites are important for activity. Thus, we have identified the DNA binding portion of RteC and the DNA site to which it binds.
not annotated - annotated - LINNAEUS only
Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides subsp. DG-6.
Oscillochloris trichoides is a mesophilic, filamentous, photoautotrophic, nonsulfur, diazotrophic bacterium which is capable of carbon dioxide fixation via the reductive pentose phosphate cycle and possesses no assimilative sulfate reduction. Here, we present the draft genome sequence of Oscillochloris trichoides subsp. DG-6, the type strain of the species, which has permitted the prediction of genes for carbon and nitrogen metabolism and for the light-harvesting apparatus.
not annotated - annotated - LINNAEUS only
Impact of density and environmental factors on population fluctuations in a migratory passerine.
1. Populations of plants and animals typically fluctuate because of the combined effects of density-dependent and density-independent processes. The study of these processes is complicated by the fact that population sizes are typically not known exactly, because population counts are subject to sampling variance. Although the existence of sampling variance is broadly acknowledged, relatively few studies on time-series data have accounted for it, which can result in wrong inferences about population processes. 2. To increase our understanding of population dynamics, we analysed time series from six Central European populations of the migratory red-backed shrike Lanius collurio by simultaneously assessing the strength of density dependence, process and sampling variance. In addition, we evaluated hypotheses predicting effects of factors presumed to operate on the breeding grounds, at stopover sites in eastern Africa during fall and spring migration and in the wintering grounds in southern Africa. We used both simple and state-space formulations of the Gompertz equation to model population size. 3. Across populations and modelling approaches, we found consistent evidence for negative density-dependent population regulation. Further, process variance contributed substantially to variation in population size, while sampling variance did not. Environmental conditions in eastern and southern Africa appear to influence breeding population size, as rainfall in the Sahel during fall migration and in the south African wintering areas were positively related to population size in the following spring in four of six populations. In contrast, environmental conditions in the breeding grounds were not related to population size. 4. Our findings suggest negative density-dependent regulation of red-backed shrike breeding populations and are consistent with the long-standing hypothesis that conditions in the African staging and wintering areas influence population numbers of species breeding in Europe. 5. This study highlights the importance of jointly investigating density-dependent and density-independent processes to improve our understanding of factors influencing population fluctuations in space and time.
not annotated - annotated - LINNAEUS only
Intraspecific trait variation and covariation in a widespread tree species (Nothofagus pumilio) in southern Chile.
* The focus of the trait-based approach to study community ecology has mostly been on trait comparisons at the interspecific level. Here we quantified intraspecific variation and covariation of leaf mass per area (LMA) and wood density (WD) in monospecific forests of the widespread tree species Nothofagus pumilio to determine its magnitude and whether it is related to environmental conditions and ontogeny. We also discuss probable mechanisms controlling the trait variation found. * We collected leaf and stem woody tissues from 30-50 trees of different ages (ontogeny) from each of four populations at differing elevations (i.e. temperatures) and placed at each of three locations differing in soil moisture. * The total variation in LMA (coefficient of variation (CV) = 21.14%) was twice that of WD (CV = 10.52%). The total variation in traits was never less than 23% when compared with interspecific studies. Differences in elevation (temperature) for the most part explained variation in LMA, while differences in soil moisture and ontogeny explained the variation in WD. Traits covaried similarly in the altitudinal gradient only. * Functional traits of N. pumilio exhibited nonnegligible variation; LMA varied for the most part with temperature, while WD mostly varied with moisture and ontogeny. We demonstrate that environmental variation can cause important trait variation without species turnover.
not annotated - annotated - LINNAEUS only
Systemic virus-induced gene silencing allows functional characterization of maize genes during biotrophic interaction with Ustilago maydis.
Infection of maize (Zea mays) plants with the corn smut fungus Ustilago maydis leads to the formation of large tumors on the stem, leaves and inflorescences. In this biotrophic interaction, plant defense responses are actively suppressed by the pathogen, and previous transcriptome analyses of infected maize plants showed massive and stage-specific changes in host gene expression during disease progression. To identify maize genes that are functionally involved in the interaction with U. maydis, we adapted a virus-induced gene silencing (VIGS) system based on the brome mosaic virus (BMV) for maize. Conditions were established that allowed successful U. maydis infection of BMV-preinfected maize plants. This set-up enabled quantification of VIGS and its impact on U. maydis infection using a quantitative real-time PCR (qRT-PCR)-based readout. In proof-of-principle experiments, an U. maydis-induced terpene synthase was shown to negatively regulate disease development while a protein involved in cell death inhibition was required for full virulence of U. maydis. The results suggest that this system is a versatile tool for the rapid identification of maize genes that determine compatibility with U. maydis.
not annotated - annotated - LINNAEUS only
The second face of a known player: Arabidopsis silencing suppressor AtXRN4 acts organ-specifically.
Plant viruses exploit the symplastic transport pathway provided by plasmodesmata by encoding for specialized movement proteins, which interact with host factors to enable viral intracellular and intercellular spread. Stable expression of the Potato leaf roll virus movement protein MP17 in Arabidopsis results in a carbohydrate export block and stunted growth. To identify host factors essential for viral infection, we screened a progeny population of EMS (ethyl methanesulfonate)-mutagenized Arabidopsis expressing a MP17:GFP fusion for suppressor mutants with restored wild type-like phenotype. Two suppressor mutants showed decreased susceptibility against Turnip mosaic virus and post-transcriptional silencing of MP17:GFP RNA in source leaves. Map based cloning identified in both lines mutations in XRN4 (Exoribonuclease 4), which was previously described as a suppressor of transgene silencing in source leaves. Importantly, silencing of MP17:GFP was not present in cotyledons and roots of the two suppressor mutants, which was confirmed in a third xrn4 T-DNA knock out line. Subsequent analysis of MP17:GFP transcript stability in xrn2 and xrn3 mutants indicated an essential role of AtXRN2 for silencing suppression in roots/cotyledons while AtXRN3 appears to act similar to AtXRN4 in source leaves, only. Overall, these findings point towards an organ-specific regulation of gene silencing in Arabidopsis.
not annotated - annotated - LINNAEUS only
Haplotype analysis of the genes encoding glutamine synthetase plastic isoforms and their association with nitrogen-use- and yield-related traits in bread wheat.
Glutamine synthetase (GS) plays a key role in the growth, nitrogen (N) use and yield potential of cereal crops. Investigating the haplotype variation of GS genes and its association with agronomic traits may provide useful information for improving wheat N-use efficiency and yield. We isolated the promoter and coding region sequences of the plastic glutamine synthetase isoform (GS2) genes located on chromosomes 2A, 2B and 2D in bread wheat. By analyzing nucleotide sequence variations of the coding region, two, six and two haplotypes were distinguished for TaGS2-A1 (a and b), TaGS2-B1 (a-f) and TaGS2-D1 (a and b), respectively. By analyzing the frequency data of different haplotypes and their association with N use and agronomic traits, four major and favorable TaGS2 haplotypes (A1b, B1a, B1b, D1a) were revealed. These favorable haplotypes may confer better seedling growth, better agronomic performance, and improved N uptake during vegetative growth or grain N concentration. Our data suggest that certain TaGS2 haplotypes may be valuable in breeding wheat varieties with improved agronomic performance and N-use efficiency.
not annotated - annotated - LINNAEUS only
The molecular basis for venation patterning of pigmentation and its effect on pollinator attraction in flowers of Antirrhinum.
Pigment stripes associated with veins (venation) is a common flower colour pattern. The molecular genetics and function of venation were investigated in the genus Antirrhinum, in which venation is determined by Venosa (encoding an R2R3MYB transcription factor). Pollinator preferences were measured by field tests with Antirrhinum majus. Venosa function was examined using in situ hybridization and transient overexpression. The origin of the venation trait was examined by molecular phylogenetics. Venation and full-red flower colouration provide a comparable level of advantage for pollinator attraction relative to palely pigmented or white lines. Ectopic expression of Venosa confers pigmentation outside the veins. Venosa transcript is produced only in small areas of the corolla between the veins and the adaxial epidermis. Phylogenetic analyses suggest that venation patterning is an ancestral trait in Antirrhinum. Different accessions of three species with full-red pigmentation with or without venation patterning have been found. Epidermal-specific venation is defined through overlapping expression domains of the MYB (myoblastoma) and bHLH (basic Helix-Loop-Helix) co-regulators of anthocyanin biosynthesis, with the bHLH providing epidermal specificity and Venosa vein specificity. Venation may be the ancestral trait, with full-red pigmentation a derived, polyphyletic trait. Venation patterning is probably not fixed once species evolve full-red floral pigmentation.
not annotated - annotated - LINNAEUS only
High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane.
Modern sugarcane (Saccharum spp.) is the leading sugar crop and a primary energy crop. It has the highest level of 'vertical' redundancy (2n=12x=120) of all polyploid plants studied to date. It was produced about a century ago through hybridization between two autopolyploid species, namely S. officinarum and S. spontaneum. In order to investigate the genome dynamics in this highly polyploid context, we sequenced and compared seven hom(oe)ologous haplotypes (bacterial artificial chromosome clones). Our analysis revealed a high level of gene retention and colinearity, as well as high gene structure and sequence conservation, with an average sequence divergence of 4% for exons. Remarkably, all of the hom(oe)ologous genes were predicted as being functional (except for one gene fragment) and showed signs of evolving under purifying selection, with the exception of genes within segmental duplications. By contrast, transposable elements displayed a general absence of colinearity among hom(oe)ologous haplotypes and appeared to have undergone dynamic expansion in Saccharum, compared with sorghum, its close relative in the Andropogonea tribe. These results reinforce the general trend emerging from recent studies indicating the diverse and nuanced effect of polyploidy on genome dynamics.
not annotated - annotated - LINNAEUS only
Aerenchyma formation in the rice stem and its promotion by H2O2.
* Gas spaces (aerenchyma) form as an adaptation to submergence to facilitate gas exchange. In rice (Oryza sativa), aerenchyma develop by cell death and lysis, which are poorly understood at the cellular level. * Aerenchyma formation was studied in rice stems by light microscopy. It was analyzed in response to submergence, ethylene and hydrogen peroxide (H(2)O(2)) treatment, and in the MT2b::Tos17 mutant. O(2)*(-) was detected with nitroblue tetrazolium and an epinephrine assay. H(2)O(2) was detected with 3,3'-diaminobenzidine. * Aerenchyma develop constitutively in all internodes of the deep-water rice variety Pin Gaew 56, but are absent from the nodes. Constitutive aerenchyma formation was also observed in two lowland rice varieties, albeit to a lesser degree. A larger number of aerenchyma are present in older internodes, and at the top of each internode, revealing developmental gradients. Submergence or treatment with the ethylene-releasing compound ethephon promoted aerenchyma formation in all genotypes analyzed. Pre-aerenchymal cells contain less starch, no chloroplasts, thinner cell walls and produce elevated levels of O(2)*(-) and H(2)O(2) compared with other parenchymal cells. Ethephon promotes O(2)*(-) formation and H(2)O(2) promotes aerenchyma formation in a dose-dependent manner. Further-more, genetic downregulation of the H(2)O(2) scavenger MT2b enhances aerenchyma formation. * Aerenchyma formation is mediated by reactive oxygen species.
not annotated - annotated - LINNAEUS only
Nitric oxide participates in cold-responsive phosphosphingolipid formation and gene expression in Arabidopsis thaliana.
Chilling triggers rapid molecular responses that permit the maintenance of plant cell homeostasis and plant adaptation. Recent data showed that nitric oxide (NO) is involved in plant acclimation and tolerance to cold. The participation of NO in the early transduction of the cold signal in Arabidopsis thaliana was investigated. The production of NO after a short exposure to cold was assessed using the NO-sensitive fluorescent probe 4, 5-diamino fluoresceine diacetate and chemiluminescence. Pharmacological and genetic approaches were used to analyze NO sources and NO-mediated changes in cold-regulated gene expression, phosphatidic acid (PtdOH) synthesis and sphingolipid phosphorylation. NO production was detected after 1-4h of chilling. It was impaired in the nia1nia2 nitrate reductase mutant. Moreover, NO accumulation was not observed in H7 plants overexpressing the A. thaliana nonsymbiotic hemoglobin Arabidopsis haemoglobin 1 (AHb1). Cold-regulated gene expression was affected in nia1nia2 and H7 plants. The synthesis of PtdOH upon chilling was not modified by NO depletion. By contrast, the formation of phytosphingosine phosphate and ceramide phosphate, two phosphorylated sphingolipids that are transiently synthesized upon chilling, was negatively regulated by NO. Taken together, these data suggest a new function for NO as an intermediate in gene regulation and lipid-based signaling during cold transduction.
not annotated - annotated - LINNAEUS only
Identification of a novel mitochondrial protein, short postembryonic roots 1 (SPR1), involved in root development and iron homeostasis in Oryza sativa.
* A rice mutant, Oryza sativa short postembryonic roots 1 (Osspr1), has been characterized. It has short postembryonic roots, including adventitious and lateral roots, and a lower iron content in its leaves. * OsSPR1 was identified by map-based cloning. It encodes a novel mitochondrial protein with the Armadillo-like repeat domain. * Osspr1 mutants exhibited decreased root cell elongation. The iron content of the mutant shoots was significantly altered compared with that of wild-type shoots. A similar pattern of alteration of manganese and zinc concentrations in shoots was also observed. Complementation of the mutant confirmed that OsSPR1 is involved in post-embryonic root elongation and iron homeostasis in rice. OsSPR1 was found to be ubiquitously expressed in various tissues throughout the plant. The transcript abundance of various genes involved in iron uptake and signaling via both strategies I and II was similar in roots of wild-type and mutant plants, but was higher in the leaves of mutant plants. * Thus, a novel mitochondrial protein that is involved in root elongation and plays a role in metal ion homeostasis has been identified.
not annotated - annotated - LINNAEUS only
Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum.
* Primary carbohydrate metabolism plays a special role related to carbon/nitrogen exchange, as well as metabolic support of fruiting body development, in ectomycorrhizal macrofungi. In this study, we used information retrieved from the recently sequenced Tuber melanosporum genome, together with transcriptome analysis data and targeted validation experiments, to construct the first genome-wide catalogue of the proteins supporting carbohydrate metabolism in a plant-symbiotic ascomycete. * More than 100 genes coding for enzymes of the glycolysis, pentose phosphate, tricarboxylic acid, glyoxylate and methylcitrate pathways, glycogen, trehalose and mannitol metabolism and cell wall precursor were annotated. Transcriptional regulation of these pathways in different stages of the T. melanosporum lifecycle was investigated using whole-genome oligoarray expression data together with real-time reverse transcription-polymerase chain reaction analysis of selected genes. * The most significant results were the identification of methylcitrate cycle genes and of an acid invertase, the first enzyme of this kind to be described in a plant-symbiotic filamentous fungus. * A subset of transcripts coding for trehalose, glyoxylate and methylcitrate enzymes was up-regulated in fruiting bodies, whereas genes involved in mannitol and glycogen metabolism were preferentially expressed in mycelia and ectomycorrhizas, respectively. These data indicate a high degree of lifecycle stage specialization for particular branches of carbohydrate metabolism in T. melanosporum.
not annotated - annotated - LINNAEUS only
An analytical model of non-photorespiratory CO2release in the light and dark in leaves of C3species based on stoichiometric flux balance.
Leaf respiration continues in the light but at a reduced rate. This inhibition is highly variable, and the mechanisms are poorly known, partly due to the lack of a formal model that can generate testable hypotheses. We derived an analytical model for non-photorespiratory CO2 release by solving steady-state supply/demand equations for ATP, NADH and NADPH, coupled to a widely used photosynthesis model. We used this model to evaluate causes for suppression of respiration by light. The model agrees with many observations, including highly variable suppression at saturating light, greater suppression in mature leaves, reduced assimilatory quotient (ratio of net CO2 and O2 exchange) concurrent with nitrate reduction and a Kok effect (discrete change in quantum yield at low light). The model predicts engagement of non-phosphorylating pathways at moderate to high light, or concurrent with processes that yield ATP and NADH, such as fatty acid or terpenoid synthesis. Suppression of respiration is governed largely by photosynthetic adenylate balance, although photorespiratory NADH may contribute at sub-saturating light. Key questions include the precise diel variation of anabolism and the ATP : 2e- ratio for photophosphorylation. Our model can focus experimental research and is a step towards a fully process-based model of CO2 exchange.
not annotated - annotated - LINNAEUS only
Complement opsonization enhances friend virus infection of B cells and thereby amplifies the virus-specific CD8+ T cell response.
B cells are one of the targets of Friend virus (FV) infection, a well-established mouse model often used to study retroviral infections in vivo. Although B cells may be effective in stimulating cytotoxic T lymphocyte responses, studies involving their role in FV infection have mainly focused on neutralizing antibody production. Here we show that polyclonal activation of B cells promotes their infection with FV both in vitro and in vivo. Furthermore, we demonstrate that complement opsonization of Friend murine leukemia virus (F-MuLV) enhances infection of B cells, which correlates with increased potency of B cells to activate FV-specific CD8(+) T cells.
not annotated - annotated - LINNAEUS only
Genetic analysis of B55alpha/Cdc55 protein phosphatase 2A subunits: association with the adenovirus E4orf4 protein.
The human adenovirus E4orf4 protein is toxic in both human tumor cells and Saccharomyces cerevisiae. Previous studies indicated that most of this toxicity is dependent on an interaction of E4orf4 protein with the B55 class of regulatory subunits of protein phosphatase 2A (PP2A) and in yeast with the B55 homolog Cdc55. We have found previously that E4orf4 inhibits PP2A activity against at least some substrates. In an attempt to understand the mechanism of this inhibition, we used a genetic approach to identify residues in the seven-bladed Beta-propeller proteins B55alpha and Cdc55 required for E4orf4 binding. In both cases, amino-terminal polypeptides composed only of blade 1 and at least part of blade 2 were found to bind E4orf4 and overexpression blocked E4orf4 toxicity in yeast. Furthermore, certain amino acid substitutions in blades 1 and 2 within full-length B55alpha and Cdc55 resulted in loss of E4orf4 binding. Recent mutational analysis has suggested that segments of blades 1 and 2 present on the top face of B55alpha form part of the "substrate-binding groove." Additionally, these segments are in close proximity to the catalytic C subunit of the PP2A holoenzyme. Thus, our results are consistent with the hypothesis that E4orf4 binding could affect the access of substrates, resulting in the failure to dephosphorylate some PP2A substrates.
not annotated - annotated - LINNAEUS only
Stepwise loss of fluorescent core protein V from human adenovirus during entry into cells.
Human adenoviruses (Ads) replicate and assemble particles in the nucleus. They organize a linear double-strand DNA genome into a condensed core with about 180 nucleosomes, by the viral proteins VII (pVII), pX, and pV attaching the DNA to the capsid. Using reverse genetics, we generated a novel, nonconditionally replicating Ad reporter by inserting green fluorescent protein (GFP) at the amino terminus of pV. Purified Ad2-GFP-pV virions had an oversized complete genome and incorporated about 38 GFP-pV molecules per virion, which is about 25% of the pV levels in Ad2. GFP-pV cofractionated with the DNA core, like pV, and newly synthesized GFP-pV had a subcellular localization indistinguishable from that of pV, indicating that GFP-pV is a valid reporter for pV. Ad2-GFP-pV completed the replication cycle, although at lower yields than Ad2. Incoming GFP-pV (or pV) was not imported into the nucleus. Virions lost GFP-pV at two points during the infection process: at entry into the cytosol and at the nuclear pore complex, where capsids disassemble. Disassembled capsids, positive for the conformation-specific antihexon antibody R70, were devoid of GFP-pV. The loss of GFP-pV was reduced by the macrolide antibiotic leptomycin B (LMB), which blocks nuclear export and adenovirus attachment to the nuclear pore complex. LMB inhibited the appearance of R70 epitopes on Ad2 and Ad2-GFP-pV, indicating that the loss of GFP-pV from Ad2-GFP-pV is an authentic step in the adenovirus uncoating program. Ad2-GFP-pV is genetically complete and hence enables detailed analyses of infection and spreading dynamics in cells and model organisms or assessment of oncolytic adenoviral potential.
not annotated - annotated - LINNAEUS only
The spatial scaling of habitat selection by African elephants.
1. Understanding and accurately predicting the spatial patterns of habitat use by organisms is important for ecological research, biodiversity conservation and ecosystem management. However, this understanding is complicated by the effects of spatial scale, because the scale of analysis affects the quantification of species-environment relationships. 2. We therefore assessed the influence of environmental context (i.e. the characteristics of the landscape surrounding a site), varied over a large range of scales (i.e. ambit radii around focal sites), on the analysis and prediction of habitat selection by African elephants in Kruger National Park, South Africa. 3. We focused on the spatial scaling of the elephants' response to their main resources, forage and water, and found that the quantification of habitat selection strongly depended on the scales at which environmental context was considered. Moreover, the inclusion of environmental context at characteristic scales (i.e. those at which habitat selectivity was maximized) increased the predictive capacity of habitat suitability models. 4. The elephants responded to their environment in a scale-dependent and perhaps hierarchical manner, with forage characteristics driving habitat selection at coarse spatial scales, and surface water at fine spatial scales. 5. Furthermore, the elephants exhibited sexual habitat segregation, mainly in relation to vegetation characteristics. Male elephants preferred areas with high tree cover and low herbaceous biomass, whereas this pattern was reversed for female elephants. 6. We show that the spatial distribution of elephants can be better understood and predicted when scale-dependent species-environment relationships are explicitly considered. This demonstrates the importance of considering the influence of spatial scale on the analysis of spatial patterning in ecological phenomena.
not annotated - annotated - LINNAEUS only
Is hunting mortality additive or compensatory to natural mortality? Effects of experimental harvest on the survival and cause-specific mortality of willow ptarmigan.
1. The effects of harvest on the annual and seasonal survival of willow ptarmigan Lagopus lagopus L. were tested in a large-scale harvest experiment. Management units were randomly assigned to one of three experimental treatments: 0%, 15% or 30% harvest. Seasonal quotas were based on the experimental treatment and estimates of bird density before the hunting season. Survival rates and hazard functions for radio-marked ptarmigan were then estimated under the competing risks of harvest and natural mortality. 2. The partially compensatory mortality hypothesis was supported: annual survival of ptarmigan was 0*54 +/- 0*08 SE under 0% harvest, 0*47 +/- 0*06 under 15% harvest, and was reduced to 0*30 +/- 0*05 under 30% harvest. Harvest mortality increased linearly from 0*08 +/- 0*05, 0*27 +/- 0*05 and 0*42 +/- 0*06 from 0% to 30% harvest, whereas natural mortality was 0*38 +/- 0*08, 0*25 +/- 0*05 and 0*28 +/- 0*06 under the same treatments. 3. Realized risk of harvest mortality was 0*08-0*12 points higher than our set harvest treatments of 0-30% because birds were exposed to risk if they moved out of protected areas. The superadditive hypothesis was supported because birds in the 30% harvest treatment had higher natural mortality during winter after the hunting season. 4. Natural mortality was mainly because of raptor predation, with two seasonal peaks in fall and spring. Natural and harvest mortality coincided during early autumn with little potential for compensation during winter months. Peak risk of harvest mortality was 5x higher than natural mortality. Low natural mortality during winter suggests that most late season harvest would be additive mortality. 5. Environmental correlates of natural mortality of ptarmigan included seasonal changes in snow cover, onset of juvenile dispersal, and periods of territorial activity. Natural mortality of ptarmigan was highest during autumn movements and nesting by gyrfalcons Falco rusticolus L. Mortality was low when gyrfalcons had departed for coastal wintering sites, and during summer when ptarmigan were attending nests and broods. 6. Our experimental results have important implications for harvest management of upland gamebirds. Seasonal quotas based on proportional harvest were effective and should be set at =< 15% of August populations for regional management plans. Under threshold harvest of a reproductive surplus, 15% harvest would be sustainable at productivity rates >= 2*5 young per pair. Impacts of winter harvest could be minimized by closing the hunting season in early November or by reducing late season quotas.
not annotated - annotated - LINNAEUS only
Possible contributions of TERMINAL FLOWER 1 to the evolution of rosette flowering in Leavenworthia (Brassicaceae).
Leavenworthia crassa is a rosette flowering species that differs from inflorescence flowering species, such as Arabidopsis thaliana, in having elongated pedicels and shortened interfloral internodes on the main axis. Based on previous experiments, we hypothesized that changes to the L. crassa TFL1 ortholog, LcrTFL1, were important in the evolution of rosette flowering. We isolated LcrTFL1 and introduced a genomic construct into tfl1 mutant A. thaliana plants. We also generated and analyzed EGFP-LcrTFL1 reporter-fusion lines, and LcrTFL1/LcrLFY doubly transgenic lines. The transgene rescued the mutant defects, but manifested gain-of-function phenotypes. However, LcrTFL1 lines differed from 35S:TFL1 lines in several regards. Defects in floral meristem identity establishment were observed, as was the production of flowers with extra petals. We also noted features that resemble rosette flowering: LcrTFL1 lines produced significantly shorter interfloral internodes and significantly longer pedicels than either wild-type or 35S:TFL1 plants. Our data show that there are substantive differences in the regulation and/or function of TFL1 orthologs between A. thaliana and L. crassa. These may reflect changes that occurred during the evolution of rosette flowering in Leavenworthia, but, if so, our results show that additional, as-yet-unidentified genes were involved in this instance of architectural evolution.
not annotated - annotated - LINNAEUS only
Gene expression changes during short day induced terminal bud formation in Norway spruce.
The molecular basis for terminal bud formation in autumn is not well understood in conifers. By combining suppression subtractive hybridization and monitoring of gene expression by qRT-PCR analysis, we aimed to identify genes involved in photoperiodic control of growth cessation and bud set in Norway spruce. Close to 1400 ESTs were generated and their functional distribution differed between short day (SD-12 h photoperiod) and long day (LD-24 h photoperiod) libraries. Many genes with putative roles in protection against stress appeared differentially regulated under SD and LD, and also differed in transcript levels between 6 and 20 SDs. Of these, PaTFL1(TERMINAL FLOWER LIKE 1) showed strongly increased transcript levels at 6 SDs. PaCCCH(CCCH-TYPE ZINC FINGER) and PaCBF2&3(C-REPEAT BINDING FACTOR 2&3) showed a later response at 20 SDs, with increased and decreased transcript levels, respectively. For rhythmically expressed genes such as CBFs, such differences might represent a phase shift in peak expression, but might also suggest a putative role in response to SD. Multivariate analyses revealed strong differences in gene expression between LD, 6 SD and 20 SD. The robustness of the gene expression patterns was verified in 6 families differing in bud-set timing under natural light with gradually decreasing photoperiod.
not annotated - annotated - LINNAEUS only
Role of nitric oxide in hydrogen peroxide-dependent induction of abiotic stress tolerance by brassinosteroids in cucumber.
Brassinosteroids (BRs) can induce plant tolerance to a variety of abiotic stresses by triggering the generation of H(2) O(2) as a signalling molecule in cucumber leaves. Whether nitric oxide (NO) also plays a signalling role and, if so, what is the relationship between NO and H(2) O(2) in BR-induced stress tolerance are unknown. Involvement of NO and H(2) O(2) in BR-induced tolerance was examined. NO accumulation and defence related gene transcripts were monitored by confocal laser-scanning microscopy and qRT-PCR, respectively. NO content was elevated after treatment with 24-epibrassinolide (EBR) and reduced with the inhibition of BR biosynthesis. EBR-induced NO production was blocked by pre-treatment with inhibitor of NADPH oxidase and a reactive oxygen species scavenger. On the other hand, EBR-induced H(2) O(2) generation was not sensitive to NO scavenger or inhibitor of NO production. Scavenging or inhibition of NO production inhibited EBR-induced tolerance to photo-oxidative and cold stress and partly blocked EBR-induced expression and activities of several antioxidant enzymes. Pre-treatment of the exogenous NO precursor, on the other hand, led to both increased stress tolerance and increased expression of antioxidant enzymes. These results strongly suggest that NO plays an important role in H(2) O(2) -dependent induction of plant stress tolerance by BR.
not annotated - annotated - LINNAEUS only
The Arabidopsis tt19-4 mutant differentially accumulates proanthocyanidin and anthocyanin through a 3' amino acid substitution in glutathione S-transferase.
The Arabidopsis transparent testa (tt) mutant tt19-4 shows reduced seed coat colour, but stains darkly with DMACA and accumulates anthocyanins in aerial tissues. Positional cloning showed that tt19-4 was allelic to tt19-1 and has a G-to-T mutation in a conserved 3'-domain in the TT19-4 gene. Soluble and unextractable seed proanthocyanidins and hydrolysis of unextractable proanthocyanidin differ between wild-type Col-4 and both mutants. However, seed quercetins, unextractable proanthocyanidin hydrolysis, and seedling anthocyanin content, and flavonoid gene expression differ between tt19-1 and tt19-4. Transformation of tt19-1 with a TT19-4 cDNA results in vegetative anthocyanins, whereas TT19-4 cDNA cannot complement the proanthocyanidin and pale seed coat phenotype of tt19-1. Both recombinant TT19 and TT19-4 enzymes are functional GSTs and are localized in the cytosol, but TT19 did not function with wide range of flavonoids and natural products to produce conjugation products. We suggest that the dark seed coat of Arabidopsis is related to soluble proanthocyanidin content and that quercetin holds the key to the function of TT19. In addition, TT19 appears to have a 5' GSH-binding domain influencing both anthocyanin and proanthocyanidin accumulation and a 3' domain affecting proanthocyanidin accumulation by a single amino acid substitution.
not annotated - annotated - LINNAEUS only
Insights into membrane association of Klebsiella pneumoniae NifL under nitrogen-fixing conditions from mutational analysis.
In Klebsiella pneumoniae nitrogen fixation is tightly controlled in response to ammonium and molecular oxygen by the NifL/NifA regulatory system. Under repressing conditions, NifL inhibits the nif-specific transcriptional activator NifA by direct protein-protein interaction, whereas under anaerobic and nitrogen-limited conditions sequestration of reduced NifL to the cytoplasmic membrane impairs inhibition of cytoplasmic NifA by NifL. We report here on a genetic screen to identify amino acids of NifL essential for sequestration to the cytoplasmic membrane under nitrogen-fixing conditions. Overall, 11,500 mutated nifL genes of three independently generated pools were screened for those conferring a Nif(-) phenotype. Based on the respective amino acid changes of nonfunctional derivatives obtained in the screen, and taking structural data into account as well, several point mutations were introduced into nifL by site-directed mutagenesis. The majority of amino acid changes resulting in a significant nif gene inhibition were located in the N-terminal domain (N46D, Q57L, Q64R, N67S, N69S, R80C, and W87G) and the Q-linker (K271E). Further analyses demonstrated that positions N69, R80, and W87 are essential for binding the FAD cofactor, whereas primarily Q64 and N46, but also Q57 and N67, appear to be crucial for direct membrane contact of NifL under oxygen and nitrogen limitation. Based on these findings, we propose that those four amino acids most likely located on the protein surface, as well as the presence of the FAD cofactor, are crucial for the correct overall protein conformation and respective surface charge, allowing NifL sequestration to the cytoplasmic membrane under derepressing conditions.
not annotated - annotated - LINNAEUS only
Complex regulation of symbiotic functions is coordinated by MucR and quorum sensing in Sinorhizobium meliloti.
In Sinorhizobium meliloti, the production of exopolysaccharides such as succinoglycan and exopolysaccharide II (EPS II) enables the bacterium to invade root nodules on Medicago sativa and establish a nitrogen-fixing symbiosis. While extensive research has focused on succinoglycan, less is known concerning the regulation of EPS II or the mechanism by which it mediates entrance into the host plant. Previously, we reported that the ExpR/Sin quorum-sensing system is required to produce the symbiotically active low-molecular-weight fraction of this exopolysaccharide. Here, we show that this system induces EPS II production by increasing expression of the expG-expC operon, encoding both a transcriptional regulator (ExpG) and a glycosyl transferase (ExpC). ExpG derepresses EPS II production at the transcriptional level from MucR, a RosR homolog, while concurrently elevating expression of expC, resulting in the synthesis of the low-molecular-weight form. While the ExpR/Sin system abolishes the role of MucR on EPS II production, it preserves a multitude of other quorum-sensing-independent regulatory functions which promote the establishment of symbiosis. In planktonic S. meliloti, MucR properly coordinates a diverse set of bacterial behaviors by repressing a variety of genes intended for expression during symbiosis and enhancing the bacterial ability to induce root nodule formation. Quorum sensing precisely modulates the functions of MucR to take advantage of both the production of symbiotically active EPS II as well as the proper coordination of bacterial behavior required to promote symbiosis.
not annotated - annotated - LINNAEUS only
Biochemical characterization of UDP-Gal:GlcNAc-pyrophosphate-lipid Beta-1,4-Galactosyltransferase WfeD, a new enzyme from Shigella boydii type 14 that catalyzes the second step in O-antigen repeating-unit synthesis.
The O antigen is the outer part of the lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria and contains many repeats of an oligosaccharide unit. It contributes to antigenic variability and is essential to the full function and virulence of bacteria. Shigella is a Gram-negative human pathogen that causes diarrhea in humans. The O antigen of Shigella boydii type 14 consists of repeating oligosaccharide units with the structure [->6-d-Galpalpha1->4-d-GlcpABeta1->6-d-GalpBeta1->4-d-GalpBeta1->4-d-GlcpNAcBeta1->]n. The wfeD gene in the O-antigen gene cluster of Shigella boydii type 14 was proposed to encode a galactosyltransferase (GalT) involved in O-antigen synthesis. We confirmed here that the wfeD gene product is a Beta4-GalT that synthesizes the GalBeta1-4GlcNAcalpha-R linkage. WfeD was expressed in Escherichia coli, and the activity was characterized by using UDP-[^3H]Gal as the donor substrate as well as the synthetic acceptor substrate GlcNAcalpha-pyrophosphate-(CH2)11-O-phenyl. The enzyme product was analyzed by liquid chromatography-mass spectrometry (LC-MS), high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR), and galactosidase digestion. The enzyme was shown to be specific for the UDP-Gal donor substrate and required pyrophosphate in the acceptor substrate. Divalent metal ions such as Mn^2(+), Ni^2(+), and, surprisingly, also Pb^2(+) enhanced the enzyme activity. Mutational analysis showed that the Glu101 residue within a DxD motif is essential for activity, possibly by forming the catalytic nucleophile. The Lys211 residue was also shown to be required for activity and may be involved in the binding of the negatively charged acceptor substrate. Our study revealed that the Beta4-GalT WfeD is a novel enzyme that has virtually no sequence similarity to mammalian Beta4-GalT, although it catalyzes a similar reaction.
not annotated - annotated - LINNAEUS only
Plasma membrane Ca^2+ transporters mediate virus-induced acquired resistance to oxidative stress.
This paper reports the phenomenon of acquired cross-tolerance to oxidative stress in plants and investigates the activity of specific Ca^2+ transport systems mediating this phenomenon. Nicotiana benthamiana plants were infected with Potato virus X (PVX) and exposed to oxidative [either ultraviolet (UV-C) or H2O2] stress. Plant adaptive responses were assessed by the combined application of a range of electrophysiological (non-invasive microelectrode ion flux measurements), biochemical (Ca^2+- and H+-ATPase activity), imaging (fluorescence lifetime imaging measurements of changes in intracellular Ca^2+ concentrations), pharmacological and cytological transmission electrone microscopy techniques. Virus-infected plants had a better ability to control UV-induced elevations in cytosolic-free Ca^2+ and prevent structural and functional damage of chloroplasts. Taken together, our results suggest a high degree of crosstalk between UV and pathogen-induced oxidative stresses, and highlight the crucial role of Ca^2+ efflux systems in acquired resistance to oxidative stress in plants.
not annotated - annotated - LINNAEUS only
Involvement of extracellular oxidative burst in salicylic acid-induced stomatal closure in Arabidopsis.
Salicylic acid (SA), a ubiquitous phenolic phytohormone, is involved in many plant physiological processes including stomatal movement. We analysed SA-induced stomatal closure, production of reactive oxygen species (ROS) and nitric oxide (NO), cytosolic calcium ion ([Ca^2+](cyt)) oscillations and inward-rectifying potassium (K+(in)) channel activity in Arabidopsis. SA-induced stomatal closure was inhibited by pre-treatment with catalase (CAT) and superoxide dismutase (SOD), suggesting the involvement of extracellular ROS. A peroxidase inhibitor, SHAM (salicylhydroxamic acid) completely abolished SA-induced stomatal closure whereas neither an inhibitor of NADPH oxidase (DPI) nor atrbohD atrbohF mutation impairs SA-induced stomatal closures. 3,3'-Diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) stainings demonstrated that SA induced H2O2 and O2- production. Guard cell ROS accumulation was significantly increased by SA, but that ROS was suppressed by exogenous CAT, SOD and SHAM. NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) suppressed the SA-induced stomatal closure but did not suppress guard cell ROS accumulation whereas SHAM suppressed SA-induced NO production. SA failed to induce [Ca^2+](cyt) oscillations in guard cells whereas K+(in) channel activity was suppressed by SA. These results indicate that SA induces stomatal closure accompanied with extracellular ROS production mediated by SHAM-sensitive peroxidase, intracellular ROS accumulation and K+(in) channel inactivation.
not annotated - annotated - LINNAEUS only
Effect of soil acidity, soil strength and macropores on root growth and morphology of perennial grass species differing in acid-soil resistance.
It is unclear whether roots of acid-soil resistant plants have significant advantages, compared with acid-soil sensitive genotypes, when growing in high-strength, acid soils or in acid soils where macropores may allow the effects of soil acidity and strength to be avoided. The responses of root growth and morphology to soil acidity, soil strength and macropores by seedlings of five perennial grass genotypes differing in acid-soil resistance were determined, and the interaction of soil acidity and strength for growth and morphology of roots was investigated. Soil acidity and strength altered root length and architecture, root hair development, and deformed the root tip, especially in acid-soil sensitive genotypes. Root length was restricted to some extent by soil acidity in all genotypes, but the adverse impact of soil acidity on root growth by acid-soil resistant genotypes was greater at high levels of soil strength. Roots reacted to soil acidity when growing in macropores, but elongation through high-strength soil was improved. Soil strength can confound the effect of acidity on root growth, with the sensitivity of acid-resistant genotypes being greater in high-strength soils. This highlights the need to select for genotypes that resist both acidity and high soil strength.
not annotated - annotated - LINNAEUS only
Enhanced formation of methane in plant cell cultures by inhibition of cytochrome c oxidase.
The claim of methane (CH4) formation in plants has caused much controversy and debate within the scientific community over the past 4 years. Here, using both stable isotope and concentration measurements, we demonstrate that CH4 formation occurs in plant cell cultures that were grown in the dark under sterile conditions. Under non-stress conditions the plant cell cultures produced trace amounts [0.3-0.6 ng g-^1 dry weight (DW) h-^1] of CH4 but these could be increased by one to two orders of magnitude (up to 12 ng g-^1 DW h-^1) when sodium azide, a compound known to disrupt electron transport flow at the cytochrome c oxidase (complex IV) in plant mitochondria, was added to the cell cultures. The addition of other electron transport chain (ETC) inhibitors did not result in significant CH4 formation indicating that a site-specific disturbance of the ETC at complex IV causes CH4 formation in plant cells. Our study is an important first step in providing more information on non-microbial CH4 formation from living plants particularly under abiotic stress conditions that might affect the electron transport flow at the cytochrome c oxidase in plant mitochondria.
not annotated - annotated - LINNAEUS only
Microbial and viral pathogens in colorectal cancer.
The heterogenetic and sporadic nature of colorectal cancer has led to many epidemiological associations with causes of this disease. As our understanding of the underlying molecular processes in colorectal-cancer develops, the concept of microbial-epithelial interactions as an oncogenic trigger might provide a plausible hypothesis for the pathogenesis of colorectal cancer. By contrast with other cancers of the gastrointestinal tract (gastric carcinoma, mucosa-associated lymphoid-tissue lymphoma), a direct causal link between microbial infection (bacteria and viruses) and colorectal carcinoma has not been established. Studies support the involvement of these organisms in oncogenesis, however, in colorectal cancer, clinical data are lacking. Here, we discuss current evidence (both in vitro and clinical studies), and focus on a putative role for bacterial and viral pathogens as a cause of colorectal cancer.
not annotated - annotated - LINNAEUS only
Activation and localization of protein kinase C in Neurospora crassa.
The Neurosporacrassa protein kinase C (NPKC) is reported to be a regulator of light responsive genes. It phosphorylates the light receptor WC-1 and regulates the levels of the circadian clock protein FRQ and transcription of the light-induced albino-2 gene. In mammals, the conventional and novel isoforms of PKC are activated by diacylglycerol (DAG), which induces PKC translocation from the cytoplasm to membranes. To investigate the interaction of NPKC and DAG in Neurospora, we constructed a strain that expresses a PKC-GFP fusion protein. We found that NPKC localizes to growing tips and sub-apical plasma membrane in actively growing hyphae, and actively participates in septum development. NPKC is activated by exogenous DAG and phorbol esters, and translocates to the plasma membrane from the cytoplasm. We have previously reported that choline depletion of the chol-1 mutant of Neurospora increases DAG levels and lengthens the period of the circadian rhythm of conidiation. We have found that the activity of NPKC is rhythmic, and that NPKC levels are increased on choline depletion. However, over-expression of NPKC did not lengthen the conidiation period, indicating that PKC in Neurospora may not be responsible for the lengthened period in low choline cultures.
not annotated - annotated - LINNAEUS only
Cercozoa comprises both EF-1alpha-containing and EFL-containing members.
Elongation factor 1alpha (EF-1alpha) and elongation factor-like protein (EFL) are considered to be functionally equivalent proteins involved in peptide synthesis. Eukaryotes can be fundamentally divided into 'EF-1alpha-containing' and 'EFL-containing' types. Recently, EF-1alpha and EFL genes have been surveyed across the diversity of eukaryotes to explore the origin and evolution of EFL genes. Although the phylum Cercozoa is a diverse group, gene data for either EFL or EF-1alpha are absent from all cercozoans except chlorarachniophytes which were previously defined as EFL-containing members. Our survey revealed that two members of the cercozoan subphylum Filosa (Thaumatomastix sp. and strain YPF610) are EFL-containing members. Importantly, we identified EF-1alpha genes from two members of Filosa (Paracercomonas marina and Paulinella chromatophora) and a member of the other subphylum Endomyxa (Filoreta japonica). All cercozoan EFL homologues could not be recovered as a monophyletic group in maximum-likelihood and Bayesian analyses, suggesting that lateral gene transfer was involved in the EFL evolution in this protist assemblage. In contrast, EF-1alpha analysis successfully recovered a monophyly of three homologues sampled from the two cercozoan subphyla. Based on the results, we postulate that cercozoan EF-1alpha genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1alpha genes.
not annotated - annotated - LINNAEUS only
Ecological conditions in wintering and passage areas as determinants of timing of spring migration in trans-Saharan migratory birds.
1. Climate change has been associated with shifts in the timing of biological events, including the spring arrival of migratory birds. Early arrival at breeding sites is an important life-history trait, usually associated with higher breeding success and therefore, susceptible to selection and evolution in response to changing climatic conditions. 2. Here, we examine the effect of changes in the environmental conditions of wintering and passage areas on the mean passage time of 13 trans-Saharan passerines during their spring migration through the western Mediterranean over the 15 years from 1993 to 2007. 3. We found that most of the species studied have been advancing the timing of their passage in recent years. However, annual variation in the mean date of passage was positively correlated with vegetation growth (measured as the normalized difference vegetation index [NDVI]) both in the Sahel (the region of departure) and in northern Africa (the passage area). Thus, migration dates were delayed in years with high primary productivity in passage and wintering zones. All species seem to respond similarly to NDVI in the Sahel; however, late migrants were less affected by ecological conditions in northern Africa than those migrating earlier, suggesting differences based on species ecology. 4. Mean timing of passage was not related to the North Atlantic Oscillation (NAO), El Nino-Southern Oscillation (ENSO), temperature or NDVI in the species-specific wintering areas (the overwintering region) when analysed in combination with the other covariates. 5. Our findings show that ecological conditions in the winter quarters (specifically the Sahel) and en route are relevant factors influencing trends in the passage dates of trans-Saharan migratory birds on the southern fringe of Europe. Possible long-term consequences for late arriving spring migrants are discussed.
not annotated - annotated - LINNAEUS only
Effects of early horn growth on reproduction and hunting mortality in female chamois.
1. Environmental conditions during early development can affect the growth patterns of vertebrates, influencing future survival and reproduction. In long-lived mammals, females that experience poor environmental conditions early in life may delay primiparity. In female bovids, annual horn growth increments may provide a record of age-specific reproduction and body growth. Horn length, however, may also be a criterion used by hunters in selecting animals to harvest, possibly leading to artificial selection. 2. We studied three populations of chamois (Rupicapra rupicapra) in the western Alps to explore the relationships between female horn length and early growth, age of primiparity and age-specific reproduction. We also compared the risk of harvest to reproductive status and horn length. 3. Early horn growth was positively correlated with body mass in pre-reproductive females and with reproduction in very young and senescent adults. Females with strong early horn growth attained primiparity at an earlier age than those with weak early growth. Horn length did not affect hunter selection, but we found a strong hunter preference for nonlactating females. 4. Our research highlights the persistent effects of early development on reproductive performance in mammals. Moderate sport harvests are unlikely to affect the evolution of phenotypic traits and reproductive strategies in female chamois. A policy of penalizing hunters that harvest lactating females, however, may increase the harvest of 2-year-old females, which have high reproductive potential.
not annotated - annotated - LINNAEUS only
FungiFun: a web-based application for functional categorization of fungal genes and proteins.
FungiFun assigns functional annotations to fungal genes or proteins and performs gene set enrichment analysis. Based on three different classification methods (FunCat, GO and KEGG), FungiFun categorizes genes and proteins for several fungal species on different levels of annotation detail. It is web-based and accessible to users without any programming skills. FungiFun is the first tool offering gene set enrichment analysis including the FunCat categorization. Two biological datasets for Aspergillus fumigatus and Candida albicans were analyzed using FungiFun, providing an overview of the usage and functions of the tool. FungiFun is freely accessible at https://www.omnifung.hki-jena.de/FungiFun/.
not annotated - annotated - LINNAEUS only
Cleavage of resveratrol in fungi: characterization of the enzyme Rco1 from Ustilago maydis.
Ustilago maydis, the causative agent of corn smut disease, contains two genes encoding members of the carotenoid cleavage oxygenase family, a group of enzymes that cleave double bonds in different substrates. One of them, Cco1, was formerly identified as a Beta-carotene cleaving enzyme. Here we elucidate the function of the protein encoded by the second gene, termed here as Ustilago maydis Resveratrol cleavage oxygenase 1 (Um Rco1). In vitro incubations of heterologously expressed and purified UM Rco1 with different carotenoid and stilbene substrates demonstrate that it cleaves the interphenyl Calpha-CBeta double bond of the phytoalexin resveratrol and its derivative piceatannol. Um Rco1 exhibits a high degree of substrate specificity, as suggested by the lack of activity on carotenoids and the other resveratrol-related compounds tested. The activity of Um Rco1 was confirmed by incubation of U. maydis rco1 deletion and over-expression strains with resveratrol. Furthermore, treatment with resveratrol resulted in striking alterations of cell morphology. However, pathogenicity assays indicated that Um rco1 is largely dispensable for biotrophic development. Our work reveals Um Rco1 as the first eukaryotic resveratrol cleavage enzyme identified so far. Moreover, Um Rco1 represents a subfamily of fungal enzymes likely involved in the degradation of stilbene compounds, as suggested by the cleavage of resveratrol by homologs from Aspergillus fumigatus, Chaetomium globosum and Botryotinia fuckeliana.
not annotated - annotated - LINNAEUS only
Medical schools in sub-Saharan Africa.
Small numbers of graduates from few medical schools, and emigration of graduates to other countries, contribute to low physician presence in sub-Saharan Africa. The Sub-Saharan African Medical School Study examined the challenges, innovations, and emerging trends in medical education in the region. We identified 168 medical schools; of the 146 surveyed, 105 (72%) responded. Findings from the study showed that countries are prioritising medical education scale-up as part of health-system strengthening, and we identified many innovations in premedical preparation, team-based education, and creative use of scarce research support. The study also drew attention to ubiquitous faculty shortages in basic and clinical sciences, weak physical infrastructure, and little use of external accreditation. Patterns recorded include the growth of private medical schools, community-based education, and international partnerships, and the benefit of research for faculty development. Ten recommendations provide guidance for efforts to strengthen medical education in sub-Saharan Africa.
not annotated - annotated - LINNAEUS only
Diversity, distribution and biogeography of testate amoebae in China: implications for ecological studies in Asia.
Testate amoebae are a group of shelled protozoa that occur in high density populations in wet environments. More than 1900 testate amoebae species or subspecies have been reported in published literature over the last 200 years, from many regions of the world. Testate amoebae are classified as Lobosea or Filosea respectively, according to the presence of lobose or filiform pseudopodia. Testate amoebae have proved an interesting group of indicator organisms in palaeoenvironmental studies and have also been used as bioindicators of human impact on ecosystems. Until recently, the testate amoebae of China were unknown to most western scientists, but our knowledge has improved greatly over the past 20 years. This paper summarizes the testate amoebae research in China along with relevant data from other countries in Asia, and provides the necessary context for future research.
not annotated - annotated - LINNAEUS only
Translation efficiency of antiterminator proteins is a determinant for the difference in glucose repression of two Beta-glucoside phosphotransferase system gene clusters in Corynebacterium glutamicum R.
Corynebacterium glutamicum R has two Beta-glucoside phosphoenolpyruvate, carbohydrate phosphotransferase systems (PTS) encoded by bglF and bglF2 located in the respective clusters, bglF-bglA-bglG and bglF2-bglA2-bglG2. Previously, we reported that whereas Beta-glucoside-dependent induction of bglF is strongly repressed by glucose, glucose repression of bglF2 is very weak. Here, we reveal the mechanism behind the different effects of glucose on the two bgl genes. Deletion of the ribonucleic antiterminator sequence and transcriptional terminator located upstream of the translation initiation codon of bglF markedly relieved the glucose repression of a bglF-lacZ fusion, indicating that glucose affects the antitermination mechanism that is responsible for the Beta-glucoside-dependent induction of the bglF cluster. The glucose repression of bglF mRNA was also relieved by introducing a multicopy plasmid carrying the bglG gene encoding an antiterminator of the bglF cluster. Moreover, replacement of the GUG translation initiation codon of bglG with AUG was effective in relieving the glucose repression of bglF and bglG. Inversely, expression of bglF2 and bglG2 was subject to strict glucose repression in a mutant strain in which the AUG translation initiation codon of bglG2 encoding antiterminator of the bglF2 cluster was replaced with GUG. These results suggest that the translation initiation efficiency of the antiterminator proteins, at least in part, determines whether the target genes are subject to glucose repression. We also found that bglF expression was induced by glucose in the BglG-overexpressing strains, which may be explained by the ability of BglF to transport glucose.
not annotated - annotated - LINNAEUS only
argC Orthologs from Rhizobiales show diverse profiles of transcriptional efficiency and functionality in Sinorhizobium meliloti.
Several factors can influence ortholog replacement between closely related species. We evaluated the transcriptional expression and metabolic performance of ortholog substitution complementing a Sinorhizobium meliloti argC mutant with argC from Rhizobiales (Agrobacterium tumefaciens, Rhizobium etli, and Mesorhizobium loti). The argC gene is necessary for the synthesis of arginine, an amino acid that is central to protein and cellular metabolism. Strains were obtained carrying plasmids with argC orthologs expressed under the speB and argC (S. meliloti) and lac (Escherichia coli) promoters. Complementation analysis was assessed by growth, transcriptional activity, enzymatic activity, mRNA levels, specific detection of ArgC proteomic protein, and translational efficiency. The argC orthologs performed differently in each complementation, reflecting the diverse factors influencing gene expression and the ability of the ortholog product to function in a foreign metabolic background. Optimal complementation was directly related to sequence similarity with S. meliloti, and was inversely related to species signature, with M. loti argC showing the poorest performance, followed by R. etli and A. tumefaciens. Different copy numbers of genes and amounts of mRNA and protein were produced, even with genes transcribed from the same promoter, indicating that coding sequences play a role in the transcription and translation processes. These results provide relevant information for further genomic analyses and suggest that orthologous gene substitutions between closely related species are not completely functionally equivalent.
not annotated - annotated - LINNAEUS only
Genetic and mass spectrometry analyses of the unusual type IV-like pili of the archaeon Methanococcus maripaludis.
The structure of pili from the archaeon Methanococcus maripaludis is unlike that of any bacterial pili. However, genetic analysis of the genes involved in the formation of these pili has been lacking until this study. Pili were isolated from a nonflagellated (DeltaflaK) mutant and shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to consist primarily of subunits with an apparent molecular mass of 17 kDa. In-frame deletions were created in three genes, MMP0233, MMP0236, and MMP0237, which encode proteins with bacterial type IV pilin-like signal peptides previously identified by in silico methodology as likely candidates for pilus structural proteins. Deletion of MMP0236 or MMP0237 resulted in mutant cells completely devoid of pili on the cell surface, while deletion of the third pilin-like gene, MMP0233, resulted in cells greatly reduced in the number of pili on the surface. Complementation with the deleted gene in each case returned the cells to a piliated state. Surprisingly, mass spectrometry analysis of purified pili identified the major structural pilin as another type IV pilin-like protein, MMP1685, whose gene is located outside the first pilus locus. This protein was found to be glycosylated with an N-linked branched pentasaccharide glycan. Deletion and complementation analysis confirmed that MMP1685 is required for piliation.
not annotated - annotated - LINNAEUS only
XerCD-mediated site-specific recombination leads to loss of the 57-kilobase gonococcal genetic island.
Most strains of Neisseria gonorrhoeae carry the 57-kb gonococcal genetic island (GGI), as do a few strains of Neisseria meningitidis. The GGI is inserted into the chromosome at the dif site (difA) and is flanked by a partial repeat of the dif site (difB). Since dif is a sequence recognized by the site-specific recombinases XerC and XerD and the GGI shows evidence of horizontal acquisition, we hypothesized that the GGI may be acquired or lost by XerCD-mediated site-specific recombination. We show that while the GGI flanked by wild-type dif sites, difA and difB, is not readily lost from the gonococcal chromosome, the substitution of difB with another copy of difA allows the frequent excision and loss of the GGI. In mutants carrying two difA sites (difA(+) difA(+)), the GGI can be detected as an extrachromosomal circle that exists transiently. A mutation of xerD diminished GGI excision from the chromosome of a difA(+) difA(+) strain, while mutations in recA or type IV secretion genes had no effect on the loss of the GGI. These data indicate that the GGI is maintained by the replication of the chromosome and that GGI excision and loss are dependent upon the dif sequence and xerD. The detection of a circular form of the GGI in a wild-type strain suggests that GGI excision may occur naturally and could function to facilitate GGI transfer. These data suggest a model of GGI excision and loss explaining the absence of the GGI from some gonococcal strains and the maintenance of variant GGIs in some gonococcal and meningococcal isolates.
not annotated - annotated - LINNAEUS only
Opposing contributions of polynucleotide phosphorylase and the membrane protein NlpI to biofilm formation by Salmonella enterica serovar Typhimurium.
CsgD and cyclic-3',5'-di-guanylate are key regulators of biofilm formation in Salmonella enterica serovar Typhimurium. Our results show that polynucleotide phosphorylase and NlpI oppositely altered expression of CsgD. Polynucleotide phosphorylase and NlpI also had opposite effects on the expression of yjcC, which codes for a cyclic-3',5'-di-guanylate phosphodiesterase affecting CsgD expression.
not annotated - annotated - LINNAEUS only
Demographic consequences of adult sex ratio in a reintroduced hihi population.
1. Male-biased adult sex ratios are frequently observed in free-ranging populations and are known to cause changes in mating behaviours including increased male harassment of females, which can cause injury to females and/or alter female behaviour during breeding. 2. Although we can explain why such behaviours may evolve and have studied their impacts on individuals when it does, we know very little about the demographic consequences of harassment caused by changes in adult sex ratio. 3. Using a 12-year longitudinal data set of a free-living and endangered New Zealand passerine, the hihi (Notiomystis cincta), we show that a changing adult sex ratio has little or no effect on adult female survival or the number of fledglings produced per female. This is despite clear evidence of male harassment of breeding females when the sex ratio was male biased (up to three males per female). 4. The length of the study and major fluctuations in sex ratio observed made it possible to obtain narrow confidence or credible intervals for effect sizes, showing that any effect of sex ratio on demographic rates were small. 5. Our results provide rare empirical evidence for the demographic consequences of biased adult sex ratios in the wild and particularly in a conservation context.
not annotated - annotated - LINNAEUS only
Ebola haemorrhagic fever.
Ebola viruses are the causative agents of a severe form of viral haemorrhagic fever in man, designated Ebola haemorrhagic fever, and are endemic in regions of central Africa. The exception is the species Reston Ebola virus, which has not been associated with human disease and is found in the Philippines. Ebola virus constitutes an important local public health threat in Africa, with a worldwide effect through imported infections and through the fear of misuse for biological terrorism. Ebola virus is thought to also have a detrimental effect on the great ape population in Africa. Case-fatality rates of the African species in man are as high as 90%, with no prophylaxis or treatment available. Ebola virus infections are characterised by immune suppression and a systemic inflammatory response that causes impairment of the vascular, coagulation, and immune systems, leading to multiorgan failure and shock, and thus, in some ways, resembling septic shock.
not annotated - annotated - LINNAEUS only
Primate communities are structured more by dispersal limitation than by niches.
1. A major goal in community ecology is to identify mechanisms that govern the assembly and maintenance of ecological communities. Current models of metacommunity dynamics differ chiefly in the relative emphasis placed on dispersal limitation and niche differentiation as causal mechanisms structuring ecological communities. Herein we investigate the relative roles of these two mechanisms in structuring primate communities in Africa, South America, Madagascar and Borneo. 2. We hypothesized that if dispersal limitation is important in structuring communities, then community similarity should depend on geographical proximity even after controlling for ecological similarity. Conversely, if communities are assembled primarily through niche processes, then community similarity should be determined by ecological similarity regardless of geographical proximity. 3. We performed Mantel and partial Mantel tests to investigate correlations among primate community similarity, ecological distance and geographical distance. Results showed significant and strongly negative relationships between diurnal primate community similarity and both ecological similarity and geographical distance in Madagascar, but significant and stronger negative relationships between community similarity and geographical distance in African, South American and Bornean metacommunities. 4. We conclude that dispersal limitation is an important determinant of primate community structure and may play a stronger role in shaping the structure of some terrestrial vertebrate communities than niche differentiation. These patterns are consistent with neutral theory. We recommend tests of functional equivalence to determine the extent to which neutral theory may explain primate community composition.
not annotated - annotated - LINNAEUS only
Candidate chemosensory ionotropic receptors in a Lepidoptera.
A new family of candidate chemosensory ionotropic receptors (IRs) related to ionotropic glutamate receptors (iGluRs) was recently discovered in Drosophila melanogaster. Through Blast analyses of an expressed sequenced tag library prepared from male antennae of the noctuid moth Spodoptera littoralis, we identified 12 unigenes encoding proteins related to D. melanogaster and Bombyx mori IRs. Their full length sequences were obtained and the analyses of their expression patterns suggest that they were exclusively expressed or clearly enriched in chemosensory organs. The deduced protein sequences were more similar to B. mori and D. melanogaster IRs than to iGluRs and showed considerable variations in the predicted ligand-binding domains; none have the three glutamate-interacting residues found in iGluRs, suggesting different binding specificities. Our data suggest that we identified members of the insect IR chemosensory receptor family in S. littoralis and we report here the first demonstration of IR expression in Lepidoptera.
not annotated - annotated - LINNAEUS only
The health of prisoners.
More than 10 million people are incarcerated worldwide; this number has increased by about a million in the past decade. Mental disorders and infectious diseases are more common in prisoners than in the general population. High rates of suicide within prison and increased mortality from all causes on release have been documented in many countries. The contribution of prisons to illness is unknown, although shortcomings in treatment and aftercare provision contribute to adverse outcomes. Research has highlighted that women, prisoners aged 55 years and older, and juveniles present with higher rates of many disorders than do other prisoners. The contribution of initiatives to improve the health of prisoners by reducing the burden of infectious and chronic diseases, suicide, other causes of premature mortality and violence, and counteracting the cycle of reoffending should be further examined.
not annotated - annotated - LINNAEUS only
Genome-wide inventory of metal homeostasis-related gene products including a functional phytochelatin synthase in the hypogeous mycorrhizal fungus Tuber melanosporum.
Ectomycorrhizal fungi are thought to enhance mineral nutrition of their host plants and to confer increased tolerance toward toxic metals. However, a global view of metal homeostasis-related genes and pathways in these organisms is still lacking. Building upon the genome sequence of Tuber melanosporum and on transcriptome analyses, we set out to systematically identify metal homeostasis-related genes in this plant-symbiotic ascomycete. Candidate gene products (101) were subdivided into three major functional classes: (i) metal transport (58); (ii) oxidative stress defence (32); (iii) metal detoxification (11). The latter class includes a small-size metallothionein (TmelMT) that was functionally validated in yeast, and phytochelatin synthase (TmelPCS), the first enzyme of this kind to be described in filamentous ascomycetes. Recombinant TmelPCS was shown to support GSH-dependent, metal-activated phytochelatin synthesis in vitro and to afford increased Cd/Cu tolerance to metal hypersensitive yeast strains. Metal transporters, especially those related to Cu and Zn trafficking, displayed the highest expression levels in mycorrhizae, suggesting extensive translocation of both metals to root cells as well as to fungal metalloenzymes (e.g., laccase) that are strongly upregulated in symbiotic hyphae.
not annotated - annotated - LINNAEUS only
Structural and functional insights into Aeropyrum pernix OppA, a member of a novel archaeal OppA subfamily.
In this study we gain insight into the structural and functional characterization of the Aeropyrum pernix oligopeptide-binding protein (OppA(Ap)) previously identified from the extracellular medium of an Aeropyrum pernix cell culture at late stationary phase. OppA(Ap) showed an N-terminal Q32 in a pyroglutamate form and C-terminal processing at the level of a threonine-rich region probably involved in protein membrane anchoring. Moreover, the OppA(Ap) protein released into the medium was identified as a "nicked" form composed of two tightly associated fragments detachable only under strong denaturing conditions. The cleavage site E569-G570 seems be located on an exposed surface loop that is highly conserved in several three-dimensional (3D) structures of dipeptide/oligopeptide-binding proteins from different sources. Structural and biochemical properties of the nicked protein were virtually indistinguishable from those of the intact form. Indeed, studies of the entire bacterially expressed OppA(Ap) protein owning the same N and C termini of the nicked form supported these findings. Moreover, in the middle exponential growth phase, OppA(Ap) was found as an intact cell membrane-associated protein. Interestingly, the native exoprotein OppA(Ap) was copurified with a hexapeptide (EKFKIV) showing both lysines methylated and possibly originating from an A. pernix endogenous stress-induced lipoprotein. Therefore, the involvement of OppA(Ap) in the recycling of endogenous proteins was suggested to be a potential physiological function. Finally, a new OppA from Sulfolobus solfataricus, SSO1288, was purified and preliminarily characterized, allowing the identification of a common structural/genetic organization shared by all "true" archaeal OppA proteins of the dipeptide/oligopeptide class.
not annotated - annotated - LINNAEUS only
Differential responses of Bacillus subtilis rRNA promoters to nutritional stress.
The in vivo expression levels of four rRNA promoter pairs (rrnp(1)p(2)) of Bacillus subtilis were determined by employing single-copy lacZ fusions integrated at the amyE locus. The rrnO, rrnJ, rrnD, and rrnB promoters displayed unique growth rate regulation and stringent responses. Both lacZ activity and mRNA levels were highest for rrnO under all growth conditions tested, while rrnJ, rrnB, and rrnD showed decreasing levels of activity. During amino acid starvation induced by serine hydroxamate (SHX), only the strong rrnO and rrnJ promoters demonstrated stringent responses. Under the growth conditions used, the rrn promoters showed responses similar to the responses to carbon source limitation induced by alpha-methyl glucoside (alpha-MG). The ratio of P2 to P1 transcripts, determined by primer extension analysis, was high for the strong rrnO and rrnJ promoters, while only P2 transcripts were detected for the weak rrnD and rrnB promoters. Cloned P1 or P2 promoter fragments of rrnO or rrnJ were differentially regulated. In wild-type (relA(+)) and suppressor [relA(S)] strains under the conditions tested, only P2 responded to carbon source limitation by a decrease in RNA synthesis, correlating with an increase in (p)ppGpp levels and a decrease in the GTP concentration. The weak P1 promoter elements remain relaxed in the three genetic backgrounds [relA(+), relA, relA(S)] in the presence of alpha-MG. During amino acid starvation, P2 was stringently regulated in relA(+) and relA(S) cells, while only rrnJp(1) was also regulated, but to a lesser extent. Both the relA(+) and relA(S) strains showed (p)ppGpp accumulation after alpha-MG treatment but not after SHX treatment. These data reveal the complex nature of B. subtilis rrn promoter regulation in response to stress, and they suggest that the P2 promoters may play a more prominent role in the stringent response.
not annotated - annotated - LINNAEUS only
Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis.
The initiation of DNA replication requires the binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. DnaA also binds to many sites around the chromosome, outside oriC, and acts as a transcription factor at several of these. In low-G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB also are required to load the replicative helicase outside oriC during replication restart, independently of DnaA. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in Bacillus subtilis. This association was dependent on DnaA, and the order of recruitment was the same as that at oriC, but it was independent of a functional oriC and suggests that DnaD and DnaB do not require open complex formation for the stable association with DNA. These secondary binding regions for DnaA could be serving as a reservoir for excess DnaA, DnaD, and DnaB to help properly regulate replication initiation and perhaps are analogous to the proposed function of the datA locus in Escherichia coli. Alternatively, DnaD and DnaB might modulate the activity of DnaA at the secondary binding regions. All three of these proteins are widely conserved and likely have similar functions in a range of organisms.
not annotated - annotated - LINNAEUS only
A LytM domain dictates the localization of proteins to the mother cell-forespore interface during bacterial endospore formation.
A large number of proteins are known to reside at specific subcellular locations in bacterial cells. However, the molecular mechanisms by which many of these proteins are anchored at these locations remains unclear. During endospore formation in Bacillus subtilis, several integral membrane proteins are located specifically at the interface of the two adjacent cells of the developing sporangium, the mother cell and forespore. The mother cell membrane protein SpoIIIAH recognizes the cell-cell interface through an interaction with the forespore membrane protein SpoIIQ, and then the other proteins are positioned there by the SpoIIIAH-SpoIIQ complex. In this study, we investigated the molecular mechanisms underlying the formation of the SpoIIIAH-SpoIIQ complex. Using gel filtration chromatography and isothermal titration calorimetry, we measured the binding parameters that characterize the SpoIIIAH-SpoIIQ interaction in vitro. We also demonstrated that the interaction of SpoIIIAH and SpoIIQ is governed by their YscJ and degenerate LytM domains, respectively. Therefore, the LytM domain of SpoIIQ provides the positional cue that dictates the localization of mother cell membrane proteins to the mother cell-forespore interface.
not annotated - annotated - LINNAEUS only
Spatial regulation of histidine kinases governing biofilm formation in Bacillus subtilis.
Bacillus subtilis is able to form architecturally complex biofilms on solid medium due to the production of an extracellular matrix. A master regulator that controls the expression of the genes involved in matrix synthesis is Spo0A, which is activated by phosphorylation via a phosphorelay involving multiple histidine kinases. Here we report that four kinases, KinA, KinB, KinC, and KinD, help govern biofilm formation but that their contributions are partially masked by redundancy. We show that the kinases fall into two categories and that the members of each pair (one pair comprising KinA and KinB and the other comprising KinC and KinD) are partially redundant with each other. We also show that the kinases are spatially regulated: KinA and KinB are active principally in the older, inner regions of the colony, and KinC and KinD function chiefly in the younger, outer regions. These conclusions are based on the morphology of kinase mutants, real-time measurements of gene expression using luciferase as a reporter, and confocal microscopy using a fluorescent protein as a reporter. Our findings suggest that multiple signals from the older and younger regions of the colony are integrated by the kinases to determine the overall architecture of the biofilm community.
not annotated - annotated - LINNAEUS only
Contributions of multiple binding sites and effector-independent binding to CodY-mediated regulation in Bacillus subtilis.
CodY is a branched-chain amino acid-responsive transcriptional regulator that controls, directly or indirectly, the expression of more than 100 genes and operons in Bacillus subtilis. Using DNase I footprinting and gel-shift experiments, we identified two CodY-binding regions upstream of a B. subtilis gene (bcaP, previously known as yhdG) that encodes a transporter of branched-chain amino acids. Mutational analysis revealed that both CodY-binding regions contribute to repression in vivo and do so independently of each other. Thus, a single CodY-binding site is apparently sufficient for substantial CodY-dependent regulation. By analyzing affinities of wild-type and mutant CodY-binding sites for CodY and their regulation by wild-type CodY and forms of CodY with various levels of activation by branched-chain amino acids, we concluded that unliganded CodY cannot repress transcription in vivo and that the level of endogenously produced effectors is sufficient for CodY-mediated regulation of promoters with stronger sites. Because the sites with higher affinity apparently respond to lower concentrations of CodY effectors and saturate faster as the concentrations of effectors increase, having two sites of binding with different affinities for CodY permits a promoter to respond to a wider range of intracellular concentrations of effectors.
not annotated - annotated - LINNAEUS only
Differences in MinC/MinD sensitivity between polar and internal Z rings in Escherichia coli.
In Escherichia coli the Z ring has the potential to assemble anywhere along the cell length but is restricted to midcell by the action of negative regulatory systems, including Min. In the current model for the Min system, the MinC/MinD division inhibitory complex is evenly distributed on the membrane and can disrupt Z rings anywhere in the cell; however, MinE spatially regulates MinC/MinD by restricting it to the cell poles, thus allowing Z ring formation at midcell. This model assumes that Z rings formed at different cellular locations have equal sensitivity to MinC/MinD in the absence of MinE. However, here we report evidence that differences in MinC/MinD sensitivity between polar and nonpolar Z rings exists even when there is no MinE. MinC/MinD at proper levels is able to block minicell production in Deltamin strains without increasing the cell length, indicating that polar Z rings are preferentially blocked. In the FtsZ-I374V strain (which is resistant to MinC(C)/MinD), wild-type morphology can be easily achieved with MinC/MinD in the absence of MinE. We also show that MinC/MinD at proper levels can rescue the lethal phenotype of a min slmA double deletion mutant, which we think is due to the elimination of polar Z rings (or FtsZ structures), which frees up FtsZ molecules for assembly of Z rings at internal sites to rescue division and growth. Taken together, these data indicate that polar Z rings are more susceptible to MinC/MinD than internal Z rings, even when MinE is absent.
not annotated - annotated - LINNAEUS only
Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K-12 strains.
The phenotypic plasticity of global regulatory networks provides bacteria with rapid acclimation to a wide range of environmental conditions, while genetic changes in those networks provide additional flexibility as bacteria evolve across long time scales. We previously identified mutations in the global regulator-encoding gene fis that enhanced organismal fitness during a long-term evolution experiment with Escherichia coli. To gain insight into the effects of these mutations, we produced two-dimensional protein gels with strains carrying different fis alleles, including a beneficial evolved allele and one with an in-frame deletion. We found that Fis controls the expression of the major porin-encoding gene ompF in the E. coli B-derived ancestral strain used in the evolution experiment, a relationship that has not been described before. We further showed that this regulatory connection evolved over two different time scales, perhaps explaining why it was not observed before. On the longer time scale, we showed that this regulation of ompF by Fis is absent from the more widely studied K-12 strain and thus is specific to the B strain. On a shorter time scale, this regulatory linkage was lost during 20,000 generations of experimental evolution of the B strain. Finally, we mapped the Fis binding sites in the ompF regulatory region, and we present a hypothetical model of ompF expression that includes its other known regulators.
not annotated - annotated - LINNAEUS only
Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli.
Iron acquisition in aerobic habitats is complicated by the low solubility of ferric hydroxides. Siderophores that bind ferric iron with high affinity are used to mobilize iron. The reduction of ferric iron to the ferrous form can be coupled to the release of iron from siderophores. Iron is also stored intracellularly as a ferric mineral in proteins, such as ferritin, and must be reduced during release. In Escherichia coli, the yqjH gene encodes a putative ferric siderophore reductase that is also part of the Fur regulon. Here we show that YqjH has ferric reductase activity and is required for iron homeostasis in E. coli. Divergently transcribed from yqjH is the yqjI gene, which encodes a novel member of the winged-helix family of transcriptional regulators and also contains an N-terminal extension similar to the Ni(2+)-binding C-terminal tail of SlyD. Deletion of yqjI leads to constitutive high-level activity of the yqjH and yqjI promoters. Purified YqjI binds inverted repeat target sequences within the yqjH and yqjI promoters. We also observed that YqjI-dependent transcriptional repression is reduced when cells are exposed to elevated nickel levels, resulting in increased expression of yqjH and yqjI. YqjI binding to nickel or iron reduces YqjI DNA-binding activity in vitro. Furthermore, we found that elevated nickel stress levels disrupt iron homeostasis in E. coli and that deletion of yqjH increases nickel toxicity. Our results suggest that the YqjI protein controls expression of yqjH to help maintain iron homeostasis under conditions (such as elevated cellular nickel levels) that disrupt iron metabolism.
not annotated - annotated - LINNAEUS only
Genome copy numbers and gene conversion in methanogenic archaea.
Previous studies revealed that one species of methanogenic archaea, Methanocaldococcus jannaschii, is polyploid, while a second species, Methanothermobacter thermoautotrophicus, is diploid. To further investigate the distribution of ploidy in methanogenic archaea, species of two additional genera-Methanosarcina acetivorans and Methanococcus maripaludis-were investigated. M. acetivorans was found to be polyploid during fast growth (t(D) = 6 h; 17 genome copies) and oligoploid during slow growth (doubling time = 49 h; 3 genome copies). M. maripaludis has the highest ploidy level found for any archaeal species, with up to 55 genome copies in exponential phase and ca. 30 in stationary phase. A compilation of archaeal species with quantified ploidy levels reveals a clear dichotomy between Euryarchaeota and Crenarchaeota: none of seven euryarchaeal species of six genera is monoploid (haploid), while, in contrast, all six crenarchaeal species of four genera are monoploid, indicating significant genetic differences between these two kingdoms. Polyploidy in asexual species should lead to accumulation of inactivating mutations until the number of intact chromosomes per cell drops to zero (called "Muller's ratchet"). A mechanism to equalize the genome copies, such as gene conversion, would counteract this phenomenon. Making use of a previously constructed heterozygous mutant strain of the polyploid M. maripaludis we could show that in the absence of selection very fast equalization of genomes in M. maripaludis took place probably via a gene conversion mechanism. In addition, it was shown that the velocity of this phenomenon is inversely correlated to the strength of selection.
not annotated - annotated - LINNAEUS only
Membrane topology and DNA-binding ability of the Streptococcal CpsA protein.
Many streptococcal pathogens require a polysaccharide capsule for survival in the host during systemic infection. The highly conserved CpsA protein is proposed to be a transcriptional regulator of capsule production in streptococci, although the regulatory mechanism is unknown. Hydropathy plots of CpsA predict an integral membrane protein with 3 transmembrane domains and only 27 cytoplasmic residues, whereas other members of the LytR_cpsA_psr protein family are predicted to have a single transmembrane domain. This unique topology, with the short cytoplasmic domain, membrane localization, and large extracellular domain, suggests a novel mechanism of transcriptional regulation. Therefore, to determine the actual membrane topology of CpsA, specific protein domains were fused to beta-galactosidase or alkaline phosphatase. Enzymatic assays confirmed that the predicted membrane topology for CpsA is correct. To investigate how this integral membrane protein may be functioning in regulation of capsule transcription, purified full-length and truncated forms of CpsA were used in electrophoretic mobility shift assays to characterize the ability to bind the capsule operon promoter. Assays revealed that full-length, purified CpsA protein binds specifically to DNA containing the capsule promoter region. Furthermore, the large extracellular domain is not required for DNA binding, but all cytoplasmic regions of CpsA are necessary and sufficient for specific binding to the capsule operon promoter. This is the first demonstration of a member of this protein family interacting with its target DNA. Taken together, CpsA, as well as other members of the LytR_cpsA_psr protein family, appears to utilize a unique mechanism of transcriptional regulation.
not annotated - annotated - LINNAEUS only
Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica.
We identified the biosynthetic gene clusters of the siderophore nocobactin NA. The nbt clusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing of Nocardia farcinica IFM 10152, consist of 10 genes separately located at two genomic regions. The gene organization of the nbt clusters and the predicted functions of the nbt genes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structure of nocobactin NA. Disruptions of the nbtA and nbtE genes, respectively, reduced and abolished the productivity of nocobactin NA. The heterologous expression of the nbtS gene revealed that this gene encoded a salicylate synthase. These results indicate that the nbt clusters are responsible for the biosynthesis of nocobactin NA. We also found putative IdeR-binding sequences upstream of the nbtA, -G, -H, -S, and -T genes, whose expression was more than 10-fold higher in the low-iron condition than in the high-iron condition. These results suggest that nbt genes are regulated coordinately by IdeR protein in an iron-dependent manner. The DeltanbtE mutant was found to be impaired in cytotoxicity against J774A.1 cells, suggesting that nocobactin NA production is required for virulence of N. farcinica.
not annotated - annotated - LINNAEUS only
Acyl-homoserine lactone binding to and stability of the orphan Pseudomonas aeruginosa quorum-sensing signal receptor QscR.
The Pseudomonas aeruginosa transcription factor QscR responds to a variety of fatty acyl-homoserine lactones (HSLs), including N-3-oxododecanoyl-HSL (3OC12-HSL), which is produced and detected by the P. aeruginosa quorum-sensing circuit LasI and LasR. As is true for LasR and many other acyl-HSL-dependent transcription factors, production of soluble QscR in sufficient amounts for purification requires growth of recombinant bacteria in the presence of an appropriate acyl-HSL. QscR is thought to bind 3OC12-HSL relatively weakly compared to LasR, and unlike LasR, binding of purified QscR to target DNA was shown to strongly depend on exogenously added 3OC12-HSL. We show that purified QscR is dimeric at sufficiently high concentrations and monomeric at lower concentrations. Furthermore, QscR bound 3OC12-HSL more tightly than previously believed. Purified QscR retained 3OC12-HSL, and at sufficiently high concentrations, it bound target DNA in the absence of added 3OC12-HSL. We also obtained soluble QscR from recombinant Escherichia coli grown in the presence of N-3-oxohexanoyl-HSL (3OC6-HSL) instead of 3OC12-HSL, and because 3OC6-HSL bound much more loosely to QscR than other acyl-HSLs tested, we were able to exchange 3OC6-HSL with other acyl-HSLs in vitro and then estimate binding affinities of QscR for different acyl-HSLs and for target DNA. Our data support a model whereby QscR polypeptides fold properly in the absence of an acyl-HSL, but soluble, acyl-HSL-free QscR does not accumulate because it is subject to rapid aggregation or proteolysis.
not annotated - annotated - LINNAEUS only
Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1.
Streptococcus pneumoniae causes several diseases, including pneumonia, septicemia, and meningitis. Phage Dp-1 is one of the very few isolated virulent S. pneumoniae bacteriophages, but only a partial characterization is currently available. Here, we confirmed that Dp-1 belongs to the family Siphoviridae. Then, we determined its complete genomic sequence of 56,506 bp. It encodes 72 open reading frames, of which 44 have been assigned a function. We have identified putative promoters, Rho-independent terminators, and several genomic clusters. We provide evidence that Dp-1 may be using a novel DNA replication system as well as redirecting host protein synthesis through queuosine-containing tRNAs. Liquid chromatography-mass spectrometry analysis of purified phage Dp-1 particles identified at least eight structural proteins. Finally, using comprehensive yeast two-hybrid screens, we identified 156 phage protein interactions, and this intraviral interactome was used to propose a structural model of Dp-1.
not annotated - annotated - LINNAEUS only
Role of the F1 region in the Escherichia coli aerotaxis receptor Aer.
In Escherichia coli, the aerotaxis receptor Aer is an atypical receptor because it senses intracellular redox potential. The Aer sensor is a cytoplasmic, N-terminal PAS domain that is tethered to the membrane by a 47-residue F1 linker. Here we investigated the function, topology, and orientation of F1 by employing random mutagenesis, cysteine scanning, and disulfide cross-linking. No native residue was obligatory for function, most deleterious substitutions had radically different side chain properties, and all F1 mutants but one were functionally rescued by the chemoreceptor Tar. Cross-linking studies were consistent with the predicted alpha-helical structure in the N-terminal F1 region and demonstrated trigonal interactions among the F1 linkers from three Aer monomers, presumably within trimer-of-dimer units, as well as binary interactions between subunits. Using heterodimer analyses, we also demonstrated the importance of arginine residues near the membrane interface, which may properly anchor the Aer protein in the membrane. By incorporating these data into a homology model of Aer, we developed a model for the orientation of the Aer F1 and PAS regions in an Aer lattice that is compatible with the known dimensions of the chemoreceptor lattice. We propose that the F1 region facilitates the orientation of PAS and HAMP domains during folding and thereby promotes the stability of the PAS and HAMP domains in Aer.
not annotated - annotated - LINNAEUS only
Genome-wide identification of Phytophthora sojae SNARE genes and functional characterization of the conserved SNARE PsYKT6.
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are central components of the machinery mediating membrane fusion and key factors for vesicular trafficking in all eukaryotic cells. Taking advantage of the available whole genome sequence of the oomycete plant pathogen Phytophthora sojae, 35 genes encoding putative SNARE proteins were identified in the genome of this organism. PsYKT6, one of the most conserved SNARE proteins, was functionally characterized by homology-dependent gene silencing. The phenotype analysis showed that PsYKT6 is important for proper asexual development, sexual reproduction, and pathogenesis on host soybean cultivars.
not annotated - annotated - LINNAEUS only
Oesophagogastric junction adenocarcinoma: which therapeutic approach?
Gastric and oesophageal cancers are among the leading causes of cancer-related death worldwide. By contrast with the decreasing prevalence of gastric cancer, incidence and prevalence of oesophagogastric junction adenocarcinoma (OGJA) are rising rapidly in developed countries. We provide an update about treatment strategies for resectable OGJA. Here we review findings from the latest randomised trials and meta-analyses, and propose guidelines regarding endoscopic, surgical, and perioperative treatments. Through a team approach, members from all diagnostic and therapeutic disciplines, such as gastroenterologists, surgeons, oncologists, radiologists, and radiotherapists, can effectively administer a range of treatment modalities.
not annotated - annotated - LINNAEUS only
Mating differentiation in Cryptococcus neoformans is negatively regulated by the Crk1 protein kinase.
Cryptococcus neoformans is a heterothallic basidiomycete that grows vegetatively as yeast and filamentous hyphae are produced in the sexual state. Previous studies have shown that C. neoformans Cwc1 and Cwc2 are two central photoregulators which form a complex to inhibit the production of sexual filaments upon light treatment. To reveal the detailed regulatory mechanisms, a genome wide mutagenesis screen was conducted and components in the Cwc1/Cwc2 complex mediated pathway have been identified. In this study, one suppressor mutant, DJ22, is characterized and T-DNA is found to disrupt the C. neoformans CRK1 gene, a homologue of Saccharomyces cerevisiae IME2 and Ustilago maydis crk1. Ime2 is a meiosis-specific gene with the conserved Ser/Thr kinase domain and TXY dual phosphorylation site. Consistent with the findings of other suppressors in our screen, C. neoformans Crk1 plays a negative role in the mating process. Dikaryotic filaments, basidia, and basidiospores are produced earlier in the crk1 mutant crosses and mating efficiency is also increased. Artificial elevation of the CRK1 mRNA level inhibits mating. Interestingly, monokaryotic fruiting is defective both in the MATalpha crk1 mutant and CRK1 overexpression strains. Our studies demonstrate that C. neoformans CRK1 gene functions as a negative regulator in the mating differentiation.
not annotated - annotated - LINNAEUS only
"Slime molds" among the Tubulinea (Amoebozoa): molecular systematics and taxonomy of Copromyxa.
Copromyxa protea is a dung-inhabiting amoeboid organism that aggregates to form simple macroscopic fruiting structures, sorocarps, which are composed of a single cell type. In a recent effort to find the phylogenetic positions of the less well-known sorocarpic protists considered to be "cellular slime molds," or aggregatively fruiting amoebae, we isolated C. protea and sequenced the nuclear-encoded small subunit ribosomal RNA gene from four samples collected from cattle farms in the central USA. Phylogenetic analyses of these data place C. protea in the eukaryotic supergroup Amoebozoa together with the Tubulinea, in which there has been no previous report of an aggregative fruiting habit. This is consistent with the morphology of the trophozoites. In fact, Copromyxa protea is found to be very closely related to Hartmannella cantabrigiensis and to a since lost amoeba isolate, Hartmannella sp. 4/3Da/10. This new grouping of Copromyxa+H. cantabrigiensis is sister to Glaeseria, which together are sister to the Amoebidae (Amoeba+Chaos). We suggest renaming, H. cantabrigiensis as C. cantabrigiensis and designate isolate 4/3Da/10 as C. protea. Future work is needed to see if these newly assigned members of the genus Copromyxa also show evidence of an ability to fruit.
not annotated - annotated - LINNAEUS only
Improved accuracy of the transcriptional profiling method of age grading in Aedes aegypti mosquitoes under laboratory and semi-field cage conditions and in the presence of Wolbachia infection.
Transcriptional profiling is an effective method of predicting age in the mosquito Aedes aegypti in the laboratory, however, its effectiveness is limited to younger mosquitoes. To address this we used a microarray to identify new gene candidates that show significant expression changes in older mosquitoes. These genes were then used to create a revised model, which upon evaluation in both laboratory and semi-field conditions, proved to have improved accuracy overall and for older mosquitoes. In association with the development of symbiont-based control strategies for Ae. aegypti, we also tested the model's accuracy for Wolbachia-infected mosquitoes and found no decline in performance. Our findings suggest that the new model is a robust and powerful tool for age determination in Australian Ae. aegypti populations.
not annotated - annotated - LINNAEUS only
Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli.
Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.
not annotated - annotated - LINNAEUS only
The three vibrio cholerae chromosome II-encoded ParE toxins degrade chromosome I following loss of chromosome II.
Three homologues of the plasmid RK2 ParDE toxin-antitoxin system are present in the Vibrio cholerae genome within the superintegron on chromosome II. Here we found that these three loci-two of which have identical open reading frames and regulatory sequences-encode functional toxin-antitoxin systems. The ParE toxins inhibit bacterial division and reduce viability, presumably due to their capacity to damage DNA. The in vivo effects of ParE1/3 mimic those of ParE2, which we have previously demonstrated to be a DNA gyrase inhibitor in vitro, suggesting that ParE1/3 is likewise a gyrase inhibitor, despite its relatively low degree of sequence identity. ParE-mediated DNA damage activates the V. cholerae SOS response, which in turn likely accounts for ParE's inhibition of cell division. Each toxin's effects can be prevented by the expression of its cognate ParD antitoxin, which acts in a toxin-specific fashion both to block toxicity and to repress the expression of its parDE operon. Derepression of ParE activity in DeltaparAB2 mutant V. cholerae cells that have lost chromosome II contributes to the prominent DNA degradation that accompanies the death of these cells. Overall, our findings suggest that the ParE toxins lead to the postsegregational killing of cells missing chromosome II in a manner that closely mimics postsegregational killing mediated by plasmid-encoded homologs. Thus, the parDE loci aid in the maintenance of the integrity of the V. cholerae superintegron and in ensuring the inheritance of chromosome II.
not annotated - annotated - LINNAEUS only
Climatic constraints on wintering bird distributions are modified by urbanization and weather.
1. Ecologists have long been interested in the role of climate in shaping species' ranges, and in recent years, this relationship has taken on greater significance because of the need for accurate predictions of the effects of climate change on wildlife populations. Bioclimatic relationships, however, are potentially complicated by various environmental factors operating at multiple spatial and temporal scales. Here, we test the hypothesis that climatic constraints on bird distributions are modified by species-specific responses to weather, urbanization and use of supplemental food. 2. Our analyses focused on 18 bird species with data from over 3000 sites across the north-eastern United States and adjacent Canadian provinces. We use hierarchal occupancy modelling to quantify the effects of short-term weather variation and surrounding urbanization on food stress and probabilities of detection, and how these fine-scale changes modify the role that climate has on the distributions of wintering bird populations at regional scales. 3. Examining site occupancy and supplemental food use across the study region, we found that average minimum temperature was an important factor limiting bird distributions, supporting the hypothesis that the occupancy of wintering birds is limited by climatic constraints. We found that 15 of 18 species (83%) were more energetically stressed (had a higher likelihood of visiting a feeder station) as minimum temperature declined from the seasonal average. Because we found these patterns in populations that regularly visit supplemental food sites and were likely not food-limited, we suggest that resource availability is less important than climate in constraining wintering bird distributions. Across a winter season, local within-winter extinction probabilities were lower and colonization probabilities higher at warmer sites supporting the role of climate-mediated range shifts. Importantly, however, these relationships were modified by the degree of urbanization and species' abilities to persist in human-modified landscapes. 4. Our results suggest that urbanization and behavioural adaptation can modify the role of climate on bird ranges and should be included in future analyses of range shifts because of climate change.
not annotated - annotated - LINNAEUS only
Molecular structure of the prothoracicotropic hormone gene in the northern house mosquito, Culex pipiens, and its expression analysis in association with diapause and blood feeding.
We cloned the gene that encodes prothoracicotropic hormone (PTTH) in the northern house mosquito, Culex pipiens, and investigated its expression profile in short-day (diapause-destined) and long-day (nondiapause-destined) individuals from the fourth-instar larval stage to 2 months of adulthood, as well as after a blood meal. The deduced C. pipiens PTTH (Cupip-PTTH) amino acid sequence contains seven cysteines with a specific spacing pattern. Sequence alignment suggests that Cupip-PTTH is 23% identical to Drosophila melanogaster PTTH, but is >=59% identical to the PTTHs of other mosquitoes. Cupip-PTTH has structural characteristics similar to those of Bombyx mori PTTH and some vertebrate nerve growth factors with cysteine-knot motifs. PTTH transcripts exhibit a daily cycling profile during the final (fourth) larval instar, with peak abundance occurring late in the scotophase. The fourth-larval instar stage is one day longer in short-day larvae than in long-day larvae, resulting in larger larvae and adults. This additional day of larval development is associated with one extra PTTH cycle. No cycling was observed in pupae, but PTTH transcripts were slightly higher in short-day pupae than in long-day pupae throughout much of the pupal stage. PTTH expression persisted at a nearly constant level in diapausing adult females for the first month but then dropped by -50%, while expression decreased at the beginning of adulthood in nondiapausing females and then remained at a low level as long as the females were denied a blood meal. However, when nondiapausing females were offered a blood meal, PTTH transcripts rose approximately 7 fold in 2 h and remained elevated for 24 h. A few diapausing females (-10%) will take a blood meal when placed in close proximity to a host, but much of the blood is ejected and such meals do not result in mature eggs. Yet, elevated PTTH mRNA expression was also observed in diapausing females that were force fed. Our results thus point to several distinctions in PTTH expression between short-day and long-day mosquitoes, but both types of females responded to a blood meal by elevating levels of PTTH mRNA.
not annotated - annotated - LINNAEUS only
Molecular events of apical bud formation in white spruce, Picea glauca.
Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome-level changes that occur during bud formation of white spruce [Picea glauca (Moench) Voss], a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day-induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod-responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for abscisic acid (ABA), cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues. These findings provide a temporal roadmap of bud formation in white spruce.
not annotated - annotated - LINNAEUS only
Linking irradiance-induced changes in pit membrane ultrastructure with xylem vulnerability to cavitation.
The effect of shading on xylem hydraulic traits and xylem anatomy was studied in hybrid poplar (Populus trichocarpa x deltoides, clone H11-11). Hydraulic measurements conducted on stem segments of 3-month-old saplings grown in shaded (SH) or control light (C) conditions indicated that shading resulted in more vulnerable and less efficient xylem. Air is thought to enter vessels through pores in inter-vessel pit membranes, thereby nucleating cavitation. Therefore, we tested if the ultrastructure and/or chemistry of pit membranes differed in SH and C plants. Transmission electron micrographs revealed that pit membranes were thinner in SH, which was paralleled by lower compound middle lamella thickness. Immunolabelling with JIM5 and JIM7 monoclonal antibodies surprisingly indicated that pectic homogalacturonans were not present in the mature pit membrane regardless of the light treatment. Porosity measurements conducted with scanning electron microscopy were significantly affected by the method used for sample dehydration. Drying through a gradual ethanol series seems to be a better alternative to drying directly from a hydrated state for pit membrane observations in poplar. Scanning electron microscopy based estimates of pit membrane porosity probably overestimated real porosity as suggested by the results from the 'rare pit' model.
not annotated - annotated - LINNAEUS only
Sensing embolism in xylem vessels: the role of sucrose as a trigger for refilling.
Refilling of embolized vessels requires a source of water and the release of energy stored in xylem parenchyma cells. Past evidence suggests that embolism presence can trigger a biological response that is switched off upon successful vessel refilling. As embolism formation is a purely physical process and most biological triggers rely on chemical sensors, we hypothesized that accumulation of osmotic compounds in walls of embolized vessels are involved in the embolism sensing mechanism. Analysis of Populus trichocarpa's response to infiltration of sucrose, monosaccharides, polyethylene glycol and potassium chloride into the xylem revealed that only presence of sucrose resulted in a simultaneous physiological and molecular response similar to that induced by embolism. This response included reduction of the starch pool in xylem parenchyma cells and significant correlation of gene expression from aquaporins, amylases and sugar transporter families. The work provides evidence of the ability of plants to sense embolism and suggests that sucrose concentration is the stimulus that allows plants to trigger a biological response to embolism.
not annotated - annotated - LINNAEUS only
Constrained preferences in nitrogen uptake across plant species and environments.
Knowledge of determining factors for nitrogen uptake preferences and how they are modified in changing environments are critical to understand ecosystem nitrogen cycling and to predict plant responses to future environmental changes. Two ^1^5N tracer experiments utilizing a unique differential labelled nitrogen source were employed in both African savannas and greenhouse settings. The results demonstrated that nitrogen uptake preferences were constrained by the climatic conditions. As mainly indicated by root delta^1^5N signatures at 1:1 ammonium/nitrate ratio, in the drier environments, plants preferred nitrate and in the wetter environments they preferred ammonium. Nitrogen uptake preferences were different across different ecosystems (e.g. from drier to wetter environments) even for the same species. More significantly, our experiments showed that the plant progeny continued to exhibit the same nitrogen preference as the parent plants in the field, even when removed from their native environment and the nitrogen source was changed dramatically. The climatic constraint of nitrogen uptake preference is likely influenced by ammonium/nitrate ratios in the native habitats of the plants. The constancy in nitrogen preference has important implications in predicting the success of plant communities in their response to climate change, to seed bank use and to reforestation efforts.
not annotated - annotated - LINNAEUS only
Molecular identification of sequestered diatom chloroplasts and kleptoplastidy in foraminifera.
Kleptoplastidy is the ability of heterotrophic organisms to preserve chloroplasts of algal preys they eat and partially digest. As the sequestered chloroplasts stay functional for months, the "host" becomes photosynthetically active. Although remaining a marginal process, kleptoplastidy was observed in different protist lineages, including foraminifera. Previous studies showed at least eight species of the foraminiferal genera Haynesina and Elphidium grazing on diatoms and husbanding their chloroplasts. In order to characterize more precisely the origin of kleptochloroplasts in these genera, we obtained 1027 chloroplastic 16S rDNA sequences from 13 specimens of two Haynesina and five Elphidium species. We identified the foraminiferal kleptochloroplasts using a reference phylogeny made of 87 chloroplastic sequences of known species of diatoms and brown algae. All the analyzed specimens were performing kleptoplastidy and according to our phylogenetic analyses they seem to retain exclusively chloroplasts of diatom origin. There is no apparent specificity for the type of diatom from which chloroplasts originated, however some foraminiferal species seem to accept a wider range of diatoms than others. Possibly the diversity of kleptochloroplasts depends on the type of diatoms the foraminiferans feed on.
not annotated - annotated - LINNAEUS only
Constitutive expression of the maltoporin LamB in the absence of OmpR damages the cell envelope.
Cells experience multiple environmental stimuli simultaneously. To survive, they must respond accordingly. Unfortunately, the proper response to one stress easily could make the cell more susceptible to a second coexistent stress. To deal with such a problem, a cell must possess a mechanism that balances the need to respond simultaneously to both stresses. Our recent studies of ompR malT(Con) double mutants show that elevated expression of LamB, the outer membrane porin responsible for maltose uptake, causes cell death when the osmoregulator OmpR is disabled. To obtain insight into the nature of the death experienced by ompR malT(Con) mutants, we described the death process. On the basis of microscopic and biochemical approaches, we conclude that death results from a loss of membrane integrity. On the basis of an unbiased genome-wide search for suppressor mutations, we conclude that this loss of membrane integrity results from a LamB-induced envelope stress that the cells do not sufficiently perceive and thus do not adequately accommodate. Finally, we conclude that this envelope stress involves an imbalance in the lipopolysaccharide/porin composition of the outer membrane and an increased requirement for inorganic phosphate.
not annotated - annotated - LINNAEUS only
Regulation of nleA in Shiga toxin-producing Escherichia coli O84:H4 strain 4795/97.
Many Shiga toxin-producing Escherichia coli (STEC) strains express a type III secretion system (TTSS) encoded by the locus of enterocyte effacement (LEE). Using the TTSS, STEC is able to inject effector proteins directly into eukaryotic host cells, where they cause characteristic attaching and effacing (A/E) lesions. In addition to the LEE-encoded effectors, a number of non-LEE-encoded effectors, located on phage-associated elements, have been described. One of them, the non-LEE-encoded effector A (NleA), is widely distributed among pathogenic E. coli. In this study, we investigated the influence of environmental conditions on the expression of the phage-encoded effector nleA gene (designated nleA(4795)) present in STEC O84:H4 strain 4795/97. We demonstrated that a particular NaCl concentration and starvation stress increase the activity of the nleA(4795) promoter. Moreover, several regulators that control nleA(4795) expression were identified. The involvement of the LEE regulators Ler, GrlA, and GrlR show that nleA(4795) is integrated in the LEE regulation circuit. Furthermore, the binding of Ler to sequences upstream of nleA(4795) underlined these findings.
not annotated - annotated - LINNAEUS only
Bacillus anthracis sin locus and regulation of secreted proteases.
Bacillus anthracis shares many regulatory loci with the nonpathogenic Bacillus species Bacillus subtilis. One such locus is sinIR, which in B. subtilis controls sporulation, biofilm formation, motility, and competency. As B. anthracis is not known to be motile, to be naturally competent, or to readily form biofilms, we hypothesized that the B. anthracis sinIR regulon is distinct from that of B. subtilis. A genome-wide expression microarray analysis of B. anthracis parental and sinR mutant strains indicated limited convergence of the B. anthracis and B. subtilis SinR regulons. The B. anthracis regulon includes homologues of some B. subtilis SinR-regulated genes, including the signal peptidase gene sipW near the sinIR locus and the sporulation gene spoIIE. The B. anthracis SinR protein also negatively regulates transcription of genes adjacent to the sinIR locus that are unique to the Bacillus cereus group species. These include calY and inhA1, structural genes for the metalloproteases camelysin and immune inhibitor A1 (InhA1), which have been suggested to be associated with virulence in B. cereus and B. anthracis, respectively. Electrophoretic mobility shift assays revealed direct binding of B. anthracis SinR to promoter DNA from strongly regulated genes, such as calY and sipW, but not to the weakly regulated inhA1 gene. Assessment of camelysin and InhA1 levels in culture supernates from sinR-, inhA1-, and calY-null mutants showed that the concentration of InhA1 in the culture supernatant is inversely proportional to the concentration of camelysin. Our data are consistent with a model in which InhA1 protease levels are controlled at the transcriptional level by SinR and at the posttranslational level by camelysin.
not annotated - annotated - LINNAEUS only
DifA, a methyl-accepting chemoreceptor protein-like sensory protein, uses a novel signaling mechanism to regulate exopolysaccharide production in Myxococcus xanthus.
DifA is a methyl-accepting chemotaxis protein (MCP)-like sensory transducer that regulates exopolysaccharide (EPS) production in Myxococcus xanthus. Here mutational analysis and molecular biology were used to probe the signaling mechanisms of DifA in EPS regulation. We first identified the start codon of DifA experimentally; this identification extended the N terminus of DifA for 45 amino acids (aa) from the previous bioinformatics prediction. This extension helped to address the outstanding question of how DifA receives input signals from type 4 pili without a prominent periplasmic domain. The results suggest that DifA uses its N-terminus extension to sense an upstream signal in EPS regulation. We suggest that the perception of the input signal by DifA is mediated by protein-protein interactions with upstream components. Subsequent signal transmission likely involves transmembrane signaling instead of direct intramolecular interactions between the input and the output modules in the cytoplasm. The basic functional unit of DifA for signal transduction is likely dimeric as mutational alteration of the predicted dimeric interface of DifA significantly affected EPS production. Deletions of 14-aa segments in the C terminus suggest that the newly defined flexible bundle subdomain in MCPs is likely critical for DifA function because shortening of this bundle can lead to constitutively active mutations.
not annotated - annotated - LINNAEUS only
The SMC-like protein complex SbcCD enhances DNA polymerase IV-dependent spontaneous mutation in Escherichia coli.
In Escherichia coli, RpoS, the general stress response sigma factor, regulates the activity of the specialized DNA polymerase DNA polymerase IV (Pol IV) both in stationary-phase and in exponential-phase cells. Because during exponential phase dinB, the gene encoding Pol IV, is transcribed independently of RpoS, RpoS must regulate Pol IV activity in growing cells indirectly via one or more intermediate factors. The results presented here show that one of these intermediate factors is SbcCD, an SMC-like protein and an ATP-dependent nuclease. By initiating or participating in double-strand break repair, SbcCD may provide DNA substrates for Pol IV polymerase activity.
not annotated - annotated - LINNAEUS only
Staphylococcus aureus ClpC divergently regulates capsule via sae and codY in strain newman but activates capsule via codY in strain UAMS-1 and in strain Newman with repaired saeS.
ClpC is an ATPase chaperone found in most Gram-positive low-GC bacteria. It has been recently reported that ClpC affected virulence gene expression in Staphylococcus aureus. Here we report that ClpC regulates transcription of the cap operon and accumulation of capsule, a major virulence factor for S. aureus. As virulence genes are regulated by a complex regulatory network in S. aureus, we have used capsule as a model to understand this regulation. By microarray analyses of strain Newman, we found that ClpC strongly activates transcription of the sae operon, whose products are known to negatively regulate capsule synthesis in this strain. Further studies indicated that ClpC repressed capsule production by activating the sae operon in strain Newman. Interestingly, the clpC gene cloned into a multiple-copy plasmid vector exhibited an activation phenotype, suggesting that ClpC overexpression has a net positive effect. In the absence of sae function, by either deletion or correction of a native mutation within saeS, we found that ClpC had a positive effect on capsule production. Indeed, in the UAMS-1 strain, which does not have the saeS mutation, ClpC functioned as an activator of capsule production. Our microarray analyses of strain Newman also revealed that CodY, a repressor of capsule production, was repressed by ClpC. Using genetic approaches, we showed that CodY functioned downstream of ClpC, leading to capsule activation both in Newman and in UAMS-1. Thus, ClpC functions in two opposite pathways in capsule regulation in strain Newman but functions as a positive activator in strain UAMS-1.
not annotated - annotated - LINNAEUS only
Flavobacterium johnsoniae sprB is part of an operon spanning the additional gliding motility genes sprC, sprD, and sprF.
Cells of Flavobacterium johnsoniae move rapidly over surfaces by a process known as gliding motility. Gld proteins are thought to comprise the gliding motor that propels cell surface adhesins, such as the 669-kDa SprB. A novel protein secretion apparatus called the Por secretion system (PorSS) is required for assembly of SprB on the cell surface. Genetic and molecular analyses revealed that sprB is part of a seven-gene operon spanning 29.3 kbp of DNA. In addition to sprB, three other genes of this operon (sprC, sprD, and sprF) are involved in gliding. Mutations in sprB, sprC, sprD, and sprF resulted in cells that failed to form spreading colonies on agar but that exhibited some motility on glass in wet mounts. SprF exhibits some similarity to Porphyromonas gingivalis PorP, which is required for secretion of gingipain protease virulence factors via the P. gingivalis PorSS. F. johnsoniae sprF mutants produced SprB protein but were defective in localization of SprB to the cell surface, suggesting a role for SprF in secretion of SprB. The F. johnsoniae PorSS is involved in secretion of extracellular chitinase in addition to its role in secretion of SprB. SprF was not needed for chitinase secretion and may be specifically required for SprB secretion by the PorSS. Cells with nonpolar mutations in sprC or sprD produced and secreted SprB and propelled it rapidly along the cell surface. Multiple paralogs of sprB, sprC, sprD, and sprF are present in the genome, which may explain why mutations in sprB, sprC, sprD, and sprF do not result in complete loss of motility and suggests the possibility that semiredundant SprB-like adhesins may allow movement of cells over different surfaces.
not annotated - annotated - LINNAEUS only
Perithecium morphogenesis in Sordaria macrospora.
The perithecium of the self-fertile ascomycete Sordaria macrospora provides an excellent model in which to analyse fungal multicellular development. This study provides a detailed analysis of perithecium morphogenesis in the wild type and eight developmental mutants of S. macrospora, using a range of correlative microscopical techniques. Fundamentally, perithecia and other complex multicellular structures produced by fungi arise by hyphal aggregation and adhesion, and these processes are followed by specialization and septation of hyphal compartments within the aggregates. Perithecial morphogenesis can be divided into the ascogonial, protoperithecial, and perithecial stages of development. At least 13 specialized, morphologically distinct cell-types are involved in perithecium morphogenesis, and these fall into three basic classes: hyphae, conglutinate cells and spores. Conglutinate cells arise from hyphal adhesion and certain perithecial hyphae develop from conglutinate cells. Various hypha-conglutinate cell transitions play important roles during the development of the perithecial wall and neck.
not annotated - annotated - LINNAEUS only
Overexpression of the trichodiene synthase gene tri5 increases trichodermin production and antimicrobial activity in Trichoderma brevicompactum.
Trichoderma brevicompactum produces trichodermin, a simple trichothecene-type toxin that shares the first steps of the sesquiterpene biosynthetic pathway with other phytotoxic trichothecenes from Fusarium spp. Trichodiene synthase catalyses the conversion of farnesyl pyrophosphate to trichodiene and it is encoded by the tri5 gene that was cloned and analysed functionally by homologous overexpression in T. brevicompactum. tri5 expression was up-regulated in media with glucose, H(2)O(2) or glycerol. tri5 repression was observed in cultures supplemented with the antioxidants ferulic acid and tyrosol. Acetone extracts of tri5-overexpressing transformants displayed higher antifungal activity than those from the wild-type. Chromatographic and spectroscopic analyses revealed that tri5 overexpression led to an increased production of trichodermin and tyrosol. Agar diffusion assays with these two purified metabolites from the tri5-overexpressing transformant T. brevicompactum Tb41tri5 showed that only trichodermin had antifungal activity against Saccharomyces cerevisiae, Kluyveromyces marxianus, Candida albicans, Candida glabrata, Candida tropicalis and Aspergillus fumigatus, in most cases such activity being higher than that observed for amphotericin B and hygromycin. Our results point to the significant role of tri5 in the production of trichodermin and in the antifungal activity of T. brevicompactum.
not annotated - annotated - LINNAEUS only
Heterotrimeric Galpha protein Pga1 from Penicillium chrysogenum triggers germination in response to carbon sources and affects negatively resistance to different stress conditions.
Heterotrimeric Galpha protein Pga1 of Penicillium chrysogenum controls vegetative growth, conidiation and secondary metabolite production. In this work we studied the role of Pga1 in spore germination and resistance to different stress conditions. Strains G203R-T (expressing the dominant inactivating pga1(G203R) allele) and Deltapga1 (deleted pga1) showed a delayed and asynchronic germination pattern, and a decrease in the percentage of germination, which occurred in only 70-80% of the total conidia. In contrast, in strains expressing the dominant activating pga1(G42R) allele, germination occurred at earlier times and in 100% of conidia. In addition, strains with the pga1(G42R) allele were able to bypass the carbon source (glucose or sucrose) requirement for germination in about 64% of conidia. Thus Pga1 plays an important, but not essential, role in germination, mediating carbon source sensing. Regulation of germination by Pga1 is probably mediated by cAMP, as intracellular levels of this secondary messenger undergo a peak before the onset of germination only in strains with an active Pga1. Pga1 activity is also a determinant factor in the resistance to different stress conditions. Absence or inactivation of Pga1 allow growth on SDS-containing minimal medium, increase resistance of conidia to thermal and oxidative stress, and increase resistance of vegetative mycelium to thermal and osmotic stress. In contrast, constitutive activation of Pga1 causes a decrease in the resistance of conidia to thermal stress and of vegetative mycelium to thermal and osmotic stress. Together with our previously reported results, we show in this work that Pga1 plays a central role in the regulation of the whole growth-developmental program of this biotechnologically important fungus.
not annotated - annotated - LINNAEUS only
Systemic therapy in the management of metastatic or locally recurrent adenoid cystic carcinoma of the salivary glands: a systematic review.
Adenoid cystic carcinomas (ACC) are rare cancers usually arising in the salivary glands. Once metastatic, the natural history can vary; some patients with indolent cancer remain asymptomatic for long periods, whereas others have rapidly progressive disease. Chemotherapy is generally reserved for the palliative treatment of symptomatic locally recurrent or metastatic disease that is not amenable to further surgery or radiation. Prospective trials of chemotherapy in advanced ACC are limited, and the optimum regimen is unclear. The aim of this systematic review is to summarise and rate the quality of trials assessing chemotherapy for treatment of ACC, by use of the European Lung Cancer Working Party scoring system. Endpoints evaluated include tumour response and rates of symptomatic improvement. 34 trials involving 441 patients are included. We give evidence-based recommendations for management of ACC with chemotherapy, along with considerations for the design of future clinical trials in this disease.
not annotated - annotated - LINNAEUS only
Disrupted energy metabolism and neuronal circuit dysfunction in cognitive impairment and Alzheimer's disease.
Epidemiological, neuropathological, and functional neuroimaging evidence implicates global and regional disruptions in brain metabolism and energetics in the pathogenesis of cognitive impairment. Nerve cell microcircuits are modified by excitatory and inhibitory synaptic activity and neurotrophic factors. Ageing and Alzheimer's disease cause perturbations in cellular energy metabolism, level of excitation or inhibition, and neurotrophic factor release, which overwhelm compensatory mechanisms and result in dysfunction of neuronal microcircuits and brain networks. A prolonged positive energy balance impairs the ability of neurons to adapt to oxidative and metabolic stress. Results from experimental studies in animals show how disruptions caused by chronic positive energy balance, such as diabetes, lead to accelerated cognitive ageing and Alzheimer's disease. Therapeutic interventions to allay cognitive dysfunction that target energy metabolism and adaptive stress responses (such as neurotrophin signalling) have been effective in animal models and in preliminary studies in humans.
not annotated - annotated - LINNAEUS only
Behavioural-variant frontotemporal dementia: diagnosis, clinical staging, and management.
Patients with behavioural-variant frontotemporal dementia (bvFTD) present with insidious changes in personality and interpersonal conduct that indicate progressive disintegration of the neural circuits involved in social cognition, emotion regulation, motivation, and decision making. The underlying pathological changes are heterogeneous and are characterised by various intraneuronal inclusions. Biomarkers to detect these histopathological changes in life are becoming increasingly important with the development of disease-modifying drugs. Gene mutations have been found that collectively account for around 10-20% of cases. Recently, criteria proposed for bvFTD define three levels of diagnostic certainty: possible, probable, and definite. Detailed history taking from family members to elicit behavioural features underpins the diagnostic process, with support from neuropsychological testing designed to detect impairment in decision making, emotion processing, and social cognition. Brain imaging is important for increasing the level of diagnostic certainty. A recently developed staging instrument shows much promise for monitoring patients and evaluating therapies, which at present are aimed at symptom amelioration. Carer education and support remain of paramount importance.
not annotated - annotated - LINNAEUS only
Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus.
We present a cryo-electron tomographic analysis of the three-dimensional architecture of a strain of the Gram-negative bacterium Bdellovibrio bacteriovorus in which endogenous MreB2 was replaced with monomeric teal fluorescent protein (mTFP)-labeled MreB2. In contrast to wild-type Bdellovibrio cells that predominantly displayed a compact nucleoid region, cells expressing mTFP-labeled MreB2 displayed a twisted spiral organization of the nucleoid. The more open structure of the MreB2-mTFP nucleoids enabled clear in situ visualization of ribosomes decorating the periphery of the nucleoid. Ribosomes also bordered the edges of more compact nucleoids from both wild-type cells and mutant cells. Surprisingly, MreB2-mTFP localized to the interface between the spiral nucleoid and the cytoplasm, suggesting an intimate connection between nucleoid architecture and MreB arrangement. Further, in contrast to wild-type cells, where a single tight chemoreceptor cluster localizes close to the single polar flagellum, MreB2-mTFP cells often displayed extended chemoreceptor arrays present at one or both poles and displayed multiple or inaccurately positioned flagella. Our findings provide direct structural evidence for spiral organization of the bacterial nucleoid and suggest a possible role for MreB in regulation of nucleoid architecture and localization of the chemotaxis apparatus.
not annotated - annotated - LINNAEUS only
A transcriptional regulator and ABC transporters link stress tolerance, (p)ppGpp, and genetic competence in Streptococcus mutans.
Streptococcus mutans, a primary agent of dental caries, has three (p)ppGpp synthases: RelA, which is required for a mupirocin-induced stringent response; RelP, which produces (p)ppGpp during exponential growth and is regulated by the RelRS two-component system; and RelQ. Transcription of relPRS and a gene cluster (SMu0835 to SMu0837) located immediately upstream was activated in cells grown with aeration and during a stringent response, respectively. Bioinformatic analysis predicted that SMu0836 and SMu0837 encode ABC exporters, which we designated rcrPQ (rel competence-related) genes, respectively. SMu0835 (rcrR) encodes a MarR family transcriptional regulator. Reverse transcriptase PCR (RT-PCR) and quantitative RT-PCR analysis showed that RcrR functions as an autogenous negative regulator of the expression of the rcrRPQ operon. A mutant in which a polar insertion replaced the SMu836 gene (Delta836polar) grew more slowly and had final yields that were lower than those of the wild-type strain. Likewise, the Delta836polar strain had an impaired capacity to form biofilms, grew poorly at pH 5.5, and was more sensitive to oxidative stressors. Optimal expression of rcrPQ required RelP and vice versa. Replacement of rcrR with a nonpolar antibiotic resistance marker (Delta835np), which leads to overexpression of rcrPQ, yielded a strain that was not transformable with exogenous DNA. Transcriptional analysis revealed that the expression of comYA and comX was dramatically altered in the Delta835np and Delta836polar mutants. Collectively, the data support the suggestion that the rcrRPQ gene products play a critical role in physiologic homeostasis and stress tolerance by linking (p)ppGpp metabolism, acid and oxidative stress tolerance, and genetic competence.
not annotated - annotated - LINNAEUS only
Mapping functional domains of colicin M.
Colicin M (Cma) lyses Escherichia coli cells by inhibiting murein biosynthesis through hydrolysis of the phosphate ester between C(55)-polyisoprenol and N-acetylmuramyl (MurNAc)-pentapeptide-GlcNAc in the periplasm. To identify Cma functional domains, we isolated 54 point mutants and small deletion mutants and examined their cytotoxicity levels. Activity and uptake mutants were distinguished by osmotic shock, which transfers Cma into the periplasm independent of the specific FhuA receptor and the Ton system. Deletion of the hydrophobic helix alpha1, which extends from the compact Cma structure, abolished interference with the antibiotic albomycin, which is transported across the outer membrane by the same system as Cma, thereby identifying alpha1 as the Cma site that binds to FhuA. Deletion of the C-terminal Lys-Arg strongly reduced Cma translocation across the outer membrane after binding to FhuA. Conversion of Asp226 to Glu, Asn, or Ala inactivated Cma. Asp226 is exposed at the Cma surface and is surrounded by Asp225, Asp229, His235, Tyr228, and Arg236; replacement of each with alanine inactivated Cma. We propose that Asp226 directly participates in phosphate ester hydrolysis and that the surrounding residues contribute to the active site. These residues are strongly conserved in Cma-like proteins of other species. Replacement of other conserved residues with alanine inactivated Cma; these mutations probably altered the Cma structure, as particularly apparent for mutants in the unique open Beta-barrel of Cma, which were isolated in lower yields. Our results identify regions in Cma responsible for uptake and activity and support the concept of a three-domain arrangement of Cma.
not annotated - annotated - LINNAEUS only
The recombinase IntA is required for excision of esp-containing ICEEfm1 in Enterococcus faecium.
Comparative genome analysis of Enterococcus faecium recently revealed that a genomic island containing the esp gene, referred to as the esp-containing pathogenicity island (esp PAI), can be transferred by conjugation and contains a partial Tn916-like element and an integrase gene, intA. Here, we characterize the role of intA in the excision of the esp PAI. An intA insertion-deletion mutant in E. faecium E1162 (E1162DeltaintA) was constructed and in trans complemented with wild-type intA (E1162DeltaintA::pEF30). Circular intermediates (CI) of excised esp PAI were determined using inverse PCR analysis on purified chromosomal DNA from strains E1162, E1162Deltaesp, E1162DeltaintA, and E1162DeltaintA::pEF30. In E1162 and E1162Deltaesp, CI of the esp PAI were detected. No CI were detected in E1162DeltaintA, while in the complemented strain E1162DeltaintA::pEF30 CI formation was restored, indicating that intA is essential for excision and subsequent mobilization of the esp-containing genomic island in E. faecium. Based on the fact that this island can be mobilized and is self-transmissible, we propose to change the name of the esp PAI to ICEEfm1.
not annotated - annotated - LINNAEUS only
Functional and phylogenetic analysis of ureD in Shiga toxin-producing Escherichia coli.
Enterohemorrhagic Escherichia coli (EHEC) is a food-borne pathogen that can cause severe health complications and utilizes a much lower infectious dose than other E. coli pathotypes. Despite having an intact ure locus, ureDABCEFG, the majority of EHEC strains are phenotypically urease negative under tested conditions. Urease activity potentially assists with survival fitness by enhancing acid tolerance during passage through the stomach or by aiding with colonization in either human or animal reservoirs. Previously, in the EHEC O157:H7 Sakai strain, a point mutation in ureD, encoding a urease chaperone protein, was identified, resulting in a substitution of an amber stop codon for glutamine. This single nucleotide polymorphism (SNP) is observed in the majority of EHEC O157:H7 isolates and correlates with a negative urease phenotype in vitro. We demonstrate that the lack of urease activity in vitro is not solely due to the amber codon in ureD. Our analysis has identified two additional SNPs in ureD affecting amino acid positions 38 and 205, in both cases determining whether the encoded amino acid is leucine or proline. Phylogenetic analysis based on Ure protein sequences from a variety of urease-encoding bacteria demonstrates that the proline at position 38 is highly conserved among Gram-negative bacteria. Experiments reveal that the L38P substitution enhances urease enzyme activity; however, the L205P substitution does not. Multilocus sequence typing analysis for a variety of Shiga toxin-producing E. coli isolates combined with the ureD sequence reveals that except for a subset of the O157:H7 strains, neither the in vitro urease-positive phenotype nor the ureD sequence is phylogenetically restricted.
not annotated - annotated - LINNAEUS only
Genome-wide identification of Mycobacterium tuberculosis exported proteins with roles in intracellular growth.
The exported proteins of Mycobacterium tuberculosis that are localized at the bacterial cell surface or secreted into the environment are ideally situated to interact with host factors and to function in virulence. In this study, we constructed a novel Beta-lactamase reporter transposon and used it directly in M. tuberculosis for genome-wide identification of exported proteins. From 177 Beta-lactam-resistant transposon mutants, we identified 111 different exported proteins. The majority of these proteins have no known function, and for nearly half of the proteins, our demonstration that they are exported when fused to a Beta-lactamase reporter is the first experimental proof of their extracytoplasmic localization. The transposon mutants in our banked library were of further value as a collection of mutants lacking individual exported proteins. By individually testing each of 111 mutants for growth in macrophages, six attenuated mutants with insertions in mce1A, mce1B, mce2F, rv0199, ctaC, and lppX were identified. Given that much of the M. tuberculosis genome encodes proteins of unknown function, our library of mapped transposon mutants is a valuable resource for efforts in functional genomics. This work also demonstrates the power of a Beta-lactamase reporter transposon that could be applied similarly to other bacterial pathogens.
not annotated - annotated - LINNAEUS only
Maternal influence on philopatry and space use by juvenile brushtail possums (Trichosurus vulpecula).
1. The causes of juvenile sex-biased philopatry and space use in mammals remain poorly understood, and results of previous research have been conflicting. Experimental interventions and manipulations on wild populations are rare, but can play an important role in establishing the factors governing offspring space use. 2. We experimentally removed mothers of independent juvenile brushtail possums from the maternal home range and examined changes in offspring space use with global positioning system collars. We examined the influence of mother absence on philopatric behaviour, and determined whether or not maternal presence affected offspring space use. 3. We fitted a longitudinal linear mixed effects model to demonstrate a change over time in the home range size of juveniles following experimental treatment by the removal of their mothers. When mothers were removed from the natal range, juveniles occupied significantly larger home range areas, with average increases of 175% in 95% kernel density estimates and 289% in minimum convex polygon estimates. This increase occurred within the first month following mother absence and was independent of juvenile sex. Home ranges of control juveniles did not change during the same time period. 4. Changes in the spatial structure of mammalian populations in response to removal of individuals have important implications for pest management. The impacts of management strategies which target particular individuals in a population may counteract conservation benefits through their effect on the space use of survivors. Studies involving experimental removals provide important information on consequences of control and also yield insights into the causes of mammalian space use, philopatric behaviours and ultimately dispersal.
not annotated - annotated - LINNAEUS only
Competitive interactions shape offspring performance in relation to seasonal timing of emergence in Atlantic salmon.
1. Timing of birth/hatching may have strong effects on offspring fitness. Breeding time is generally considered to have evolved to match offspring arrival with optimal seasonal environmental conditions, though this is rarely tested experimentally and factors shaping the relations between timing of birth and reproductive success are often poorly understood. 2. By manipulating incubation temperature of Atlantic salmon embryos, and hence controlling for maternal and genetic effects, we obtained offspring emerging from nests prior to (accelerated), during and after (decelerated) normal emergence times, and accordingly experienced widely different seasonal environmental conditions at emergence (stream temperature range 4-16 ^0C). The accelerated group emerged at temperatures that are generally considered to be highly sub-optimal for growth and likely imposes strong constraints on feeding and activity, and during a peak in water discharge which is expected to negatively influence habitat availability. 3. In the wild, overall mortality during the period after emergence was 79%, and was significantly affected by both release density and emergence timing. Accelerated offspring, which emerged earliest and experienced the harshest environmental conditions, had both highest survival and largest final body size. The effect was particularly strong at the high density release site, where survival of accelerated offspring was significantly higher than both the normal and decelerated groups. 4. In more controlled semi-natural environments, all developmental groups were able to perform well, but accelerated offspring had a relatively better performance than the later emerging offspring when density was high. Furthermore, the relative performance of the different groups was not sensitive to water discharge regimes (temporally stable vs. fluctuating). 5. These results suggest that the performance of offspring in relation to seasonal timing of emergence is highly affected by competitive interactions in Atlantic salmon. Although a match between phenology and optimal seasonal environmental conditions may be highly important for organisms depending on specific resources that are only available during a limited period of the season, such resources may be available in variable amounts year around for many organisms. For these, offspring success may to a larger degree be shaped by the timing of their hatching/birth relative to each other, and particularly so under high population densities.
not annotated - annotated - LINNAEUS only
Disentangling the effects of predator hunting mode and habitat domain on the top-down control of insect herbivores.
1. Polyphagous predatory invertebrates play a key role in the top-down control of insect herbivores. However, predicting predation risk for herbivores is not a simple function of predator species richness. Predation risk may be reduced or enhanced depending on the functional characteristics predator species. We predict that where predator species spatially overlap this will reduce predation risk for herbivores by allowing negative inter-specific interaction between predators to occur. Where increased predation risk occurs, we also predict that this will have a cascading effect through the food chain reducing plant growth. 2. We used a substitutive replicated block design to identify the effect of similarity and dissimilarity in predator hunting mode (e.g. 'sit and wait', 'sit and pursue', and 'active') and habitat domain (e.g. canopy or ground) on the top-down control of planthoppers in grasslands. Predators included within the mesocosms were randomly selected from a pool of 17 local species. 3. Predation risk was reduced where predators shared the same habitat domain, independent of whether they shared hunting modes. Where predators shared the same habitat domains, there was some evidence that this had a cascading negative effect on the re-growth of grass biomass. Where predator habitat domains did not overlap, there were substitutable effects on predation risk to planthoppers. Predation risk for planthoppers was affected by taxonomic identity of predator species, i.e. whether they were beetles, spiders or true bugs. 4. Our results indicated that in multi-predator systems, the risk of predation is typically reduced. Consideration of functional characteristics of individual species, in particular aspects of habitat domain and hunting mode, are crucial in predicting the effects of multi-predator systems on the top-down control of herbivores.
not annotated - annotated - LINNAEUS only
Clinical experience and laboratory investigations in patients with anti-NMDAR encephalitis.
Since its discovery in 2007, the encephalitis associated with antibodies against the N-methyl-D-aspartate receptor (NMDAR) has entered the mainstream of neurology and other disciplines. Most patients with anti-NMDAR encephalitis develop a multistage illness that progresses from psychosis, memory deficits, seizures, and language disintegration into a state of unresponsiveness with catatonic features often associated with abnormal movements, and autonomic and breathing instability. The disorder predominantly affects children and young adults, occurs with or without tumour association, and responds to treatment but can relapse. The presence of a tumour (usually an ovarian teratoma) is dependent on age, sex, and ethnicity, being more frequent in women older than 18 years, and slightly more predominant in black women than it is in white women. Patients treated with tumour resection and immunotherapy (corticosteroids, intravenous immunoglobulin, or plasma exchange) respond faster to treatment and less frequently need second-line immunotherapy (cyclophosphamide or rituximab, or both) than do patients without a tumour who receive similar initial immunotherapy. More than 75% of all patients have substantial recovery that occurs in inverse order of symptom development and is associated with a decline of antibody titres. Patients' antibodies cause a titre-dependent, reversible decrease of synaptic NMDAR by a mechanism of crosslinking and internalisation. On the basis of models of pharmacological or genetic disruption of NMDAR, these antibody effects reveal a probable pathogenic relation between the depletion of receptors and the clinical features of anti-NMDAR encephalitis.
not annotated - annotated - LINNAEUS only
Acute encephalopathy with inflammation-mediated status epilepticus.
Fever-induced refractory epileptic encephalopathy in school-aged children (FIRES), and idiopathic hemiconvulsion-hemiplegia syndrome (IHHS) are both triggered by fever, although evidence for a causal microorganism or an autoimmune phenomenon is lacking. FIRES begins in school age with status epilepticus lasting several weeks, involves perisylvian areas including mesial temporal structures, and is followed by pharmacoresistant epilepsy with major cognitive deterioration. IHHS begins in infancy with unilateral clonic status epilepticus and is followed by hemiplegia with pharmacoresistant epilepsy. The aetiology of FIRES and IHHS remains unknown, although clinical features and experimental models point to a likely vicious cycle involving inflammation and seizure activity that depends on the stage of brain maturation. We therefore propose to group these conditions under the concept of acute encephalopathy with inflammation-mediated status epilepticus. In addition to preliminary but encouraging clinical observations, there are theoretical reasons to consider the ketogenic diet as an early means to control both seizures and inflammation.
not annotated - annotated - LINNAEUS only
The ribonucleotide reductase large subunit (RRM1) as a predictive factor in patients with cancer.
The large subunit of human ribonucleotide reductase, RRM1, is involved in the regulation of cell proliferation, cell migration, tumour and metastasis development, and the synthesis of deoxyribonucleotides for DNA synthesis. It is also a cellular target for the chemotherapeutic agent, gemcitabine. RRM1 has been studied in a large number of patients with different types of cancer, such as non-small-cell lung cancer, pancreatic cancer, breast cancer, and biliary tract cancer, to establish its prognostic or predictive value when patients were treated with gemcitabine, and mRNA expression and genetic variants as determined by genotyping have in some cases been associated with clinical outcome of patients with cancer. Here, we review preclinical and clinical studies of RRM1 assessment and discuss the further steps in the development of this clinically pertinent biomarker.
not annotated - annotated - LINNAEUS only
KRAS, BRAF, PIK3CA, and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer.
The discovery of mutant KRAS as a predictor of resistance to epidermal growth-factor receptor (EGFR) monoclonal antibodies brought a major change in the treatment of metastatic colorectal cancer. This seminal finding also highlighted our sparse knowledge about key signalling pathways in colorectal tumours. Drugs that inhibit oncogenic alterations such as phospho-MAP2K (also called MEK), phospho-AKT, and mutant B-RAF seem promising as single treatment or when given with EGFR inhibitors. However, our understanding of the precise role these potential drug targets have in colorectal tumours, and the oncogenic dependence that tumours might have on these components, has not progressed at the same rate. As a result, patient selection and prediction of treatment effects remain problematic. We review the role of mutations in genes other than KRAS on the efficacy of anti-EGFR therapy, and discuss strategies to target these oncogenic alterations alone or in combination with receptor tyrosine-kinase inhibition.
not annotated - annotated - LINNAEUS only
Conserved function of the Kruppel gap gene in the blowfly Lucilia sericata, despite anterior shift of expression.
To determine whether expression patterns of segmentation genes found in Drosophila melanogaster can be scaled to pattern larger insects, we studied the expression of the Kruppel (Kr) gene in the blowfly Lucilia sericata. Compared with Drosophila Kr, L. sericata Kr showed an unexpected 10% shift of expression towards the anterior pole. Furthermore, expression domains not found in D. melanogaster were present at the blastoderm stage of L. sericata. To compare Kr activity and function, we employed RNA interference-mediated gene silencing. We found Kr phenotypes in L. sericata comparable with those observed in D. melanogaster, demonstrating that L. sericata Kr functions as a gap gene as it does in Drosophila. Our results show that, despite an anterior shift in expression, Kr function has remained conserved during the evolution of the blowflies.
not annotated - annotated - LINNAEUS only
Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila.
Natural transformation by competence is a major mechanism of horizontal gene transfer in bacteria. Competence is defined as the genetically programmed physiological state that enables bacteria to actively take up DNA from the environment. The conditions that signal competence development are multiple and elusive, complicating the understanding of its evolutionary significance. We used expression of the competence gene comEA as a reporter of competence development and screened several hundred molecules for their ability to induce competence in the freshwater living pathogen Legionella pneumophila. We found that comEA expression is induced by chronic exposure to genotoxic molecules such as mitomycin C and antibiotics of the fluoroquinolone family. These results indicated that, in L. pneumophila, competence may be a response to genotoxic stress. Sunlight-emitted UV light represents a major source of genotoxic stress in the environment and we found that exposure to UV radiation effectively induces competence development. For the first time, we show that genetic exchanges by natural transformation occur within an UV-stressed population. Genotoxic stress induces the RecA-dependent SOS response in many bacteria. However, genetic and phenotypic evidence suggest that L. pneumophila lacks a prototypic SOS response and competence development in response to genotoxic stress is RecA independent. Our results strengthen the hypothesis that competence may have evolved as a DNA damage response in SOS-deficient bacteria. This parasexual response to DNA damage may have enabled L. pneumophila to acquire and propagate foreign genes, contributing to the emergence of this human pathogen.
not annotated - annotated - LINNAEUS only
Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota.
Two autotrophic carbon fixation cycles have been identified in Crenarchaeota. The dicarboxylate/4-hydroxybutyrate cycle functions in anaerobic or microaerobic autotrophic members of the Thermoproteales and Desulfurococcales. The 3-hydroxypropionate/4-hydroxybutyrate cycle occurs in aerobic autotrophic Sulfolobales; a similar cycle may operate in autotrophic aerobic marine Crenarchaeota. Both cycles form succinyl-coenzyme A (CoA) from acetyl-CoA and two molecules of inorganic carbon, but they use different means. Both cycles have in common the (re)generation of acetyl-CoA from succinyl-CoA via identical intermediates. Here, we identified several missing enzymes/genes involved in the seven-step conversion of succinyl-CoA to two molecules of acetyl-CoA in Thermoproteus neutrophilus (Thermoproteales), Ignicoccus hospitalis (Desulfurococcales), and Metallosphaera sedula (Sulfolobales). The identified enzymes/genes include succinyl-CoA reductase, succinic semialdehyde reductase, 4-hydroxybutyrate-CoA ligase, bifunctional crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase, and beta-ketothiolase. 4-Hydroxybutyryl-CoA dehydratase, which catalyzes a mechanistically intriguing elimination of water, is well conserved and rightly can be considered the key enzyme of these two cycles. In contrast, several of the other enzymes evolved from quite different sources, making functional predictions based solely on genome interpretation difficult, if not questionable.
not annotated - annotated - LINNAEUS only
Unexpected coregulator range for the global regulator Lrp of Escherichia coli and Proteus mirabilis.
The Lrp/AsnC family of transcription factors links gene regulation to metabolism in bacteria and archaea. Members of this family, collectively, respond to a wide range of amino acids as coregulators. In Escherichia coli, Lrp regulates over 200 genes directly and is well known to respond to leucine and, to a somewhat lesser extent, alanine. We focused on Lrp from Proteus mirabilis and E. coli, orthologs with 98% identity overall and identical helix-turn-helix motifs, for which a previous study nevertheless found functional differences. Sequence differences between these orthologs, within and adjacent to the amino acid-responsive RAM domain, led us to test for differential sensitivity to coregulatory amino acids. In the course of this investigation, we found, via in vivo reporter fusion assays and in vitro electrophoretic mobility shift experiments, that E. coli Lrp itself responded to a broader range of amino acids than was previously appreciated. In particular, for both the E. coli and P. mirabilis orthologs, Lrp responsiveness to methionine was similar in magnitude to that to leucine. Both Lrp orthologs are also fairly sensitive to Ile, His, and Thr. These observations suggest that Lrp ties gene expression in the Enterobacteriaceae rather extensively to physiological status, as reflected in amino acid pools. These findings also have substantial implications for attempts to model regulatory architecture from transcriptome measurements or to infer such architecture from genome sequences, and they suggest that even well-studied regulators deserve ongoing exploration.
not annotated - annotated - LINNAEUS only
Labeling and enzyme studies of the central carbon metabolism in Metallosphaera sedula.
Metallosphaera sedula (Sulfolobales, Crenarchaeota) uses the 3-hydroxypropionate/4-hydroxybutyrate cycle for autotrophic carbon fixation. In this pathway, acetyl-coenzyme A (CoA) and succinyl-CoA are the only intermediates that can be considered common to the central carbon metabolism. We addressed the question of which intermediate of the cycle most biosynthetic routes branch off. We labeled autotrophically growing cells by using 4-hydroxy[1-^1^4C]butyrate and [1,4-^1^3C1]succinate, respectively, as precursors for biosynthesis. The labeling patterns of protein-derived amino acids verified the operation of the proposed carbon fixation cycle, in which 4-hydroxybutyrate is converted to two molecules of acetyl-CoA. The results also showed that major biosynthetic flux does not occur via acetyl-CoA, except for the formation of building blocks that are directly derived from acetyl-CoA. Notably, acetyl-CoA is not assimilated via reductive carboxylation to pyruvate. Rather, our data suggest that the majority of anabolic precursors are derived from succinyl-CoA, which is removed from the cycle via oxidation to malate and oxaloacetate. These C4intermediates yield pyruvate and phosphoenolpyruvate (PEP). Enzyme activities that are required for forming intermediates from succinyl-CoA were detected, including enzymes catalyzing gluconeogenesis from PEP. This study completes the picture of the central carbon metabolism in autotrophic Sulfolobales by connecting the autotrophic carbon fixation cycle to the formation of central carbon precursor metabolites.
not annotated - annotated - LINNAEUS only
The sensor kinase CbrA is a global regulator that modulates metabolism, virulence, and antibiotic resistance in Pseudomonas aeruginosa.
Pseudomonas aeruginosa is an opportunistic pathogen that possesses a large arsenal of virulence factors enabling the pathogen to cause serious infections in immunocompromised patients, burn victims, and cystic fibrosis patients. CbrA is a sensor kinase that has previously been implied to play a role with its cognate response regulator CbrB in the metabolic regulation of carbon and nitrogen utilization in P. aeruginosa. Here it is demonstrated that CbrA and CbrB play an important role in various virulence and virulence-related processes of the bacteria, including swarming, biofilm formation, cytotoxicity, and antibiotic resistance. The cbrA deletion mutant was completely unable to swarm while exhibiting an increase in biofilm formation, supporting the inverse regulation of swarming and biofilm formation in P. aeruginosa. The cbrA mutant also exhibited increased cytotoxicity to human lung epithelial cells as early as 4 and 6 h postinfection. Furthermore, the cbrA mutant demonstrated increased resistance toward a variety of clinically important antibiotics, including polymyxin B, ciprofloxacin, and tobramycin. Microarray analysis revealed that under swarming conditions, CbrA regulated the expression of many genes, including phoPQ, pmrAB, arnBCADTEF, dnaK, and pvdQ, consistent with the antibiotic resistance and swarming impairment phenotypes of the cbrA mutant. Phenotypic and real-time quantitative PCR (RT-qPCR) analyses of a PA14 cbrB mutant suggested that CbrA may be modulating swarming, biofilm formation, and cytotoxicity via CbrB and that the CrcZ small RNA is likely downstream of this two-component regulator. However, as CbrB did not have a resistance phenotype, CbrA likely modulates antibiotic resistance in a manner independent of CbrB.
not annotated - annotated - LINNAEUS only
Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-gamma-pyrone.
The genome sequencing of the fungus Aspergillus niger uncovered a large cache of genes encoding enzymes thought to be involved in the production of secondary metabolites yet to be identified. Identification and structural characterization of many of these predicted secondary metabolites are hampered by their low concentration relative to the known A. niger metabolites such as the naphtho-gamma-pyrone family of polyketides. We deleted a non-reducing PKS gene in A. niger strain ATCC 11414, a daughter strain of A. niger ATCC strain 1015 whose genome was sequenced by the DOE Joint Genome Institute. This PKS encoding gene we name albA is a predicted ortholog of alb1 from Aspergillus fumigatus which is responsible for production of the naphtho-gamma-pyrone precursor for the 1,8-dihydroxynaphthalene (DHN) melanin/spore pigment. Our results show that the A. nigeralbA PKS is responsible for both the production of the spore pigment precursor and a family of naphtho-gamma-pyrones commonly found in significant quantity in A. niger culture extracts. The generation of an A. niger strain devoid of naphtho-gamma-pyrones will greatly facilitate the elucidation of cryptic biosynthetic pathways in this organism.
not annotated - annotated - LINNAEUS only
Drivers of age-specific survival in a long-lived seabird: contributions of observed and hidden sources of heterogeneity.
1. We assessed the relative influence of variability in recruitment age, dynamic reproductive investment (time-specific reproductive states) and frailty (unobserved differences in survival abilities across individuals) on survival in the black-legged kittiwake. Furthermore, we examined whether observed variability in survival trajectories was best explained by immediate reproductive investment, cumulative investment, or both. 2. Individuals that delayed recruitment (>= age 7) suffered a higher mortality risk than early recruits (age 3), especially later in life, suggesting that recruitment age may be an indicator of individual quality. Although recruitment age helped explain variation in survival, time-varying reproductive investment had a more substantial influence. 3. The dichotomy of attempting to breed or not explained variability in survival across life better than other parameterizations of reproductive states such as clutch size, brood size or breeding success. In the kittiwake, the sinequanon condition to initiate reproduction is to hold a nest site, which is considered a very competitive activity. This might explain why attempting to breed is the key level of investment that affects survival, independent of the outcome (failure or success). 4. Interestingly, the more individuals cumulate reproductive attempts over life, the lower their mortality risk, indicating that breeding experience may be a good indicator of parental quality as well. In contrast, attempting to breed at time t increased the risk of mortality between t and t + 1. We thus detected an immediate trade-off between attempting to breed and survival in this population; however, the earlier individuals recruited, and the more breeding experience they accumulated, the smaller the cost. 5. Lastly, unobserved heterogeneity across individuals improved model fit more (1*3 times) than fixed and dynamic sources of observed heterogeneity in reproductive investment, demonstrating that it is critical to account for both sources of individual heterogeneity when studying survival trajectories. Only after simultaneously accounting for both sources of heterogeneity were we able to detect the 'cost' of immediate reproductive investment on survival and the 'benefit' of cumulative breeding attempts (experience), a proxy to individual quality.
not annotated - annotated - LINNAEUS only
Developmental plasticity of immune defence in two life-history ecotypes of the garter snake, Thamnophis elegans - a common-environment experiment.
1. Ecoimmunological theory predicts a link between life-history and immune-defence strategies such that fast-living organisms should rely more on constitutive innate defences compared to slow-living organisms. An untested assumption of this hypothesis is that the variation in immune defence associated with variation in life history has a genetic basis. 2. Replicate populations of two life-history ecotypes of the garter snake Thamnophis elegans provide an ideal system in which to test this assumption. Free-ranging snakes of the fast-living ecotype, which reside in lakeshore habitats, show higher levels of three measures of constitutive innate immunity than those of the slow-living ecotype, which inhabit meadows around the lake. Although this pattern is consistent with the ecoimmunological pace-of-life hypothesis, environmental differences between the lakeshore and meadow habitats could also explain the observed differences in immune defence. 3. We performed a common-environment experiment to distinguish between these alternatives. Snakes born and raised in common-environment conditions reflected the immune phenotype of their native habitats when sampled at 4 months of age (i.e. fast-living lakeshore snakes showed higher levels of natural antibodies, complement activity and bactericidal competence than slow-living meadow snakes), but no longer showed differences when 19 months old. 4. This suggests that the differences in innate immunity observed between the two ecotypes have an important - and likely age-specific - environmental influence, with these immune components showing developmental plasticity. A genetic effect in early life may also be present, but further research is needed to confirm this possibility and therefore provide a more definitive test of the ecoimmunological pace-of-life hypothesis in this system.
not annotated - annotated - LINNAEUS only
Prey, predators, parasites: intraguild predation or simpler community modules in disguise?
1. Competition and predation are at the heart of community ecology. The theoretical concept of intraguild predation (IGP) combines these key interactions in a single community module. Because IGP is believed to be ubiquitous in nature, it has been subject to extensive research, and there exists a well-developed theoretical framework. 2. We show that a general class of IGP models can be transformed to simpler, but equivalent community structures. This rather unexpected simplification depends critically on the property of 'indiscriminate predation', which we define broadly as the top-predator not distinguishing between its two different prey species. 3. In a broader context, the great importance of IGP and of the simplifying transformation we report here is enhanced by the recent insight that the basic IGP structure extends naturally to host-parasitoid and host-pathogen communities. We show that parasites infecting prey (predators) tend to render IGP effectively into exploitative competition (tritrophic food chain, respectively). 4. The equivalence between the original and simplified community module makes it possible to take advantage from already existing insights. We illustrate this by means of an eco-epidemiological IGP model that is strikingly similar to a classical exploitative competition model. 5. The change of perspective on certain community modules may contribute to a better understanding of food web dynamics. In particular, it may help explain the interactions in food webs that include parasites. Given the ubiquity of parasitism, food webs may appear in a different light when they are transformed to their simplified analogue.
not annotated - annotated - LINNAEUS only
Individual differences in reproductive costs examined using multi-state methods.
1. Trade-offs among life-history traits are common because individuals have to partition limited resources between multiple traits. Reproductive costs are generally assumed to be high, resulting in reduced survival and fecundity in the following year. However, it is common to find positive rather than negative correlations between life-history traits. 2. Here, we use a data set from the individual-based study of red deer on the Isle of Rum to examine how these costs vary between individuals and at different ages, using multi-state mark-recapture methodology. 3. Females that had reproduced frequently in the past incurred lower costs of reproduction in terms of survival in the following year and were more likely to reproduce in two consecutive years. Older individuals and those that had not reproduced frequently exhibited higher costs. 4. These results highlight the importance of considering heterogeneity and individual quality when examining trade-offs and demonstrate the effectiveness of using detailed long-term data sets to explore life-history strategies using multi-state mark-recapture models.
not annotated - annotated - LINNAEUS only
Functional analysis of the fungal/plant class chitinase family in Aspergillus fumigatus.
A quintuple mutant was constructed to delete the entire family of the fungal/plant (class III) chitinases of Aspergillus fumigatus. Only a limited reduction in the total chitinolytic activity was seen for the different chitinase mutants including the quintuple mutant. In spite of this reduction in chitinolytic activity, no growth or germination defects were observed in these chitinase mutants. This result demonstrated that the fungal/plant chitinases do not have an essential role in the morphogenesis of A. fumigatus. A slight diminution of the growth during autolysis was seen for the quintuple mutant suggesting that class III chitinases may play only a nutritional role during this phase of the cycle, retarding fungal death.
not annotated - annotated - LINNAEUS only
Early-onset versus late-onset Alzheimer's disease: the case of the missing APOE epsilo4 allele.
Some patients with early-onset Alzheimer's disease (AD) present with a distinct phenotype. Typically, the first and most salient characteristic of AD is episodic memory impairment. A few patients, however, present with focal cortical, non-memory symptoms, such as difficulties with language, visuospatial, or executive functions. These presentations are associated with specific patterns of atrophy and frequently with a young age at onset. Age is not, however, the only determinant of phenotype; underlying factors, especially genetic factors, seem also to affect phenotype and predispose patients to younger or older age at onset. Importantly, patients with atypical early-onset disease seldom carry the APOE epsilo4 allele, which is the most important risk factor for lowering the age of onset in patients with AD. Additionally, theAPOE epsilo4 genotype seems to predispose patients to vulnerability in the medial temporal areas, which leads to memory loss. Conversely, patients negative for the APOE epsilo4 allele and with early-onset AD are more likely to be predisposed to vulnerability of cerebral networks beyond the medial temporal lobes. Other factors are probably involved in determining the pattern of atrophy, but these are currently unknown.
not annotated - annotated - LINNAEUS only
Breathing some air into the single-species vacuum: multi-species responses to environmental change.
Studies of ecological responses to climate change have often analysed species independently of each other, yet interactions between species are fundamental aspects of ecology. Mutshinda, O'Hara & Woiwod (2011) used light-trapping data for Lepidoptera (moths) to examine population responses to intraspecific effects and effects of winter rainfall and temperature. They show how Bayesian hierarchical models can analyse residual correlations among species' responses, illustrating an approach to account for and measure dependencies that are not fully explained by the candidate explanatory variables. A key result is that the responses of the different moth species did not appear to have strong residual correlation (Mutshinda, O'Hara & Woiwod 2011). These analyses provide an approach for synthesising across species and can better inform ecological responses to environmental change.
not annotated - annotated - LINNAEUS only
Functional analysis of a mitochondrial phosphopantetheinyl transferase (PPTase) gene pptB in Aspergillus fumigatus.
The mitochondrial phosphopantetheinyl transferase gene pptB of the opportunistic pathogen Aspergillus fumigatus has been identified and characterised. Unlike pptA, which is required for lysine biosynthesis, secondary metabolism, and iron assimilation, pptB is essential for viability. PptB is located in the mitochondria. In vitro expression of pptA and pptB has shown that PptB is specific for the mitochondrial acyl carrier protein AcpA.
not annotated - annotated - LINNAEUS only
Borderline personality disorder.
Recent research findings have contributed to an improved understanding and treatment of borderline personality disorder. This disorder is characterised by severe functional impairments, a high risk of suicide, a negative effect on the course of depressive disorders, extensive use of treatment, and high costs to society. The course of this disorder is less stable than expected for personality disorders. The causes are not yet clear, but genetic factors and adverse life events seem to interact to lead to the disorder. Neurobiological research suggests that abnormalities in the frontolimbic networks are associated with many of the symptoms. Data for the effectiveness of pharmacotherapy vary and evidence is not yet robust. Specific forms of psychotherapy seem to be beneficial for at least some of the problems frequently reported in patients with borderline personality disorder. At present, there is no evidence to suggest that one specific form of psychotherapy is more effective than another. Further research is needed on the diagnosis, neurobiology, and treatment of borderline personality disorder.
not annotated - annotated - LINNAEUS only
Spatio-temporal variation in territory quality and oxidative status: a natural experiment in the Seychelles warbler (Acrocephalus sechellensis).
1. Fluctuations in the quality of the habitat in which an animal lives can have major consequences for its behaviour and physiological state. In poor-quality habitat with low food availability, metabolically intensive foraging activity is likely to result in increased generation of reactive oxygen species, while scarcity of food can lead to a weakening of exogenously derived antioxidant defences. The consequent oxidant/antioxidant imbalance may lead to elevated oxidative stress. 2. Although the link between food availability and oxidative stress has been studied in the laboratory, very little is known about this relationship in the wild. Here, we investigate the association between territory quality (measured through food availability) and oxidative stress in the Seychelles warbler (Acrocephalus sechellensis). 3. Seychelles warblers are insectivorous birds that inhabit a fixed feeding territory year round. Individuals experience profound and rapid local fluctuations in territory quality within these territories, owing to changing patterns of vegetation defoliation resulting from seasonal changes in prevailing wind direction and wind-borne salt spray. 4. As expected, oxidant generation (measured as reactive oxygen metabolites; ROMs) was higher when territory quality was low, but there was no correlation between territory quality and antioxidant capacity (OXY). The negative correlation between territory quality and ROMs was significant between individuals and approached significance within individuals, indicating that the pattern resulted from individual responses to environmental variation. 5. ROMs and OXY levels within individuals were positively correlated, but the relationship between territory quality and ROMs persisted after including OXY as a covariate, implying that oxidative stress occurs in low territory quality conditions. 6. Our results indicate that the oxidative stress balance of an individual is sensitive to relatively short-term changes in territory quality, which may have consequences for the birds' fitness.
not annotated - annotated - LINNAEUS only
Ice-cover effects on competitive interactions between two fish species.
1. Variations in the strength of ecological interactions between seasons have received little attention, despite an increased focus on climate alterations on ecosystems. Particularly, the winter situation is often neglected when studying competitive interactions. In northern temperate freshwaters, winter implies low temperatures and reduced food availability, but also strong reduction in ambient light because of ice and snow cover. Here, we study how brown trout [Salmo trutta (L.)] respond to variations in ice-cover duration and competition with Arctic charr [Salvelinus alpinus (L.)], by linking laboratory-derived physiological performance and field data on variation in abundance among and within natural brown trout populations. 2. Both Arctic charr and brown trout reduced resting metabolic rate under simulated ice-cover (darkness) in the laboratory, compared to no ice (6-h daylight). However, in contrast to brown trout, Arctic charr was able to obtain positive growth rate in darkness and had higher food intake in tank experiments than brown trout. Arctic charr also performed better (lower energy loss) under simulated ice-cover in a semi-natural environment with natural food supply. 3. When comparing brown trout biomass across 190 Norwegian lakes along a climate gradient, longer ice-covered duration decreased the biomass only in lakes where brown trout lived together with Arctic charr. We were not able to detect any effect of ice-cover on brown trout biomass in lakes where brown trout was the only fish species. 4. Similarly, a 25-year time series from a lake with both brown trout and Arctic charr showed that brown trout population growth rate depended on the interaction between ice breakup date and Arctic charr abundance. High charr abundance was correlated with low trout population growth rate only in combination with long winters. 5. In conclusion, the two species differed in performance under ice, and the observed outcome of competition in natural populations was strongly dependent on duration of the ice-covered period. Our study shows that changes in ice phenology may alter species interactions in Northern aquatic systems. Increased knowledge of how adaptations to winter conditions differ among coexisting species is therefore vital for our understanding of ecological impacts of climate change.
not annotated - annotated - LINNAEUS only
Predicting the post-fire responses of animal assemblages: testing a trait-based approach using spiders.
1. Developing a predictive understanding of how species assemblages respond to fire is a key conservation goal. In moving from solely describing patterns following fire to predicting changes, plant ecologists have successfully elucidated generalizations based on functional traits. Using species traits might also allow better predictions for fauna, but there are few empirical tests of this approach. 2. We examined whether species traits changed with post-fire age for spiders in 27 sites, representing a chronosequence of 0-20 years post-fire. We predicted a priori whether spiders with ten traits associated with survival, dispersal, reproduction, resource-utilization and microhabitat occupation would increase or decrease with post-fire age. We then tested these predictions using a direct (fourth-corner on individual traits and composite traits) and an indirect (emergent groups) approach, comparing the benefits of each and also examining the degree to which traits were intercorrelated. 3. For the seven individual traits that were significant, three followed predictions (body size, abundance of burrow ambushers and burrowers was greater in recently burnt sites); two were opposite (species with heavy sclerotisation of the cephalothorax and longer time to maturity were in greater abundance in long unburnt and recently burnt sites respectively); and two displayed response patterns more complex than predicted (abdominal scutes displayed a U-shaped response and dispersal ability a hump shaped curve). However, within a given trait, there were few significant differences among post-fire ages. 4. Several traits were intercorrelated and scores based on composite traits used in a fourth-corner analysis found significant patterns, but slightly different to those using individual traits. Changes in abundance with post-fire age were significant for three of the five emergent groups. The fourth-corner analysis yielded more detailed results, but overall we consider the two approaches complementary. 5. While we found significant differences in traits with post-fire age, our results suggest that a trait-based approach may not increase predictive power, at least for the assemblages of spiders we studied. That said, there are many refinements to faunal traits that could increase predictive power.
not annotated - annotated - LINNAEUS only
Analysis of expressed sequence tags from Maize mosaic rhabdovirus-infected gut tissues of Peregrinus maidis reveals the presence of key components of insect innate immunity.
The corn planthopper, Peregrinus maidis, causes direct feeding damage to plants and transmits Maize mosaic rhabdovirus (MMV) in a persistent-propagative manner. MMV must cross several insect tissue layers for successful transmission to occur, and the gut serves as an important barrier for rhabdovirus transmission. In order to facilitate the identification of proteins that may interact with MMV either by facilitating acquisition or responding to virus infection, we generated and analysed the gut transcriptome of P. maidis. From two normalized cDNA libraries, we generated a P. maidis gut transcriptome composed of 20,771 expressed sequence tags (ESTs). Assembly of the sequences yielded 1860 contigs and 14,032 singletons, and biological roles were assigned to 5793 (36%). Comparison of P. maidis ESTs with other insect amino acid sequences revealed that P. maidis shares greatest sequence similarity with another hemipteran, the brown planthopper Nilaparvata lugens. We identified 202 P. maidis transcripts with putative homology to proteins associated with insect innate immunity, including those implicated in the Toll, Imd, JAK/STAT, Jnk and the small-interfering RNA-mediated pathways. Sequence comparisons between our P. maidis gut EST collection and the currently available National Center for Biotechnology Information EST database collection for Ni. lugens revealed that a pathogen recognition receptor in the Imd pathway, peptidoglycan recognition protein-long class (PGRP-LC), is present in these two members of the family Delphacidae; however, these recognition receptors are lacking in the model hemipteran Acyrthosiphon pisum. In addition, we identified sequences in the P. maidis gut transcriptome that share significant amino acid sequence similarities with the rhabdovirus receptor molecule, acetylcholine receptor (AChR), found in other hosts. This EST analysis sheds new light on immune response pathways in hemipteran guts that will be useful for further dissecting innate defence response pathways to rhabdovirus infection.
not annotated - annotated - LINNAEUS only
Genetic analysis of the xenobiotic resistance-associated ABC gene subfamilies of the Lepidoptera.
Some ATP-binding cassette (ABC) transporters of subfamilies B, C and G confer resistance to xenobiotics including insecticides. We identified genes of these subfamilies expressed by the lepidopterans Trichoplusia ni and Bombyx mori. The B. mori genome includes eight, six and 13 ABC-B, -C and -G genes, respectively, which encode P-glycoprotein, multidrug resistance protein, MRP, and breast cancer resistance protein, BCRP, homologues. Among the ABC-C and -G subfamilies, gene duplication contributes to protein diversity. We have identified three ABC-B and two ABC-C T. ni genes. Analyses of the T. ni MRP (TrnMRP) revealed unique features, including the potential for TrnMRP4 hyperglycosylation and the alternative splicing of TrnMRP1. Taken together, these attributes of moth multidrug resistance-associated ABCs may confer distinct functional capacities to xenobiotic efflux.
not annotated - annotated - LINNAEUS only
Effects of Wolbachia on mtDNA variation and evolution in natural populations of Tetranychus urticae Koch.
We investigated the effects of Wolbachia infection on mtDNA variation in spider mites by sequencing a portion of the mitochondrial cytochrome oxidase I (COI) gene from 198 individuals of known infection status. Four Wolbachia strains were described in the current study, namely wUrtOri1, wUrtOri2, wUrtOri3 and wUrtCon1. As predicted, the haplotype and nucleotide diversity were lower in infected individuals than in uninfected individuals. However, these mtDNA haplotype data are not entirely concordant with the surface protein of wolbachia (wsp) sequence data and both infected and uninfected individuals were found of the same haplotype. Although values of Tajima's D and Fu & Li's F were consistently less than zero for most infected groups, McDonald-Kreitman tests suggested that the patterns of variation were different from those expected under neutrality in only the uninfected group. Thus, the neutrality tests do not show a clear effect of Wolbachia infection on patterns of mtDNA variation and substitution in spider mites.
not annotated - annotated - LINNAEUS only
Decompression illness.
Decompression illness is caused by intravascular or extravascular bubbles that are formed as a result of reduction in environmental pressure (decompression). The term covers both arterial gas embolism, in which alveolar gas or venous gas emboli (via cardiac shunts or via pulmonary vessels) are introduced into the arterial circulation, and decompression sickness, which is caused by in-situ bubble formation from dissolved inert gas. Both syndromes can occur in divers, compressed air workers, aviators, and astronauts, but arterial gas embolism also arises from iatrogenic causes unrelated to decompression. Risk of decompression illness is affected by immersion, exercise, and heat or cold. Manifestations range from itching and minor pain to neurological symptoms, cardiac collapse, and death. First-aid treatment is 100% oxygen and definitive treatment is recompression to increased pressure, breathing 100% oxygen. Adjunctive treatment, including fluid administration and prophylaxis against venous thromboembolism in paralysed patients, is also recommended. Treatment is, in most cases, effective although residual deficits can remain in serious cases, even after several recompressions.
not annotated - annotated - LINNAEUS only
The genetic basis for 3-ADON and 15-ADON trichothecene chemotypes in Fusarium.
Certain Fusarium species cause head blight of wheat and other small grains worldwide and produce trichothecene mycotoxins. These mycotoxins can induce toxicoses in animals and humans and can contribute to the ability of some fusaria to cause plant disease. Production of the trichothecene 3-acetyldeoxynivalenol (3-ADON) versus 15-acetyldeoxynivalenol (15-ADON) is an important phenotypic difference within and among some Fusarium species. However, until now, the genetic basis for this difference in chemotype has not been identified. Here, we identified consistent DNA sequence differences in the coding region of the trichothecene biosynthetic gene TRI8 in 3-ADON and 15-ADON strains. Functional analyses of the TRI8 enzyme (Tri8) in F. graminearum, the predominant cause of wheat head blight in North America and Europe, revealed that Tri8 from 3-ADON strains catalyzes deacetylation of the trichothecene biosynthetic intermediate 3,15-diacetyldeoxynivalenol at carbon 15 to yield 3-ADON, whereas Tri8 from 15-ADON strains catalyzes deacetylation of 3,15-diacetyldeoxynivalenol at carbon 3 to yield 15-ADON. Fusarium strains that produce the trichothecene nivalenol have a Tri8 that functions like that in 15-ADON strains. TRI3, which encodes a trichothecene carbon 15 acetyltransferase, was found to be functional in all three chemotypes. Together, our data indicate that differential activity of Tri8 determines the 3-ADON and 15-ADON chemotypes in Fusarium.
not annotated - annotated - LINNAEUS only
Influence of proximity to a geographical range limit on the physiology of a tropical bird.
1. Species' geographical ranges can be limited by a variety of biotic and abiotic factors. Physiological challenge in response to unsuitable environmental conditions can establish limits to geographical ranges. 2. We studied the physiology of Song Wrens (Cyphorhinus phaeocephalus) across their geographical range on the isthmus of Panama, an area characterized by a strong rainfall gradient. Wrens are common on the Caribbean slope of the isthmus where annual rainfall is greatest, but wren abundance declines towards the south as annual rainfall declines. Song Wrens are completely absent from the driest third of the isthmus. 3. We searched for the existence of a physiologically induced distribution limit by measuring body condition (an integrative measure of energy balance), hematocrit (% packed red blood cells in a given blood sample), and corticosterone levels (CORT, a steroid hormone that regulates the availability of energy and the endocrine stress response) in males and females. We caught birds by luring them into nets when they responded to playback of conspecific song. 4. Wrens living in drier habitat near the geographical range edge were significantly more likely to have abnormally low hematocrit scores. Baseline CORT levels were negatively associated with rainfall in one of our three best-fit path models, indicating potential energetic challenge in some individuals. Maximum CORT levels during a 60-min period of restraint correlated significantly only with sex, being higher in females. Birds with the poorest body condition lived at the dry end of the gradient. Birds on the wet end of the gradient responded fastest to conspecific song. 5. Environmental conditions vary across geographical ranges and may influence the physiological conditions of organisms, thereby enforcing limits to species' distributions. Highly specialized species, such as birds of the rain forest understory, may be especially susceptible to environmental variation associated with changing climatic conditions.
not annotated - annotated - LINNAEUS only
New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina).
Sensing of environmental signals is often mediated by G-protein coupled receptors and their cognate heterotrimeric G-proteins. In Trichoderma reesei (Hypocrea jecorina) the signals transmitted via the G-protein alpha subunits GNA1 and GNA3 cause considerable modulation of cellulase transcript levels and the extent of this adjustment is dependent on the light status. We therefore intended to elucidate the underlying mechanism connecting light response and heterotrimeric G-protein signaling. Analysis of double mutant strains showed that constitutive activation of GNA1 or GNA3 in the absence of the PAS/LOV domain protein ENVOY (ENV1) leads to the phenotype of constitutive G-alpha activation in darkness. In light, however the deletion-phenotype of Deltaenv1 was observed with respect to growth, conidiation and cellulase gene transcription. Additionally deletion of env1 causes decreased intracellular cAMP accumulation, even upon constitutive activation of GNA1 or GNA3. While supplementation of cAMP caused an even more severe growth phenotype of all strains lacking env1 in light, addition of the phosphodiesterase inhibitor caffeine rescued the growth phenotype of these strains. ENV1 is consequently suggested to connect the light response pathway with nutrient signaling by the heterotrimeric G-protein cascade by adjusting transcript levels of gna1 and gna3 and action on cAMP levels - presumably through inhibition of a phosphodiesterase.
not annotated - annotated - LINNAEUS only
Chronic diseases and injuries in India.
Chronic diseases (eg, cardiovascular diseases, mental health disorders, diabetes, and cancer) and injuries are the leading causes of death and disability in India, and we project pronounced increases in their contribution to the burden of disease during the next 25 years. Most chronic diseases are equally prevalent in poor and rural populations and often occur together. Although a wide range of cost-effective primary and secondary prevention strategies are available, their coverage is generally low, especially in poor and rural populations. Much of the care for chronic diseases and injuries is provided in the private sector and can be very expensive. Sufficient evidence exists to warrant immediate action to scale up interventions for chronic diseases and injuries through private and public sectors; improved public health and primary health-care systems are essential for the implementation of cost-effective interventions. We strongly advocate the need to strengthen social and policy frameworks to enable the implementation of interventions such as taxation on bidis (small hand-rolled cigarettes), smokeless tobacco, and locally brewed alcohols. We also advocate the integration of national programmes for various chronic diseases and injuries with one another and with national health agendas. India has already passed the early stages of a chronic disease and injury epidemic; in view of the implications for future disease burden and the demographic transition that is in progress in India, the rate at which effective prevention and control is implemented should be substantially increased. The emerging agenda of chronic diseases and injuries should be a political priority and central to national consciousness, if universal health care is to be achieved.
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Health care and equity in India.
In India, despite improvements in access to health care, inequalities are related to socioeconomic status, geography, and gender, and are compounded by high out-of-pocket expenditures, with more than three-quarters of the increasing financial burden of health care being met by households. Health-care expenditures exacerbate poverty, with about 39 million additional people falling into poverty every year as a result of such expenditures. We identify key challenges for the achievement of equity in service provision, and equity in financing and financial risk protection in India. These challenges include an imbalance in resource allocation, inadequate physical access to high-quality health services and human resources for health, high out-of-pocket health expenditures, inflation in health spending, and behavioural factors that affect the demand for appropriate health care. Use of equity metrics in monitoring, assessment, and strategic planning; investment in development of a rigorous knowledge base of health-systems research; development of a refined equity-focused process of deliberative decision making in health reform; and redefinition of the specific responsibilities and accountabilities of key actors are needed to try to achieve equity in health care in India. The implementation of these principles with strengthened public health and primary-care services will help to ensure a more equitable health care for India's population.
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Reproductive health, and child health and nutrition in India: meeting the challenge.
India, with a population of more than 1 billion people, has many challenges in improving the health and nutrition of its citizens. Steady declines have been noted in fertility, maternal, infant and child mortalities, and the prevalence of severe manifestations of nutritional deficiencies, but the pace has been slow and falls short of national and Millennium Development Goal targets. The likely explanations include social inequities, disparities in health systems between and within states, and consequences of urbanisation and demographic transition. In 2005, India embarked on the National Rural Health Mission, an extraordinary effort to strengthen the health systems. However, coverage of priority interventions remains insufficient, and the content and quality of existing interventions are suboptimum. Substantial unmet need for contraception remains, adolescent pregnancies are common, and access to safe abortion is inadequate. Increases in the numbers of deliveries in institutions have not been matched by improvements in the quality of intrapartum and neonatal care. Infants and young children do not get the health care they need; access to effective treatment for neonatal illness, diarrhoea, and pneumonia shows little improvement; and the coverage of nutrition programmes is inadequate. Absence of well functioning health systems is indicated by the inadequacies related to planning, financing, human resources, infrastructure, supply systems, governance, information, and monitoring. We provide a case for transformation of health systems through effective stewardship, decentralised planning in districts, a reasoned approach to financing that affects demand for health care, a campaign to create awareness and change health and nutrition behaviour, and revision of programmes for child nutrition on the basis of evidence. This agenda needs political commitment of the highest order and the development of a people's movement.
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Human resources for health in India.
India has a severe shortage of human resources for health. It has a shortage of qualified health workers and the workforce is concentrated in urban areas. Bringing qualified health workers to rural, remote, and underserved areas is very challenging. Many Indians, especially those living in rural areas, receive care from unqualified providers. The migration of qualified allopathic doctors and nurses is substantial and further strains the system. Nurses do not have much authority or say within the health system, and the resources to train them are still inadequate. Little attention is paid during medical education to the medical and public health needs of the population, and the rapid privatisation of medical and nursing education has implications for its quality and governance. Such issues are a result of underinvestment in and poor governance of the health sector--two issues that the government urgently needs to address. A comprehensive national policy for human resources is needed to achieve universal health care in India. The public sector will need to redesign appropriate packages of monetary and non-monetary incentives to encourage qualified health workers to work in rural and remote areas. Such a policy might also encourage task-shifting and mainstreaming doctors and practitioners who practice traditional Indian medicine (ayurveda, yoga and naturopathy, unani, and siddha) and homoeopathy to work in these areas while adopting other innovative ways of augmenting human resources for health. At the same time, additional investments will be needed to improve the relevance, quantity, and quality of nursing, medical, and public health education in the country.
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Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys.
In recent years, a substantial amount of data on aquatic protists has been obtained from culture-independent molecular approaches, unveiling a large diversity and the existence of new lineages. However, sequences affiliated with minor groups (in terms of clonal abundance) have often been under-analyzed, and this hides a potentially relevant source of phylogenetic information. Here we have searched public databases for 18S rDNA sequences of chrysophytes, choanoflagellates and bicosoecids retrieved from molecular surveys of protists. These three groups are often considered to account for most of the heterotrophic flagellates, an important functional component in microbial food webs. They represented a significant fraction of clones in freshwater studies, whereas their relative clonal abundance was low in marine studies. The novelty displayed by this dataset was notable. Most environmental sequences were distant to sequences of cultured organisms, indicating a significant bias in the representation of taxa in culture. Moreover, they were often distant to sequences from other molecular surveys, suggesting an insufficient sequencing effort to characterize the in situ diversity of these groups. Phylogenetic trees with complete sequences present the most accurate representation of the diversity of these groups, with the emergence of several new clades formed exclusively by environmental sequences. Exhaustive data mining in sequence databases allowed the identification of new diversity hidden inside chrysophytes, choanoflagellates and bicosoecids.
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Gene expression analysis of wounding-induced root-to-shoot communication in Arabidopsis thaliana.
Root-to-shoot communication plays an important role in the adaptation to environmental stress. In this study, we established a model system for root-to-shoot signalling to observe global gene expression in Arabidopsis thaliana. The roots of Arabidopsis seedlings were wounded and the expression in the shoots of 68 and 5 genes was up-regulated threefold at 30 min and 6 h post-injury, respectively. These genes were designated early and late Root-to-Shoot responsive (RtS) genes, respectively. Many of the early RtS genes were found to encode transcription factors such as AtERFs, whereas others were associated with jasmonic acid (JA) and ethylene (ET). Some of the late RtS genes were shown to be regulated by 12-oxo-phytodienoic acid (OPDA). In fact, elevated levels of JA and OPDA were detected in the shoots of seedlings 30 min and 6 h, respectively, after wounding of the roots. A mutant analysis revealed that JA and ET are involved in the expression of the early RtS genes. Thus, root-to-shoot communication for many RtS genes is associated with the systemic production of JA, OPDA and possibly ET.
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Effects of the hydraulic coupling between xylem and phloem on diurnal phloem diameter variation.
Measurements of diurnal diameter variations of the xylem and phloem are a promising tool for studying plant hydraulics and xylem-phloem interactions in field conditions. However, both the theoretical framework and the experimental verification needed to interpret phloem diameter data are incomplete. In this study, we analytically evaluate the effects of changing the radial conductance between the xylem and the phloem on phloem diameter variations and test the theory using simple manipulation experiments. Our results show that phloem diameter variations are mainly caused by changes in the radial flow rate of water between the xylem and the phloem. Reducing the hydraulic conductance between these tissues decreases the amplitude of phloem diameter variation and increases the time lag between xylem and phloem diameter variation in a predictable manner. Variation in the amplitude and timing of diameter variations that cannot be explained by changes in the hydraulic conductance, could be related to changes in the osmotic concentration in the phloem.
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Light exerts multiple levels of influence on the Arabidopsis wound response.
Light plays important roles in modulating plant responses to attack by pests and pathogens. Here, we test the hypothesis that darkness modifies the response to wounding, and examine possible mechanisms for such an effect. We investigated changes in the Arabidopsis transcriptome following a light-dark transition and the response to wounding either in the light or in the dark. The transcriptional response to the light-dark transition strongly resembles responses associated with carbon depletion. The dark shift and wound responses acted largely independently, but more complex interactions were identified at a number of levels. Darkness attenuates the overall transcriptional response to wounding, and we identified genes and physiological processes, such as anthocyanin accumulation, that exhibit light-dependent wound responses. Transcriptional activation of light-dependent wound-induced genes requires a chloroplast-derived signal originating from photosynthetic electron transport. We also present evidence of a role for the circadian clock in modifying wound responses. Our results show that darkness impacts on the wound response at a number of levels, which may imply differences in induced herbivore defences during the day and night.
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The effect of competition from neighbours on stomatal conductance in lettuce and tomato plants.
Competition decreased transpiration from young lettuce plants after 2 days, before any reductions in leaf area became apparent, and stomatal conductance (g(s) ) of lettuce and tomato plants was also reduced. Stomatal closure was not due to hydraulic signals or competition for nutrients, as soil water content, leaf water status and leaf nitrate concentrations were unaffected by neighbours. Competition-induced stomatal closure was absent in an abscisic acid (ABA)-deficient tomato mutant, flacca, indicating a fundamental involvement of ABA. Although tomato xylem sap ABA concentrations were unaffected by the presence of neighbours, ABA/pH-based stomatal modulation is still likely to underlie the response to competition, as soil and xylem sap alkalization was observed in competing plants. Competition also modulated leaf ethylene production, and treatment of lettuce plants with an ethylene perception inhibitor (1-methylcyclopropene) diminished the difference in g(s) between single and competing plants grown in a controlled environment room, but increased it in plants grown in the greenhouse: ethylene altered the extent of the stomatal response to competition. Effects of competition on g(s) are discussed in terms of the detection of the absence of neighbours: increases in g(s) and carbon fixation may allow faster initial space occupancy within an emerging community/crop.
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The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis.
In Arabidopsis, there are four homologs of class A1 heat shock factor (HSFA1) genes, which likely encode the master regulators of heat shock response (HSR). However, previous studies with double knockout (KO) mutants were unable to confirm this point probably due to functional redundancy. Here, we generated a quadruple KO (QK) and four triple KO mutants to dissect their functions. Our data show that members of the HSFA1 group not only play a pivotal role in HSR but also are involved in growth and development. Alterations in morphology and retardation in growth were observed in the quadruple but not in triple KO mutants. The basal and acquired thermotolerance capacity was dramatically decreased in the QK mutant but varied in triple KO mutants at different developmental stages. The transcriptomics profiles suggested that more than 65% of the heat stress (HS)-up-regulated genes were HSFA1 dependent. HSFA1s were also involved in the expression of several HS genes induced by H(2) O(2) , salt and mannitol, which is consistent with the increased sensitive phenotype of the QK mutant to the stress factors. In conclusion, the Arabidopsis HSFA1s function as the master regulators of HSR and participate as important components in other abiotic stress responses as well.
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Predicting the optimal prey group size from predator hunting behaviour.
1. How group size affects predator attack and success rate, and so prey vulnerability, is important in determining the nonlethal consequences of predation risk on animal populations and communities. Theory predicts that both predator attack success rate and the dilution effect decline exponentially with group size and that selection generates optimal group sizes at a 'risk threshold' above which antipredation benefits are outweighed by costs, such as those owing to higher attack rates. 2. We examined whether flock size risk thresholds for attack rate, success rate or dilution differed, and therefore whether the strength of selection for group size differed for these three factors, using a system of redshank Tringa totanus flocks being hunted by Eurasian sparrowhawks Accipiter nisus. We also asked which of the three thresholds, on their own or in combination, predicted the most commonly observed group size. 3. Mean redshank flock size increased with a very gradual quadratic function (i.e. approximately linearly) with population size, although at a rate half that possible; when population size was not limiting, individuals almost always avoided flocks of less than 30 and birds were frequently in flocks up to at least 80. Sparrowhawk attack rate showed a quadratic relationship with flock size and peaked at 55 redshanks. Sparrowhawk attack success rate, however, declined exponentially, becoming less steep at flock sizes of about 40 and remaining uniformly low (a 95% decrease) by 70. Combined with dilution, individual risk of death per attack decreased by 95% when group size reached 30 (20 for the dilution effect alone). 4. Redshanks most commonly formed group sizes that gained the maximum individual predation risk reduction. They also commonly formed group sizes far above any further substantial advantages from the dilution effect or from reducing attack rate, but that continued to reduce predation risk by lowering attack success rate. Individuals did not always form the largest groups possible which we suggest is because individual variation in risk-taking subdivides the population. This places a constraint on the ability of individuals to compensate for predation risk and will have a variety of important effects on animal populations.
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Ecosystem engineering and predation: the multi-trophic impact of two ant species.
1. Ants are ubiquitous ecosystem engineers and generalist predators and are able to affect ecological communities via both pathways. They are likely to influence any other terrestrial arthropod group either directly or indirectly caused by their high abundance and territoriality. 2. We studied the impact of two ant species common in Central Europe, Myrmica rubra and Lasius niger, on an arthropod community. Colony presence and density of these two ant species were manipulated in a field experiment from the start of ant activity in spring to late summer. 3. The experiment revealed a positive influence of the presence of one ant colony on densities of decomposers, herbivores and parasitoids. However, in the case of herbivores and parasitoids, this effect was reversed in the presence of two colonies. 4. Generally, effects of the two ant species were similar with the exception of their effect on Braconidae parasitoid densities that responded positively to one colony of M. rubra but not of L. niger. 5. Spider density was not affected by ant colony manipulation, but species richness of spiders responded positively to ant presence. This effect was independent of ant colony density, but where two colonies were present, spider richness was significantly greater in plots with two M. rubra colonies than in plots with one colony of each ant species. 6. To test whether the positive ecosystem engineering effects were purely caused by modified properties of the soil, we added in an additional experiment (i) the soil from ant nests (without ants) or (ii) unmodified soil or (iii) ant nests (including ants) to experimental plots. Ant nest soil on its own did not have a significant impact on densities of decomposers, herbivores or predators, which were significantly, and positively, affected by the addition of an intact nest. 7. The results suggest an important role of both ant species in the grassland food web, strongly affecting the densities of decomposers, herbivores and higher trophic levels. We discuss how the relative impact via bottom-up and top-down effects of ants depends on nest density, with a relatively greater top-down predatory impact at higher densities.
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Constraints on host choice: why do parasitic birds rarely exploit some common potential hosts?
1. Why are some common and apparently suitable resources avoided by potential users? This interesting ecological and evolutionary conundrum is vividly illustrated by obligate brood parasites. Parasitic birds lay their eggs into nests of a wide range of host species, including many rare ones, but do not parasitize some commonly co-occurring potential hosts. 2. Attempts to explain the absence of parasitism in common potential hosts are limited and typically focused on single-factor explanations while ignoring other potential factors. We tested why thrushes Turdus spp. are extremely rarely parasitized by common cuckoos Cuculus canorus despite breeding commonly in sympatry and building the most conspicuous nests among forest-breeding passerines. 3. No single examined factor explained cuckoo avoidance of thrushes. Life-history traits of all six European thrush species and the 10 most frequently used cuckoo hosts in Europe were similar except body/egg size, nest design and nestling diet. 4. Experiments (n = 1211) in several populations across Europe showed that host defences at egg-laying and incubation stages did not account for the lack of cuckoo parasitism in thrushes. However, cross-fostering experiments disclosed that various factors during the nestling period prevent cuckoos from successfully parasitizing thrushes. Specifically, in some thrush species, the nest cup design forced cuckoo chicks to compete with host chicks with fatal consequences for the parasite. Other species were reluctant to care even for lone cuckoo chicks. 5. Importantly, in an apparently phylogenetically homogenous group of hosts, there were interspecific differences in factors responsible for the absence of cuckoo parasitism. 6. This study highlights the importance of considering multiple potential factors and their interactions for understanding absence of parasitism in potential hosts of parasitic birds. In the present study, comparative and experimental procedures are integrated, which represent a novel approach that should prove useful for the understanding of interspecific ecological relationships in general.
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Neurological complications of acute ischaemic stroke.
Complications after ischaemic stroke, including both neurological and medical complications, are a major cause of morbidity and mortality. Neurological complications, such as brain oedema or haemorrhagic transformation, occur earlier than do medical complications and can affect outcomes with potential serious short-term and long-term consequences. Some of these complications could be prevented or, when this is not possible, early detection and proper management could be effective in reducing the adverse effects. However, there is little evidence-based data to guide the management of these neurological complications. There is a clear need for improved surveillance and specific interventions for the prevention, early diagnosis, and proper management of neurological complications during the acute phase of stroke to reduce stroke morbidity and mortality.
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The decoupling of abundance and species richness in lizard communities.
1. Patterns of species richness often correlate strongly with measures of energy. The more individuals hypothesis (MIH) proposes that this relationship is facilitated by greater resources supporting larger populations, which are less likely to become extinct. Hence, the MIH predicts that community abundance and species richness will be positively related. 2. Recently, Buckley & Jetz (2010, Journal of Animal Ecology, 79, 358-365) documented a decoupling of community abundance and species richness in lizard communities in south-west United States, such that richer communities did not contain more individuals. They predicted, as a consequence of the mechanisms driving the decoupling, a more even distribution of species abundances in species-rich communities, evidenced by a positive relationship between species evenness and species richness. 3. We found a similar decoupling of the relationship between abundance and species richness for lizard communities in semi-arid south-eastern Australia. However, we note that a positive relationship between evenness and richness is expected because of the nature of the indices used. We illustrate this mathematically and empirically using data from both sets of lizard communities. When we used a measure of evenness, which is robust to species richness, there was no relationship between evenness and richness in either data set. 4. For lizard communities in both Australia and the United States, species dominance decreased as species richness increased. Further, with the iterative removal of the first, second and third most dominant species from each community, the relationship between abundance and species richness became increasingly more positive. 5. Our data support the contention that species richness in lizard communities is not directly related to the number of individuals an environment can support. We propose an alternative hypothesis regarding how the decoupling of abundance and richness is accommodated; namely, an inverse relationship between species dominance and species richness, possibly because of ecological release.
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Food chain length and omnivory determine the stability of a marine subtidal food web.
1. Using a subtidal marine food web as a model system, we examined how food chain length (predators present or absent) and the prevalence of omnivory influenced temporal stability (and its components) of herbivores and plants. We held the density of top predators constant but manipulated their identity to generate a gradient in omnivory prevalence. 2. We measured temporal stability as the inverse of the coefficient of variation of abundance over time. Predators and omnivory could influence temporal stability through effects on abundance (the 'abundance' effect), summed variance across taxa (the 'portfolio effect') or summed covariances among taxa (the 'covariance effect'). 3. We found that increasing food chain length by predator addition destabilized aggregate herbivore abundance through their cascading effects on abundances. Thus, predators destabilized herbivores through the overyielding effect. We also found that the stability of herbivore abundance and microalgae declined with increasing prevalence of omnivory among top predators. Aggregate macroalgae was not affected, but the stability of one algal taxon increased with the prevalence of omnivory. 4. Our results suggest that herbivores are more sensitive than plants to changes in food web structure because of predator additions by invasion or deletions such as might occur via harvesting and habitat loss.
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Are numbers enough? Colonizer phenotype and abundance interact to affect population dynamics.
1. Ecologists have long recognized that the number of colonizers entering a population can be a major driver of population dynamics, but still struggle to explain why the importance of colonizer supply varies so dramatically. While there are indications that differences in the phenotype among dispersing individuals could also be important to populations, the role of phenotypic variation relative to the number of individuals, and the extent to which they interact, remains unknown. 2. We simultaneously manipulated the phenotype (dispersal duration) and abundance of settlers of a marine bryozoan and measured subsequent population structure in the field. 3. Increases in the number of colonizing individuals increased the subsequent recruitment and biomass of populations, regardless of colonizer phenotype. However, the relationship between colonizer abundance and the subsequent reproductive yield of the population was strongly reduced in populations containing individuals that had long dispersal durations. 4. The interactive effects of colonizer phenotype and abundance on the reproductive yield of populations occurred because longer dispersal durations decreased the proportion of individuals that reproduced. In fact, populations established from a few individuals with short dispersal durations had similar reproductive yield to populations c. 30 times larger established from individuals with long dispersal durations. 5. Interactions between colonizer phenotype and abundance have important implications for predicting population dynamics beyond those previously provided by numerical abundance or recruit phenotype alone.
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A bicistronic, Ubiquitin-10 promoter-based vector cassette for transient transformation and functional analysis of membrane transport demonstrates the utility of quantitative voltage clamp studies on intact Arabidopsis root epidermis.
To date the use of fluorescent reporter constructs in analysing membrane transport has been limited primarily to cell lines expressing stably either the tagged transporter protein(s) or markers to identify lineages of interest. Strategies for transient expression have yet to be exploited in transport analysis, despite their wide application in cellular imaging studies. Here we describe a Gateway-compatible, bicistronic vector, incorporating the constitutive Ubiqutin-10 gene promoter of Arabidopsis that gives prolonged expression after transient transformation and enables fluorescence marking of cells without a fusion construct. We show that Arabidopsis root epidermal cells are readily transformed by co-cultivation with Agrobacterium and are tractable for quantitative electrophysiological analysis. As a proof of principle, we transiently transformed Arabidopsis with the bicistronic vector carrying GFP as the fluorescent marker and, separately, the integral plasma membrane protein SYP121 essential for the inward K+ channel current. We demonstrate that transient expression of SYP121 in syp121 mutant plants is sufficient to rescue the K+ current in vivo. The combination of transient expression and use of the bicistronic vector promises significant advantages for studies of membrane transport and nutrient acquisition in roots.
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Treatment of patients with essential tremor.
Essential tremor is a common movement disorder. Tremor severity and handicap vary widely, but most patients with essential tremor do not receive a diagnosis and hence are never treated. Furthermore, many patients abandon treatment because of side-effects or poor efficacy. A newly developed algorithm, based on the logarithmic relation between tremor amplitude and clinical tremor ratings, can be used to compare the magnitude of effect of available treatments. Drugs with established efficacy (propranolol and primidone) produce a mean tremor reduction of about 50%. Deep brain stimulation (DBS) in the thalamic nucleus ventrointermedius or neighbouring subthalamic structures reduces tremor by about 90%. However, no controlled trials of DBS have been done, and the best target is still uncertain. Better drugs are needed, and controlled trials are required to determine the safety and efficacy of DBS in the nucleus ventrointermedius and neighbouring subthalamic structures.
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Mechanisms of epileptogenesis and potential treatment targets.
Prevention of epileptogenesis after brain trauma is an unmet medical challenge. Recent molecular profiling studies have provided an insight into molecular changes that contribute to formation of ictogenic neuronal networks, including genes regulating synaptic or neuronal plasticity, cell death, proliferation, and inflammatory or immune responses. These mechanisms have been targeted to prevent epileptogenesis in animal models. Favourable effects have been obtained using immunosuppressants, antibodies blocking adhesion of leucocytes to endothelial cells, gene therapy driving expression of neurotrophic factors, pharmacological neurostimulation, or even with conventional antiepileptic drugs by administering them before the appearance of genetic epilepsy. Further studies are needed to clarify the optimum time window and aetiological specificity of treatments. Questions related to adverse events also need further consideration. Encouragingly, the recent experimental studies emphasise that the complicated process of epileptogenesis can be favourably modified, and that antiepileptogenesis as a treatment indication might not be an impossible mission.
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Pterin-based ornamental coloration predicts yolk antioxidant levels in female striped plateau lizards (Sceloporus virgatus).
1. Maternal investment in egg quality can have important consequences for offspring fitness. For example, yolk antioxidants can affect embryonic development as well as juvenile and adult phenotype. Thus, females may be selected to advertise their yolk antioxidant deposition to discriminatory males via ornamental signals, perhaps depending on the reproductive costs associated with signal production. 2. Female striped plateau lizards (Sceloporus virgatus) develop pterin-based orange colour patches during the reproductive season that influence male behaviour and that are positively associated with the phenotypic quality of the female and her offspring. Here, we assessed one potential developmental mechanism underlying the relationship between offspring quality and female ornamentation in S. virgatus, by examining the relationship between ornament expression and yolk antioxidant levels. 3. As expected, concentrations of the yolk antioxidants vitamin A, vitamin E and carotenoids (lutein and zeaxanthin) were strongly positively intercorrelated. Eggs from larger clutches had fewer antioxidants than eggs from smaller clutches, suggesting that females may be limited in antioxidant availability or use. Fertilized and unfertilized eggs did not differ in yolk antioxidant levels. 4. The size of a female's ornament was positively related to both the concentration and total amount of yolk antioxidants, and ornament colour was positively related to yolk antioxidant concentration. Thus, in S. virgatus, female ornaments may advertise egg quality. In addition, these data suggest that more ornamented females may produce higher-quality offspring, in part because their eggs contain more antioxidants. As the colour ornament of interest is derived from pterins, not carotenoids, direct resource trade-offs between ornaments and eggs may be eliminated, reducing reproductive costs associated with signalling. 5. This is the first example of a positive relationship between female ornamentation and yolk antioxidants in reptiles and may indicate the general importance of these patterns in oviparous vertebrates.
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Human resources for health in southeast Asia: shortages, distributional challenges, and international trade in health services.
In this paper, we address the issues of shortage and maldistribution of health personnel in southeast Asia in the context of the international trade in health services. Although there is no shortage of health workers in the region overall, when analysed separately, five low-income countries have some deficit. All countries in southeast Asia face problems of maldistribution of health workers, and rural areas are often understaffed. Despite a high capacity for medical and nursing training in both public and private facilities, there is weak coordination between production of health workers and capacity for employment. Regional experiences and policy responses to address these challenges can be used to inform future policy in the region and elsewhere. A distinctive feature of southeast Asia is its engagement in international trade in health services. Singapore and Malaysia import health workers to meet domestic demand and to provide services to international patients. Thailand attracts many foreign patients for health services. This situation has resulted in the so-called brain drain of highly specialised staff from public medical schools to the private hospitals. The Philippines and Indonesia are the main exporters of doctors and nurses in the region. Agreements about mutual recognition of professional qualifications for three groups of health workers under the Association of Southeast Asian Nations Framework Agreement on Services could result in increased movement within the region in the future. To ensure that vital human resources for health are available to meet the needs of the populations that they serve, migration management and retention strategies need to be integrated into ongoing efforts to strengthen health systems in southeast Asia. There is also a need for improved dialogue between the health and trade sectors on how to balance economic opportunities associated with trade in health services with domestic health needs and equity issues.
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Emerging infectious diseases in southeast Asia: regional challenges to control.
Southeast Asia is a hotspot for emerging infectious diseases, including those with pandemic potential. Emerging infectious diseases have exacted heavy public health and economic tolls. Severe acute respiratory syndrome rapidly decimated the region's tourist industry. Influenza A H5N1 has had a profound effect on the poultry industry. The reasons why southeast Asia is at risk from emerging infectious diseases are complex. The region is home to dynamic systems in which biological, social, ecological, and technological processes interconnect in ways that enable microbes to exploit new ecological niches. These processes include population growth and movement, urbanisation, changes in food production, agriculture and land use, water and sanitation, and the effect of health systems through generation of drug resistance. Southeast Asia is home to about 600 million people residing in countries as diverse as Singapore, a city state with a gross domestic product (GDP) of US$37,500 per head, and Laos, until recently an overwhelmingly rural economy, with a GDP of US$890 per head. The regional challenges in control of emerging infectious diseases are formidable and range from influencing the factors that drive disease emergence, to making surveillance systems fit for purpose, and ensuring that regional governance mechanisms work effectively to improve control interventions.
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Health-financing reforms in southeast Asia: challenges in achieving universal coverage.
In this sixth paper of the Series, we review health-financing reforms in seven countries in southeast Asia that have sought to reduce dependence on out-of-pocket payments, increase pooled health finance, and expand service use as steps towards universal coverage. Laos and Cambodia, both resource-poor countries, have mostly relied on donor-supported health equity funds to reach the poor, and reliable funding and appropriate identification of the eligible poor are two major challenges for nationwide expansion. For Thailand, the Philippines, Indonesia, and Vietnam, social health insurance financed by payroll tax is commonly used for formal sector employees (excluding Malaysia), with varying outcomes in terms of financial protection. Alternative payment methods have different implications for provider behaviour and financial protection. Two alternative approaches for financial protection of the non-poor outside the formal sector have emerged-contributory arrangements and tax-financed schemes-with different abilities to achieve high population coverage rapidly. Fiscal space and mobilisation of payroll contributions are both important in accelerating financial protection. Expanding coverage of good-quality services and ensuring adequate human resources are also important to achieve universal coverage. As health-financing reform is complex, institutional capacity to generate evidence and inform policy is essential and should be strengthened.
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Health and health-care systems in southeast Asia: diversity and transitions.
Southeast Asia is a region of enormous social, economic, and political diversity, both across and within countries, shaped by its history, geography, and position as a major crossroad of trade and the movement of goods and services. These factors have not only contributed to the disparate health status of the region's diverse populations, but also to the diverse nature of its health systems, which are at varying stages of evolution. Rapid but inequitable socioeconomic development, coupled with differing rates of demographic and epidemiological transitions, have accentuated health disparities and posed great public health challenges for national health systems, particularly the control of emerging infectious diseases and the rise of non-communicable diseases within ageing populations. While novel forms of health care are evolving in the region, such as corporatised public health-care systems (government owned, but operating according to corporate principles and with private-sector participation) and financing mechanisms to achieve universal coverage, there are key lessons for health reforms and decentralisation. New challenges have emerged with rising trade in health services, migration of the health workforce, and medical tourism. Juxtaposed between the emerging giant economies of China and India, countries of the region are attempting to forge a common regional identity, despite their diversity, to seek mutually acceptable and effective solutions to key regional health challenges. In this first paper in the Lancet Series on health in southeast Asia, we present an overview of key demographic and epidemiological changes in the region, explore challenges facing health systems, and draw attention to the potential for regional collaboration in health.
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Field tests of interspecific competition in ant assemblages: revisiting the dominant red wood ants.
1. There has been considerable debate on the importance of competition in ecological communities, but its importance in structuring ant assemblages has often been uncritically accepted. Here, we briefly review field experiments examining competition in ant assemblages and use a removal experiment to test the effect of the classical territorial dominant ant, Formica aquilonia. Ants of this species group are thought to structure communities through a dominance hierarchy. 2. First, we used pitfall traps to compare the abundance of other ants in replicated sites with low and high densities of F. aquilonia. We found differences in community composition, in particular, Camponotus herculeanus was more common in low-density sites, in accordance with predictions. Differences in ant assemblages were not owing to differences in measured habitat variables. 3. We removed F. aquilonia from a set of high-density sites, using physical and chemical methods, and repeated these procedures at procedural control sites. One year after removal, abundances of F. aquilonia at removal sites were similar to those at low-density sites. However, the composition of other species did not change in response to F. aquilonia removal. Replication rates were identical in the mensurative and experimental components of this study, so this is unlikely to be owing to the analysis being insufficiently powerful. 4. We suggest three possibilities for the lack of difference. First, the study may have been too short term or small scale to detect differences. However, previous studies have shown effects on smaller spatial- and temporal-scales. Second, priority effects may be important in the successful colonisation by F. aquilonia. Thirdly, boreal ant assemblages may be too depauperate for redundancy in ecological roles and for competition to play an important structuring role. 5. We thus recommend that long-term large-scale experiments be considered essential if we are to distinguish between competing hypotheses in community ecology.
not annotated - annotated - LINNAEUS only
Effective management in clusters of pneumococcal disease: a systematic review.
Outbreaks of serious pneumococcal disease can occur with high attack rates in certain settings. We systematically reviewed studies of interventions implemented in pneumococcal clusters and those reporting the effect of antibiotics on carriage reduction to assess the effectiveness of interventions. Evidence was graded according to the Scottish Intercollegiate Guidelines Network system. Of 28 identified cluster reports, one showed that administration of antibiotics to close contacts reduced risk of pneumococcal disease. In three of four clusters where rifampicin chemoprophylaxis was used and in four of five clusters where penicillin was used no further cases were seen after intervention. In clusters where pneumococcal polysaccharide vaccine was used, subsequent cases occurred, all within around 2 weeks of vaccination, which suggests delayed benefit with this approach (evidence grade D). Use of infection control measures alone was reported in eight clusters, with no further cases being reported in seven (grade D). From 21 selected carriage studies, large carriage reductions were observed consistently with use of penicillin and azithromycin, with median values being 90% and 73%, respectively (grade C). The findings were presented to a working group for pneumococcal cluster guidelines and used to develop key recommendations on the management of clusters that supported prompt use of amoxicillin or azithromycin chemoprophylaxis, pneumococcal vaccination for close contacts, and implementation of infection control measures.
not annotated - annotated - LINNAEUS only
Urbanisation and infectious diseases in a globalised world.
The world is becoming urban. The UN predicts that the world's urban population will almost double from 3*3 billion in 2007 to 6*3 billion in 2050. Most of this increase will be in developing countries. Exponential urban growth is having a profound effect on global health. Because of international travel and migration, cities are becoming important hubs for the transmission of infectious diseases, as shown by recent pandemics. Physicians in urban environments in developing and developed countries need to be aware of the changes in infectious diseases associated with urbanisation. Furthermore, health should be a major consideration in town planning to ensure urbanisation works to reduce the burden of infectious diseases in the future.
not annotated - annotated - LINNAEUS only
Emerging opportunistic yeast infections.
A growing population of immunosuppressed patients has resulted in increasingly frequent diagnoses of invasive fungal infections, including those caused by unusual yeasts. The incidence of non-albicans species of Candida is increasing compared with that of Candida albicans, and several species, such as Candida glabrata and Candida krusei, may be resistant to azole antifungal therapy. Trichosporon species are the second most common cause of fungaemia in patients with haematological malignant disease and are characterised by resistance to amphotericin and echinocandins and poor prognosis. Rhodotorula species belong to the family Cryptococcaceae, and are a cause of catheter-related fungaemia, sepsis, and invasive disease in severely immunosuppressed patients. An increasing number of sporadic cases of invasive fungal infections by non-neoformans cryptococci have been reported in immunocompromised hosts, especially for patients with advanced HIV infection or cancer who are undergoing transplant. Other uncommon yeasts that can cause invasive disease in severely immunosuppressed patients include Geotrichum, Hansenula, Malassezia, and Saccharomyces. Host immune status is a crucial determinant of the type of invasive fungal infection a patient is at risk for. Diagnosis can be challenging and relies heavily on traditional cultures of blood and other sterile sites, although serum (1,3)-Beta-D-glucan testing might have an adjunctive role. Although rare yeasts are emerging as opportunistic human pathogens, diagnosis remains challenging and treatment suboptimal.
not annotated - annotated - LINNAEUS only
Protist-like inclusions in amber, as evidenced by Charentes amber.
The mid-Cretaceous amber of France contains thousands of protist-like inclusions similar in shape to some ciliates, flagellates and amoebae. The sheer abundance of these inclusions and their size variation within a single amber piece are not concordant with true fossil protists. French amber is coniferous in origin, which generally does not preserve well protists without cell walls. Thus, it would be surprising if French Cretaceous amber had preserved millions of protists. Here, we present a survey of the protist-like inclusions from French amber and attempt to elucidate their origins. Diverse Cretaceous ambers (from Spain, Germany and Lebanon), also derived from conifer resins, contain thousands of protist-like inclusions. In contrast, Tertiary ambers and modern resins are poor in protist-like fossils. This suggests these inclusions originated from early Cretaceous plant resins, probably secreted with the resin by trees that did not survive after the Cretaceous (such as the Cheirolepidiaceae). A review of the recent literature on amber microfossils indicates several protist-like inclusions that are unlikely to have a biological origin have already been described as real fossil protists. This is problematic in that it will bias our understanding of protist evolution.
not annotated - annotated - LINNAEUS only
Management of uncommon chemotherapy-induced emergencies.
Chemotherapy can induce various clinical emergencies. Prompt recognition and management of these adverse events are important for avoiding further morbidity and mortality. Some events such as hypersensitivity and extravasation are quite common, whereas emergencies such as neutropenic typhlitis, pancreatitis, and acute haemolysis are very rare. Little information exists on the management of rare chemotherapy-induced emergencies that affect fewer than 1% of patients. We review these uncommon chemotherapy-induced life-threatening emergencies, their pathogenesis and management, and recommendations for rechallenge with the offending chemotherapy.
not annotated - annotated - LINNAEUS only
New driver mutations in non-small-cell lung cancer.
Treatment decisions for patients with lung cancer have historically been based on tumour histology. Some understanding of the molecular composition of tumours has led to the development of targeted agents, for which initial findings are promising. Clearer understanding of mutations in relevant genes and their effects on cancer cell proliferation and survival, is, therefore, of substantial interest. We review current knowledge about molecular subsets in non-small-cell lung cancer that have been identified as potentially having clinical relevance to targeted therapies. Since mutations in EGFR and KRAS have been extensively reviewed elsewhere, here, we discuss subsets defined by so-called driver mutations in ALK, HER2 (also known as ERBB2), BRAF, PIK3CA, AKT1, MAP2K1, and MET. The adoption of treatment tailored according to the genetic make-up of individual tumours would involve a paradigm shift, but might lead to substantial therapeutic improvements.
not annotated - annotated - LINNAEUS only
Thermal performance curves of Paramecium caudatum: a model selection approach.
The ongoing climate change has motivated numerous studies investigating the temperature response of various organisms, especially that of ectotherms. To correctly describe the thermal performance of these organisms, functions are needed which sufficiently fit to the complete optimum curve. Surprisingly, model-comparisons for the temperature-dependence of population growth rates of an important ectothermic group, the protozoa, are still missing. In this study, temperature reaction norms of natural isolates of the freshwater protist Paramecium caudatum were investigated, considering nearly the entire temperature range. These reaction norms were used to estimate thermal performance curves by applying a set of commonly used model functions. An information theory approach was used to compare models and to identify the best ones for describing these data. Our results indicate that the models which can describe negative growth at the high- and low-temperature branch of an optimum curve are preferable. This is a prerequisite for accurately calculating the critical upper and lower thermal limits. While we detected a temperature optimum of around 29 ^0C for all investigated clonal strains, the critical thermal limits were considerably different between individual clones. Here, the tropical clone showed the narrowest thermal tolerance, with a shift of its critical thermal limits to higher temperatures.
not annotated - annotated - LINNAEUS only
The molecular and genetic basis of conidial pigmentation in Aspergillus niger.
A characteristic hallmark of Aspergillus niger is the formation of black conidiospores. We have identified four loci involved in spore pigmentation of A. niger by using a combined genomic and classical complementation approach. First, we characterized a newly isolated color mutant, colA, which lacked pigmentation resulting in white or colorless conidia. Pigmentation of the colA mutant was restored by a gene (An12g03950) which encodes a putative 4'phosphopantetheinyl transferase protein (PptA). 4'Phosphopantetheinyl transferase activity is required for the activation of Polyketide Synthases (PKSs) and/or Non-Ribosomal Peptide Synthases (NRPSs). The loci whose mutation resulted in fawn, olive, and brown color phenotypes were identified by complementation. The fawn phenotype was complemented by a PKS protein (FwnA, An09g05730), the ovlA mutant by An14g05350 (OlvA) and the brnA mutant by An14g05370 (BrnA), the respective homologs of alb1/pksP, ayg1 and abr1 in A. fumigatus. Targeted disruption of the pptA, fwnA, olvA and brnA genes confirmed the complementation results. Disruption of the pptA gene abolished synthesis of all polyketides and non-ribosomal peptides, while the naphtho-gamma-pyrone subclass of polyketides were specifically dependent on fwnA, and funalenone on fwnA, olvA and brnA. Thus, secondary metabolite profiling of the color mutants revealed a close relationship between polyketide synthesis and conidial pigmentation in A. niger.
not annotated - annotated - LINNAEUS only
Identification and characterization of putative osmosensors, HwSho1A and HwSho1B, from the extremely halotolerant black yeast Hortaea werneckii.
In Saccharomyces cerevisiae, the Sho1 protein is one of two potential osmosensors that can activate the kinase cascade of the HOG pathway in response to increased extracellular osmolarity. Two novel SHO1-like genes, HwSHO1A and HwSHO1B, have been cloned from the saltern-inhabiting, extremely halotolerant black yeast Hortaea werneckii. The HwSho1 protein isoforms are 93.8% identical in their amino-acid sequences, and have a conserved SH3 domain. When the HwSHO1 genes were transferred into S. cerevisae cells lacking the SHO1 gene, both of the HwSho1 isoforms fully complemented the function of the native S. cerevisiae Sho1 protein. Through microscopic and biochemical validation, we demonstrate that in S. cerevisiae, both of the HwSho1 proteins have characteristic subcellular localizations similar to the S. cerevisiae Sho1 protein, and they can both activate the HOG pathway under conditions of osmotic stress. To a lower extent, crosstalk to the mating pathway expressing HwSho1 proteins is conserved in the PBS2 deleted S. cerevisiae strain. These data show that the HwSho1 proteins from H. werneckii are true functional homologs of the Sho1 protein of S. cerevisiae.
not annotated - annotated - LINNAEUS only
Polymorphism of Paramecium pentaurelia (Ciliophora, Oligohymenophorea) strains revealed by rDNA and mtDNA sequences.
Paramecium pentaurelia is one of 15 known sibling species of the Paramecium aurelia complex. It is recognized as a species showing no intra-specific differentiation on the basis of molecular fingerprint analyses, whereas the majority of other species are polymorphic. This study aimed at assessing genetic polymorphism within P. pentaurelia including new strains recently found in Poland (originating from two water bodies, different years, seasons, and clones of one strain) as well as strains collected from distant habitats (USA, Europe, Asia), and strains representing other species of the complex. We compared two DNA fragments: partial sequences (349 bp) of the LSU rDNA and partial sequences (618 bp) of cytochrome B gene. A correlation between the geographical origin of the strains and the genetic characteristics of their genotypes was not observed. Different genotypes were found in Kraksigmaw in two types of water bodies (Opatkowice-natural pond; Jordan's Park-artificial pond). Haplotype diversity within a single water body was not recorded. Likewise, seasonal haplotype differences between the strains within the artificial water body, as well as differences between clones originating from one strain, were not detected. The clustering of some strains belonging to different species was observed in the phylogenies.
not annotated - annotated - LINNAEUS only
Determinants of reproductive success in dominant pairs of clownfish: a boosted regression tree analysis.
1. Central questions of behavioural and evolutionary ecology are what factors influence the reproductive success of dominant breeders and subordinate nonbreeders within animal societies? A complete understanding of any society requires that these questions be answered for all individuals. 2. The clown anemonefish, Amphiprion percula, forms simple societies that live in close association with sea anemones, Heteractis magnifica. Here, we use data from a well-studied population of A. percula to determine the major predictors of reproductive success of dominant pairs in this species. 3. We analyse the effect of multiple predictors on four components of reproductive success, using a relatively new technique from the field of statistical learning: boosted regression trees (BRTs). BRTs have the potential to model complex relationships in ways that give powerful insight. 4. We show that the reproductive success of dominant pairs is unrelated to the presence, number or phenotype of nonbreeders. This is consistent with the observation that nonbreeders do not help or hinder breeders in any way, confirming and extending the results of a previous study. 5. Primarily, reproductive success is negatively related to male growth and positively related to breeding experience. It is likely that these effects are interrelated because males that grow a lot have little breeding experience. These effects are indicative of a trade-off between male growth and parental investment. 6. Secondarily, reproductive success is positively related to female growth and size. In this population, female size is positively related to group size and anemone size, also. These positive correlations among traits likely are caused by variation in site quality and are suggestive of a silver-spoon effect. 7. Noteworthily, whereas reproductive success is positively related to female size, it is unrelated to male size. This observation provides support for the size advantage hypothesis for sex change: both individuals maximize their reproductive success when the larger individual adopts the female tactic. 8. This study provides the most complete picture to date of the factors that predict the reproductive success of dominant pairs of clown anemonefish and illustrates the utility of BRTs for analysis of complex behavioural and evolutionary ecology data.
not annotated - annotated - LINNAEUS only
Novel cultured protists identify deep-branching environmental DNA clades of cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia.
We describe three new orders of filosan Cercozoa, five new deep-branching genera, eight new species of Thaumatomonas, Reckertia, Spongomonas, Rhogostoma, Agitata, Neoheteromita and Paracercomonas, sequence their 18S rDNA, and construct 18S rDNA trees for 148 Cercozoa. Our phylogeny indicates that Filosa were ancestrally gliding flagellates; non-flagellate filose amoebae evolved from them five times independently. The new genera are more closely related to environmental DNA sequences than cultured organisms. Tremula longifila, a zooflagellate glider on both flagella (unlike other Cercozoa), is the most divergent filosan (Tremulida ord. n.). Micrometopion nutans is a eukaryote-eating gliding zooflagellate like Metopion and Metromonas. Minimassisteria diva is a widespread trimorphic marine amoeboflagellate granofilosan. Peregrinia clavideferens, a non-testate, scale-bearing, filose amoeba, branches deeply in Thaumatomonadida, which are probably sisters to Spongomonadida. Nudifila producta is a filose amoeboflagellate related to Clautriavia and Marimonadida (ord. n., e.g. Pseudopirsonia, Auranticordis). We substantially revise Imbricatea, now including Spongomonadida, and Thecofilosea to include Phaeodaria. Thecofilosea and Imbricatea and Thecofilosea are sisters, both arguably ancestrally rigid gliding flagellates with ventral pseudopod-emitting grooves. Scale-free Ovulinata parva is sister to Paulinella, so imbricate silica scales can be lost. Internal hollow silica skeletons evolved twice in Thecofilosea (Ebriida, Phaeodaria) or were multiply lost. Protaspa replaces preoccupied 'Protaspis'.
not annotated - annotated - LINNAEUS only
Amyotrophic lateral sclerosis.
Amyotrophic lateral sclerosis (ALS) is an idiopathic, fatal neurodegenerative disease of the human motor system. In this Seminar, we summarise current concepts about the origin of the disease, what predisposes patients to develop the disorder, and discuss why all cases of ALS are not the same. In the 150 years since Charcot originally described ALS, painfully slow progress has been made towards answering these questions. We focus on what is known about ALS and where research is heading-from the small steps of extending longevity, improving therapies, undertaking clinical trials, and compiling population registries to the overarching goals of establishing the measures that guard against onset and finding the triggers for this neurodegenerative disorder.
not annotated - annotated - LINNAEUS only
Tyrosine phosphorylation of actin during microcyst formation and germination in Polysphondylium pallidum.
High osmolarity causes amoebae of the cellular slime mould Polysphondylium pallidum to individually encyst, forming microcysts. During microcyst differentiation, actin is tyrosine phosphorylated. Tyrosine phosphorylation of actin is independent of encystment conditions and occurs during the final stages of microcyst formation. During microcyst germination, actin undergoes dephosphorylation prior to amoebal emergence. Renewed phosphorylation of actin in germinating microcysts can be triggered by increasing the osmolarity of the medium which inhibits emergence. Immunofluorescence reveals that actin is dispersed throughout the cytoplasm in dormant microcysts. Following the onset of germination, actin is observed around vesicles where it co-localizes with phosphotyrosine. Prior to emergence, actin localizes to patches near the cell surface. Increasing osmolarity disrupts this localization and causes actin to redistribute throughout the cytoplasm, a situation similar to that observed in dormant microcysts. The tyrosine phosphorylation state of actin does not appear to influence the long-term viability of dormant microcysts. Together, these results indicate an association between actin tyrosine phosphorylation, organization of the actin cytoskeleton, and microcyst dormancy.
not annotated - annotated - LINNAEUS only
Mechanisms of unisexual mating in Cryptococcus neoformans.
Sex serves a pivotal role in genetic exchange and it contributes to the fitness and genetic diversity for eukaryotic populations. Although the importance of the canonical bisexual mating has been widely accepted, the significance of the evolution and maintenance of unisexual mating observed in some eukaryotes is unclear. The recent discovery of same-sex mating in the human fungal pathogen Cryptococcus neoformans and the revelation of its impact on the Cryptococcus global population structure provide a platform to elucidate the molecular mechanisms and significance of unisexual mating. Here, we review the evidence of unisexual mating in Cryptococcus and provide some perspective on the biological significance of this life style on the survival of this important fungal pathogen in the environment and in animal hosts. We also summarize our current understanding of the molecular mechanisms governing this unconventional mode of reproduction.
not annotated - annotated - LINNAEUS only
Patchy bed disturbance and fish predation independently influence the distribution of stream invertebrates and algae.
1. The identification of factors determining the patchy distribution of organisms in space and time is a central concern of ecology. Predation and abiotic disturbance are both well-known drivers of this patchiness, but their interplay is still poorly understood, especially for communities dominated by mobile organisms in frequently disturbed ecosystems. 2. We investigated the separate and interactive influences of bed disturbance by floods and predation by fish on the benthic community in a flood-prone stream. Electric fields excluded fish predators from half of 48 stream bed patches (area 0*49 m(2) ) with contrasting disturbance treatments. Three types of bed disturbance were created by either scouring or filling patches to a depth of 15-20 cm or by leaving the patches undisturbed, thus mimicking the mosaic of scour and fill caused by a moderate flood. Benthic invertebrates and algae were sampled repeatedly until 57 days after the disturbance. 3. Disturbance influenced all ten investigated biological response variables, whereas predation affected four variables. Averaged across time, invertebrate taxon richness and total abundance were highest in stable patches. Algal biomass and densities of five of the seven most common invertebrate taxa (most of which were highly mobile) were higher in fill than in scour patches, whereas two taxa were more abundant in scour and stable than in fill patches. Furthermore, two common invertebrate grazers were more abundant and algal biomass tended to be reduced in fish exclusion patches, suggesting a patch-scale trophic cascade from fish to algae. 4. Our results highlight the importance of patchy physical disturbance for the microdistribution of mobile stream organisms and indicate a notable, but less prevalent, influence of fish predation at the patch scale in this frequently disturbed environment. Disturbance and predation treatments interacted only once, suggesting that the observed predation effects were largely independent of local bed disturbance patterns.
not annotated - annotated - LINNAEUS only
Contrasting cascade effects of carnivores on plant fitness: a meta-analysis.
1. Although carnivores indirectly improve plant fitness by decreasing herbivory, they may also decrease plant reproduction by disrupting plant-pollinator mutualism. The overall magnitude of the resulting net effect of carnivores on plant fitness and the factors responsible for the variations in strength and direction of this effect have not been explored quantitatively to date. 2. We performed a meta-analysis of 67 studies containing 163 estimates of the effects of carnivores on plant fitness and examined the relative importance of several potential sources of variation in carnivore effects. 3. Carnivores significantly increased plant fitness via suppression of herbivores and decreased fitness by consuming pollinators. The overall net effect of carnivores on plant fitness was positive (32% increase), indicating that effects via herbivores were stronger than effects via pollinators. 4. Parasitoids had stronger positive effect on plant fitness than predators. Active hunters increased plant fitness, whereas stationary predators had no significant effect, presumably because they were more prone to disrupt plant-pollinator mutualism. Carnivores with broader habitat domain had negative effects on plant fitness, whereas those with narrow habitat domain had positive effects. 5. Predator effects were positive for plants which offered rewards (e.g. extrafloral nectaries) and negative for plants which lacked any attractors. 6. This study adds new knowledge on the factors that determine the strength of terrestrial trophic cascades and highlights the importance of considering simultaneous contrasting interactions in the same study system.
not annotated - annotated - LINNAEUS only
Shrinking by numbers: landscape context affects the species composition but not the quantitative structure of local food webs.
1. With habitat fragmentation spreading around the world, there is a pressing need to understand its impacts on local food webs. To date, few studies have examined the effects of landscape context on multiple local communities in a quantitative, spatially realistic setting. 2. To examine how the isolation of a food web affects its structure, we construct local food webs of specialist herbivores and their natural enemies on 82 individual oaks (Quercus robur) growing in different landscape contexts. 3. Across this set of webs, we find that communities in isolated habitat patches not only contained fewer species than did well-connected ones, but also differed in species composition. 4. Surprisingly, the effects observed in terms of species composition were not reflected in the quantitative interaction structure of local food webs: landscape context had no detectable effect on either the interaction evenness, linkage density, connectance, generality or vulnerability of local webs. 5. We conclude that the quantitative structure of food webs may be stable in the face of habitat fragmentation, despite clear-cut impacts on individual species. This finding offers hope-inspiring news for conservation, but should clearly be verified by empirical studies across both naturally and more recently fragmented systems.
not annotated - annotated - LINNAEUS only
Comparative immunofluorescence and ultrastructural analysis of microtubule organization in Uronema sp., Klebsormidium flaccidum, K. subtilissimum, Stichococcus bacillaris and S. chloranthus (Chlorophyta).
A detailed comparative examination of microtubule (MT) organization in interphase and dividing cells of Uronema sp., Klebsormidium flaccidum, K. subtilissimum, Stichococcus bacillaris and S. chloranthus was made using tubulin immunofluorescence and transmission electron microscopy (TEM). During interphase all the species bear a well-organized cortical MT system, consisting of parallel bundles with different orientations. In Uronema sp. the cortical MT bundles are longitudinally oriented, whereas in the other species they are in transverse orientation to the axis of the cells. Considerable differences in MT organization were also observed during stages of mitosis, mainly preprophase, as well as cytokinesis. In Uronema sp., a particular radial MT assembly is organized during preprophase-early prophase, which was not observed in the other species. In Stichococcus a fine MT ring surrounded the nucleus during preprophase and prophase. An MT ring, together with single cytoplasmic MTs, was also found associated with the developing diaphragm during cytokinesis in Stichococcus. A phycoplast participates in cytokinesis in Uronema sp., but not in the other species. In Uronema sp. the centrosome functions as a microtubule organizing center (MTOC) during mitosis, but not during interphase and cytokinesis. The phylogenetic significance of these differences is discussed in combination with SSU/ITS sequencing and other, existing molecular data.
not annotated - annotated - LINNAEUS only
Intentional genetic introgression influences survival of adults and subadults in a small, inbred felid population.
1. Inbreeding and low genetic diversity can cause reductions in individual fitness and increase extinction risk in animal populations. Intentional introgression, achieved by releasing genetically diverse individuals into inbred populations, has been used as a conservation tool to improve demographic performance in endangered populations. 2. By the 1980s, Florida panthers (Puma concolor coryi) had been reduced to a small, inbred population that appeared to be on the brink of extinction. In 1995, female pumas from Texas (P. c. stanleyana) were released in occupied panther range as part of an intentional introgression programme to restore genetic variability and improve demographic performance of panthers. 3. We used 25 years (1981-2006) of continuous radiotelemetry and genetic data to estimate and model subadult and adult panther survival and cause-specific mortality to provide rigorous sex and age class-specific survival estimates and evaluate the effect of the introgression programme on these parameters. 4. Genetic ancestry influenced annual survival of subadults and adults after introgression, as F(1) generation admixed panthers ( = 0*98) survived better than pre-introgression type panthers ( = 0*77) and other admixed individuals ( = 0*82). Furthermore, heterozygosity was higher for admixed panthers relative to pre-introgression type panthers and positively influenced survival. 5. Our results are consistent with hybrid vigour; however, extrinsic factors such as low density of males in some areas of panther range may also have contributed to higher survival of F(1) panthers. Regardless, improved survival of F(1) subadults and adults likely contributed to the numerical increase in panthers following introgression, and our results indicate that intentional admixture, achieved here by releasing individuals from another population, appears to have been successful in improving demographic performance in this highly endangered population.
not annotated - annotated - LINNAEUS only
Projectin PEVK domain, splicing variants and domain structure in basal and derived insects.
The third elastic filament of striated muscles consists of giant proteins: titin (in vertebrates) and kettin/projectin (in insects). In all three proteins, elasticity is at least partly associated with the so-called PEVK domain. The projectin PEVK domains of diverse insects are highly divergent compared with an otherwise conserved protein organization. We present the characterization of the PEVK domain in two dragonflies and in human lice. A conserved segment at the end of the PEVK, the NH(2)-terminal conserved segment-1 (NTCS-1), may serve as an anchor point for projectin to either myosin or actin, providing a mechanical link. The analysis of alternative splicing variants identifies the shortest PEVK isoform as the predominant form in the flight muscles of several insects, possibly contributing to myofibrillar stiffness.
not annotated - annotated - LINNAEUS only
Paediatric stroke: genetic insights into disease mechanisms and treatment targets.
In children, stroke is as common as brain tumour and causes substantial mortality and long-term morbidity, with recurrence in up to 20%. There are three sets of international clinical guidelines relating to childhood stroke; however, acute and preventive treatment recommendations are based on interventions effective in adults, rather than data regarding efficacy in children. A wide spectrum of risk factors underlies childhood stroke, and these risk factors vary from those encountered in adults. Specific disease mechanisms implicated in childhood arterial ischaemic stroke have received little attention, but an increased understanding of disease pathogenesis could lead to novel targeted treatment approaches. Here, we consider insights into the pathogenesis of childhood arterial ischaemic stroke and cerebral arteriopathy, provided by current knowledge of Mendelian diseases that are associated with an increased risk of these conditions. We give particular attention to aspects of vascular development, homoeostasis, and response to environmental effects. Our analysis highlights a potential role for interventions already licensed for pharmaceutical use, as well as new therapeutic targets and avenues for further research.
not annotated - annotated - LINNAEUS only
The sirtuin pathway in ageing and Alzheimer disease: mechanistic and therapeutic considerations.
BACKGROUND: Advances in gerontology have yielded crucial insights into the molecular and biochemical aspects of the ageing process. The sirtuin pathway, which is most notable for its association with the anti-ageing effects of calorie restriction, has received particular attention, and pharmacological or transgenic upregulation of the sirtuin pathway has shown promising results in laboratory models of ageing. Alzheimer's disease is a neurodegenerative disease that is imposing an increasing burden on society, and is the leading cause of senile dementia worldwide. The lack of therapies for Alzheimer's disease provides a strong incentive for the development of an effective treatment strategy and, interestingly, research has uncovered a mechanism of action of the sirtuin pathway that might have therapeutic potential for Alzheimer's disease. RECENT DEVELOPMENTS: SIRT1, one of the seven mammalian proteins of the sirtuin family of NAD(+)-dependent deacetylases, has recently been shown to attenuate amyloidogenic processing of amyloid-Beta protein precursor (APP) in cell culture studies in vitro and in transgenic mouse models of Alzheimer's disease. Mechanistically, SIRT1 increases alpha-secretase production and activity through activation of the alpha-secretase gene ADAM10. Because alpha-secretase is the enzyme responsible for the non-amyloidogenic cleavage of APP, upregulation of alpha-secretase shifts APP processing to reduce the pathological accumulation of the presumptive toxic ABeta species that results from Beta-secretase and gamma-secretase activity. Interestingly, the spatial patterns of ABeta deposition in the brain might correlate with increased aerobic glycolysis in those regions. Because aerobic glycolysis depletes cellular levels of NAD(+) (through a decreased NAD(+)/NADH ratio), it is possible that a corresponding downregulation of the NAD(+)-dependent sirtuin pathway contributes to the amyloidogenic processing of APP. WHERE NEXT?: The specific inhibition of ABeta generation by SIRT1 coupled with the potential link between aerobic glycolysis, NAD(+) depletion, and amyloidogenesis through the sirtuin pathway has translational implications. On the one hand, the possible underlying role of the sirtuin pathway in Alzheimer's disease onset and development might increase our understanding of this devastating condition. On the other hand, therapeutic upregulation of SIRT1 might provide opportunities for the amelioration of Alzheimer's-disease-type neuropathology through inhibition of amyloidogenesis. Ultimately, further analysis into both aspects is necessary if any progress is to be made.
not annotated - annotated - LINNAEUS only
Ventricular septal defect.
Ventricular septal defects account for up to 40% of all congenital cardiac malformations. The diagnosis encompasses a broad range of anomalies, including isolated defects and those associated with other congenital cardiac malformations. Presentation, symptoms, natural history, and management of ventricular septal defects depend on size and anatomical associations of the anomaly, patient's age, and local diagnostic and interventional expertise. In this Seminar, we describe the anatomical range of ventricular septal defects and discuss present management of these malformations. Genetic determinants, diagnostic techniques, physiological considerations, and management challenges are examined in detail. Unfortunately, in many circumstances, evidence on which to guide optimum management is scarce. We present some longer term considerations of ventricular septal defects in adolescents and adults, with particular emphasis on patients with raised pulmonary vascular resistance and Eisenmenger's syndrome.
not annotated - annotated - LINNAEUS only
Interplay between the parasite Amoebophrya sp. (Alveolata) and the cyst formation of the red tide dinoflagellate Scrippsiella trochoidea.
Syndiniales (Alveolata) are marine parasites of a wide range of hosts, from unicellular organisms to Metazoa. Many Syndiniales obligatorily kill their hosts to accomplish their life cycle. This is the case for Amoebophrya spp. infecting dinoflagellates. However, several dinoflagellate species known to be infected by these parasites produce diploid resting cysts as part of their life history. These resting cysts may survive several seasons in the sediment before germinating. How these parasites survive during the dormancy of their host remained an open question. We successfully established infections by Amoebophrya sp. in the red tide dinoflagellate Scrippsiella trochoidea. This host strain was homothallic and able to continuously produce typical calcified cysts covered by calcareous spines. Presence of the parasite significantly speeded up the host cyst production, and cysts produced were the only cells to resist infections. However, some of them were clearly infected, probably earlier in their formation. After 10 months, cysts produced in presence of the parasite were able to germinate and new infective cycles of the parasite were rapidly observed. Thus, a very novel relationship for protists is demonstrated, one in which parasite and host simultaneously enter dormancy, emerging months later to propagate both species.
not annotated - annotated - LINNAEUS only
Treatment implications of the emerging molecular classification system for melanoma.
Melanoma is an aggressive disease with few standard treatment options. The conventional classification system for this disease is based on histological growth patterns, with division into four subtypes: superficial spreading, lentigo maligna, nodular, and acral lentiginous. Major limitations of this classification system are absence of prognostic importance and little correlation with treatment outcomes. Recent preclinical and clinical findings support the notion that melanoma is not one malignant disorder but rather a family of distinct molecular diseases. Incorporation of genetic signatures into the conventional histopathological classification of melanoma has great implications for development of new and effective treatments. Genes of the mitogen-associated protein kinase (MAPK) pathway harbour alterations sometimes identified in people with melanoma. The mutation Val600Glu in the BRAF oncogene (designated BRAF(V600E)) has been associated with sensitivity in vitro and in vivo to agents that inhibit BRAF(V600E) or MEK (a kinase in the MAPK pathway). Melanomas arising from mucosal, acral, chronically sun-damaged surfaces sometimes have oncogenic mutations in KIT, against which several inhibitors have shown clinical efficacy. Some uveal melanomas have activating mutations in GNAQ and GNA11, rendering them potentially susceptible to MEK inhibition. These findings suggest that prospective genotyping of patients with melanoma should be used increasingly as we work to develop new and effective treatments for this disease.
not annotated - annotated - LINNAEUS only
Ciliate community associated with aquatic macrophyte roots: effects of nutrient enrichment on the community composition and species richness.
The objective of this study was to identify the impact of nutrient enrichment on the diversity of the ciliate community associated with the roots of the aquatic macrophyte Eichhornia crassipes. The experiment was performed in the Garsigmaas Lake, located in the Upper Parana River floodplain, Brazil. We conducted two treatments (fertilized and control) with three replicates each. To increase the initial nutrient concentrations in each mesocosm of the fertilized treatment, we added 1000 mugL(-1) of KNO(3) and 200 mugL(-1) of KH(2)PO(4) during each sampling date. We found a relative high number of ciliate species (85 species) and a predominance of hypotrichs. Among the recorded species, about 25% occurred exclusively in the fertilized treatment. Moreover, detrended correspondence analysis demonstrated that the ciliate community associated with E. crassipes roots changed significantly in response to the nutrient input in such a way that the species composition of the fertilized treatment was remarkably different from that of the control. In contrast to our expectations, species richness in the fertilized treatment was significantly higher than that in the control, refuting our hypothesis that species richness decreases under eutrophic conditions.
not annotated - annotated - LINNAEUS only
International Cognition and Cancer Task Force recommendations to harmonise studies of cognitive function in patients with cancer.
It has become increasingly apparent that cytotoxic drugs given systemically for non-CNS tumours might have cognitive side-effects, but many fundamental questions require further elucidation, and large samples from several institutions are needed. Two working groups brought together by the International Cognition and Cancer Task Force (ICCTF) developed recommendations for a core set of neuropsychological tests, common criterion for defining cognitive impairment and cognitive changes, and common approaches to improve the homogeneity of study methods. These recommendations will improve research design and facilitate study combinations, between-study comparisons, and meta-analyses, which will allow more accurate estimates of incidence, severity, individual risk factors, and causes of cognitive problems associated with chemotherapy for non-CNS tumours.
not annotated - annotated - LINNAEUS only
Low functional richness and redundancy of a predator assemblage in native forest fragments of Chiloe island, Chile.
1. Changes in land use and habitat fragmentation are major drivers of global change, and studying their effects on biodiversity constitutes a major research programme. However, biodiversity is a multifaceted concept, with a functional component linking species richness to ecosystem function. Currently, the interaction between functional and taxonomic components of biodiversity under realistic scenarios of habitat degradation is poorly understood. 2. The expected functional richness (FR)-species richness relationship (FRSR) is positive, and attenuated for functional redundancy in species-rich assemblages. Further, environmental filters are expected to flatten that association by sorting species with similar traits. Thus, analysing FRSR can inform about the response of biodiversity to environmental gradients and habitat fragmentation, and its expected functional consequences. 3. Top predators affect ecosystem functioning through prey consumption and are particularly vulnerable to changes in land use and habitat fragmentation, being good indicators of ecosystem health and suitable models for assessing the effects of habitat fragmentation on their FR. 4. Thus, this study analyses the functional redundancy of a vertebrate predator assemblage at temperate forest fragments in a rural landscape of Chiloe island (Chile), testing the existence of environmental filters by contrasting an empirically derived FRSR against those predicted from null models, and testing the association between biodiversity components and the structure of forest fragments. 5. Overall, contrasts against null models indicate that regional factors determine low levels of FR and redundancy for the vertebrate predator assemblage studied, while recorded linear FRSR indicates proportional responses of the two biodiversity components to the structure of forest fragments. Further, most species were positively associated with either fragment size or shape complexity, which are highly correlated. This, and the absence of ecological filters at the single-fragment scale, rendered taxonomically and functionally richer predator assemblages at large complex-shaped fragments. 6. These results predict strong effects of deforestation on both components of biodiversity, potentially affecting the functioning of remnants of native temperate forest ecosystems. Thus, the present study assesses general responses of functional and taxonomic components of biodiversity to a specific human-driven process.
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Fluorescent proteins illuminate the structure and function of the hyphal tip apparatus.
Fungal hyphae show extreme polarized growth at the tip. Electron microscope studies have revealed a apical body called the Spitzenkorper that is thought to drive polarized growth. Studies of polarized growth in S. cerevisiae have identified the protein components of the polarized growth machinery, that are conserved in other fungi. Fusion of these proteins to GFP and its variants has for the first time allowed the localization of these proteins in real time to the hyphal tip without the need for drastic fixation procedures. Such studies showed that vesicle-associated proteins localize to the Spitzenkorper and identified a second compartment located at the tip surface composed of exocyst and other proteins that mediate the fusion of secretory vesicles with the plasma membrane.
not annotated - annotated - LINNAEUS only
One step construction of Agrobacterium-Recombination-ready-plasmids (OSCAR), an efficient and robust tool for ATMT based gene deletion construction in fungi.
Increasing availability of genomic data and sophistication of analytical methodology in fungi has elevated the need for functional genomics tools in these organisms. Previously we reported a method called DelsGate for rapid preparation of deletion constructs for protoplast-mediated fungal transformation systems, which is based on Gateway(R) technology. However, over the past several years Agrobacteriumtumefaciens-mediated transformation (ATMT) has become the preferred genetic transformation method for an increasing number of fungi. Therefore, we developed a method for One Step Construction of Agrobacterium-Recombination-ready-plasmids (OSCAR), to rapidly create deletion constructs for ATMT systems. The OSCAR methodology involves PCR amplification of the upstream and downstream flanks of the gene of interest, using gene specific primers each with a 5' extension containing one of four different attB recombination sites, modified from the Invitrogen MultiSite Gateway(R) system. Amplified gene flanks are then mixed with specifically designed marker and binary vectors and treated with BP clonase, generating the deletion construct in a single cloning step. The entire process of deletion construct preparation can be accomplished in just 2days. Using OSCAR we generated eight targeted deletion constructs and used two of them to generate deletion mutants in Verticillium dahliae by ATMT. In summary, OSCAR methodology combines PCR and Gateway(R) technology to rapidly and robustly generate precise deletion constructs for fungal ATMT and homologous gene replacement.
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Scales of orientation, directed walks and movement path structure in sharks.
1. Animal search patterns reflect sensory perception ranges combined with memory and knowledge of the surrounding environment. 2. Random walks are used when the locations of resources are unknown, whereas directed walks should be optimal when the location of favourable habitats is known. However, directed walks have been quantified for very few species. 3. We re-analysed tracking data from three shark species to determine whether they were using directed walks, and if so, over which spatial scales. Fractal analysis was used to quantify how movement structure varied with spatial scale and determine whether the sharks were using patches. 4. Tiger sharks performed directed walks at large spatial scales (at least 6-8 km). Thresher sharks also showed directed movement (at scales of 400-1900 m), and adult threshers were able to orient at greater scales than juveniles, which may suggest that learning improves the ability to perform directed walks. Blacktip reef sharks had small home ranges, high site fidelity and showed no evidence of oriented movements at large scales. 5. There were inter- and intraspecific differences in path structure and patch size, although most individuals showed scale-dependent movements. Furthermore, some individuals of each species performed movements similar to a correlated random walk. 6. Sharks can perform directed walks over large spatial scales, with scales of movements reflecting site fidelity and home range size. Understanding when and where directed walks occur is crucial for developing more accurate population-level dispersal models.
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El Nino in the warm tropics: local sea temperature predicts breeding parameters and growth of blue-footed boobies.
1. There is increasing interest in the impacts of El Nino Southern Oscillation (ENSO) on reproduction of apical predators such as seabirds and marine mammals. Long-term studies documenting ENSO effects on reproduction of seabirds in the warm tropics are scarce, and differential sensitivity of breeding parameters to ENSO has rarely been explored. 2. Analysis of 18 years of breeding data from a colony of the blue-footed booby Sula nebouxii (Milne-Edwards) showed a delay in onset of breeding when the global Southern Oscillation Index was negative; each unit of the atmospheric pressure differential (hPa) across the Pacific Ocean meant a delay of 7 days. 3. ENSO conditions also produced declines in breeding participation, clutch size, brood size, hatching success and fledging success, especially when surface waters surrounding the colony were warmer during winter and spring. Each additional degree (^0C) of water temperature produced a reduction of 0.45 fledglings per nest. Different breeding parameters were sensitive to ENSO indices in different blocks of months. 4. Warming of local waters during the winter was associated with decline in ocean productivity in the current year and the following year, consistent with ENSO impacts on breeding parameters being mediated by effects on local productivity and prey availability. However, there was no evidence of lagged effects of ENSO on any breeding parameter. 5. Comparison of 5 years revealed that when local surface waters were warm, chicks grew more slowly, but no effects of ENSO on weight and size of eggs were evident in data of 9 and 7 years, respectively. 6. Our findings extend evidence of impacts of ENSO on seabird reproduction to the eastern tropical Pacific and indicate that several breeding parameters of blue-footed boobies (but not egg size) are affected in the short term by ENSO conditions, particularly by local anomalies in sea surface temperature associated with decline in ocean productivity.
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Partial diel vertical migrations in pelagic fish.
1. Field studies on diel vertical migration (DVM) usually report uniform behaviour with population-wide ascents and descents during crepuscular periods. This contrasts partial seasonal migrations of many animal populations, where individuals choose either the resident or the migrant strategy depending on population density, feeding opportunity and predation risk in the resident and migrant habitats. 2. We tested whether DVM of freshwater zooplanktivorous fish (Coregonus spp.) resembles partial migrations. Twenty-eight hydroacoustic surveys were performed in the deep Lake Stechlin (Germany) between 2000 and 2010, with samplings encompassing all months between March and December. Zooplankton samples were simultaneously taken in epilimnetic and hypolimnetic layers. Fish obtained from depth-stratified samplings by a midwater trawl were used to test for individual differences between residents and migrants. 3. We show for the first time that DVMs of freshwater fish resemble patterns of partial migrations often found in seasonal environments. Across all samplings, 7-33% of fish did not ascend at dusk, but exhibited the resident strategy. The proportion or residents increased at low zooplankton feeding rates in the daytime habitat and during months when the temperature difference between daytime and night-time habitats was minor. 4. Slightly larger size and higher caloric density of migrants over residents in one of the coexisting Coregonus species suggested that individual differences contributed to the migration strategy performed. However, these results were based on one sample only, and extrapolation to the entire data set is not possible. 5. Our results are indirect evidence that the balance between migrants and residents may primarily depend on the trade-off between feeding gains and metabolic and predation costs of migration. However, the results also suggest that the global fitness consequences for the resident and migrant strategies may not be identical, rendering the importance of individual traits in the 'decision to migrate' likely.
not annotated - annotated - LINNAEUS only
Clinical management of Staphylococcus aureus bacteraemia.
Staphylococcus aureus bacteraemia is one of the most common serious bacterial infections worldwide. In the UK alone, around 12,500 cases each year are reported, with an associated mortality of about 30%, yet the evidence guiding optimum management is poor. To date, fewer than 1500 patients with S aureus bacteraemia have been recruited to 16 controlled trials of antimicrobial therapy. Consequently, clinical practice is driven by the results of observational studies and anecdote. Here, we propose and review ten unanswered clinical questions commonly posed by those managing S aureus bacteraemia. Our findings define the major areas of uncertainty in the management of S aureus bacteraemia and highlight just two key principles. First, all infective foci must be identified and removed as soon as possible. Second, long-term antimicrobial therapy is required for those with persistent bacteraemia or a deep, irremovable focus. Beyond this, the best drugs, dose, mode of delivery, and duration of therapy are uncertain, a situation compounded by emerging S aureus strains that are resistant to old and new antibiotics. We discuss the consequences on clinical practice, and how these findings define the agenda for future clinical research.
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Seasonal influenza epidemiology in sub-Saharan Africa: a systematic review.
Acute respiratory infection (ARI) is a leading cause of mortality worldwide, of which influenza is an important cause that can be prevented with vaccination. We did a systematic review of research published from 1980 to 2009 on seasonal influenza epidemiology in sub-Saharan Africa to identify data strengths and weaknesses that might affect policy decisions, to assess the state of knowledge on influenza disease burden, and to ascertain unique features of influenza epidemiology in the region. We assessed 1203 papers, reviewed 104, and included 49 articles. 1-25% of outpatient ARI visits were caused by influenza (11 studies; mean 9*5%; median 10%), whereas 0*6-15*6% of children admitted to hospital for ARI had influenza identified (15 studies; mean 6*6%; median 6*3%). Influenza was highly seasonal in southern Africa. Other data were often absent, particularly direct measurement of influenza incidence rates for all ages, within different patient settings (outpatient, inpatient, community), and for all countries. Data from sub-Saharan Africa are insufficient to allow most countries to prioritise strategies for influenza prevention and control. Key data gaps include incidence and case-fatality ratios for all ages, the contribution of influenza towards admission of adults to hospital for ARI, representative seasonality data, economic burden, and the interaction of influenza with prevalent disorders in Africa, such as malaria, HIV, and malnutrition.
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Population biological principles of drug-resistance evolution in infectious diseases.
The emergence of resistant pathogens in response to selection pressure by drugs and their possible disappearance when drug use is discontinued are evolutionary processes common to many pathogens. Population biological models have been used to study the dynamics of resistance in viruses, bacteria, and eukaryotic microparasites both at the level of the individual treated host and of the treated host population. Despite the existence of generic features that underlie such evolutionary dynamics, different conclusions have been reached about the key factors affecting the rate of resistance evolution and how to best use drugs to minimise the risk of generating high levels of resistance. Improved understanding of generic versus specific population biological aspects will help to translate results between different studies, and allow development of a more rational basis for sustainable drug use than exists at present.
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Guidelines for hospital-acquired pneumonia and health-care-associated pneumonia: a vulnerability, a pitfall, and a fatal flaw.
The 2005 American Thoracic Society and Infectious Disease Society of America's guidelines for pneumonia introduced the new category of health-care-associated pneumonia, which increased the number of people to whom the guidelines for multidrug-resistant pathogens applied. Three fundamental issues inherent in the definition of hospital-acquired pneumonia and health-care-associated pneumonia undermined the credibility of these guidelines and the applicability of their recommendations: a vulnerability, a pitfall, and a fatal flaw. The vulnerability is the extreme heterogeneity of the population of patients. The fatal flaw is the failure to accurately diagnose hospital-acquired pneumonia and ventilator-associated pneumonia; inability to distinguish colonisation from infection in respiratory-tract cultures renders the guidelines inherently unstable. The pitfall is spiralling empiricism of antibiotic use for severely ill patients in whom infection might not be present. A vicious circle of antibiotic overuse leading to emergence of resistant microflora can become established, leading to unnecessary use of empirical broad-spectrum combination antibiotics and increased mortality. Controlled studies now show that administration of broad-spectrum combination antibiotic therapy can lead to increased mortality in uninfected patients. Proposed solutions include the use of individualised assessment of patients. Health-care-associated pneumonia should be broken down into several distinct subgroups so narrow-spectrum antibiotic therapy can be used. Emphasis should be placed on defining the microbial cause of the pneumonia rather than reflex administration of empirical combination therapy.
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Alzheimer's disease.
An estimated 24 million people worldwide have dementia, the majority of whom are thought to have Alzheimer's disease. Thus, Alzheimer's disease represents a major public health concern and has been identified as a research priority. Although there are licensed treatments that can alleviate symptoms of Alzheimer's disease, there is a pressing need to improve our understanding of pathogenesis to enable development of disease-modifying treatments. Methods for improving diagnosis are also moving forward, but a better consensus is needed for development of a panel of biological and neuroimaging biomarkers that support clinical diagnosis. There is now strong evidence of potential risk and protective factors for Alzheimer's disease, dementia, and cognitive decline, but further work is needed to understand these better and to establish whether interventions can substantially lower these risks. In this Seminar, we provide an overview of recent evidence regarding the epidemiology, pathogenesis, diagnosis, and treatment of Alzheimer's disease, and discuss potential ways to reduce the risk of developing the disease.
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Serum c testing in patients with HER2-positive breast cancer: the death knell tolls.
Determination of the human epidermal growth factor receptor 2 (HER2; also known as ERBB2) status of breast tumours is emphasised in various national guidelines as a necessary step for the diagnosis of breast cancer. As an alternative to tissue-based diagnostic methods, there has been substantial interest in the establishment of an easily accessible serum-based alternative that could be used for prognosis and diagnosis. Detection of serum-soluble-HER2 extracellular domain (ECD) and establishment of its potential clinical usefulness has created much debate. We assessed whether identification of circulating concentrations of HER2 ECD have clinical usefulness for management of patients with HER2-positive breast cancer. We examined data from 63 studies of patients with breast cancer. Prevalence of increased concentrations varied greatly between studies. Some studies showed significant associations between raised concentrations and poor prognosis, poor response to treatments including trastuzumab, or tumour characteristics associated with aggressive disease, whereas others did not. Examination of existing data showed that concentrations of HER2 ECD are not consistently related to patient outcomes; therefore, there is insufficient evidence to support the clinical use of serum HER2 ECD testing. Design and execution of future large-scale trials to investigate the clinical use of HER2 ECD testing, in view of the progressive non-supportive evidence, is not recommended. Oncologists should continue to adhere to national guidelines for determining HER2 status. Furthermore, oncologists should continue to use clinical parameters when making decisions about initiation, continuation, and discontinuation of HER2-targeted treatments.
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Breast-cancer early detection in low-income and middle-income countries: do what you can versus one size fits all.
In general, rates of breast cancer are lower in low-income and middle-income countries (LMCs) than they are in more industrialised countries of North America and Europe. This lower incidence means that screening programmes aimed at early detection in asymptomatic women would have a lower yield--ie, substantially more women would need to be examined to find a true case of breast cancer. Because the average age of breast cancer is generally younger in LMCs, it has been suggested that breast-cancer screening programmes begin at an earlier age in these settings. However, the younger average age of breast cancer is mainly driven by the age distribution of the population, and fewer older women with breast cancer, rather than by higher age-specific incidence rates in younger women. Resources in LMCs might be better used to raise awareness and encourage more women with palpable breast lumps to seek and receive treatment in a timely manner.
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Towards a conceptual framework to support one-health research for policy on emerging zoonoses.
In the past two decades there has been a growing realisation that the livestock sector was in a process of change, resulting from an expansion of intensive animal production systems and trade to meet a globalised world's increasing demand for livestock products. One unintended consequence has been the emergence and spread of transboundary animal diseases and, more specifically, the resurgence and emergence of zoonotic diseases. Concurrent with changes in the livestock sector, contact with wildlife has increased. This development has increased the risk of transmission of infections from wildlife to human beings and livestock. Two overarching questions arise with respect to the real and perceived threat from emerging infectious diseases: why are these problems arising with increasing frequency, and how should we manage and control them? A clear conceptual research framework can provide a guide to ensure a research strategy that coherently links to the overarching goals of policy makers. We propose such a new framework in support of a research and policy-generation strategy to help to address the challenges posed by emerging zoonoses.
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Compartmentalization of a glycolytic enzyme in Diplonema, a non-kinetoplastid euglenozoan.
Glycosomes are peroxisome-related organelles containing glycolytic enzymes that have been found only in kinetoplastids. We show here that a glycolytic enzyme is compartmentalized in diplonemids, the sister group of kinetoplastids. We found that, similar to kinetoplastid aldolases, the fructose 1,6-bisphosphate aldolase of Diplonema papillatum possesses a type 2-peroxisomal targeting signal. Western blotting showed that this aldolase was present predominantly in the membrane/organellar fraction. Immunofluorescence analysis showed that this aldolase had a scattered distribution in the cytosol, suggesting its compartmentalization. In contrast, orotidine-5'-monophosphate decarboxylase, a non-glycolytic glycosomal enzyme in kinetoplastids, was shown to be a cytosolic enzyme in D. papillatum. Since euglenoids, the earliest diverging branch of Euglenozoa, do not possess glycolytic compartments, these findings suggest that the routing of glycolytic enzymes into peroxisomes may have occurred in a common ancestor of diplonemids and kinetoplastids, followed by diversification of these newly established organelles in each of these euglenozoan lineages.
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Responses of the pea aphid transcriptome to infection by facultative symbionts.
Serratia symbiotica is a facultative symbiont of pea aphids (Acyrthosiphon pisum) that provides tolerance to heat stress. Although the phenotypic effects of facultative symbionts upon hosts have been studied in some detail, little is known about the molecular and genomic basis of these interactions. Previous studies show a large impact of S. symbiotica upon the aphid metabolome. Whole-genome transcriptional profiling and next-generation sequencing demonstrated expression of 94% of RefSeq genes from the pea aphid genome, providing the largest dataset to date on aphid gene expression. However, only 28 genes showed changes in expression with S. symbiotica infection, and these changes were of small magnitude. No expression differences in genes involved in innate immunity in other insects were observed. Therefore, the large metabolic impact of S. symbiotica is most likely a result of metabolism of the symbiont itself, or of post-transcriptional modification of host gene expression. Although S. symbiotica has a major influence on its host's metabolome and resistance to heat, it induces little change in gene expression in its host.
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Molecular cloning and characterization of a thioredoxin peroxidase gene from Apis cerana cerana.
Thioredoxin peroxidases (Tpxs) play important roles in protecting organisms against the toxicity of reactive oxygen species (ROS) and regulating intracellular signal transduction. In the present study, we cloned the full cDNA of Tpx1 encoding a 195-amino acid protein from Apis cerana cerana (Acc). Based on the genomic DNA sequence, a 1442-bp 5'-flanking region was obtained, and the putative transcription factor binding sites were predicted. Quantitative PCR analysis showed that AccTpx1 was highly expressed in thorax and that the AccTpx1 transcript reached its highest level in two-week-old adult worker honeybees. Moreover, expression of the AccTpx1 transcript was increased by various abiotic stresses, such as ultraviolet light, HgCl(2) , and insecticide treatments. In addition, the recombinant AccTpx1 protein exhibited antioxidant activity; it removed hydrogen peroxide and protected DNA. These results suggest that AccTpx1 plays an important role in protecting honeybees from oxidative injury and may act in extending the lifespan of them.
not annotated - annotated - LINNAEUS only
Predation and patchiness in the tropical litter: do swarm-raiding army ants skim the cream or drain the bottle?
1. Swarm-raiding army ants have long been considered as episodic, catastrophic agents of disturbance in the tropical litter, but few quantitative data exist on their diets, preferences, and, critically, their ability to deplete prey. 2. Here, we provide such data for two common species of swarm raiders broadly sympatric throughout the Neotropics: the iconic Eciton burchellii and the more secretive, less studied Labidus praedator. In Ecuador, Costa Rica, Venezuela and Panama, patches of forest floor were sampled for litter invertebrates immediately before and after army ant raids. These invertebrates have been shown to regulate decomposition and vary 100-fold in local densities across the forest floor. 3. Contrary to Eciton's popular image, only Labidus consistently reduced the biomass of litter invertebrates and only then by an average of 25%. Eciton's impacts were concentrated on rich patches of invertebrates, while Labidus prey depletion showed no such density dependence. Labidus reduced the biomass of some invertebrates-isopods, larviforms and coleoptera-by up to 75%; Eciton showed no such prey preferences. 4. Our results suggest that Eciton specializes on high biomass patches, while Labidus feeds profitably from any litter patch. Combined, these swarm raiders sum to be chronic, but not catastrophic, predators of common litter invertebrates of the brown food web.
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Community-wide character displacement in the presence of clines: a test of Holarctic weasel guilds.
1. Competition is thought to be a major influence on community assembly, ecology and evolution; presence of competitors may cause divergence in traits related to resource use (character displacement). 2. Such traits, however, often vary clinally, and this phenomenon may be independent of the presence or absence of competing species. 3. The presence of such clines can either obscure the effects of competition, or create an impression that competition is operating when, in fact, it is not. 4. We corrected for clinal variation while testing for character displacement in two well-studied weasel (Mustela) guilds, in the Nearctic and the west Palaearctic. 5. Without accounting for clines, our results agreed with previous studies suggesting character displacement in these guilds. 6. However, when we corrected for clines, predictions of competition theory were not met - and often we obtained evidence for character convergence in sympatry. 7. This may suggest that the nature of the resource base may be more important than interspecific competition in shaping morphology and size in these carnivores. 8. Our results highlight the need to account for geographic variation when studying character displacement and cast some doubt on prevailing ideas regarding the effect of competition on morphological evolution.
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Agrobacterium tumefasciens-mediated transformation of the aquatic fungus Blastocladiella emersonii.
Agrobacterium tumefaciens is widely used for plant DNA transformation and more recently, has also been used to transform yeast, filamentous fungi and even human cells. Using this technique, we developed the first transformation protocol for the saprobic aquatic fungus Blastocladiella emersonii, a Blastocladiomycete localized at the base of fungal phylogenetic tree, which has been shown as a promising and interesting model of study of cellular function and differentiation. We constructed binary T-DNA vectors containing hygromycin phosphotransferase (hph) or enhanced green fluorescent protein (egfp) genes, under the control of Aspergillus nidulans trpC promoter and terminator sequences. 24 h of co-cultivation in induction medium (IM) agar plates, followed by transfer to PYG-agar plates containing cefotaxim to kill Agrobacterium tumefsciens and hygromycin to select transformants, resulted in growth and sporulation of resistant transformants. Genomic DNA from the pool o resistant zoospores were shown to contain T-DNA insertion as evidenced by PCR amplification of hph gene. Using a similar protocol we could also evidence the expression of enhanced green fluorescent protein (EGFP) in zoospores derived from transformed cells. This protocol can also open new perspectives for other non-transformable closely related fungi, like the Chytridiomycete class.
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Chronic pancreatitis.
Chronic pancreatitis is a progressive fibroinflammatory disease that exists in large-duct (often with intraductal calculi) or small-duct form. In many patients this disease results from a complex mix of environmental (eg, alcohol, cigarettes, and occupational chemicals) and genetic factors (eg, mutation in a trypsin-controlling gene or the cystic fibrosis transmembrane conductance regulator); a few patients have hereditary or autoimmune disease. Pain in the form of recurrent attacks of pancreatitis (representing paralysis of apical exocytosis in acinar cells) or constant and disabling pain is usually the main symptom. Management of the pain is mainly empirical, involving potent analgesics, duct drainage by endoscopic or surgical means, and partial or total pancreatectomy. However, steroids rapidly reduce symptoms in patients with autoimmune pancreatitis, and micronutrient therapy to correct electrophilic stress is emerging as a promising treatment in the other patients. Steatorrhoea, diabetes, local complications, and psychosocial issues associated with the disease are additional therapeutic challenges.
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Occurrence of the lobose testate amoeba Pseudonebela africana (Amoebozoa, Arcellinida) in the Brazilian "cerrado".
Flagship species are defined as microbial eukaryote species with characteristic morphologies and restricted geographic distributions. These are proposed as ideal systems to elucidate patterns of geographical distribution in microbial eukaryotes. Here we present new records of the putative flagship species Pseudonebela africana, a lobose testate amoeba (Arcellinida) characterized by a cross or clover-shaped aperture and geographic distribution previously believed to be restricted to Africa. We have sampled P. africana from 5 separate ponds in the Central and Southwest Brazillian "cerrado", and characterized individuals both by light and electron microscopy. We provide a brief description to facilitate further studies on this poorly understood taxon, and show that light microscopy is sufficient for identification, an important feature for ecological and biogeographical studies.
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Comparing isotopic niche widths among and within communities: SIBER - Stable Isotope Bayesian Ellipses in R.
1. The use of stable isotope data to infer characteristics of community structure and niche width of community members has become increasingly common. Although these developments have provided ecologists with new perspectives, their full impact has been hampered by an inability to statistically compare individual communities using descriptive metrics. 2. We solve these issues by reformulating the metrics in a Bayesian framework. This reformulation takes account of uncertainty in the sampled data and naturally incorporates error arising from the sampling process, propagating it through to the derived metrics. 3. Furthermore, we develop novel multivariate ellipse-based metrics as an alternative to the currently employed Convex Hull methods when applied to single community members. We show that unlike Convex Hulls, the ellipses are unbiased with respect to sample size, and their estimation via Bayesian inference allows robust comparison to be made among data sets comprising different sample sizes. 4. These new metrics, which we call SIBER (Stable Isotope Bayesian Ellipses in R), open up more avenues for direct comparison of isotopic niches across communities. The computational code to calculate the new metrics is implemented in the free-to-download package Stable Isotope Analysis for the R statistical environment.
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The role of body mass in diet contiguity and food-web structure.
1. The idea that species occupy distinct niches is a fundamental concept in ecology. Classically, the niche was described as an n-dimensional hypervolume where each dimension represents a biotic or abiotic characteristic. More recently, it has been hypothesised that a single dimension may be sufficient to explain the system-level organization of trophic interactions observed between species in a community. 2. Here, we test the hypothesis that species body mass is that single dimension. Specifically, we determine how the intervality of food webs ordered by body size compares to that of randomly ordered food webs. We also extend this analysis beyond the community level to the effect of body mass in explaining the diets of individual species. 3. We conclude that body mass significantly explains the ordering of species and the contiguity of diets in empirical communities. 4. At the species-specific level, we find that the degree to which body mass is a significant explanatory variable depends strongly on the phylogenetic history, suggesting that other evolutionarily conserved traits partly account for species' roles in the food web. 5. Our investigation of the role of body mass in food webs thus helps us to better understand the important features of community food-web structure and the evolutionary forces that have led us to the communities we observe.
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Beyond phytohaemagglutinin: assessing vertebrate immune function across ecological contexts.
1. Over the past decade, there has been a substantial increase in interest in the immune system and the role it plays in the regulation of disease susceptibility, giving rise to the field of eco-immunology. 2. Eco-immunology aims to understand changes in host immune responses in the broader framework of an organism's evolutionary, ecological and life-history contexts. 3. The immune system, however, is complex and multifaceted and can be intimidating for the nonimmunologist interested in incorporating immunological questions into their research. Which immune responses should one measure and what is the biological significance of these measures? 4. The focus of this review is to describe a wide range of eco-immunology techniques, from the simple to the sophisticated, with the goal of providing researchers with a range of options to consider incorporating in their own research programs. 5. These techniques were chosen because they provide relatively straightforward, biologically meaningful assessments of immune function, many of which can be performed across a range of ecological contexts (i.e. field vs. laboratory) and in a wide range of vertebrate animals without relying on species-specific reagents. 6. By incorporating assessments of immune function into their specific research questions, animal ecologists will gain a more comprehensive understanding of organism-environment interactions.
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Genome-wide analysis of brain transcriptional changes in honey bee (Apis mellifera L.) queens exposed to carbon dioxide and physical manipulation.
Mating is a complex process causing many behavioural and physiological changes, but the factors triggering them and the underlying molecular processes are not well characterized. In the present study we examine the effects of CO(2) (a commonly used anaesthetic in instrumental insemination that causes changes similar to those occurring after mating) and physical manipulation (which may mimic certain aspects of copulation) on the behavioural, physiological and brain transcriptional changes in honey bee queens. We show that while CO(2) causes cessation of mating flights and ovary activation, physical manipulation has additional effects on ovary activation and brain transcriptional changes. Comparisons with previous studies of honey bees and female Drosophila indicate that common molecular mechanisms may be responsible for regulating reproductive changes across different mating regimes and insect orders.
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Does variation in movement tactics and trophic interactions among American alligators create habitat linkages?
1. Highly mobile top predators are hypothesized to spatially and/or temporally link disparate habitats through the combination of their movement and feeding patterns, but recent studies suggest that individual specialization in habitat use and feeding could keep habitats compartmentalized. 2. We used passive acoustic telemetry and stable isotope analysis to investigate whether specialization in movement and feeding patterns of American alligators (Alligator mississippiensis) in an oligotrophic subtropical estuary created habitat linkages between marine and estuarine/freshwater food webs. 3. Individual alligators adopted one of the three relatively distinct movement tactics that were linked to variation in diets. Fifty-six per cent of alligators regularly travelled from the upstream (freshwater/mid-estuary) areas into the downstream (marine-influenced) areas where salinities exceed those typically tolerated by alligators. Thirty-one per cent of the alligators made regular trips from the mid-estuarine habitat into the upstream habitat; 13% remained in the mid-estuary zone year-round. 4. Stable isotopic analysis indicated that, unlike individuals remaining in the mid-estuary and upstream zones, alligators that used the downstream zone fed at least partially from marine food webs and likely moved to access higher prey abundance at the expense of salt stress. Therefore, 'commuting' alligators may link marine food webs with those of the estuary and marshes in the coastal Everglades and create an upstream vector for allochthonous nutrient inputs into the estuary. 5. This study lends further support to the hypothesis that large-bodied highly mobile predators faced with trade-offs are likely to exhibit individual specialization leading to habitat linkages, rather than compartmentalization. However, the conditions under which this scenario occurs require further investigation.
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Relative fitness of alternative male reproductive tactics in a mammal varies between years.
1. In many species, males can use different behavioural tactics to achieve fertilization, so-called alternative reproductive tactics (ARTs). Few field studies have measured fitness consequences of ARTs under varying environmental conditions. 2. Here, we describe fitness consequences of three phenotypically plastic ARTs in the African striped mouse (Rhabdomys pumilio) and show that relative fitness of ARTs differs between years. Each year represents a different generation. 3. For the generation living under high population density, tactics differed in relative fitness in accordance with the theory of conditional strategies, with highly successful territorial breeding males having 10 times higher success than solitary roaming males and 102 times higher success than adult natally philopatric males. 4. For the generation living under intermediate population density, the territorial breeding and roaming tactics yielded similar fitness, which would be in agreement with the theory of mixed strategies. No philopatric males occurred. 5. For the generation living under low population density, roaming was the only tactic used and some roamers had very high fitness. 6. The main prediction of status-dependent selection for conditional strategies is a correlation between fitness and status, often measured as body mass, but we did not find this correlation within tactics when more than one tactic was expressed in the population. 7. Female distribution seems to have an effect on which reproductive tactics male chose: female defence polygyny when females are clumped (interference competition), but a searching tactic when females are dispersed (scramble competition). In contrast to predictions arising from theory on scramble competition, male body mass was important in determining fitness only in the year when females were dispersed, but not in other years. 8. Our results indicate that the differentiation between conditional and mixed strategies is not an absolute one. In many other species, environmental conditions might fluctuate temporally and spatially so that the normally suboptimal tactic yields similar fitness to the (usually) dominant tactic or that only a single tactic prevails. 9. We suggest the term single strategy, independent of current fitness consequences, for systems where tactics are not genetically determined, in contrast to genetically determined alternative strategies.
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Predicting diet and consumption rate differences between and within species using gut ecomorphology.
1. Rapid environmental changes and pressing human needs to forecast the consequences of environmental change are increasingly driving ecology to become a predictive science. The need for effective prediction requires both the development of new tools and the refocusing of existing tools that may have previously been used primarily for purposes other than prediction. One such tool that historically has been more descriptive in nature is ecomorphology (the study of relationships between ecological roles and morphological adaptations of species and individuals). 2. Here, we examine relationships between diet and gut morphology for 15 species of brachyuran crabs, a group of pervasive and highly successful consumers for which trophic predictions would be highly valuable. 3. We show that patterns in crab stomach volume closely match some predictions of metabolic theory and demonstrate that individual diet differences and associated morphological variation reflect, at least in some instances, individual choice or diet specialization. 4. We then present examples of how stomach volume can be used to predict both the per cent herbivory of brachyuran crabs and the relative consumption rates of individual crabs.
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Completing the purine utilisation pathway of Aspergillus nidulans.
We have previously identified by classical genetics and biochemistry, all the genes of Aspergillus nidulans predicted to be involved in purine utilisation, together with cognate regulatory genes and one gene encoding a novel xanthine hydroxylation activity. In this article we complete the description of the purine utilisation pathway with the identification of the two genes (uaX and uaW) encoding the enzymes catalysing the conversion of the product of urate oxidation by urate oxidase, 5-hydroxyisourate, to optically active allantoin. The identification of these additional genes confirms the complete absence of clustering of the genes involved in purine utilisation in A. nidulans.
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The ultrastructure of Ancyromonas, a eukaryote without supergroup affinities.
The small heterotrophic flagellate Ancyromonas (=Planomonas) lacks close relatives in most molecular phylogenies, and it is suspected that it does not belong to any of the recognized eukaryote 'supergroups', making it an organism of great evolutionary interest. Proposed relatives include apusomonads and excavates, but limited understanding of the ancyromonad cytoskeleton has precluded identification of candidate structural homologies. We present a detailed analysis of the ultrastructure of Ancyromonas through computer-based reconstruction of serial sections. We confirm or extend previous observations of its major organelles (mitochondria, Golgi body, extrusomes, etc.) and pellicle, and distinguish a system of stacked endomembranes that may be developmentally connected to the glycocalyx. Ancyromonas has two basal bodies, each with its own flagellar pocket. The anterior basal body associates with two microtubular elements: a doublet root that runs from between the basal bodies to support the cell's rostrum, and a short singlet root. The posterior basal body is associated with two multi-microtubular structures and a singlet root. One multi-microtubular structure, L1, is a conventional microtubular root. The other structure appears as a curved ribbon of -8 microtubules near the basal body, but then flares out into two multi-microtubular elements, L2 and L3, plus two single microtubules. The posterior singlet root originates independently near this second complex. L1, the singlet, L2, and L3 all support the posterior flagellar pocket and channel. We also identified several groups of peripheral microtubules. Possible homologies with the flagellar apparatus of both apusomonads and excavates include a splitting root on the right side of the posterior basal body and a singlet root, both supporting a longitudinal channel or groove associated with the posterior flagellum. The anterior flagellar apparatus in each includes a root supporting structures to the left of the anterior flagellum. Given the probable deep divergences of Ancyromonas, apusomonads and excavates within eukaryotes, it is possible that the eukaryotic cenancestor also possessed these features.
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Phylogenetic validation of the genera Angomonas and Strigomonas of trypanosomatids harboring bacterial endosymbionts with the description of new species of trypanosomatids and of proteobacterial symbionts.
We comparatively examined the nutritional, molecular and optical and electron microscopical characteristics of reference species and new isolates of trypanosomatids harboring bacterial endosymbionts. Sequencing of the V7V8 region of the small subunit of the ribosomal RNA (SSU rRNA) gene distinguished six major genotypes among the 13 isolates examined. The entire sequences of the SSU rRNA and glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) genes were obtained for phylogenetic analyses. In the resulting phylogenetic trees, the symbiont-harboring species clustered as a major clade comprising two subclades that corresponded to the proposed genera Angomonas and Strigomonas. The genus Angomonas comprised 10 flagellates including former Crithidia deanei and C. desouzai plus a new species. The genus Strigomonas included former Crithidia oncopelti and Blastocrithidia culicis plus a new species. Sequences from the internal transcribed spacer of ribosomal DNA (ITS rDNA) and size polymorphism of kinetoplast DNA (kDNA) minicircles revealed considerable genetic heterogeneity within the genera Angomonas and Strigomonas. Phylogenetic analyses based on 16S rDNA and ITS rDNA sequences demonstrated that all of the endosymbionts belonged to the Betaproteobacteria and revealed three new species. The congruence of the phylogenetic trees of trypanosomatids and their symbionts support a co-divergent host-symbiont evolutionary history.
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Introduced brown trout alter native acanthocephalan infections in native fish.
1. Native parasite acquisition provides introduced species with the potential to modify native host-parasite dynamics by acting as parasite reservoirs (with the 'spillback' of infection increasing the parasite burdens of native hosts) or sinks (with the 'dilution' of infection decreasing the parasite burdens of native hosts) of infection. 2. In New Zealand, negative correlations between the presence of introduced brown trout (Salmo trutta) and native parasite burdens of the native roundhead galaxias (Galaxias anomalus) have been observed, suggesting that parasite dilution is occurring. 3. We used a multiple-scale approach combining field observations, experimental infections and dynamic population modelling to investigate whether native Acanthocephalus galaxii acquisition by brown trout alters host-parasite dynamics in native roundhead galaxias. 4. Field observations demonstrated higher infection intensity in introduced trout than in native galaxias, but only small, immature A. galaxii were present in trout. Experimental infections also demonstrated that A. galaxii does not mature in trout, although parasite establishment and initial growth were similar in the two hosts. Taken together, these results support the hypothesis that trout may serve as an infection sink for the native parasite. 5. However, dynamic population modelling predicts that A. galaxii infections in native galaxias should at most only be slightly reduced by dilution in the presence of trout. Rather, model exploration indicates parasite densities in galaxias are highly sensitive to galaxias predation on infected amphipods, and to relative abundances of galaxias and trout. Hence, trout presence may instead reduce parasite burdens in galaxias by either reducing galaxias density or by altering galaxias foraging behaviour.
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Fitness effects of endemic malaria infections in a wild bird population: the importance of ecological structure.
1. Parasites can have important effects on host populations influencing either fecundity or mortality, but understanding the magnitude of these effects in endemic host-parasite systems is challenging and requires an understanding of ecological processes affecting both host and parasite. 2. Avian blood parasites (Haemoproteus and Plasmodium) have been much studied, but the effects of these parasites on hosts in areas where they are endemic remains poorly known. 3. We used a multistate modelling framework to explore the effects of chronic infection with Plasmodium on survival and recapture probability in a large data set of breeding blue tits, involving 3424 individuals and 3118 infection diagnoses over nine years. 4. We reveal strong associations between chronic malaria infection and both recapture and survival, effects that are dependent on the clade of parasite, on host traits and on the local risk of infection. 5. Infection with Plasmodium relictum was associated with reduced recapture probability and increased survival, compared to P. circumflexum, suggesting that these parasites have differing virulence and cause different types of selection on this host. 6. Our results suggest a large potential survival cost of acute infections revealed by modelling host survival as a function of the local risk of infection. 7. Our analyses suggest not only that endemic avian malaria may have multiple fitness effects on their hosts and that these effects are species dependent, but also that adding ecological structure (in this case parasite species and spatial variation in disease occurrence) to analyses of host-parasite interactions is an important step in understanding the ecology and evolution of these systems.
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Host phylogeography and beta diversity in avian haemosporidian (Plasmodiidae) assemblages of the Lesser Antilles.
1. We estimated the correlation between host phylogeographical structure and beta diversity of avian haemosporidian assemblages of passerine birds to determine the degree to which parasite communities change with host evolution, expressed as genetic divergence between island populations, and we investigated whether differences among islands in the haemosporidia of a particular host species reflect beta diversity in the entire parasite assemblage, beta diversity in vectors, turnover of bird species and/or geographical distance. 2. We used Mantel tests to assess the significance of partial correlations between host nucleotide difference (based on cytochrome b) and haemosporidian (Haemoproteus spp. and Plasmodium spp.) mitochondrial lineage beta diversity within a given host species and between Plasmodium mitochondrial lineage beta diversity and mosquito and bird species beta diversity (or turnover). Three abundant and widespread host species (Tiaris bicolor, Coereba flaveola and Loxigilla noctis/barbadensis) were included in the study. Haemosporidian lineage beta diversity among nine islands was assessed using the Chao-Jaccard, Chao-Sorensen and Morisita-Horn indices of community similarity. Beta diversity indices of mosquito species and turnover of bird species were calculated from data in published records and field guides. 3. In Loxigilla spp., we found a positive correlation with geographical distance and an unexpected negative correlation between haemosporidian beta diversity and host genetic distance. Tiaris bicolor exhibited a significant positive correlation between haemosporidian beta diversity and beta diversity within the entire parasite assemblage. We did not find significant correlations between parasite beta diversity and mosquito beta diversity or bird species turnover. 4. Host phylogeographical structure does not appear to drive within-host beta diversity of haemosporidian lineages. Instead, the array of parasites on one host can reflect the haemosporidian assemblage on other hosts.
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Dermamoeba algensis n. sp. (Amoebozoa, Dermamoebidae): an algivorous lobose amoeba with complex cell coat and unusual feeding mode.
The genus Dermamoeba unifies oblong, flattened amoebae of lingulate morphotype, possessing a thick multilayered cell coat. It includes two species, D. granifera and D. minor. In this paper we describe a third species of this genus, D. algensis n. sp. This species is algivorous; engulfing a large algal cell, it destroys part of the cell coat liberating the plasma membrane, which forms the food vacuole. Thus the glycocalyx never appears inside the phagosome. This observation confirms that some of the thick-coated amoebae may use this way to avoid energetically costly digestion of their own glycocalyx. Studies of the physiology of this organism show that it feeds most actively at a temperature of 22-25 ^0C. Below and above this temperature the feeding intensity drastically decreases. The new species can survive NaCl concentrations up to 5%, which roughly corresponds to 50 ppt salinity. Accordingly, D. algensis has a wide range of salinity tolerance.
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European guidelines on the clinical management of HIV-1 tropism testing.
Viral tropism is the ability of viruses to enter and infect specific host cells and is based on the ability of viruses to bind to receptors on those cells. Testing for HIV tropism is recommended before prescribing a chemokine receptor blocker. In most European countries, HIV tropism is identified with tropism phenotype testing. New data support genotype analysis of the HIV third hypervariable loop (V3) for the identification of tropism. The European Consensus Group on clinical management of tropism testing was established to make recommendations to clinicians and clinical virologists. The panel recommends HIV-tropism testing for the following groups: drug-naive patients in whom toxic effects are anticipated or for whom few treatment options are available; patients who have poor tolerability to or toxic effects from current treatment or who have CNS pathology; and patients for whom therapy has failed and a change in treatment is considered. In general, an enhanced sensitivity Trofile assay and V3 population genotyping are the recommended methods. Genotypic methods are anticipated to be used more frequently in the clinical setting because of their greater accessibility, lower cost, and faster turnaround time than other methods. For the interpretation of V3 loop genotyping, clinically validated systems should be used when possible. Laboratories doing HIV tropism tests should have adequate quality assurance measures. Similarly, close collaboration between HIV clinicians and virologists is needed to ensure adequate diagnostic and treatment decisions.
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Causal involvement of mammalian-type cryptochrome in the circadian cuticle deposition rhythm in the bean bug Riptortus pedestris.
Mammalian-type CRYPTOCHROME (CRY-m) is considered to be a core repressive component of the circadian clock in various insect species. However, this role is based only on the molecular function of CRY-m in cultured cells and it therefore remains unknown whether CRY-m is indispensable for governing physiological rhythms at the organismal level. In the present study, we show that RNA interference (RNAi) targeting of cry-m in the bean bug Riptortus pedestris disrupts the circadian clock governing the cuticle deposition rhythm and results in the generation of a single cuticle layer. Furthermore, period expression was induced in cry-m RNAi insects. These results verified that CRY-m functions as a negative regulator in the circadian clock that generates physiological rhythm at the organismal level.
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Induced pluripotent stem cells: a new revolution for clinical neurology?
Why specific neuronal populations are uniquely susceptible in neurodegenerative diseases remains a mystery. Brain tissue samples from patients are rarely available for testing, and animal models frequently do not recapitulate all features of a specific disorder; therefore, pathophysiological investigations are difficult. An exciting new avenue for neurological research and drug development is the discovery that patients' somatic cells can be reprogrammed to a pluripotent state; these cells are known as induced pluripotent stem cells. Once pluripotency is reinstated, cell colonies can be expanded and differentiated into specific neural populations. The availability of these cells enables the monitoring in vitro of temporal features of disease initiation and progression, and testing of new drug treatments on the patient's own cells. Hence, this swiftly growing area of research has the potential to contribute greatly to our understanding of the pathophysiology of neurodegenerative and neurodevelopmental diseases.
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Viral pneumonia.
About 200 million cases of viral community-acquired pneumonia occur every year-100 million in children and 100 million in adults. Molecular diagnostic tests have greatly increased our understanding of the role of viruses in pneumonia, and findings indicate that the incidence of viral pneumonia has been underestimated. In children, respiratory syncytial virus, rhinovirus, human metapneumovirus, human bocavirus, and parainfluenza viruses are the agents identified most frequently in both developed and developing countries. Dual viral infections are common, and a third of children have evidence of viral-bacterial co-infection. In adults, viruses are the putative causative agents in a third of cases of community-acquired pneumonia, in particular influenza viruses, rhinoviruses, and coronaviruses. Bacteria continue to have a predominant role in adults with pneumonia. Presence of viral epidemics in the community, patient's age, speed of onset of illness, symptoms, biomarkers, radiographic changes, and response to treatment can help differentiate viral from bacterial pneumonia. However, no clinical algorithm exists that will distinguish clearly the cause of pneumonia. No clear consensus has been reached about whether patients with obvious viral community-acquired pneumonia need to be treated with antibiotics. Apart from neuraminidase inhibitors for pneumonia caused by influenza viruses, there is no clear role for use of specific antivirals to treat viral community-acquired pneumonia. Influenza vaccines are the only available specific preventive measures. Further studies are needed to better understand the cause and pathogenesis of community-acquired pneumonia. Furthermore, regional differences in cause of pneumonia should be investigated, in particular to obtain more data from developing countries.
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Preventive therapy for breast cancer: a consensus statement.
In March, 2010, a group of breast cancer experts met to develop a consensus statement on breast cancer prevention, with a focus on medical and therapeutic interventions. We present the conclusions in this Review. First we agreed that the term chemoprevention is inappropriate and suggested that the term preventive therapy better represents this feature of management. Two selective oestrogen-receptor modulators--tamoxifen and raloxifene--are so far the only medical options approved by the US Food and Drug Administration for preventive therapy. Of these tamoxifen has greater efficacy and can be used in premenopausal women, but raloxifene has fewer side-effects. Two newer drugs in this class, lasofoxifene and arzoxifene, also show efficacy and possibly a better overall risk-benefit profile, but need further assessment. Aromatase inhibitors might be more efficacious, and results of prevention trials are eagerly awaited. Newer agents, notably bisphosphonates and metformin, have shown promise in observational studies and need to be assessed in randomised prevention trials. Other agents, such as aspirin, other non-steroidal anti-inflammatory drugs, COX-2 inhibitors, retinoids, rexinoids, and dietary components have limited effects or are in the early phases of investigation. New contralateral tumours in women with breast cancer might be generally useful as a model for prevention, as has been seen for tamoxifen. If valid such a model would facilitate the design of simpler, cheaper, and better-focused trials for assessing new agents.
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Structure and evolution of the Fusarium mating type locus: new insights from the Gibberellafujikuroi complex.
Mating type genes are central to sexual reproduction and compatibility in Ascomycete fungi. However the "MAT" loci experience unique evolutionary pressures that can result in rapid divergence and enhanced inter-specific gene-flow (lateral gene transfer). In this study, molecular evolution of MAT loci was considered using the genus Fusarium (Teleomorph: Gibberella) as a model. Both MAT1-1 and MAT1-2 "idiomorphs" from eleven species of the Gibberellafujikuroi species complex were sequenced. Molecular evolution of the MAT loci from these heterothallic (self-sterile) species was compared with that of the MAT loci from nine homothallic (self-fertile) species in the Fusariumgraminearum species complex. Although Fusarium has previously been thought to have the same complement of four MAT genes that are found in Neurospora, we found evidence of a novel gene, MAT1-2-3, that may be specific to the Hypocreales. All MAT genes share a similar set of cis-regulatory motifs, although homothallic species might have recruited novel regulatory elements, which could potentially facilitate alternate expression of MAT1-1-1 and MAT1-2-1. FusariumMAT loci displayed evidence consistent with historical lateral gene-flow. Most notably, the MAT1-1 idiomorph of Fusariumsacchari appears to be unrelated to those of other species in the G.fujikuroi complex. In general, FusariumMAT genes are highly divergent. Both positive selection and relaxed selective constraint could account for this phenomenon. However, the extent of both recombination and inter-specific gene-flow in the MAT locus also appears to affect the rate of divergence.
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Mucormycosis: its contemporary face and management strategies.
Several countries have seen rising frequencies of mucormycosis among patients with haematological disorders, malignancies, or diabetes mellitus, and among transplant recipients. Growing numbers of immunocompromised hosts, widespread use of antifungal agents inactive against mucormycosis, or other unidentified factors, could be contributing to this situation. The predominant clinical manifestations of mucormycosis vary from host to host. Additionally, risk factors specific to different subgroups have been identified, such as leukaemia, allogeneic haemopoietic stem-cell transplant, voriconazole prophylaxis, diabetes, and malnutrition. We summarise the current state of knowledge of characteristics and risk factors and discuss topical developments in therapeutic methods and strategies in the management of mucormycosis.
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Hygiene: new hopes, new horizons.
Although promotion of safe hygiene is the single most cost-effective means of preventing infectious disease, investment in hygiene is low both in the health and in the water and sanitation sectors. Evidence shows the benefit of improved hygiene, especially for improved handwashing and safe stool disposal. A growing understanding of what drives hygiene behaviour and creative partnerships are providing fresh approaches to change behaviour. However, some important gaps in our knowledge exist. For example, almost no trials of the effectiveness of interventions to improve food hygiene in developing countries are available. We also need to figure out how best to make safe hygiene practices matters of daily routine that are sustained by social norms on a mass scale. Full and active involvement of the health sector in getting safe hygiene to all homes, schools, and institutions will bring major gains to public health.
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Visceral leishmaniasis: elimination with existing interventions.
The world's burden of infectious diseases can be substantially reduced by more-effective use of existing interventions. Advances in case detection, diagnosis, and treatment strategies have made it possible to consider the elimination of visceral leishmaniasis in the Indian subcontinent. The priority must now be to effectively implement existing interventions at the community level by actively finding cases in endemic villages and treating them with single-dose liposomal amphotericin B at primary-health-care centres. Once the elimination target of one case per 10,000 population has been reached, combination therapies involving miltefosine and paromomycin can be introduced to ensure long-term availability of several drugs for visceral leishmaniasis and to protect against resistance.
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Glaucoma.
Most medical practitioners have regular contact with adults who have one of the two forms of glaucoma: open-angle glaucoma or angle-closure glaucoma. Data from population-based surveys indicate that one in 40 adults older than 40 years has glaucoma with loss of visual function, which equates to 60 million people worldwide being affected and 8*4 million being bilaterally blind. Even in developed countries, half of glaucoma cases are undiagnosed. Glaucoma is mostly asymptomatic until late in the disease when visual problems arise. Vision loss from glaucoma cannot be recovered, and improved case-detection methods for glaucoma are needed. Glaucoma is commonly treated with daily eye-drop drugs, but adherence to treatment is often unsatisfactory. As a usually asymptomatic and chronic disease, glaucoma has similar treatment challenges to chronic systemic diseases. Similarities to the pathogenesis of common CNS diseases mean that common neuroprotective strategies might exist. Successful gene therapy, which has been used for other eye diseases might be possible for the treatment of glaucoma in the future.
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Heating up relations between cold fish: competition modifies responses to climate change.
Most predictions about species responses to climate change ignore species interactions. Helland and colleagues (2011) test whether this assumption is valid by evaluating whether ice cover affects competition between brown trout [Salmo trutta (L.)] and Arctic charr [Salvelinus alpines (L.)]. They show that increasing ice cover correlates with lower trout biomass when Arctic charr co-occur, but not in charr's absence. In experiments, charr grew better in the cold, dark environments that typify ice-covered lakes. Decreasing ice cover with warmer winters could mean more trout and fewer charr. More generally, their results provide an excellent example, suggesting that species interactions can strongly modify responses to climate change.
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An empirical link between the spectral colour of climate and the spectral colour of field populations in the context of climate change.
1. The spectral colour of population dynamics and its causes have attracted much interest. The spectral colour of a time series can be determined from its power spectrum, which shows what proportion of the total variance in the time series occurs at each frequency. A time series with a red spectrum (a negative spectral exponent) is dominated by low-frequency oscillations, and a time series with a blue spectrum (a positive spectral exponent) is dominated by high-frequency oscillations. 2. Both climate variables and population time series are characterised by red spectra, suggesting that a population's environment might be partly responsible for its spectral colour. Laboratory experiments and models have been used to investigate this potential link. However, no study using field data has directly tested whether populations in redder environments are redder. 3. This study uses the Global Population Dynamics Database together with climate data to test for this effect. We found that the spectral exponent of mean summer temperatures correlates positively and significantly with population spectral exponent. 4. We also found that over the last century, temperature climate variables on most continents have become bluer. 5. Although population time series are not long or abundant enough to judge directly whether their spectral colours are changing, our two results taken together suggest that population spectral colour may be affected by the changing spectral colour of climate variables. Population spectral colour has been linked to extinction; we discuss the potential implications of our results for extinction probability.
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Response assessment in neuro-oncology (a report of the RANO group): assessment of outcome in trials of diffuse low-grade gliomas.
Although low-grade gliomas (LGG) have a less aggressive course than do high-grade gliomas, the outcome of these tumours is ultimately fatal in most patients. Both the tumour and its treatment can cause disabling morbidity, particularly of cognitive functions. Because many patients present with seizures only, with no other signs and symptoms, maintenance of quality of life and function constitutes a particular challenge in LGG. The slow growth pattern of most LGG, and the rare radiological true responses despite a favourable clinical response to treatment, interferes with the use of progression-free survival as the primary endpoint in trials. Overall survival as an endpoint brings logistical challenges, and is sensitive to other non-investigational salvage therapies. Clinical trials for LGG need to consider other measures of patient benefit such as cognition, symptom burden, and seizure activity, to establish whether improved survival is reflected in prolonged wellbeing. This Review investigates clinical and imaging endpoints in trials of LGG, and provides response assessment in neuro-oncology (RANO) criteria for non-enhancing tumours. Additionally, other measures for patients with brain tumours that assess outcome are described. Similar considerations are relevant for trials of high-grade gliomas, although for these tumours survival is shorter and survival endpoints generally have more value than they do for LGG.
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Baculovirus cyclobutane pyrimidine dimer photolyases show a close relationship with lepidopteran host homologues.
Cyclobutane pyrimidine dimer (CPD) photolyases repair ultraviolet (UV)-induced DNA damage using blue light. To get insight in the origin of baculovirus CPD photolyase (phr) genes, homologues in the lepidopteran insects Chrysodeixis chalcites, Spodoptera exigua and Trichoplusia ni were identified and characterized. Lepidopteran and baculovirus phr genes each form a monophyletic group, and together form a well-supported clade within the insect photolyases. This suggests that baculoviruses obtained their phr genes from an ancestral lepidopteran insect host. A likely evolutionary scenario is that a granulovirus, Spodoptera litura GV or a direct ancestor, obtained a phr gene. Subsequently, it was horizontally transferred from this granulovirus to several group II nucleopolyhedroviruses (NPVs), including those that infect noctuids of the Plusiinae subfamily.
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The importance of marine vs. human-induced subsidies in the maintenance of an expanding mesocarnivore in the arctic tundra.
1. Most studies addressing the causes of the recent increases and expansions of mesopredators in many ecosystems have focused on the top-down, releasing effect of extinctions of large apex predators. However, in the case of the northward expansion of the red fox into the arctic tundra, a bottom-up effect of increased resource availability has been proposed, an effect that can counteract prey shortage in the low phase of the multi-annual rodent cycle. Resource subsidies both with marine and with terrestrial origins could potentially be involved. 2. During different phases of a multi-annual rodent cycle, we investigated the seasonal dynamics and spatial pattern of resource use by red foxes across a coast to inland low arctic tundra gradient, Varanger Peninsula, Norway. We employed two complementary methods of diet analyses: stomach contents and stable isotope analysis. 3. We found that inland red foxes primarily subsisted on reindeer carrions during the low phase of a small rodent population cycle. Lemmings became the most important food item towards the peak phase of the rodent cycle, despite being less abundant than sympatric voles. Isotopic signatures of tissue from both predator and prey also revealed that red foxes near the coast used marine-derived subsidies in the winter, but these allochthonous resources did not spillover to adult foxes living beyond 20-25 km from the coast. 4. Although more needs to be learned about the link between increasing primary productivity due to climatic warming and trophic dynamics in tundra ecosystems, we suggest that changes in reindeer management through a bottom-up effect, at least regionally, may have paved the way towards the establishment of a new mesopredator in the tundra biome.
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Mathematical models in the evaluation of health programmes.
Modelling is valuable in the planning and evaluation of interventions, especially when a controlled trial is ethically or logistically impossible. Models are often used to calculate the expected course of events in the absence of more formal assessments. They are also used to derive estimates of rare or future events from recorded intermediate points. When developing models, decisions are needed about the appropriate level of complexity to be represented and about model structure and assumptions. The degree of rigor in model development and assessment can vary greatly, and there is a danger that existing beliefs inappropriately influence judgments about model assumptions and results.
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Scale and state dependence of the relationship between personality and dispersal in a great tit population.
1. Dispersal is a key process in population biology and ecology. Although the general ecological conditions that lead to dispersal have been well studied, the causes of individual variation in dispersal are less well understood. A number of recent studies suggest that heritable temperament - or personality - traits are correlated with dispersal in the wild but the extent to which these 'personality-dispersal syndromes' are general, how they depend on an individual's state and on spatial scale and whether they are temporally stable, both within and across individuals, remains unclear. 2. Here, we examine the relationship between exploration behaviour - an axis of personality that appears to be important in animals generally - and a variety of dispersal processes over 6 years in a population of the great tit Parus major. 3. Exploration behaviour was higher in immigrant than in locally born juveniles, but the difference was much larger for individuals with a small body mass, though independent of sex, representing one of the first examples of a state-dependent effect in a personality-dispersal syndrome. 4. Despite a temporal trend in exploration behaviour at the population level, the difference between immigrants and locally born birds remained stable over time, both across and within individuals. This suggests that the personality difference between immigrants and locally born birds is established early in development, but that the process of immigration interacts with both personality and state. 5. We found that the number of immigrant parents a locally born bird had did not influence exploration behaviour, suggesting either the difference between immigrants and residents was environmental or that the effect is overridden by local environmental sources of variation. 6. In contrast to previous work, we found no evidence for links between personality and natal dispersal distance within the population, either in terms of an individual's own exploration behaviour or that of its parents. 7. Our results suggest that there are links between individual differences in personality and dispersal, but that these can be dependent on differences in state among individuals and on the scale over which dispersal is measured. Future work should aim to understand the differences between dispersal within and between populations and the ways in which personality and state interact to determine the outcome of these processes.
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A role for endosomal proteins in alphavirus dissemination in mosquitoes.
Little is known about endosomal pathway proteins involved in arthropod-borne virus (arbovirus) assembly and cell-to-cell spread in vector mosquitoes. UNC93A and synaptic vesicle-2 (SV2) proteins are involved in intracellular transport in mammals. They show amino acid sequence conservation from mosquitoes to humans, and their transcripts are highly enriched in Aedes aegypti during arbovirus infection. Transient gene silencing of SV2 or UNC93A in mosquitoes infected with the recombinant alphavirus Sindbis MRE16-enhanced green fluorescent protein (SINV; family Togaviridae) resulted in the accumulation of viral positive- and negative-strand RNA, congregation of virus envelope antigen in intracellular networks, and reduced virus dissemination outside of the midgut. Further, UNC93A silencing, but not SV2 silencing, resulted in a 10-fold reduction in viral titres at 4 days post-infection. Together, these data support a role for UNC93A and SV2 in virus assembly or budding. Cis-regulatory elements (CREs) were identified at the 5'-ends of genes from the original data set in which SV2 and UNC93A were identified. Common CREs at the 5'-end genomic regions of a subset of enriched transcripts support the hypothesis that UNC93A transcription may be co-regulated with that of other ion transport and endosomal trafficking proteins.
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Pyrethroid resistance in Sitophilus zeamais is associated with a mutation (T929I) in the voltage-gated sodium channel.
The maize weevil, Sitophilus zeamais, is the most important pest affecting stored grain in Brazil and its control relies heavily on the use of insecticides. The intensive use of compounds such as the pyrethroids has led to the emergence of resistance, and previous studies have suggested that resistance to both pyrethroids and 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) may result from reduced sensitivity of the insecticide target, the voltage-gated sodium channel. To identify the molecular mechanisms underlying pyrethroid resistance in S. zeamais, the domain II region of the voltage-gated sodium channel (para-orthologue) gene was amplified by PCR and sequenced from susceptible and resistant laboratory S. zeamais strains that were selected with a discriminating dose of DDT. A single point mutation, T929I, was found in the para gene of the resistant S. zeamais populations and its presence in individual weevils was strongly associated with survival after DDT exposure. This is the first identification of a target-site resistance mutation in S. zeamais and unusually it is a super-kdr type mutation occurring in the absence of the more common kdr (L1014F) substitution. A high-throughput assay based on TaqMan single nucleotide polymorphism genotyping was developed for sensitive detection of the mutation and used to screen field-collected strains of S. zeamais. This showed that the mutation is present at low frequency in field populations and is a useful tool for informing control strategies.
not annotated - annotated - LINNAEUS only
Stillbirths: the way forward in high-income countries.
Stillbirth rates in high-income countries declined dramatically from about 1940, but this decline has slowed or stalled over recent times. The present variation in stillbirth rates across and within high-income countries indicates that further reduction in stillbirth is possible. Large disparities (linked to disadvantage such as poverty) in stillbirth rates need to be addressed by providing more educational opportunities and improving living conditions for women. Placental pathologies and infection associated with preterm birth are linked to a substantial proportion of stillbirths. The proportion of unexplained stillbirths associated with under investigation continues to impede efforts in stillbirth prevention. Overweight, obesity, and smoking are important modifiable risk factors for stillbirth, and advanced maternal age is also an increasingly prevalent risk factor. Intensified efforts are needed to ameliorate the effects of these factors on stillbirth rates. Culturally appropriate preconception care and quality antenatal care that is accessible to all women has the potential to reduce stillbirth rates in high-income countries. Implementation of national perinatal mortality audit programmes aimed at improving the quality of care could substantially reduce stillbirths. Better data on numbers and causes of stillbirth are needed, and international consensus on definition and classification related to stillbirth is a priority. All parents should be offered a thorough investigation including a high-quality autopsy and placental histopathology. Parent organisations are powerful change agents and could have an important role in raising awareness to prevent stillbirth. Future research must focus on screening and interventions to reduce antepartum stillbirth as a result of placental dysfunction. Identification of ways to reduce maternal overweight and obesity is a high priority for high-income countries.
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Stillbirths: Where? When? Why? How to make the data count?
Despite increasing attention and investment for maternal, neonatal, and child health, stillbirths remain invisible-not counted in the Millennium Development Goals, nor tracked by the UN, nor in the Global Burden of Disease metrics. At least 2*65 million stillbirths (uncertainty range 2*08 million to 3*79 million) were estimated worldwide in 2008 (>=1000 g birthweight or >=28 weeks of gestation). 98% of stillbirths occur in low-income and middle-income countries, and numbers vary from 2*0 per 1000 total births in Finland to more than 40 per 1000 total births in Nigeria and Pakistan. Worldwide, 67% of stillbirths occur in rural families, 55% in rural sub-Saharan Africa and south Asia, where skilled birth attendance and caesarean sections are much lower than that for urban births. In total, an estimated 1*19 million (range 0*82 million to 1*97 million) intrapartum stillbirths occur yearly. Most intrapartum stillbirths are associated with obstetric emergencies, whereas antepartum stillbirths are associated with maternal infections and fetal growth restriction. National estimates of causes of stillbirths are scarce, and multiple (>35) classification systems impede international comparison. Immediate data improvements are feasible through household surveys and facility audit, and improvements in vital registration, including specific perinatal certificates and revised International Classification of Disease codes, are needed. A simple, programme-relevant stillbirth classification that can be used with verbal autopsy would provide a basis for comparable national estimates. A new focus on all deaths around the time of birth is crucial to inform programmatic investment.
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Stillbirths: the vision for 2020.
Stillbirth is a common adverse pregnancy outcome, with nearly 3 million third-trimester stillbirths occurring worldwide each year. 98% occur in low-income and middle-income countries, and more than 1 million stillbirths occur in the intrapartum period, despite many being preventable. Nevertheless, stillbirth is practically unrecognised as a public health issue and few data are reported. In this final paper in the Stillbirths Series, we call for inclusion of stillbirth as a recognised outcome in all relevant international health reports and initiatives. We ask every country to develop and implement a plan to improve maternal and neonatal health that includes a reduction in stillbirths, and to count stillbirths in their vital statistics and other health outcome surveillance systems. We also ask for increased investment in stillbirth-related research, and especially research aimed at identifying and addressing barriers to the aversion of stillbirths within the maternal and neonatal health systems of low-income and middle-income countries. Finally, we ask all those interested in reducing stillbirths to join with advocates for the improvement of other pregnancy-related outcomes, for mothers and their offspring, so that a united front for improved pregnancy and neonatal care for all will become a reality.
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Stillbirths: why they matter.
In this first paper of The Lancet's Stillbirths Series we explore the present status of stillbirths in the world-from global health policy to a survey of community perceptions in 135 countries. Our findings highlight the need for a strong call for action. In times of global focus on motherhood, the mother's own aspiration of a liveborn baby is not recognised on the world's health agenda. Millions of deaths are not counted; stillbirths are not in the Global Burden of Disease, nor in disability-adjusted life-years lost, and they are not part of the UN Millennium Development Goals. The grief of mothers might be aggravated by social stigma, blame, and marginalisation in regions where most deaths occur. Most stillborn babies are disposed of without any recognition or ritual, such as naming, funeral rites, or the mother holding or dressing the baby. Beliefs in the mother's sins and evil spirits as causes of stillbirth are rife, and stillbirth is widely believed to be a natural selection of babies never meant to live. Stillbirth prevention is closely linked with prevention of maternal and neonatal deaths. Knowledge of causes and feasible solutions for prevention is key to health professionals' priorities, to which this Stillbirths Series paper aims to contribute.
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Dynamic behaviour of stationary pronuclei during their positioning in Paramecium caudatum.
During conjugation of Paramecium caudatum, there are two well-known stages when nuclear migration occurs. What happens to the nuclei is closely related to their localisations in cells. The first of these stages is the entrance of one meiotic product into the paroral region. This nucleus survives, while the remaining three outside this area degenerate. The second stage is the antero-posterior localisation of eight synkaryon division products. Four posterior nuclei are differentiated into macronuclear anlagen, whereas four anterior nuclei remain as the presumptive micronuclei. In this experiment, the process of the third prezygotic division of P. caudatum was studied with the help of protargol staining. Here, a third nuclear migration was discovered. By two spindle turnings and two spindle elongations, stationary pronuclei were positioned near migratory pronuclei. This positioning of stationary pronuclei could shorten the distance for transferred migratory pronuclei to recognise and reach the stationary pronuclei. This fosters the synkaryon formation of P. caudatum.
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Complete sructure of nuclear rDNA of the obligate plant parasite Plasmodiophora brassicae: intraspecific polymorphisms in the exon and group I intron of the large subunit rDNA.
Plasmodiophora brassicae is a soil-borne obligate intracellular parasite in the phylum Cercozoa of the Rhizaria that causes clubroot disease of crucifer crops. To control the disease, understanding the distribution and infection routes of the pathogen is essential, and thus development of reliable molecular markers to discriminate geographic populations is required. In this study, the nuclear ribosomal RNA gene (rDNA) repeat unit of P. brassicae was determined, with particular emphasis on the structure of large subunit (LSU) rDNA, in which polymorphic regions were expected to be present. The complete rDNA complex was 9513bp long, which included the small subunit, 5.8S and LSU rDNAs as well as the internal transcribed spacer and intergenic spacer regions. Among eight field populations collected from throughout Honshu Island, Japan, a 1.1 kbp region of the LSU rDNA, including the divergent 8 domain, exhibited intraspecific polymorphisms that reflected geographic isolation of the populations. Two new group I introns were found in this region in six out of the eight populations, and the sequences also reflected their geographic isolation. The polymorphic region found in this study may have potential for the development of molecular markers for discrimination of field populations/isolates of this organism.
not annotated - annotated - LINNAEUS only
Taxonomy and phylogeny of a new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov. (Gymnodiniales, Dinophyceae), and its cryptophyte symbiont.
A new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov., was described using light microscopy, electron microscopy and phylogengetic analysis based on partial LSU rDNA sequences. Cells were dorsiventrally flattened, elongate-elliptical in ventral view. There was no displacement of the cingulum encircling the anterior part of the cell. The cingulum was curved posteriorly at the terminal junction with the sulcus. The sulcus was generally narrow but expanded in the posterior end. The epicone possessed an apical groove made of one and one-half counterclockwise revolutions. Phylogenetic analysis based on LSU rDNA showed that the sequence of G. myriopyrenoides was included in the Gymnodiniales sensu stricto clade and had special affinities with the species Amphidinium poecilochroum and Gymnodinium acidotum, which also harbor kleptochloroplasts. Phylogenetic analysis based on plastid-encoded SSU rDNA and ultrastructural observations suggested that the symbionts of G. myriopyrenoides were cryptophytes of the genus Chroomonas or Hemiselmis. Organelles including the nucleus, the nucleomorph, mitochondria, Golgi bodies and large chloroplasts remained in the cytoplasm of the symbionts, but not the periplast, ejectosomes or flagellar apparatus. The symbiotic level of G. myriopyrenoides was estimated to be a relatively early stage in the unarmored kleptoplastidal dinoflagellates.
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No paradox, no progress: inverse cancer comorbidity in people with other complex diseases.
In the past 5 years, several leading groups have attempted to explain why individuals with Down's syndrome have a reduced risk of many solid tumours and an increased risk of leukaemia and testicular cancer. Niels Bohr, the Danish physicist, noted that a paradox could initiate progress. We think that the paradox of a medical disorder protecting against cancer could be formalised in a new model of inverse cancer morbidity in people with other serious diseases. In this Personal View, we review evidence from epidemiological and clinical studies that supports a consistently lower than expected occurrence of cancer in patients with Down's syndrome, Parkinson's disease, schizophrenia, diabetes, Alzheimer's disease, multiple sclerosis, and anorexia nervosa. Intriguingly, most comorbidities are neuropsychiatric or CNS disorders. We provide a brief overview of evidence indicating genetic and molecular connections between cancer and these complex diseases. Inverse comorbidity could be a valuable model to investigate common or related pathways or processes and test new therapies, but, most importantly, to understand why certain people are protected from the malignancy.
not annotated - annotated - LINNAEUS only
Milestones in Candida albicans gene manipulation.
In the United States, candidemia is one of the most common hospital-acquired infections and is estimated to cause 10,000 deaths per year. The species Candida albicans is responsible for the majority of these cases. As C. albicans is capable of developing resistance against the currently available drugs, understanding the molecular basis of drug resistance, finding new cellular targets, and further understanding the overall mechanism of C. albicans pathogenesis are important goals. To study this pathogen it is advantageous to manipulate its genome. Numerous strategies of C. albicans gene manipulation have been introduced. This review evaluates a majority of these strategies and should be a helpful guide for researchers to identify gene targeting strategies to suit their requirements.
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The pharmacological treatment of epilepsy in adults.
Treatment decisions in epilepsy need to be individualised on the basis of careful analysis of the risk-benefit ratio of each available option. Key decision steps include the time at which antiepileptic drug treatment should be started, which drug should be chosen for first-line therapy, and which strategy is most appropriate for people who did not respond to the initially prescribed drug. With more than 20 antiepileptic drugs currently available to treat epilepsy in adults, opportunities to tailor drug therapy have never been greater, but optimum use of such a complex armamentarium is a challenge even for the epilepsy specialist. Antiepileptic drug choice is primarily based on evidence of efficacy and effectiveness for the individual's seizure type, but other patient-specific factors need to be considered, including age, sex, childbearing potential, comorbidities, and concomitant medications.
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Stroke and the immune system: from pathophysiology to new therapeutic strategies.
Stroke is the second most common cause of death worldwide and a major cause of acquired disability in adults. Despite tremendous progress in understanding the pathophysiology of stroke, translation of this knowledge into effective therapies has largely failed, with the exception of thrombolysis, which only benefits a small proportion of patients. Systemic and local immune responses have important roles in causing stroke and are implicated in the primary and secondary progression of ischaemic lesions, as well as in repair, recovery, and overall outcome after a stroke. However, potential therapeutic targets in the immune system and inflammatory responses have not been well characterised. Development of novel and effective therapeutic strategies for stroke will require further investigation of these pathways in terms of their temporal profile (before, during, and after stroke) and risk-to-benefit therapeutic ratio of modulating them.
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Emerging targets and treatments in amyotrophic lateral sclerosis.
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that is currently untreatable. Many compounds have been tested in laboratory-based models and in patients with ALS, but so far only one drug, riluzole, has shown efficacy, yet it only slightly slows disease progression. Several new insights into the causes of motor neuron death have led to the identification of some important novel targets for intervention. At no time have studies involved such a wide range of innovations and such advanced technologies. Many promising studies are underway to test potential targets that will hopefully translate into meaningful therapeutics for patients with ALS.
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Hepatitis delta virus.
Hepatitis delta virus (HDV) is a small, defective RNA virus that can infect only individuals who have hepatitis B virus (HBV); worldwide more than 15 million people are co-infected. There are eight reported genotypes of HDV with unexplained variations in their geographical distribution and pathogenicity. The hepatitis D virion is composed of a coat of HBV envelope proteins surrounding the nucleocapsid, which consists of a single-stranded, circular RNA genome complexed with delta antigen, the viral protein. HDV is clinically important because although it suppresses HBV replication, it causes severe liver disease with rapid progression to cirrhosis and hepatic decompensation. The range of clinical presentation is wide, varying from mild disease to fulminant liver failure. The prevalence of HDV is declining in some endemic areas but increasing in northern and central Europe because of immigration. Treatment of HDV is with pegylated interferon alfa; however, response rates are poor. Increased understanding of the molecular virology of HDV will identify novel therapeutic targets for this most severe form of chronic viral hepatitis.
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Altering sexual reproductive mode by interspecific exchange of MAT loci.
Sexual fungi can be self-sterile (heterothallic, requiring genetically distinct partners) or self-fertile (homothallic, no partner required). In most ascomycetes, a single mating type locus (MAT) controls the ability to reproduce sexually. In the genus Cochliobolus, all heterothallic species have either MAT1-1 or MAT1-2 (but never both) in different individuals whereas all homothallic species carry both MAT1-1 and MAT1-2 in the same nucleus of an individual. It has been demonstrated, previously, that a MAT gene from homothallic Cochliobolus luttrellii can confer self-mating ability on a mat-deleted strain of its heterothallic relative, Cochliobolus heterostrophus. In this reciprocal study, we expressed, separately, the heterothallic C. heterostrophus MAT1-1-1 and MAT1-2-1 genes in a mat-deleted homothallic C. luttrellii strain and asked if this converts homothallic C. luttrellii to heterothallism. We report that: (1) A C. luttrellii transgenic strain carrying C. heterostrophus MAT1-1-1 and a C. luttrellii transgenic strain carrying C. heterostrophus MAT1-2-1 can mate in a heterothallic manner and the fertility of the cross is similar to that of a wild type C. luttrellii self. Full tetrads are always found. (2) A C. luttrellii transgenic strain carrying C. heterostrophus MAT1-1-1 can mate with the parental wild type C. luttrellii MAT1-1;MAT1-2 strain, indicating the latter is able to outcross, a result which was expected but has not been demonstrated previously. (3) A C. luttrellii transgenic strain carrying C. heterostrophus MAT1-2-1 cannot mate with the parental wild type C. luttrellii MAT1-1;MAT1-2 strain, indicating outcrossing specificity. (4) Each transgenic C. luttrellii strain, carrying only a single C. heterostrophus MAT gene, is able to self, although all pseudothecia produced are smaller than those of wild type and fertility is low (about 4-15% of the number of wild type asci). These data support the argument that in Cochliobolus spp., the primary determinant of reproductive mode is MAT itself, and that a heterothallic strain can be made homothallic or a homothallic strain can be made heterothallic by exchange of MAT genes. The selfing ability of transgenic C. luttrellii strains also suggests that both MAT1-1-1 and MAT1-2-1 genes of C. heterostrophus carry equivalent transcription regulatory activities, each capable of promoting sexual development when alone, in a suitable genetic background.
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Rate of egg maturation in marine turtles exhibits 'universal temperature dependence'.
1. The metabolic theory of ecology (MTE) predicts that, after correcting for body mass variation among organisms, the rates of most biological processes will vary as a universal function of temperature. However, empirical support for 'universal temperature dependence' (UTD) is currently equivocal and based on studies of a limited number of traits. 2. In many ectothermic animals, the rate at which females produce mature eggs is temperature dependent and may be an important factor in determining the costs of reproduction. 3. We tested whether the rate of egg maturation in marine turtles varies with environmental temperature as predicted by MTE, using the time separating successive clutches of individual females to estimate the rate at which eggs are formed. We also assessed the phenotypic contribution to this rate, by using radio telemetry to make repeated measurements of interclutch intervals for individual green turtles (Chelonia mydas). 4. Rates of egg maturation increased with seasonally increasing water temperatures in radio-tracked green turtles, but were not repeatable for individual females, and did not vary according to maternal body size or reproductive investment (number and size of eggs produced). 5. Using a collated data set from several different populations and species of marine turtles, we then show that a single relationship with water temperature explains most of the variation in egg maturation rates, with a slope that is statistically indistinguishable from the UTD predicted by MTE. However, several alternative statistical models also described the relationship between temperature and egg maturation rates equally parsimoniously. 6. Our results offer novel support for the MTE's predicted UTD of biological rates, although the underlying mechanisms require further study. The strong temperature dependence of egg maturation combined with the apparently weak phenotypic contribution to this rate has interesting behavioural implications in ectothermic animals. We suggest that maternal thermoregulatory behaviour in marine turtles, and many other reptiles, is consistent with a strategy of adaptively increasing body temperatures to accelerate egg maturation.
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Host plant effects on alkaline phosphatase activity in the whiteflies, Bemisia tabaci Biotype B and Trialeurodes vaporariorum.
Bemisia tabaci (Gennadius) B-biotype and Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) often coexist on greenhouse-grown vegetable crops in northern China. The recent spread of B. tabaci B-biotype has largely replaced T. vaporariorum, and B-biotype now overlaps with T. vaporariorum where common hosts occur in most invaded areas. The impact of the B-biotype on the agro eco system appears to be widespread, and involves the ability to compete with and perhaps replace other phytophages like T. vaporariorum. An emerging hypothesis is that the B-biotype is physiologically superior due at least in part to an improved ability to metabolically utilize the alkaline phosphatase pathway. To test this hypothesis, alkaline phosphatase activity was studied in the B-biotype and T. vaporariorum after feeding on a number of different hosts for a range of durations, with and without host switching. Alkaline phosphatase activity in T. vaporariorum was 1.45 to 2.53-fold higher than that of the B-biotype when fed on tomato for 4 and 24 h, or switched from tomato to cotton and cabbage for the same durations. However, alkaline phosphatase activity in the B-biotype was 1.40 to 3.35-fold higher than that of T. vaporariorum when the host switching time was -72 and -120 h on the same plant. Both short-term (4 h) and long-term (72 h) switching of plant hosts can significantly affect the alkaline phosphatase activity in the two species. After -120 h, feeding on tomato and cotton alkaline phosphatase activity in the B-biotype was significantly higher than that of T. vaporariorum. It was shown that alkaline phosphatase aids the species feeding on different plant species, and that the B-biotype is physiologically superior to T. vaporariorum in utilizing the enzyme compared to T. vaporariorum over longer periods of feeding.
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Evidence to support karyotypic variation of the mosquito, Anopheles peditaeniatus in Thailand.
Eight isoline colonies of Anopheles peditaeniatus Leicester (Diptera: Culicidae) were established from wild-caught females collected from buffalo-baited traps at 8 localities in Thailand. They showed 2 types of X (X(2), X(3)) and 4 types of Y (Y(2), Y(3), Y(4), Y(5)) chromosomes based on the number and amount of major block(s) of heterochromatin present in the heterochromatic arm, and were tentatively designated as Forms B (X(2), X(3), Y(2)), C (X(3), Y(3)), D (X(3), Y(4)) and E (X(2), X(3), Y(5)). Form B was found in Nan, Ratchaburi, and Chumphon provinces; Form C was obtained in Chon Buri province; Form D was recovered in Kamphaeng Phet province; and Form E was acquired in Chiang Mai, Udon Thani, and Ubon Ratchathani provinces. Crossing studies among the 8 isoline colonies, which were representative of 4 karyotypic forms of An. peditaeniatus, revealed genetic compatibility in providing viable progenies and synaptic salivary gland polytene chromosomes through F(2)-generations, thus suggesting the conspecific nature of these karyotypic forms. These results were supported by the very low intraspecific sequence variations (0.0 - 1.1%) of the nucleotide sequences in ribosomal DNA (ITS2) and mitochondrial DNA (COI and COII) of the 4 forms.
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A review of the implications of heterozygosity and inbreeding on germplasm biodiversity and its conservation in the silkworm, Bombyx mori.
Abstract Silkworm genebanks assume paramount importance as the reservoirs of biodiversity and source of alleles that can be easily retrieved for genetic enhancement of popular breeds. More than 4000 Bombyx mori L (Lepidoptera: Bombycidae) strains are currently available and these strains are maintained through continuous sibling mating. This repeated sibling mating makes the populations of each strain more homozygous, but leads to loss of unique and valuable genes through the process of inbreeding depression. Hence, it is essential to maintain a minimal degree of heterozygosity within the population of each silkworm strain, especially in the traditional geographic strains, to avoid such loss. As a result, accurate estimation of genetic diversity is becoming more important in silkworm genetic resources conservation. Application of molecular markers help estimate genetic diversity much more accurately than that of morphological traits. Since a minimal amount of heterozygosity in each silkworm strain is essential for better conservation by avoiding inbreeding depression, this article overviews both theoretical and practical importance of heterozygosity together with impacts of inbreeding depression and the merits and demerits of neutral molecular markers for measurements of both heterozygosity and inbreeding depression in the silkworm Bombyx mori.
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Characterization of nonjunctional hemichannels in caterpillar cells.
Recent studies have demonstrated that hemichannels, which form gap junctions when paired from apposing cells, may serve additional roles when unpaired including cell adhesion and paracrine communication. Hemichannels in mammals are formed by connexins or pannexins, while in insects they are formed by pannexin homologues termed innexins. The formation of functional gap junctions by insect innexins has been established, although their ability to form functional nonjunctional hemichannels has not been reported. Here the characteristics of nonjunctional hemichannels were examined in three lepidopteran cell types, two cell lines (High Five and Sf9) and explanted hemocytes from Heliothis virescens (Fabricius) (Lepidoptera: Noctuidae). Selective fluorescent dye uptake by hemichannels was observed in a significant minority of cells, using fluorescence microscopy and flow cytometry. Carbenoxelone, an inhibitor of mammalian junctions, disrupted dye uptake, while flufenamic acid and mefloquine did not. The presence of Ca(2+) and Mg(2+) in the media increased hemichannel activity. Additionally, lipopolysaccharide, a stimulator of immune activity in lepidopterans, decreased dye uptake. These results demonstrate for the first time the activity of nonjunctional hemichannels in insect cells, as well as pharmacological tools to manipulate them. These results will facilitate the further examination of the role of innexins and nonjunctional hemichannels in insect cell biology, including paracrine signaling, and comparative studies of mammalian pannexins and insect innexins.
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Post-egression host tissue feeding is another strategy of host regulation by the Koinobiont wasp, Toxoneuron nigriceps.
Koinobiont wasps start their lives as hemolymph feeders inside the host body, but before they egress from the host many become tissue predators. One species, the endoparasitoid Toxoneuron nigriceps Viereck (Hymenoptera: Braconidae), exhibits the unusual behavior of egressing before initiating tissue predation. After egression from the host, it reinserts its head into the host body to begin tissue feeding. These third instar T. nigriceps larvae show a significant increase in body size and mass after post-egression feeding. Through this project the importance of post-egression feeding in the development of T. nigriceps in its host the tobacco budworm, Heliothis virescens Fabricius (Lepidoptera: Noctuidae), has been evaluated. The study was conducted by preventing the egressed third instar T. nigriceps larvae from feeding on host tissue and observing whether they could undergo further development. Though some of the larvae that were prevented from post-egression feeding did undergo cocoon formation, pupation, and adult emergence they were inferior in terms of size, body mass, and survival to those that developed from larvae allowed to feeding after egression. Hence, it is concluded that post-egression host tissue feeding is essential for the normal development of T. nigriceps, as the prevention of feeding resulted in significantly lighter and smaller larvae, cocoons, and adults as well as deformed adults and reduced adult survival. Post-egression feeding as a host regulatory strategy is discussed.
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Evaluating aggregation membership and copulatory success in the stink bug, Euschistus conspersus, using field and laboratory experiments.
The aggregation and mating behavior of the stink bug, Euschistus conspersus Uhler (Hemiptera: Pentatomidae) was investigated in a series of field and laboratory experiments. Marking of E. conspersus mating in aggregations in the field demonstrated that both sexes mate multiple times within aggregations on successive nights and with different partners, although = 20% of the individuals of both sexes returned to aggregations but did not mate. Further analysis of mating patterns in caged aggregations revealed that heavy males and light females mated more frequently than their respective counterparts. Data are interpreted in terms of elucidating the function of benefits of multiple mating within aggregations for males and females.
not annotated - annotated - LINNAEUS only
Occurrence of entomopathogenic fungi from agricultural and natural ecosystems in Saltillo, Mexico, and their virulence towards thrips and whiteflies.
Entomopathogenic fungi were collected from soil in four adjacent habitats (oak forest, agricultural soil, pine reforestation and chaparral habitat) in Saltillo, Mexico using the insect bait method with Tenebrio molitor (L.) (Coleoptera: Tenebrionidae) larvae as bait. Overall, of the larvae exposed to soil, 171 (20%) hosted Beauveria bassiana (Balsamo) Vuillemin (Hypocreales: Cordycipitaceae), 25 (3%) hosted Metarhizium anisopliae (Metschnikoff) Sorokin (Hypocreales: Clavicipitaceae) and 1 (0.1%) hosted lsaria (=Paecilomyces) sp. (Hypocreales: Cordycipitaceae). B. bassiana was significantly more frequent on larvae exposed to oak forest soil. M. anisopliae was significantly more frequent on larvae exposed to agricultural soil. From the infected bait insects, 93 isolates of B. bassiana and 24 isolates of M. anisopliae were obtained. Strains were tested for their infectivity against Cuban laurel thrips, Gynaikothrips uzeli Zimmerman (Thysanoptera: Phlaeothripidae) and the greenhouse whitefly, Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae). B. bassiana isolates caused the highest mortality on thrips (some causing 88% mortality after 6 days); both fungal species caused similarly high mortality levels against whiteflies (75%) after 6 days. Large amounts of germplasm of entomopathogenic fungi, fundamentally B. bassiana and M. anisopliae, exist in the habitats sampled; pathogenicity varied among strains, and some strains possessed significant virulence. Soils in these habitats are reservoirs of diverse strains with potential for use in biocontrol.
not annotated - annotated - LINNAEUS only
Lasting effects of maternal behaviour on the distribution of a dispersive stream insect.
1. Predicting population dynamics at large spatial scales requires integrating information about spatial distribution patterns, inter-patch movement rates and within-patch processes. Advective dispersal of aquatic species by water movement is considered paramount to understanding their population dynamics. Rivers are model advective systems, and the larvae of baetid mayflies are considered quintessential dispersers. Egg laying of baetids along channels is patchy and reflects the distribution of oviposition sites, but larvae are assumed to drift frequently and far, thereby erasing patterns created during oviposition. Dispersal kernels are often overestimated, however, and empirical tests of such assumptions are warranted because of the pivotal role distribution patterns can have on populations. 2. We tested empirically whether the egg distribution patterns arising from oviposition behaviours persisted and were reflected in the distribution patterns of larval Baetis rhodani. In field surveys, we tested for associations between egg mass and larval densities over 1 km lengths of four streams. A control species, the mayfly Ephemerella ignita, was employed to test for covarying environmental factors. We estimated drift rates directly to test whether larvae dispersed between riffles (patches of high egg mass density) and whether drift rates were density-dependent or density-related - expected outcomes if drift erases patterns established by maternal behaviours. 3. Positive associations between egg masses and larval benthic densities were found for neonate and mid-stage larvae of Baetis, but not the control species, suggesting persistence of the patchy distribution patterns established at oviposition. Drift rates were high, and riffles were net exporters of neonate and mid-stage larvae, but drift rates were unrelated to benthic densities and few drifters reached the next riffle. Riffles were sinks for large larvae, suggesting ontogenetic shifts in habitat use, but little long-distance dispersal. 4. Overall, the results suggest that most neonate and mid-stage larvae of B. rhodani remain close to the natal riffle, and late-stage larvae disperse shorter distances than routinely assumed. The persistence of maternal effects on distribution patterns well into juvenile life of an allegedly iconic disperser suggests that traditional models of how dispersal influences the population dynamics of many lotic invertebrates may be incorrect.
not annotated - annotated - LINNAEUS only
Effects of individual condition and habitat quality on natal dispersal behaviour in a small rodent.
1. Individuals should benefit from settling in high-quality habitats, but dispersers born under favourable conditions have a better physical condition and should therefore be more successful at settling in high-quality habitats. 2. We tested these predictions with root voles (Microtus oeconomus) by a manipulation of individual condition through litter-size enlargement and reduction during lactation combined with a manipulation of habitat quality through degradation of the vegetation cover. We accurately monitored movements of 149 juveniles during a settlement and breeding period of 3 months. 3. The litter size treatment had long-lasting effects on body size, life-history traits and home range size, but did not influence dispersal behaviour. 4. Different stages of dispersal were influenced by habitat quality. In low-quality patches, females dispersed earlier, spent more time prospecting their environment before settling, and settlers had a smaller adult body size than in high-quality patches. Preference and competition for high-quality patches is likely adaptive as it increased fitness both in terms of survival and reproduction. 5. We found no interactive effect of individual condition and habitat quality on natal dispersal and habitat selection. 6. These findings suggest that immediate conditions are more important determinants of dispersal decisions than conditions experienced early in life.
not annotated - annotated - LINNAEUS only
Nesting biology and fungiculture of the fungus-growing ant, Mycetagroicus cerradensis: new light on the origin of higher attine agriculture.
The genus Mycetagroicus is perhaps the least known of all fungus-growing ant genera, having been first described in 2001 from museum specimens. A recent molecular phylogenetic analysis of the fungus-growing ants demonstrated that Mycetagroicus is the sister to all higher attine ants (Trachymyrmex, Sericomyrmex, Acromyrmex, Pseudoatta, and Atta), making it of extreme importance for understanding the transition between lower and higher attine agriculture. Four nests of Mycetagroicus cerradensis near Uberlandia, Minas Gerais, Brazil were excavated, and fungus chambers for one were located at a depth of 3.5 meters. Based on its lack of gongylidia (hyphal-tip swellings typical of higher attine cultivars), and a phylogenetic analysis of the ITS rDNA gene region, M. cerradensis cultivates a lower attine fungus in Clade 2 of lower attine (G3) fungi. This finding refines a previous estimate for the origin of higher attine agriculture, an event that can now be dated at approximately 21-25 mya in the ancestor of extant species of Trachymyrmex and Sericomyrmex.
not annotated - annotated - LINNAEUS only
The role of body size and shape in understanding competitive interactions within a community of Neotropical dung beetles.
Geometric morphometrics is helpful for understanding how body size and body shape influence the strength of inter-specific competitive interactions in a community. Dung beetles, characterized by their use of decomposing organic material, provide a useful model for understanding the structuring of ecological communities and the role of competition based on their size and morphology. The relationship between body size and shape in a dung beetle community from the Atlantic Forest in Serra do Japi, Brazil was analyzed for 39 species. Fifteen anatomical landmarks on three-dimensional Cartesian coordinates were used to describe both the shape and the size of the body of each species on the basis of the centroid located along homologous points in all of the species. The first vector of a principal components analysis explained 38.5% of the morphological variation among species, and represents a gradient of body shape from elongated, flattened bodies with narrow abdomen to rounded or convex bodies. The second component explained 17.8% of the remaining variation in body shape, which goes from species with an abdomen that is larger than the elytra to species with constricted abdomens and large elytra. The relationship between body size and shape was analyzed separately for diurnal and nocturnal species. In both guilds not only were there differences in body size, but also in body shape, suggesting a reduction in their level of competition.
not annotated - annotated - LINNAEUS only
Analysis of genetic variation and phylogeny of the predatory bug, Pilophorus typicus, in Japan using mitochondrial gene sequences.
Pilophorus typicus (Distant) (Heteroptera: Miridae) is a predatory bug occurring in East, Southeast, and South Asia. Because the active stages of P. typicus prey on various agricultural pest insects and mites, this species is a candidate insect as an indigenous natural enemy for use in biological control programs. However, the mass releasing of introduced natural enemies into agricultural fields may incur the risk of affecting the genetic integrity of species through hybridization with a local population. To clarify the genetic characteristics of the Japanese populations of P. typicus two portions of the mitochondrial DNA, the cytochrome oxidase subunit I (COI) (534 bp) and the cytochrome B (cytB) (217 bp) genes, were sequenced for 64 individuals collected from 55 localities in a wide range of Japan. Totals of 18 and 10 haplotypes were identified for the COI and cytB sequences, respectively (25 haplotypes over regions). Phylogenetic analysis using the maximum likelihood method revealed the existence of two genetically distinct groups in P. typicus in Japan. These groups were distributed in different geographic ranges: one occurred mainly from the Pacific coastal areas of the Kii Peninsula, the Shikoku Island, and the Ryukyu Islands; whereas the other occurred from the northern Kyushu district to the Kanto and Hokuriku districts of mainland Japan. However, both haplotypes were found in a single locality of the southern coast of the Shikoku Island. COI phylogeny incorporating other Pilophorus species revealed that these groups were only recently differentiated. Therefore, use of a certain population of P. typicus across its distribution range should be done with caution because genetic hybridization may occur.
not annotated - annotated - LINNAEUS only
Fire ant decapitating fly cooperative release programs (1994-2008): two Pseudacteon species, P. tricuspis and P. curvatus, rapidly expand across imported fire ant populations in the southeastern United States.
Natural enemies of the imported fire ants, Solenopsis invicta Buren S. richteri Forel (Hymenoptera: Formicidae), and their hybrid, include a suite of more than 20 fire ant decapitating phorid flies from South America in the genus Pseudacteon. Over the past 12 years, many researchers and associates have cooperated in introducing several species as classical or self-sustaining biological control agents in the United States. As a result, two species of flies, Pseudacteon tricuspis Borgmeier and P. curvatus Borgmeier (Diptera: Phoridae), are well established across large areas of the southeastern United States. Whereas many researchers have published local and state information about the establishment and spread of these flies, here distribution data from both published and unpublished sources has been compiled for the entire United States with the goal of presenting confirmed and probable distributions as of the fall of 2008. Documented rates of expansion were also used to predict the distribution of these flies three years later in the fall of 2011. In the fall of 2008, eleven years after the first successful release, we estimate that P. tricuspis covered about 50% of the fire ant quarantined area and that it will occur in almost 65% of the quarantine area by 2011. Complete coverage of the fire ant quarantined area will be delayed or limited by this species' slow rate of spread and frequent failure to establish in more northerly portions of the fire ant range and also, perhaps, by its preference for red imported fire ants (S. invicta). Eight years after the first successful release of P. curvatus, two biotypes of this species (one biotype occurring predominantly in the black and hybrid imported fire ants and the other occurring in red imported fire ants) covered almost 60% of the fire ant quarantined area. We estimate these two biotypes will cover almost 90% of the quarantine area by 2011 and 100% by 2012 or 2013. Strategic selection of several distributional gaps for future releases will accelerate complete coverage of quarantine areas. However, some gaps may be best used for the release of additional species of decapitating flies because establishment rates may be higher in areas without competing species.
not annotated - annotated - LINNAEUS only
Factors of susceptibility of human myiasis caused by the New World screw-worm, Cochliomyia hominivorax in Sao Gonsigmaalo, Rio de Janeiro, Brazil.
This study was carried out between July 2007 and June 2008 and reports on the occurrence of human myiasis caused by the New World screwworm, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae) in Sao Gonsigmaalo in the state of Rio de Janeiro, Brazil. Liquid or solid vaseline was used to suffocate the larvae, which were then preserved in 70% ethanol and sent to the Instituto Oswaldo Cruz for identification. C. hominivorax were identified in all 22 cases of myiasis. There were 12 male and 10 female patients with ages ranging from 03 to 71. Ethnically the highest incidence was among black people, with 17 cases. Open wounds were the main cause of the parasitosis, whereas poor personal hygiene, the low educational level, alcoholism, bedridden patients, and physical or mental disability were possibly secondary factors; in addition to all these factors the income of the patients was very low.
not annotated - annotated - LINNAEUS only
Assessment of attractiveness of cassava as a roosting plant for the melon fly, Bactrocera cucurbitae, and the Oriental fruit fly, B. dorsalis.
Application of bait spray to crop borders is a standard approach for suppression of melon fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae) populations and may also be of value for suppression of oriental fruit fly, B. dorsalis (Hendel) populations. Establishment of preferred roosting hosts as crop borders may help to improve suppression of both fruit fly species by providing sites for bait spray applications. In an area-wide B. cucurbitae suppression trial, the question was raised as to whether cassava, Manihot esculenta Crantz (Euphorbiales: Euphorbiaceae), could be used as a B. cucurbitae roosting host. M. esculenta was of interest as a roosting host because, in contrast to many other identified preferred roosting hosts, it would also be a crop potentially increasing the productivity of the crop production system overall. As a short-lived and shrubby perennial, M. esculenta potentially constitutes a crop with more persistent roosting foliage than an annual crop such as corn, Zea mays L. (Cyperales: Poaceae), that has often been planted as a roosting host for B. cucurbitae control. Using protein-baited traps set amidst potted plants placed adjacent to a papaya Carica papaya L. (Violales: Caricaceae) orchard known to have established populations of B. cucurbitae and B. dorsalis, the effectiveness of M. esculenta as a roosting host was assessed by comparing its attractiveness to that of castor bean, Ricinus communis L (Malpighiales: Euphorbiaceae), previously identified as one of the most attractive roosting hosts for B. cucurbitae, and to corn, a crop which has been planted as a roosting host for help in B. cucurbitae control. The results showed that use of M. esculenta as a roosting host is comparable to use of R. communis by both B. cucurbitae and B. dorsalis. These results provide encouragement to incorporate M. esculenta on a farm as a trap crop (i.e. site for bait spray application). This has the advantage of having the trap crop be a crop on its own (as opposed to castor bean) and, among prospective crops that could be used as a trap crop, has foliage more persistent than an annual trap crop such as corn.
not annotated - annotated - LINNAEUS only
A comparison of the pitfall trap, Winkler extractor and Berlese funnel for sampling ground-dwelling arthropods in tropical montane cloud forests.
Little is known about the ground-dwelling arthropod diversity in tropical montane cloud forests (TMCF). Due to unique habitat conditions in TMCFs with continuously wet substrates and a waterlogged forest floor along with the innate biases of the pitfall trap, Berlese funnel and Winkler extractor are certain to make it difficult to choose the most appropriate method to sample the ground-dwelling arthropods in TMCFs. Among the three methods, the Winkler extractor was the most efficient method for quantitative data and pitfall trapping for qualitative data for most groups. Inclusion of floatation method as a complementary method along with the Winkler extractor would enable a comprehensive quantitative survey of ground-dwelling arthropods. Pitfall trapping is essential for both quantitative and qualitative sampling of Diplopoda, Opiliones, Orthoptera, and Diptera. The Winkler extractor was the best quantitative method for Psocoptera, Araneae, Isopoda, and Formicidae; and the Berlese funnel was best for Collembola and Chilopoda. For larval forms of different insect orders and the Acari, all the three methods were equally effective.
not annotated - annotated - LINNAEUS only
The organization of foraging in the fire ant, Solenopsis invicta.
Although natural selection in ants acts most strongly at the colony, or superorganismal level, foraging patterns have rarely been studied at that level, focusing instead on the behavior of individual foragers or groups of foragers. The experiments and observations in this paper reveal in broad strokes how colonies of the fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae), allocate their available labor to foraging, how they disperse that force within their territory, and how this force changes with colony size, season and worker age. Territory area is positively related to colony size and the number of foragers, more so during the spring than fall. Changes of colony size and territory area are driven by seasonal variation of sexual and worker production, which in turn drive seasonal variation of worker age-distribution. During spring sexual production, colonies shrink because worker production falls below replacement. This loss is proportional to colony size, causing forager density in the spring to be negatively related to colony and territory size. In the fall, colonies emphasize worker production, bringing colony size back up. However, because smaller colonies curtailed spring worker production less than larger ones, their fall forager populations are proportionally greater, causing them to gain territory at the expense of large colonies. Much variation of territory area remains unexplained and can probably be attributed to pressure from neighboring colonies. Boundaries between territories are characterized by "no ants' zones" mostly devoid of fire ants. The forager population can be divided into a younger group of recruitable workers that wait for scouts to activate them to help retrieve large food finds. About one-third of the recruits wait near openings in the foraging tunnels that underlie the entire territory, while two-thirds wait in the nest. Recruitment to food is initially very rapid and local from the foraging tunnels, while sustained recruitment gradually involves the recruits waiting in the nest. As recruits age, they become scouts searching for food on the surface, and die about two weeks later. Foraging tunnels decrease in cross-sectional area with distance from the nest, in keeping with the gradual bleeding off of workers to the surface with distance. Foragers lack route-faithfulness, and having been marked and released at one point within the territory, they can be recaptured at any other point a day later. The size of the territory actually occupied may be limited during dry weather, resulting in very large no-ants' zones.
not annotated - annotated - LINNAEUS only
Pollen preference for Psychotria sp. is not learned in the passion flower butterfly, Heliconius erato.
Heliconius butterflies are known to maximize fitness by feeding on pollen from Gurania sp. and Psiguria sp. (Cucurbitales: Curcurbitaceae), and Psychotria sp. (Gentianales: Rubiaceae). This specialization involves specific physical, physiological, and behavioral adaptations including efficient search strategies in the forest to locate pollen host plants, pollen removal, and pollen external digestion. Reducing pollen host plant search time is crucial to out-compete other flower visitors and to reduce exposure to predators. One way in which this can be achieved is by using chemical cues to learn from experienced foragers in roosting aggregations. Similar strategies have been documented in bumblebees, where inexperienced individuals learn floral odors from experienced foragers. Behavioral experiments using plants preferred by Heliconius erato suggest that pollen preference in H. erato is an innate trait and consequently learning of chemical cues at roosting aggregations is unlikely.
not annotated - annotated - LINNAEUS only
Description of the immatures of the ant, Myrmelachista catharinae.
The Neotropical ant genus Myrmelachista Roger comprises 69 described species and subspecies, and still is a poorly studied group. Larvae play a paramount role in colony nutrition in social hymenopterans and bear considerable value in the reconstruction of group phylogenies, however, they are generally neglected. Larvae of different instars of Myrmelachista catharinae Mayr (Hymenoptera: Formicidae) are herein described in detail by light and scanning electron microscopy. The number of larval instars was estimated as three based on the frequency distribution of maximum head capsule widths. The described larvae confirmed some traits typical of the genus: general shape of body and mandibles, general aspect and distribution of body hairs, and the number of sensilla on the palps and galea. Differently from other Myrmelachista larvae previously described, M. catharinae presented two distinct kinds of second instars, some additional types of body hairs, different number of antennal sensilla, and a distinct labrum shape. M. catharinae presented ten pairs of spiracles, which is the first record for this genus.
not annotated - annotated - LINNAEUS only
Morphological redescriptions of four marine ciliates (Ciliophora: Cyrtophorida: Dysteriidae) from Qingdao, China.
The morphology and infraciliature of four marine cyrtophorid ciliates isolated from Qingdao, China, were investigated. Based on the present work and on previous data, improved diagnoses for three rarely known species are provided: (1) Mirodysteria decora; small-sized marine Mirodysteria about 35-60 x 25-35 mum in vivo, oval in outline; body surface with two or three conspicuous dorsal spines and one caudal spine; three right kineties, the rightmost one extending dorso-apically; left frontal kineties reduced, each consisting of three basal bodies only; podite subcaudally positioned; two ventrally located contractile vacuoles. (2) Dysteria legumen; body oval with two longitudinal grooves on different plates; six right kineties, the rightmost two of which extend dorso-apically; two left frontal kineties and two ventrally located contractile vacuoles. (3) Dysteria proraefrons; body about 60x35 mum in vivo; six right kineties, the two rightmost of which extend dorso-apically and the leftmost one is considerably shortened; three left frontal kineties; two ventrally located contractile vacuoles. A population of D. derouxi with eight or nine right kineties is also briefly described. The current investigation further demonstrates high diversity and cosmopolitan distribution of this highly specialized group of benthic ciliates.
not annotated - annotated - LINNAEUS only
Morphological and molecular information of a new species of Geleia (Ciliophora, Karyorelictea), with redescriptions of two Kentrophoros species from China.
The morphology and infraciliature of three karyorelictean ciliates, Geleia sinica spec. nov. and two poorly known Kentrophoros species, K. flavus and K. gracilis, isolated from the intertidal zone of a beach at Qingdao, China, were investigated. Geleia sinica spec. nov. is distinguished from its congeners by the following combination of characters: body medium-sized and slender-cylindrical; with a conspicuous prebuccal fossa; 28-34 somatic kineties; about 40 short adoral polykineties; intrabuccal kinety composed of 25-34 dikinetids; paroral kineties composed of closely spaced dikinetids. The comparison with similar congeners clearly supports the validity of this new species based on morphological and small subunit (SSU) rRNA gene sequence data. In light of these new data the "well-known" morphotype, Geleia simplex (Faure-Fremiet, 1951), is redefined. Two Kentrophoros species are redescribed and improved diagnoses are supplied. Kentrophoros flavus Raikov and Kovaleva, 1968 is mainly characterized by having about 33 macronuclei and 12 micronuclei forming a row that extends along the cell meridian, and 12-19 ciliary rows on the right side of the cell. Kentrophoros gracilis Raikov, 1963 is characterized by having about 14 macronuclei, 13 micronuclei and 10-13 kineties on the right side of the cell.
not annotated - annotated - LINNAEUS only
Morphological description of three marine ciliates (Ciliophora, Scuticociliatia), with establishment of a new genus and two new species.
Three marine scuticociliates, Falcicyclidium fangi nov. gen., nov. spec., Falcicyclidium atractodes nov. spec., and Cristigera media Kahl, 1928 were investigated using live observation and silver impregnation methods. The genus Falcicyclidium is distinguished by the combination of: (i) dorsoventrally flattened body, (ii) hook-like (falciform) paroral membrane, (iii) anterior end of paroral membrane posterior to anterior end of membranelle 1, and (iv) multiple caudal cilia. Falcicyclidium fangi nov. spec., the type of the new genus, can be recognized by the combination of its large size, extremely dorsoventrally flattened (3:1) body, consistently 10 somatic kineties, and the broad, elongate buccal area occupying 60% of the body length. Falcicyclidium atractodes nov. spec. is mainly characterized by a unique spine projecting from both the anterior and posterior end. The uncommon form, Cristigera media is redescribed based on the population from Qingdao, the statistic data and additional features, especially the morphology of the living cells, are documented.
not annotated - annotated - LINNAEUS only
Influence of helix 12 of Ultraspiracle on Drosophila melanogaster ecdysone receptor function.
Although it has no ligand, helix 12 in the ligand binding domain of Ultraspiracle (USP) is locked in an antagonistic position. To investigate whether this position is of functional importance, we enhanced the flexibility of helix 12 by mutating two amino acids (259, located in L1-3 and F491 in helix 12). Mutated USP reduces the stability of USP and all isoforms of the ecdysone receptor (EcR) and impairs nuclear localization and DNA binding of EcR/USP(L259A/F491/A), resulting in lower levels of basal transcriptional activity. Although the affinity of the ligand ponasterone A to EcR/USP(L259/F491) is moderately diminished, hormone-induced stimulation of transcriptional activity is normal. Potentiation of the ecdysone response by juvenile hormone (JH) is selectively increased in mutated heterodimers with EcR-B1, demonstrating that the antagonistic position impairs functional interaction of the EcR complex with JHIII.
not annotated - annotated - LINNAEUS only
Physiological and molecular evidence that environmental changes elicit morphological interconversion in the model diatom Phaeodactylum tricornutum.
Over the last decades Phaeodactylum tricornutum has become a model to study diatom biology at the molecular level. Cells have the peculiarity to be pleiomorphic and it is thought that this character is triggered by culture conditions, although few quantitative studies have been performed and nothing is known at the molecular level. Our aim was to quantify the effect of growth conditions on cell morphology of different P. tricornutum strains by quantitative microscopy, cellular imaging, and non-targeted transcriptomics. We show that morphotype changes can be regulated by changing culture conditions, depending on the strain, and show a common trend of increased oval cell abundance as a response to stress. Examination of expressed sequence tags (ESTs) from triradiate cells infers the importance of osmoregulation in the maintenance of this morphotype, whereas ESTs derived from oval cells grown in hyposaline and low temperature conditions show a predominance of genes encoding typical components of stress pathways, especially in signaling, cell homeostasis and lipid metabolism. This work contributes to better understand the importance of the unique capability of morphotype conversion in P. tricornutum and its relevance in acclimation to changing environmental conditions.
not annotated - annotated - LINNAEUS only
Phr1p, a glycosylphosphatidylinsitol-anchored Beta(1,3)-glucanosyltransferase critical for hyphal wall formation, localizes to the apical growth sites and septa in Candida albicans.
Cell wall biogenesis is a dynamic process relying on the coordinated activity of several extracellular enzymes. PHR1 is a pH-regulated gene of Candida albicans encoding a glycosylphosphatidylinositol-anchored Beta(1,3)-glucanosyltransferase of family GH72 which acts as a cell wall remodelling enzyme and is crucial for morphogenesis and virulence. In order to explore the function of Phr1p, we obtained a green fluorescent protein (GFP) fusion to determine its localization. During induction of vegetative growth, Phr1p-GFP was concentrated in the plasma membrane of the growing bud, in the mother-bud neck, and in the septum. Phr1p-GFP was recovered in the detergent-resistant membranes indicating its association with the lipid rafts as the wild type Phr1p. Upon induction of hyphal growth, Phr1p-GFP highly concentrated at the apex of the germ tubes and progressively distributed along the lateral sides of the hyphae. Phr1p-GFP also labelled the hyphal septa, where it colocalized with chitin. Localization to the hyphal septa was perturbed in nocodazole-treated cells, whereas inhibition of actin polymerization hindered the apical localization. Electron Microscopy analysis of the hyphal wall ultrastructure of a PHR1 null mutant showed loss of compactness and irregular organization of the surface layer. These observations indicate that Phr1p plays a crucial role in hyphal wall formation, a highly regulated process on which morphogenesis and virulence rely.
not annotated - annotated - LINNAEUS only
Dynamics in space and time of four testate amoebae (Difflugia spp.) co-existing in the zooplankton of a reservoir in southern China.
We studied a long time series of the dynamics in space and time of four species of Difflugia (thecamoebae) that co-exist in the pelagic plankton of Liuxihe Reservoir, an oligo-mesotrophic impoundment in southern China, during 8-9 months ("summer" form March to November), and retreat to the benthos during the rest of the year ("winter"). We discuss the reasons for the winter retreat, and suggest that predator evasion may be involved, although temperature-linked physiological effects (like the rate of gas bubble production) appear more probable. Clear diel vertical migration of Difflugia was not observed, but patchiness was common. We found no evident lake edge-effects in the spatial pattern either, but the abundances were strongly influenced by trophic conditions and increased by up to one order of magnitude in the upstream, eutrophic sections of the reservoir.
not annotated - annotated - LINNAEUS only
Pathways to immunity: temporal dynamics of the bumblebee (Bombus terrestris) immune response against a trypanosomal gut parasite.
Immune response dynamics in insects from natural host-parasite associations are poorly understood, despite accumulating evidence of ecological immune phenomena in these systems. Using a gene discovery approach, we have identified genes relating to signalling, enzymatic processes and respiration that were up-regulated in the bumblebee, Bombus terrestris, during infection with the trypanosomatid parasite, Crithidia bombi. In addition, we have mapped dynamic changes in the temporal expression of these genes and three candidate antimicrobial peptide (AMP) immune genes, Abaecin, Defensin and Hymenoptaecin, from 1 to 24 h after C. bombi infection. We show that dynamic changes in expression occur for individual genes at distinct phases of the immune response to C. bombi that correspond to early, intermediate and late stages of infection.
not annotated - annotated - LINNAEUS only
Carnivorous planktonic Difflugia (Protista, Amoebina Testacea) and their predators.
Four planktonic species of Difflugia co-occurring in a south Chinese reservoir were found to be carnivorous, but the diet was widest in the largest species (D. tuberspinifera) and narrowest in the smallest (D. hydrostatica). It included rotifers, ciliates, dinoflagellates, floating eggs, and small particles associated with organic debris. Scavenging and cannibalism were also observed. Species with a collared test (D. biwae, D. mulanensis) showed a form of suction-feeding, while species with teeth on the pseudostome used these, together with their pseudopods, as "inverted crown corks", providing leverage for opening the lorica of their (rotifer) prey. Predators of Difflugia included cyclopoid copepods. In addition, the rotifers Asplanchna priodonta, Ploesoma hudsoni and, occasionally, big ciliates (Stentor sp.) all ingested their prey as a whole.
not annotated - annotated - LINNAEUS only
Ca(2+)-dependent in vivo protein phosphorylation and encystment induction in the ciliated protozoan Colpoda cucullus.
Encystment induction of Colpoda cucullus is promoted by an increase in external Ca(2+) and overpopulation of Colpoda vegetative cells. Using phos-tag detection assays, the present study revealed that the in vivo phosphorylation level in several proteins [33 kDa, 37 kDa, 37.5 kDa, 43 kDa, 47 kDa, 49 kDa, etc.] was raised when the vegetative cells were stimulated by overpopulation to encyst in a medium containing 0.1 mM Ca(2+) or without the addition of Ca(2+). Both overpopulation-mediated encystment induction and protein phosphorylation were suppressed by the addition of EGTA. Ca(2+)/overpopulation-stimulated encystment induction and protein phosphorylation were also suppressed by the addition of BAPTA-AM. These results suggest that the Ca(2+) inflow promoted by cell-to-cell stimulation due to overpopulation may activate signaling pathways involving protein phosphorylation and encystment induction. In the presence of cAMP-AM, the phosphorylation levels of 33 kDa, 37 kDa, 37.5 kDa, 43 kDa, 47 kDa and 49 kDa proteins were enhanced, and encystment induction was promoted. Enzyme immunoassays (EIAs) showed that intracellular cAMP concentration was raised prior to encystment when the cells were stimulated by overpopulation. These results suggest that cAMP/PKA-dependent protein phosphorylation, which is an event on Ca(2+)-triggered signaling pathways, may be involved in encystment induction.
not annotated - annotated - LINNAEUS only
Intestinal ciliate composition found in the feces of the Turk rahvan horse Equus caballus, Linnaeus 1758.
Species composition and distribution of large intestinal ciliates were investigated in the feces from 15 Turk rahvan horses, living in the vicinity of Izmir, Turkey. Twenty-two ciliate genera consisting of 36 species were identified. This is the first report on intestinal ciliates in Turk rahvan horses and no previously unknown species were observed. The mean number of ciliates was 14.2+/-13.9x10(4) cells ml(-1) of feces and the mean number of ciliate species per host was 9.9+/-7.1. No ciliates were observed in 2 horses. Bundleia and Blepharocorys were considered to be the major genera since these ciliates were constantly found in high proportions. In contrast, Paraisotricha, Didesmis and Gassovskiella were only observed at low frequencies. The ciliates found in this survey had almost the same characteristics as those described in previous reports, suggesting that there was no significant geographic variation in the intestinal ciliate fauna of equids.
not annotated - annotated - LINNAEUS only
Morphological and molecular phylogeny of dileptid and tracheliid ciliates: Resolution at the base of the class Litostomatea (Ciliophora, Rhynchostomatia).
Dileptid and tracheliid ciliates have been traditionally classified within the subclass Haptoria of the class Litostomatea. However, their phylogenetic position among haptorians has been controversial and indicated that they may play a key role in understanding litostomatean evolution. In order to reconstruct the evolutionary history of dileptids and tracheliids, and to unravel their affinity to other haptorians, we have used a cladistic approach based on morphological evidence and a phylogenetic approach based on 18S rRNA gene sequences, including eight new ones. The molecular trees demonstrate that dileptids and tracheliids represent a separate subclass, Rhynchostomatia, that is sister to the subclasses Haptoria and Trichostomatia. The Rhynchostomatia are characterized by a ventrally located oral opening at the base of a proboscis that carries a complex oral ciliature. We have recognized two orders within Rhynchostomatia. The new order Tracheliida is monotypic, while the order Dileptida comprises two families: the new, typically bimacronucleate family Dimacrocaryonidae and the multimacronucleate family Dileptidae. The Haptoria evolved from the last common ancestor of the Litostomatea by polarization of the body, the oral opening locating more or less apically and the oral ciliature simplifying. The Trichostomatia originated from a microaerophylic haptorian by further simplification of the oral ciliature, possibly due to an endosymbiotic lifestyle.
not annotated - annotated - LINNAEUS only
Compatible interaction with its rice host leads to enhanced expression of the gamma subunit of oligosaccharyl transferase in the Asian rice gall midge, Orseolia oryzae.
The Asian rice gall midge, Orseolia oryzae, is a fast evolving, damaging pest of rice. Understanding the underlying molecular mechanism of interaction between the gall midge and rice will help in devising strategies to control and manage the pest. The present study aims to identify rice-responsive genes in the gall midge that aid pest survival. The abundance of transcripts coding for enzymes related to glycosylation, in a cDNA library prepared from maggots of the rice gall midge feeding on susceptible hosts, indicated their probable involvement in the gall midge-rice interaction. Hence, a full-length transcript for a gamma subunit of the oligosaccharyl transferase gene (OoOST) from the gall midge was cloned and characterized. It has 72% similarity to its orthologue cloned from Aedes aegypti. Tissue-specific analysis of the expression of OoOST revealed an increase (> sevenfold) in the transcripts of the gene in the salivary glands of maggots in susceptible plants when compared with the transcript level in the salivary glands of maggots feeding on resistant hosts. Using quantitative PCR, performed on different developmental stages of the maggots in two susceptible and two resistant hosts, we observed similar expression patterns (i.e. overexpression in the compatible interaction). These results indicate the involvement of OoOST in maggot survival and establishment in the susceptible host. In order to identify polymorphism in the gene, OoOST was cloned from three gall midge biotypes GMB1, GMB4 and GMB4M.
not annotated - annotated - LINNAEUS only
Transcript analysis and comparative evaluation of shaker and slowmo gene homologues from the European corn borer, Ostrinia nubilalis.
The movement and dispersal of larval Lepidoptera impact their survival and distribution within the natural landscape. Homologues of the Drosophila behaviour-linked genes shaker (shkr) and slowmo (slmo) were identified from Ostrinia nubilalis (Lepidoptera: Crambidae). Onshkr was isolated as a 1610-nucleotide (nt) constitutively expressed transcript encoding a membrane-localized 469-amino-acid (aa) protein with a conserved tetramerization domain and the six-domain architecture necessary for the molecule to fold into an active K(+) channel. Three expressed splice variants of 682, 970 and 1604 nt were identified for the Onslmo gene, and encode predicted 141 and 228 aa proteins with a conserved protein of relevant evolutionary and lymphoid interest (PRELI) domain that may function in mitochondrial protein sorting and perinuclear protein localization. Onshkr and Onslmo protein sequences aligned within monophyletic lepidopteran groups.
not annotated - annotated - LINNAEUS only
Identification of predicted seminal fluid proteins in Tribolium castaneum.
In several insect species, seminal fluid proteins (SFPs) have been demonstrated to be key regulators of male and female fitness through their ability to alter female physiology and behaviour. Tribolium castaneum is an economically important pest species and a model system for sexual selection research, but little is known about SFPs in this insect. To create a foundation for the study of T. castaneum SFPs, we used mass spectrometry to identify putative SFPs by comparing proteins detected in the male reproductive glands with those found in the reproductive tracts of virgin and mated females. Fourteen putative SFPs, thirteen with male biased expression, were identified through this approach. We also used reverse transcription PCR (RT-PCR) to examine expression levels across different tissue types. We found strongly male-biased expression in 13 genes, nine of which were expressed only in male accessory gland tissue. This represents the first proteomic-based method of identifying putative SFPs in any coleopteran species, and is the first study in this species to identify putative SFPs that are likely transferred to the female. This work could lead to functional analyses of the role of SFPs in sexual selection, sexual conflict and potential control of a pest species.
not annotated - annotated - LINNAEUS only
Comparison of transgene expression in Aedes aegypti generated by mariner Mos1 transposition and PhiC31 site-directed recombination.
Transgenic mosquitoes generated by transposable elements (TEs) often poorly express transgenes owing to position effects. To avoid these effects, the PhiC31 site-directed recombination system was used to insert transgenes into a locus favourable for gene expression in Aedes aegypti. We describe phenotypes of mariner Mos1 TE and PhiC31 transgenic mosquitoes expressing the enhanced green fluorescent protein (EGFP) reporter in midguts of blood-fed females. Mosquitoes of nine TE-generated lines [estimated transformation frequency (TF): 9.3%] clearly expressed the eye-specific selection marker but only 2/9 lines robustly expressed the EGFP reporter. The piggyBac TE-generated PhiC31 docking strain, attP26, supported recombination with attB site containing donors at an estimated TF of 1.7-4.9%. Using a codon-optimized PhiC31 integrase mutant instead of the 'wild-type' enzyme did not affect TF. Site-directed recombination of line attP26 with an attB-containing donor expressing EGFP from the Ae. aegypti carboxypeptidase promoter produced one transgenic line with blood-fed females expressing the reporter in midgut tissue. Docking strain attP26 also supported robust expression of Flock House virus B2 from the Ae. aegypti polyubiquitin promoter. Our data confirm that eye-specific selection marker expression alone is not a reliable indicator for robust gene-of-interest expression in Ae. aegypti and that the PhiC31 system can ensure predictable transgene expression in this mosquito species.
not annotated - annotated - LINNAEUS only
Optimization of the Gal4-UAS system in an Anopheles gambiae cell line.
The development of the bipartite Gal4-UAS system in Anopheles gambiae would improve the functional characterization of genes in this important malaria vector. Towards this aim, we used Gal4 driver plasmids to successfully activate expression of the reporter gene, luciferase, from UAS responder plasmids when cotransfected into an An. gambiae cell line. To optimize Gal4-regulated gene expression in mosquitoes, we compared the efficiency of a series of alternative Gal4 transactivators to drive reporter gene expression from responder plasmids incorporating different numbers of tandemly arrayed Gal4 binding sites or upstream activation sequences (UAS). The results indicated that the native Gal4 is only weakly active in these cells. Modified forms of Gal4, including those carrying minimal VP16 activation domains, as well as a deleted form of Gal4, give up to 20-fold greater activity than the native protein, when used in conjunction with a responder plasmid having 14 UAS repeats. The identification of Gal4-UAS vectors that are efficiently expressed in a mosquito cell line should facilitate the transfer of this versatile expression system to An. gambiae, and potentially to other insects of medical importance.
not annotated - annotated - LINNAEUS only
Host translational control of a polydnavirus, Cotesia plutellae bracovirus, by sequestering host eIF4A to prevent formation of a translation initiation complex.
Host translational control is a viral strategy to exploit host cellular resources. Parasitization by some endoparasitoids containing polydnaviruses inhibits the synthesis of specific host proteins at post-transcriptional level. Two host translation inhibitory factors (HTIFs) have been proposed in Cotesia plutellae bracovirus (CpBV). Parasitization by C. plutellae inhibited storage protein 1 (SP1) synthesis of Plutella xylostella at post-transcriptional level. One HTIF, CpBV15Beta, inhibited the translation of SP1 mRNA in an in vitro translation assay using rabbit reticulocyte lysate, but did not inhibit its own mRNA. To further analyse the discrimination of target and nontarget mRNAs of the inhibitory effect of HTIF, 5' untranslated regions (UTRs) of SP1 and CpBV15Beta mRNA were reciprocally exchanged. In the presence of HTIFs, the chimeric CpBV15Beta mRNA that contained SP1 5' UTR was not translated, whereas the chimeric SP1 mRNA that contained CpBV15Beta 5' UTR was translated. There was a difference in the 5' UTR secondary structures between target (SP1) and nontarget (CpBV15alpha and CpBV15Beta) mRNAs in terms of thermal stability. Different mutant 5' UTRs of SP1 mRNA were prepared by point mutations to modify their secondary structures. The constructs containing 5' UTRs of high thermal stability in their secondary structures were inhibited by HTIF, but those of low thermal stability were not. Immunoprecipitation with CpBV15Beta antibody coprecipitated eIF4A, which would be required for unwinding the secondary structure of the 5' UTR. These results indicate that the viral HTIF discriminates between host mRNAs according to their dependency on eIF4A to form a functional initiation complex for translation.
not annotated - annotated - LINNAEUS only
Identification and expression analysis of the genes involved in serotonin biosynthesis and transduction in the field cricket Gryllus bimaculatus.
Serotonin (5-HT) modulates various aspects of behaviours such as aggressive behaviour and circadian behaviour in the cricket. To elucidate the molecular basis of the cricket 5-HT system, we identified 5-HT-related genes in the field cricket Gryllus bimaculatus DeGeer. Complementary DNA of tryptophan hydroxylase and phenylalanine-tryptophan hydroxylase, which convert tryptophan into 5-hydroxy-L-tryptophan (5-HTP), and that of aromatic L-amino acid decarboxylase, which converts 5-HTP into 5-HT, were isolated from a cricket brain cDNA library. In addition, four 5-HT receptor genes (5-HT(1A) , 5-HT(1B) , 5-HT(2alpha) , and 5-HT(7) ) were identified. Expression analysis of the tryptophan hydroxylase gene TRH and phenylalanine-tryptophan hydroxylase gene TPH, which are selectively involved in neuronal and peripheral 5-HT synthesis in Drosophila, suggested that two 5-HT synthesis pathways co-exist in the cricket neuronal tissues. The four 5-HT receptor genes were expressed in various tissues at differential expression levels, suggesting that the 5-HT system is widely distributed in the cricket.
not annotated - annotated - LINNAEUS only
The influence of fundamental design parameters on ciliates community structure in Irish activated sludge systems.
The protozoan community in eleven activated sludge wastewater treatment plants (WWTPs) in the greater Dublin area has been investigated and correlated with key physio-chemical operational and effluent quality parameters. The plants represented various designs, including conventional and biological nutrient removal (BNR) systems. The aim of the study was to identify differences in ciliate community due to key design parameters including anoxic/anaerobic stages and to identify suitable bioindicator species for performance evaluation. BNR systems supported significantly different protozoan communities compared to conventional systems. Total protozoan abundance was reduced in plants with incorporated anoxic and anaerobic stages, whereas species diversity was either unaffected or increased. Plagiocampa rouxi and Holophrya discolor were tolerant to anoxic/anaerobic conditions and associated with high denitrification. Apart from process design, influent wastewater characteristics affect protozoan community structure. Aspidisca cicada was associated with low dissolved oxygen and low nitrate concentrations, while Trochilia minuta was indicative of good nitrifying conditions and good sludge settleability. Trithigmostoma cucullulus was sensitive to ammonia and phosphate and could be useful as an indicator of high effluent quality. The association rating assessment procedure of Curds and Cockburn failed to predict final effluent biological oxygen demand (BOD(5)) indicating the method might not be applicable to treatment systems of different designs.
not annotated - annotated - LINNAEUS only
Identification and characterization of the cysteine protease inhibitor gene MdCPI from Musca domestica.
Cysteine proteinase inhibitors (CPIs) are involved in many vital cellular processes such as signalling pathways, apoptosis, immune response and development; however, no CPIs have yet been reported from the housefly Musca domestica. Here we report the isolation and characterization of a housefly CPI gene designated MdCPI. The gene contains an open reading frame of 357 bp encoding a protein of 118 amino acid residues with a putative signal peptide of 17 amino acid residues. Protein alignment demonstrated a high homology to that of Sarcophaga crassipalpis (identity = 51%). Phylogenetic analysis suggested that all CPIs from dipterans, including the housefly, belong to the I25A family and may be descended from a single common ancestor. The gene was expressed in and purified from Escherichia coli. Biochemical studies showed that MdCPI exerts an inhibiting function on papain, which is a classical assay to confirm CPIs. Real-time quantitative PCR and immunolocalization analysis revealed that MdCPI is specifically expressed in haemocytes and fat bodies. It is highly down-regulated in larvae and markedly up-regulated in the pupal stage, suggesting that it may be related to development.
not annotated - annotated - LINNAEUS only
Functions of the mitotic B-type cyclins CLB1, CLB2, and CLB3 at mitotic exit antagonized by the CDC14 phosphatase.
In the budding yeast Saccharomyces cerevisiae, cell cycle progression and cytokinesis at mitotic exit are proposed to be linked by CDC14 phosphatase antagonizing the function of mitotic B-type cyclin (CLBs). We have isolated a temperature-sensitive mutant, cdc14(A280V), with a mutation in the conserved phosphatase domain. Prolonged arrest in the cdc14(A280V) mutant partially uncoupled cell cycle progression from the completion of cytokinesis as measured by bud re-emergence, in the form of elongated apical projections, and DNA re-replication. In contrast to previous mitotic exit mutants, cdc14(A280V) mutants displayed a strong bias for the first apical projection to form in the mother cell body. Using cdc14(A280V) mutant phenotypes, the functions of the B-type cyclins at mitotic exit were investigated. The preference in mother-daughter apical projection formation was observed to be independent of any individual CLB function. However, cdc14(A280V)clb1Delta cells displayed a pronounced increase in apical projections, while cdc14(A280V)clb3Delta cells were observed to form round cellular chains. While cdc14(A280V) cells arrested at mitotic exit, both cdc14(A280V)clb1Delta and cdc14(A280V)clb3Delta cells completed cytokinesis, but failed cell separation. cdc14(A280V)clb2Delta cells displayed a defect in actin ring assembly. These observations differentiate the functions of CLB1, CLB2, and CLB3 at mitotic exit, and are consistent with the hypothesis that CLB activities are antagonized by the CDC14 phosphatase in order to couple cell cycle progression with cytokinesis at mitotic exit.
not annotated - annotated - LINNAEUS only
Insect insulin receptors: insights from sequence and caste expression analyses of two cloned hymenopteran insulin receptor cDNAs from the fire ant.
The insulin and insulin-like growth factor (IGF) signalling (IIS) pathway in the honey bee (Apis mellifera) is linked to reproductive division of labour and foraging behaviour. Two insulin receptor genes are present in the released genomes of other social hymenopterans. Limited information is available on the IIS pathway role in ants. The predicted insulin receptor sequences from the recently released draft genome of the fire ant Solenopsis invicta (Hymenoptera: Formicidae) are incomplete and biologically significant data are also lacking. To elucidate the role of the IIS pathway in the fire ant, two putative insulin receptors (SiInR-1 and SiInR-2) were cloned; the first InR cDNAs cloned from social insects. Analyses of putative post-translational modification sites in SiInRs revealed the potential for differential regulation. We investigated the transcriptional expression of both receptors at different developmental stages, castes and queen tissues. In last instar larvae and pharate pupae of workers and reproductive, transcriptional abundance of both receptors was negatively correlated with body size and nutritional status. The expression level of both receptors in different queen tissues appears to correlate with requirements for queen reproductive physiology and behaviours. This study contributes new information to the understanding of social insects because in fire ants juvenile hormone acts as a gonadotropin and workers are fully sterile, contrary to honey bees.
not annotated - annotated - LINNAEUS only
The transcriptional response of Saccharomyces cerevisiae to proapoptotic concentrations of Pichia membranifaciens killer toxin.
PMKT (Pichia membranifaciens killer toxin) reportedly has antimicrobial activity against yeasts and filamentous fungi. In previous research we posited that high PMKT concentrations pose a serious challenge for cell survival by disrupting plasma membrane electrochemical gradients, inducing a transcriptional response similar to that of certain stimuli such as hyperosmotic shock. This response was related to the HOG-pathway with Hog1p phosphorylation and a transitional increase in intracellular glycerol accumulation. Such a response was consistent with the notion that the effect induced by high PMKT concentrations lies in an alteration to the ionic homeostasis of the sensitive cell. By contrast, the evidence presented here shows that low PMKT doses lead to a cell death process in Saccharomyces cerevisiae accompanied by cytological and biochemical indicators of apoptotic programmed cell death, namely, the production of reactive oxygen species, DNA strand breaks, metacaspase activation and cytochrome c release. Furthermore, dying cells progressed from an apoptotic state to a secondary necrotic state, and the rate at which this change occurred was proportional to the intensity of the stimulus. We have explored the global gene expression response of S. cerevisiae during that stimulus. The results obtained from DNA microarrays indicate that genes related with an oxidative stress response were induced in response to proapoptotic concentrations of PMKT, showing that the coordinated transcriptional response is not coincident with that obtained when ionophoric concentrations of PMKT are used. By contrast, cwp2Delta mutants showed no signs of apoptosis, indicating that the initial steps of the killer mechanism coincide when proapoptotic (low) or ionophoric (high) PMKT concentrations are used. Additionally, low dosages of PMKT promoted Hog1p phosphorylation and glycerol accumulation.
not annotated - annotated - LINNAEUS only
Limitation of Sludge Biotic Index application for control of a wastewater treatment plant working with shock organic and ammonium loadings.
This study aimed to determine the relationship between activated sludge microfauna, the sludge biotic index (SBI) and the effluent quality of a full-scale municipal wastewater treatment plant (WWTP) working with shock organic and ammonium loadings caused by periodic wastewater delivery from septic tanks. Irrespective of high/low effluent quality in terms of COD, BOD(5), ammonium and suspended solids, high SBI values (8-10), which correspond to the first quality class of sludge, were observed. High SBI values were connected with abundant taxonomic composition and the domination of crawling ciliates with shelled amoebae and attached ciliates. High SBI values, even at a low effluent quality, limit the usefulness of the index for monitoring the status of an activated sludge system and the effluent quality in municipal WWTP-treated wastewater from septic tanks. It was shown that a more sensitive indicator of effluent quality was a change in the abundance of attached ciliates with a narrow peristome (Vorticella infusionum and Opercularia coarctata), small flagellates and crawling ciliates (Acineria uncinata) feeding on flagellates.
not annotated - annotated - LINNAEUS only
Microtubule dynamics in mitosis in Aspergillus nidulans.
Mitosis in Aspergillus nidulans is very rapid, requiring less than 5 min at 37 ^0C in germlings (Bergen and Morris, 1983). In this time the cytoplasmic microtubules (MTs) must disassemble, the mitotic spindle assemble, function and disassemble, and cytoplasmic MTs reassemble. It follows that cytoplasmic MTs must be extremely dynamic in this period and we were interested, in particular, in examining the processes of MT disassembly in prophase and reassembly in anaphase and telophase. We observed a diploid strain that expressed GFP-alpha-tubulin. We used a spinning disk confocal microscope that allowed rapid image capture, which proved necessary because microtubule dynamics were extremely rapid. We found, for the first time, that microtubule severing occurs in prophase in a filamentous fungus and that catastrophe rather than nucleation limits astral microtubule growth.
not annotated - annotated - LINNAEUS only
Fluorescent protein fusions in Candida guilliermondii.
Candida guilliermondii is an emerging fungal agent of candidiasis often associated with oncology patients. This yeast also remains a promising biotechnological model for the industrial production of value-added metabolites. In the present study, we developed a recipient strain as well as a set of plasmids for construction of fluorescent protein (FP) fusions in this species. We demonstrated that C. guilliermondii phosphoglycerate kinase transcription-regulating sequences allow a constitutive expression of codon-optimized green, cyan, yellow and mCherry FP genes in C. guilliermondii cells and the fluorescence signal could be directly observed at the colony and blastospore level by epifluorescence microcopy. To illustrate differential targeting of the FPs into specified cellular compartments, we studied and validated the expected subcellular localization of various C. guilliermondii predicted proteins fused to FPs. Furthermore, co-expression experiments of various couples of FP-tagged C. guilliermondii predicted proteins in the same cell showed that the fluorescence of each FP could be detected independently, providing firm evidences that YFP/CFP and GFP/mCherry pairs can be used for dual labeling in C. guilliermondii cells. This technical advance will facilitate future studies of protein co-expression and co-localization in C. guilliermondii and will give precious help for elucidating new molecular events supporting pathogenicity, antifungal resistance and for exploring the potential of yeast metabolic engineering.
not annotated - annotated - LINNAEUS only
Insertion of an intact CR1 retrotransposon in a cadherin gene linked with Bt resistance in the pink bollworm, Pectinophora gossypiella.
Three mutations in the Pectinophora gossypiella cadherin gene PgCad1 are linked with resistance to Bacillus thuringiensis (Bt) toxin Cry1Ac. Here we show that the r3 mutation entails recent insertion into PgCad1 of an active chicken repeat (CR1) retrotransposon, designated CR1-1_Pg. Unlike most other CR1 elements, CR1-1_Pg is intact, transcribed by a flanking promoter, contains target site duplications and has a relatively low number of copies. Examination of transcripts from the PgCad1 locus revealed that CR1-1_Pg disrupts both the cadherin protein and a long noncoding RNA of unknown function. Together with previously reported data, these findings show that transposable elements disrupt eight of 12 cadherin alleles linked with resistance to Cry1Ac in three lepidopteran species, indicating that the cadherin locus is a common target for disruption by transposable elements.
not annotated - annotated - LINNAEUS only
Application of the systematic "DAmP" approach to create a partially defective C. albicans mutant.
An understanding of gene function often relies upon creating multiple kinds of alleles. Functional analysis in Candida albicans, a major fungal pathogen, has generally included characterization of mutant strains with insertion or deletion alleles and over-expression alleles. Here we use in C. albicans another type of allele that has been employed effectively in the model yeast Saccharomyces cerevisiae, a "Decreased Abundance by mRNA Perturbation" (DAmP) allele (Yan et al., 2008). DAmP alleles are created systematically through replacement of 30 noncoding regions with nonfunctional heterologous sequences, and thus are broadly applicable. We used a DAmP allele to probe the function of Sun41, a surface protein with roles in cell wall integrity, cell-cell adherence, hyphal formation, and biofilm formation that has been suggested as a possible therapeutic target (Firon et al., 2007; Hiller et al., 2007; Norice et al., 2007). A SUN41-DAmP allele results in approximately 10-fold reduced levels of SUN41 RNA, and yields intermediate phenotypes in most assays. We report that a sun41Delta/Delta mutant is defective in biofilm formation in vivo, and that the SUN41-DAmP allele complements that defect. This finding argues that Sun41 may not be an ideal therapeutic target for biofilm inhibition, since a 90% decrease in activity has little effect on biofilm formation in vivo. We anticipate that DAmP alleles of C. albicans genes will be informative for analysis of other prospective drug targets, including essential genes.
not annotated - annotated - LINNAEUS only
The metalloreductase FreB is involved in adaptation of Aspergillus fumigatus to iron starvation.
Aspergillus fumigatus employs two high affinity iron uptake mechanisms, siderophore mediated iron uptake and reductive iron assimilation (RIA). The A. fumigatus genome encodes 15 putative metalloreductases (MR) but the ferrireductasesinvolved in RIA remained elusive so far. Expression of the MR FreB was found to be transcriptionally repressed by iron via SreA, a repressor of iron acquisition during iron sufficiency, indicating a role in iron metabolism. FreB-inactivation by gene deletion was phenotypically largely inconspicuous unless combined with inactivation of the siderophore system, which then decreased growth rate, surface ferrireductase activity and oxidative stress resistance during iron starvation. This study also revealed that loss of copper-independent siderophore-mediated iron uptake increases sensitivity of A. fumigatus to copper starvation due to copper-dependence of RIA.
not annotated - annotated - LINNAEUS only
Expression and functional characterisation of TNC, a high-affinity nickel transporter from Neurospora crassa.
Our previous in silico studies identified a high-affinity nickel transporter,TNC, from the metal transportome of Neurospora crassa. A knockout mutant of the tnc gene in N. crassa failed to transport nickel, showed phenotypic growth defects and diminished urease activity under physiological levels of nickel. Transport assays conducted in wild type and knockout mutant strains showed that TNC transports nickel withhigh affinity but exhibits selectivity for other transition metal ions like cobalt. Heterologous complementation of Schizosaccharomyces pombe nickel uptake mutant by TNC further substantiates its nickel transport function. Transcriptional analysis of the nickel transporter encoding gene, tnc in N. crassa by qRT-PCR showed its constitutive expression in various phases of its life cycle. However, levels of the corresponding protein TNC were down-regulated only by increasing the nickel, but not cobalt concentration in the media. Immunolocalisation data suggested that TNC is distributed in the plasma membrane of N. crassa. Thus, the present study establishes TNC as a functional plasma membrane nickel transporter necessary for physiological acquisition of nickel in the multicellular fungi N. crassa.
not annotated - annotated - LINNAEUS only
The effects of dsRNA mycoviruses on growth and murine virulence of Aspergillus fumigatus.
Some isolates of the opportunistic human pathogenic fungus Aspergillus fumigatus are known to be infected with mycoviruses. The dsRNA genomes of two of these mycoviruses, which include a chrysovirus and a partitivirus, have been completely sequenced and an RT-PCR assay for the viruses has been developed. Through curing virus-infected A. fumigatus isolates by cycloheximide treatment and transfecting virus-free isolates with purified virus, as checked by RT-PCR, isogenic virus-free and virus-infected lines of the fungus were generated whose phenotypes and growth have been directly compared. Mycovirus infection of A. fumigatus with either the chrysovirus or the partitivirus resulted in significant aberrant phenotypic alterations and attenuation of growth of the fungus but had no effect on susceptibility to common antifungals. Chrysovirus infection of A. fumigatus caused no significant alterations to murine pathogenicity.
not annotated - annotated - LINNAEUS only
Gene expression associated with vegetative incompatibility in Amylostereum areolatum.
In filamentous fungi, vegetative compatibility among individuals of the same species is determined by the genes encoded at the heterokaryon incompatibility (het) loci. The hyphae of genetically similar individuals that share the same allelic specificities at their het loci are able to fuse and intermingle, while different allelic specificities at the het loci result in cell death of the interacting hyphae. In this study, suppression subtractive hybridization (SSH) followed by pyrosequencing and quantitative reverse transcription PCR were used to identify genes that are selectively expressed when vegetatively incompatible individuals of Amylostereum areolatum interact. The SSH library contained genes associated with various cellular processes, including cell-cell adhesion, stress and defence responses, as well as cell death. Some of the transcripts encoded proteins that were previously implicated in the stress and defence responses associated with vegetative incompatibility. Other transcripts encoded proteins known to be associated with programmed cell death, but have not previously been linked with vegetative incompatibility. Results of this study have considerably increased our knowledge of the processes underlying vegetative incompatibility in Basidiomycetes in general and A. areolatum in particular.
not annotated - annotated - LINNAEUS only
Brief exposures of human body lice to sublethal amounts of ivermectin over-transcribes detoxification genes involved in tolerance.
Transcriptional profiling results, using our non-invasive induction assay {short exposure intervals (2-5 h) to sublethal amounts of insecticides [<lethal concentration 3% (LC(3)) at 24 h] administered by stress-reducing means (contact vs. immersion screen) and with induction assessed in a time frame when tolerance is still present [~lethal concentration 90% (LC(90)) in 2-4 h]}, showed that ivermectin-induced detoxification genes from body lice are identified by quantitative real-time PCR analyses. Of the cytochrome P450 monooxygenase and ATP binding cassette transporter genes induced by ivermectin, CYP6CJ1, CYP9AG1, CYP9AG2 and PhABCC4 were respectively most significantly over-expressed, had high basal expression levels and were most closely related to genes from other organisms that metabolized insecticides, including ivermectin. Injection of double-stranded RNAs (dsRNAs) against either CYP9AG2 or PhABCC4 into non-induced female lice reduced their respective transcript level and resulted in increased sensitivity to ivermectin, indicating that these two genes are involved in the xenobiotic metabolism of ivermectin and in the production of tolerance.
not annotated - annotated - LINNAEUS only
Influence of hormone response elements (HREs) on ecdysteroid receptor concentration.
Transcriptional activity of nuclear receptors is the result of transactivation capability and receptor protein concentration. The concentration of ecdysteroid receptor (EcR) constitutively expressed in vertebrate cells varies depending on the isoforms. Besides ligand binding and heterodimerization with ultraspiracle (USP), which stabilizes receptor protein concentration, degradation is regulated by interaction of the receptor complex with different ecdysteroid response elements (EcREs). Coexpression of EcREs significantly reduces ecdysteroid receptor concentration depending on the type of EcRE. Transcriptional activity and interaction with hormone response elements (HREs) as determined by Electrophoretic Mobility Shift Assay (EMSA) are often inversely related to receptor protein concentration. The complex regulation of receptor protein concentration offers an additional opportunity to regulate transcriptional activity in an isoform- and target cell-specific manner and allows the temporal limitation of hormone action.
not annotated - annotated - LINNAEUS only
Galleria mellonella as model host for the trans-kingdom pathogen Fusarium oxysporum.
Fusarium oxysporum, the causal agent of vascular wilt disease, affects a wide range of plant species and can produce disseminated infections in humans. F. oxysporum f. sp. lycopersici isolate FGSC 9935 causes disease both on tomato plants and immunodepressed mice, making it an ideal model for the comparative analysis of fungal virulence on plant and animal hosts. Here we tested the ability of FGSC 9935 to cause disease in the greater wax moth Galleria mellonella, an invertebrate model host that is widely used for the study of microbial human pathogens. Injection of living but not of heat-killed microconidia into the hemocoel of G. mellonella larvae resulted in dose-dependent killing both at 30^0C and at 37^0C. Fluorescence microscopy of larvae inoculated with a F. oxysporum transformant expressing GFP revealed hyphal proliferation within the hemocoel, interaction with G. mellonella hemocytes, and colonization of the killed insects by the fungus. Fungal gene knockout mutants previously tested in the tomato and immunodepressed mouse systems displayed a good correlation in virulence between the Galleria and the mouse model. Thus, Galleria represents a useful non-vertebrate infection model for studying virulence mechanisms of F. oxysporum on animal hosts.
not annotated - annotated - LINNAEUS only
The structure-function relationship of the Aspergillus fumigatuscyp51A L98H conversion by site-directed mutagenesis: the mechanism of L98H azole resistance.
Since 1998, the rapid emergence of multi-azole-resistance (MAR) was observed in Aspergillus fumigatus in the Netherlands. Two dominant mutations were found in the cyp51A gene, a 34bp tandem repeat (TR) in the promoter region combined with a leucine to histidine substitution at codon 98 (L98H). In this study, we show that molecular dynamics simulations combined with site-directed mutagenesis of amino acid substitutions in the cyp51A gene, correlate to the structure-function relationship of the L98H substitution conferring to MAR in A. fumigatus. Because of a L98H directed change in the flexibility of the loops, that comprise a gate-like structure in the protein, the capacity of the two ligand entry channels is modified by narrowing the diameter and thereby binding of azoles is obstructed. Moreover, the L98H induced relocation of tyrosine 121 and tyrosine 107 seems to be related to the MAR phenotype, without affecting the biological activity of the CYP51A protein. Site-directed mutagenesis showed that both the 34bp TR and the L98H mutation are required to obtain the MAR phenotype. Furthermore, the amino acid leucine in codon 98 in A. fumigatus is highly conserved and important for maintaining the structure of the CYP51A protein that is essential for azole docking.
not annotated - annotated - LINNAEUS only
Overexpression of a cytochrome P450 monooxygenase, CYP6ER1, is associated with resistance to imidacloprid in the brown planthopper, Nilaparvata lugens.
The brown planthopper, Nilaparvata lugens, is an economically significant pest of rice throughout Asia and has evolved resistance to many insecticides including the neonicotinoid imidacloprid. The resistance of field populations of N. lugens to imidacloprid has been attributed to enhanced detoxification by cytochrome P450 monooxygenases (P450s), although, to date, the causative P450(s) has (have) not been identified. In the present study, biochemical assays using the model substrate 7-ethoxycoumarin showed enhanced P450 activity in several resistant N. lugens field strains when compared with a susceptible reference strain. Thirty three cDNA sequences encoding tentative unique P450s were identified from two recent sequencing projects and by degenerate PCR. The mRNA expression level of 32 of these was examined in susceptible, moderately resistant and highly resistant N. lugens strains using quantitative real-time PCR. A single P450 gene (CYP6ER1) was highly overexpressed in all resistant strains (up to 40-fold) and the level of expression observed in the different N. lugens strains was significantly correlated with the resistance phenotype. These results provide strong evidence for a role of CYP6ER1 in the resistance of N. lugens to imidacloprid.
not annotated - annotated - LINNAEUS only
Differential PbP27 expression in the yeast and mycelial forms of the Paracoccidioides brasiliensis species complex.
p27 is an antigenic protein produced by Paracoccidioides brasiliensis, the etiologic agent of paracoccidioidomycosis (PCM). Despite its unknown function, it has been suggested as a putative virulence factor, proposed as a suitable target for the design of diagnostic tools and vaccines, and considered as an enhancer in antifungal treatment of PCM. We evaluated sequence polymorphisms of PbP27 gene sequence among isolates, finding some polymorphisms associated with the isolates' phylogenetic origin. In order to determine if there was a differential expression pattern between morphological states and among isolates, we also evaluated PbP27 expression, at transcriptional and translational levels, in mycelia and yeast cultures in 14 isolates belonging to the P. brasiliensis species complex (S1, PS2, PS3, and "Pb01-like", proposed to be named Paracoccidioides lutzii) by two techniques, real time RT-PCR (RT-qPCR) and protein dot blot. For the latter, four protein extracts from different cell localizations (SDS or Beta-mercaptoethanol, cytoplasmic and extracellular proteins) were analyzed for each isolate. p27 was present in the four extracts evaluated, mainly in the SDS extract, corresponding to an extract containing proteins loosely attached to the cell wall. This information correlates with immunohistochemical analysis, where positive staining of the yeasts' cell wall was observed. We found that p27 was present in all isolates, mainly in the yeast form. This pattern was corroborated by RT-qPCR results, with higher expression levels found in the yeast form for most of the isolates. The results provide new insights into the expression patterns of this protein, and further characterize it in view of potential uses as a diagnostic and/or therapeutic tool.
not annotated - annotated - LINNAEUS only
Involvement of a helix-loop-helix transcription factor CHC-1 in CO(2)-mediated conidiation suppression in Neurospora crassa.
The morphological switch from vegetative growth to conidiation in filamentous fungi is highly regulated, but the understanding of the regulatory mechanisms is limited. In this study, by screening a set of knock-out mutants corresponding to 103 transcription factor encoding genes in Neurospora crassa, a mutant was found to produce abundant conidia in race tubes in which conidiation in the wild-type strain was suppressed. The corresponding gene NCU00749 encodes a protein containing a helix-loop-helix DNA binding region. Unlike enhanced conidiation in ras-1 and sod-1 mutants, which was completely suppressed by antioxidant N-acetyl cysteine, enhanced conidiation in the NCU00749 mutant was only slightly affected by N-acetyl cysteine. When grown on slants, the NCU00749 deletion mutant exhibited earlier conidial formation than the wild-type strain, and this was more evident at a higher (5%) CO(2) concentration. Therefore, we named NCU00749 as conidiation at high carbon dioxide-1 (chc-1). Genes that are highly expressed during conidial development, eas, con-6, con-8 and con-10, were transcribed at a higher rate in the chc-1 deletion mutant than the wild-type strain in response to conidiation induction. To determine the mechanisms by which CHC-1 regulates conidiation, we conducted a RNA sequencing analysis and found that 404 genes exhibited >= 2 fold changes in transcription in response to chc-1 deletion. Among them, fluffy and ada-6, two transcription factor genes that positively regulate conidiation in N. crassa, and rca-1, whose homolog flbD in Aspergillus nidulans is essential for conidiation, were upregulated in the chc-1 deletion mutant. Results of RNA sequencing also suggest that signal transduction via the cAMP and the MAK-2 mediated signal pathways, and ROS generation and removal, mechanisms known to regulate conidiation, are not involved in chc-1 mediated control of conidiation. In addition, chc-1 also influences expression of genes involved in other important biological processes besides conidiation such as carbon metabolism, sphingolipid synthesis, cell wall synthesis, and calcium signaling.
not annotated - annotated - LINNAEUS only
Identification and characterization of a putative basic helix-loop-helix transcription factor involved in the early stage of conidiophore development in Aspergillus oryzae.
The helix-loop-helix (HLH) family of transcriptional factors is a key player in a wide range of developmental processes. HLH proteins form homo- and/or heterodimers with other HLH proteins and bind to E-box motifs. The regulation and functions of these proteins can be complex due to their bifunctional roles as activators and repressors of gene transcription. In this study, we isolated and characterized a novel predicted bHLH protein-encoding gene, AO090023000902, designated ecdR (early conidiophore development regulator), in Aspergillus oryzae. The ecdR gene disruptant produced very few conidia. Conversely, the overexpression of ecdR resulted in the formation of a large number of conidia at an early stage, suggesting that the EcdR protein is required for early asexual development. Additionally, when serially diluted conidia were spread-cultivated onto malt agar medium, we found that conidial number of the control strain depended on the cultivated conidium density, while the ecdR-overexpressing strain showed no significant change in conidiation. These phenotypes of ecdR-disruptant and ecdR-overexpressing strains are partially similar to those of the sclR-overexpressing strain and sclR-disruptant, respectively. Yeast two-hybrid assays and sclR, ecdR-double deletion experiment indicated that EcdR plays a major role in conidiation, and SclR represses this function by competitively interacting with EcdR in A. oryzae.
not annotated - annotated - LINNAEUS only
Meiotic silencing by unpaired DNA is expressed more strongly in the early than the late perithecia of crosses involving most wild-isolated Neurospora crassa strains and in self-crosses of N. tetrasperma.
Meiotic silencing by unpaired DNA is a presumed RNAi-mediated elimination of the transcripts of any gene that is not properly paired with a homolog in meiosis. Eighty wild-isolated strains of Neurospora crassa were classified into three types based on the apparent strength of meiotic silencing of the bml (Beta-tubulin) and mei-3 genes in crosses with the ::Bml(r) and ::mei-3 tester strains. "OR" and "Sad" type wild-isolates, respectively, did or did not silence both the genes, whereas the "Esm" type (68 strains) silenced bml but not mei-3(+), suggesting an intermediate strength of silencing. Many wild strains, especially of the Esm type, gave fertile crosses with strains bearing the 148kbp chromosome segment duplication Dp(EB4) but their crosses with the 405kbp Dp(IBj5) were barren. Larger Dps might include more genes whose sensitivity to silencing is comparable with that of bml, consequently their crosses with the OR and Esm type strains would be about equally barren, whereas small Dps, with presumably few or no bml-like genes suffer little gene silencing in crosses with Esm and Sad strains and thus remain fertile. Using lollipop-shaped asci as indicators of silencing in crosses of the ::act tester with Esm type strains, and white-spored asci in Neurospora tetrasperma self-crosses heterozygous for an ectopic insertion of the asm-1 gene, we found that meiotic silencing was expressed more strongly in the early but not in the late perithecia of these crosses.
not annotated - annotated - LINNAEUS only
Accumulation of P-bodies in Candida albicans under different stress and filamentous growth conditions.
Candida albicans is an opportunistic fungal pathogen that grows as budding yeast, pseudohyphal, and hyphal forms. In response to external signals, C. albicans switches rapidly among these forms. mRNA-containing cytoplasmic granules, termed processing bodies (P-bodies), have been reported to accumulate under various environmental stress conditions in diverse species from yeast to mammals. Here, we provide the first microscopic and genetic characterization of P-bodies in C. albicans. The core components of P-bodies, including the decapping machinery (Dcp2 and Dhh1), 5'-3' exoribonuclease (Kem1/Xrn1), and the P-body scaffolding protein (Edc3), were identified and their localizations with respect to P-bodies were demonstrated. Various growth conditions, including glucose deprivation, hyperosmotic stress, and heat stress, stimulated the accumulation of P-bodies. In addition, we observed P-body aggregation during hyphal development. The deletion mutant strain edc3/edc3 had a defect in filamentation and exhibited a dramatic reduction in the number of P-bodies. These results suggest that Edc3 plays an essential role in the assembly and maintenance of P-bodies in C. albicans, and that the switch to filamentous growth appears to accompany P-body accumulation.
not annotated - annotated - LINNAEUS only
A heme peroxidase of the ascomyceteous lichen Leptogium saturninum oxidizes high-redox potential substrates.
Lichens belonging to the order Peltigerales display strong activity of multi-copper oxidases (e.g. tyrosinase) as well as heme-containing peroxidases. The lichen peroxidase was purified to homogeneity from the thallus of Leptogium saturninum (LsaPOX) by fast protein liquid chromatography and then partially characterized. The oligomeric protein occurs as both 79kDa dimeric and 42kDa monomeric forms, and displayed broad substrate specificity. In addition to an ability to oxidize classic peroxidase substrates (e.g. 2,6-dimethoxyphenol), the enzyme could convert recalcitrant compounds such as synthetic dyes (e.g. Azure B and Reactive Blue 5), 4-nitrophenol and non-phenolic methoxylated aromatics (e.g. veratryl alcohol). Comparing LsaPOX with a basidiomycete dye-decolorizing (DyP)-type peroxidase from Auricularia auricula-judae showed that the lichen enzyme has a high-redox potential, with oxidation capabilities ranging between those of known plant and fungal peroxidases. Internal peptide fragments show homology (up to 60%) with putative proteins from free-living ascomycetes (e.g. Penicillium marneffei and Neosartorya fischeri), but not to sequences of algal or cyanobacterial peptides or to known fungal, bacterial or plant peroxidases. LsaPOX is the first heme peroxidase purified from an ascomyceteous lichen that may help the organism to successfully exploit the extreme micro-environments in which they often grow.
not annotated - annotated - LINNAEUS only
Cannibalism and intraguild predation of eggs within a diverse predator assemblage.
Greater biodiversity among aphid predators sometimes leads to greater predator reproductive success. This could occur if cannibalism of predator eggs is consistently stronger than intraguild predation, such that diversity dilutes cannibalism risk when total predator densities remain constant across diversity levels. We compared the frequency of cannibalism versus intraguild predation by adult predators of four species [the lady beetles Coccinella septempunctata L. and Hippodamia convergens Guerin-Meneville, and the predatory bugs Geocoris bullatus (Say) and Nabis alternatus Parshley] on the eggs of three predator species (all of these predators but Nabis). For both coccinellid species, egg predation averaged across all intraguild predators was less frequent than cannibalism. In contrast, Geocoris eggs were generally more likely to be consumed by intraguild predators than by conspecifics. Closer inspection of the data revealed that Geocoris consistently consumed fewer eggs than the other species, regardless of egg species. Indeed, for lady beetle eggs it was relatively infrequent egg predation by Geocoris that brought down the average across all heterospecific predators, masking the fact that adults of the two lady beetles were no more likely to act as egg cannibals than as intraguild predators. Nabis ate eggs of the two beetles at approximately equal rates, but rarely ate Geocoris eggs. Female predators generally consumed more eggs than did males, but this did not alter any of the patterns described above. Altogether, our results suggest that species-specific differences in egg predation rates determined the relative intensity of egg intraguild-predation versus cannibalism, rather than any more general trend for egg cannibalism to always exceed intraguild predation.
not annotated - annotated - LINNAEUS only
Sunflower stem weevil and its larval parasitoids in native sunflowers: is parasitoid abundance and diversity greater in the u.s. Southwest?
Classical biological control programs often target a pest's region of origin as a likely source for new biological control agents. Here, we use this approach to search for biological control agents of the sunflower stem weevil (Cylindrocopturus adspersus LeConte), an economically important pest of commercial sunflower. We conducted surveys of weevil natural enemy diversity and abundance across a transect running from the northern Great Plains to the southwestern U.S. (the presumed area of endemism of annual sunflower species in the genus Helianthus). Accordingly, natural enemy diversity and abundance were expected to be greater in the southwestern U.S. C. adspersus and their larval parasitoids were collected from stems of four native sunflower species (Helianthus annuus, H. nuttallii, H. pauciflorus, and H. petiolaris) from 147 sites across eight states. Native H. annuus constituted the majority of the sunflower populations. Mean weevil densities were significantly higher in sunflower stalks that were larger in diameter. Mean weevil densities within sites did not differ across the range of longitudes and latitudes sampled. After accounting for the effects of stalk diameter and location, weevil densities did not differ among the four sunflower species nor did they differ as a function of elevation. C. adspersus in H. annuus and H. petiolaris were attacked by seven species of parasitoids. No parasitoids were found attacking C. adspersus in H. nuttallii or H. pauciflorus stalks. C. adspersus were twice as likely to be attacked by a parasitoid when feeding on H. petiolaris than H. annuus. Furthermore, the likelihood that C. adspersus would be parasitized decreased with increasing elevation and increasing stem diameters. All parasitoid species have been previously reported attacking C. adspersus larvae in cultivated sunflower. Species richness was less diverse in these collections than from previous studies of cultivated sunflower. Our findings suggest that the species of larval parasitoids attacking C. adspersus in native sunflowers have successfully made the transition to cultivated sunflower.
not annotated - annotated - LINNAEUS only
Interactions Between Extrafloral Nectaries, Ants (Hymenoptera: Formicidae), and Other Natural Enemies Affect Biological Control of Grapholita molesta (Lepidoptera: Tortricidae) on Peach (Rosales: Rosaceae).
Extrafloral nectaries (EFNs) are reported to benefit some plants when ants (Hymenoptera: Formicidae) use their secretions and fend off herbivores, but in some cases resulting competitive interactions may reduce biological control of specific herbivores. This research examined the interactions between ants and other natural enemies associated with the EFNs of peach [Prunus persica (L.) Batcsh] and the implications for biological control of a key pest, the oriental fruit moth [Grapholita molesta (Busck)]. Studies using sentinel G. molesta placed on peach trees ('Lovell' cultivar) with EFNs present and absent revealed that several natural enemy groups associated with the EFNs contribute to reductions in G. molesta eggs, larvae, and pupae in peach orchards. Ants on trees with EFNs antagonized the G. molesta egg parasitoid Trichogramma minutum (Riley), but the ants were crucial in reducing G. molesta in both the larval and pupal stages. Overall, individual trees with EFNs experienced higher ant and other (nonant) natural enemy densities and subsequent pest reductions, as compared with trees without EFNs. However, the implications of EFN-natural enemy-pest interactions to orchard-level biological control will likely depend on local G. molesta population dynamics.
not annotated - annotated - LINNAEUS only
Laboratory and Field Evaluation of Formulated Bacillus thuringiensis var. israelensis as a Feed Additive and Using Topical Applications for Control of Musca domestica (Diptera: Muscidae) Larvae in Caged-Poultry Manure.
Infestations of house flies, Musca domestica L., are a continual problem around poultry establishments. Acute toxicity of two commercial Bacillus thuringiensis variety israelensis (Bti) formulations (water-dispersible granules and bran formulation) was evaluated against larvae in the laboratory and against natural populations of M. domestica larvae in the field applied in feed to chickens and as topical applications in the poultry houses. Bioassay data showed that susceptibility of M. domestica larvae increased to a given concentration of Bti as the duration of exposure increased. In the laboratory studies, the LC(50) values of Bti for the larvae ranged between 65 and 77.4 mug/ml. In the field, a concentration of 10 g Bti/kg of feed resulted in 90% reduction of larvae at 4 wk after treatment. A higher concentration (2 g/liter) of Bti in spray applications was not significantly more effective than the lower concentration of 1 g/liter. Adding Bti to chicken feed is potentially an efficient measure for the management and control of house flies in caged-poultry facilities.
not annotated - annotated - LINNAEUS only
Short-Term Population Redistribution of Pseudacteon tricuspis (Diptera: Phoridae) From Point Source Releases.
There is a need for quantitative data on patterns and rates of movement of organisms to understand their movement behavior and predict their rates of spread. Opportunities for studying movement of biological control agents are presented during release programs. However, despite these opportunities, patterns and range of dispersal are often not considered. For example, information about effects of wind on dispersal patterns and heterogeneities in rates of movement is critical to predicting future range expansion of biological control agents and determining proximity of multiple releases. Here, the pattern and range of movement of a fire ant parasitoid, Pseudacteon tricuspis Borgmeier, was investigated by performing a series of mass-release-resighting experiments. Flies were released at a central location surrounded by radial transects containing trays of host ants at variable distances along four axes. Resighted flies were censused at these trays at 30 min intervals, up to 2 h postrelease. The dispersal pattern of P. tricuspis in the short term was consistent with a simple diffusion model. On average, 50% of P. tricuspis dispersed =<10 m, and 95% dispersed =<29 m. Diffusion rates were variable, depending on release densities, but tended to decline over time after release. Drift of dispersing flies was detected in several trials, and was attributed to prevailing wind dynamics. Data from this assessment of the short term redistribution pattern of P. tricuspis could be useful in determining proximity of releases of this, and other fire ant parasitoids.
not annotated - annotated - LINNAEUS only
Age and Sex Related Responsiveness of Tribolium castaneum (Coleoptera: Tenebrionidae) in Novel Behavioral Bioassays.
The hardiness and mobile nature of Tribolium castaneum (Herbst) make them easy to work with but are the same factors that make their responses to behavior-modifying chemical stimuli difficult to evaluate. To overcome these difficulties two bioassays were developed: a two-choice test with airflow and a diffusion-based test to evaluate responses to chemical stimuli. The two-choice assay is excellent for rapidly comparing two stimuli or examining the response to one stimulus against a control. The diffusion assay determines differences in orientation behavior to multiple simultaneous stimuli and can examine other behaviors during exposure. Preparation of individuals for bioassay is also important, because disturbance increases the activity level of individual beetles beyond the duration of the disturbance. The age and the sex of beetles affect responsiveness to chemical cues. These bioassays and a better understanding of T. castaneum's activity have revealed approaches for evaluating its responsiveness to behavior-modifying chemicals.
not annotated - annotated - LINNAEUS only
Evaluation of tag entanglement as a factor in harmonic radar studies of insect dispersal.
The observation of insects and other small organisms entangled in the habitat after the addition of vertical or trailing electronic tags to their body has generated concerns on the suitability of harmonic radars to track the dispersal of insects. This study compared the walking behavior of adult Colorado potato beetle (Leptinotarsa decemlineata (Say) Chrysomelidae), plum curculio (Conotrachelus nenuphar (Herbst) Curculionidae), and western corn rootworm (Diabrotica virgifera virgifera (LeConte) Chrysomelidae) with and without vertical and or trailing tags in field plots or arenas. The frequency of the larger Colorado potato beetles crossing bare ground or grassy plots was unaffected by the presence of an 8 cm trailing harmonic radar tag. However, plum curculios and western corn rootworms, were either unable to walk with a 4 cm trailing tag (plum curculio) or displayed a reduced ability to successfully cross a bare ground arena. Our results revealed the significant impact of vegetation on successful insect dispersal, whether tagged or not. The vertical movement of these insects on stems, stalks, and tubes was also unaffected by the presence of vertical tags. Trailing tags had a significant negative effect on the vertical movement of the western corn rootworm. Results show that harmonic radar technology is a suitable method for studying the walking paths of the three insects with appropriate tag type and size. The nuisance factor generated by appropriately sized tags was small relative to that of vegetation.
not annotated - annotated - LINNAEUS only
Influence of Sticky Trap Color and Height Above Ground on Capture of Alate Elatobium abietinum (Hemiptera: Aphididae) in Sitka Spruce Plantations.
A series of field trials were used to assess the practicality of using sticky traps to monitor populations of green spruce aphid, Elatobium abietinum (Walker), in plantations of Sitka spruce. The highest numbers of alate E. abietinum were caught on sticky traps placed in the upper third of the live canopy at 9-17 m above the ground, whereas low numbers of aphids were caught just below the live canopy or at 2 m above the ground. Trials in 2005 with sticky traps of different colors showed that significantly more alate E. abietinum were caught on yellow, red, and green sticky traps than on white, blue, and black traps. A repeat trial in 2007 resulted in significantly more alate aphids being caught on red sticky traps than on traps of any other color except for green. Attraction to red is unusual among aphids, as aphids are thought not to possess a red-sensitive photoreceptor. The attraction of E. abietinum to red-colored sticky traps suggests that conifer-feeding aphids might have a fundamentally different color response compared with aphids that live on cereals, grasses, or herbaceous plants. Alternatively, the attraction to red might be a physiological artifact related to the presence of red-screening pigments in the aphid's compound eye.
not annotated - annotated - LINNAEUS only
The Role of Frass and Cocoon Volatiles in Host Location by Monodontomerus aeneus, a Parasitoid of Megachilid Solitary Bees.
Monodontomerus aeneus (Fonscolombe) is a parasitic wasp that oviposits on the prepupae and pupae of Osmia cornuta (Latreille) and other solitary bee species. A two-armed olfactometer was used to test the olfactory attractiveness of O. cornuta prepupae, cocoon, and larval frass to female M. aeneus. Both cocoon and frass attracted the female parasitoids, but frass alone was more attractive than the cocoon and the cocoon with frass was more attractive than frass alone. Female parasitoids were not attracted by the host prepupa. M33 (methanol) was the organic volatile most emitted by cocoons and m61 (acetic acid) was the compound most emitted by frass. However, cocoons showed higher emission for almost all compounds, including m61 (acetic acid). Although acetic acid alone attracted M. aeneus, a complex volatile signal is probably involved in the attraction process because the ratio of acetic acid and acetaldehyde characteristic of the frass was more attractive than other ratios.
not annotated - annotated - LINNAEUS only
Rapid Cold Hardening and Expression of Heat Shock Protein Genes in the B-Biotype Bemisia tabaci.
This paper describes the rapid cold hardening processes of the sweetpotato whitefly, Bemisia tabaci (Gennadius). It was found that all developmental stages of B. tabaci have the capacity of rapid cold hardening and the length of time required to induce maximal cold hardiness at 0^0C varies with stage. There was only 18.3% survival when adult whiteflies were transferred directly from 26^0C to -8.5^0C for 2 h. However, exposure to 0^0C for 1 h before transfer to -8.5^0C increased the survival to 81.2%. The whiteflies show "prefreeze" mortality when they were exposed to temperatures above the supercooling point (SCP), although the range of SCP of whiteflies is -26^0C to -29^0C. The rapid cold hardening had no effect on SCP and reduced the lower lethal temperature of adults from -9^0C to -11^0C. Rapid cold-hardened adults had a similar lifespan as the control group but deposited fewer eggs than nonhardened individuals. The expression profiles during cold hardening and recovery from this process revealed that HSP90 did not respond to cold stress. However, HSP70 and HSP20 were significantly induced by cold with different temporal expression patterns. These results suggest that the rapid cold hardening response is possibly advantageous to whiteflies that are often exposed to drastic temperature fluctuations in spring or autumn in northern China, and the expression of HSP70 and HSP20 may be associated with the cold tolerance of B. tabaci.
not annotated - annotated - LINNAEUS only
Interspecific Interactions Between Bemisia tabaci Biotype B and Trialeurodes vaporariorum (Hemiptera: Aleyrodidae).
Bemisia tabaci (Gennadius) biotype B and Trialeurodes vaporariorum (Westwood) are invasive whitefly species that often co-occur on greenhouse-grown vegetables in northern China. Although B. tabaci biotype B has been present in China for a relatively short period of time, it has become dominant over T. vaporariorum. We studied the interspecific competitive interactions between the two species in single or mixed cultures at 24 +/- 1^0C, 40 +/- 5% RH, and L14:D10 h photoperiod. Female longevity on tomato was not significantly different between species, but B. tabaci reproduced 4.3 to 4.9 fold more progeny. The ratio of female to male progeny in both instances was greater for B. tabaci. When cultured on tomato, cotton, and tobacco, B. tabaci developed 0.8, 3.3, and 4.7 d earlier in single culture, and 1.8, 3.9, and 4.3 d earlier in mixed culture. B. tabaci displaced T. vaporariorum in four, five and six generations when the initial ratios of B. tabaci to T. vaporariorum were 15:15, 20:10, or 10:20 on tomato. Populations of B. tabaci were 2.3 fold higher than that of T. vaporariorum on tomato plants for seven consecutive generations in single culture. B. tabaci performed better in development, survival, fecundity, and female ratio. We conclude that B. tabaci could displace T. vaporariorum in as short as four generations in a controlled greenhouse environment when they start at equal proportions. Warmer greenhouse conditions and an increase in total greenhouse area could be contributing factors in the recent dominance of B. tabaci.
not annotated - annotated - LINNAEUS only
Streptococcus ursoris sp. nov., isolated from the oral cavities of bears.
Three Gram-positive, catalase-negative, coccus-shaped organisms were isolated from the oral cavities of bears. The isolates were tentatively identified as a streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the new isolates was Streptococcus ratti ATCC 19645(T) (98.6 %), however, DNA-DNA hybridization analysis showed that the isolates displayed less than 15 % DNA-DNA relatedness with the type strain of S. ratti. Colonies of the novel strains grown on mitis salivarius agar showed an extracellular polysaccharide-producing colony morphology. Based on phenotypic and phylogenetic evidence, it is proposed that the novel isolates are classified in the genus Streptococcus as Streptococcus ursoris sp. nov. The type strain of S. ursoris is NUM 1615(T) (=JCM 16316(T)=DSM 22768(T)).
not annotated - annotated - LINNAEUS only
Larkinella bovis sp. nov., isolated from fermented bovine products, and emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006.
A novel bacterial strain, designated M2T2B15(T), was isolated from fermented bovine products and was characterized by using a polyphasic approach. Colonies were reddish pink and circular with entire margins. Cells were strictly aerobic, Gram-reaction-negative, oxidase- and catalase-positive rods that lacked flagella and were motile by gliding. Flexirubin-type pigments were absent. 16S rRNA gene sequence analysis indicated that strain M2T2B15(T) was related most closely to Larkinella insperata LMG 22510(T) (94.4 % similarity) but shared <87 % similarity with other members of the phylum Bacteroidetes. The major cellular fatty acids were C(16 : 1)omega5c, iso-C(15 : 0) and iso-C(17 : 0) 3-OH. The polar lipids were phosphatidylethanolamine, phosphatidylserine, two unidentified aminophospholipids and two unidentified polar lipids. Menaquinone 7 (MK-7) was the major respiratory quinone. The G+C content of the DNA of strain M2T2B15(T) was 52 mol%. The phenotypic, genotypic and phylogenetic data presented clearly indicate that strain M2T2B15(T) represents a novel species of the genus Larkinella, for which the name Larkinella bovis sp. nov. is proposed. The type strain is M2T2B15(T) (=KACC 14040(T) =NBRC 106324(T)). Emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006 are also proposed.
not annotated - annotated - LINNAEUS only
Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost.
A mesophilic, non-motile, hydrogenotrophic, rod-shaped methanogen, designated M2(T), was isolated from Holocene permafrost sediments of the Kolyma lowland in the Russian Arctic. Cells were 3-6 mum long and 0.45-0.5 mum wide. Strain M2(T) grew on H(2)/CO(2) and formate. Optimum conditions for growth were 37^0C, pH 6.8-7.2 and 0.1 M NaCl. The DNA G+C content was 38.1 mol%. On the basis of 16S rRNA gene sequence comparison with known methanogens, strain M2(T) was affiliated with the genus Methanobacterium and was most closely related to Methanobacterium veterum MK4(T) and Methanobacterium bryantii DSM 863(T) (both 99 % 16S rRNA gene sequence similarity). However, no significant DNA-DNA relatedness was observed between strain M2(T) and these type strains. We propose that strain M2(T) represents a novel species, with the name Methanobacterium arcticum sp. nov., with type strain M2(T) (=DSM 19844(T) =VKM B-2371(T)).
not annotated - annotated - LINNAEUS only
Thiomonas islandica sp. nov., a moderately thermophilic, hydrogen- and sulfur-oxidizing betaproteobacterium isolated from a hot spring.
A novel, hydrogen- and sulfur-oxidizing bacterium, designated strain 6C(T), was isolated from a hot spring in Graendalur, south-western Iceland. Cells of this organism were Gram-reaction-negative, rod-shaped and motile. The strain grew aerobically and was capable of chemolithotrophic growth on thiosulfate and hydrogen, heterotrophic growth on pyruvate, oxalate, acetate and on glutamate in the presence of yeast extract and mixotrophic growth on several organic compounds, thiosulfate and/or hydrogen. During growth on thiosulfate, the final product was sulfate, resulting in a drop in pH from 6.8 to 2.7. Heterotrophic growth on pyruvate was observed at pH 4-7 (optimum pH 4) and 35-50 ^0C (optimum 45 ^0C). The DNA G+C content was 65.2 mol%. As determined by 16S rRNA gene sequence analysis, strain 6C(T) represents a distinct species belonging to the class Betaproteobacteria and is most closely related to Thiomonas intermedia DSM 18155(T) and Thiomonas perometabolis DSM 18570(T). DNA-DNA hybridization between strain 6C(T) and Thiomonas intermedia DSM 18155(T) and Thiomonas perometabolis DSM 18570(T) gave relatedness values below 32 %. These results, together with physiological characteristics, showed that strain 6C(T) represents a novel species within the genus Thiomonas, for which the name Thiomonas islandica sp. nov. is proposed. The type strain is 6C(T) (=DSM 21436(T) =JCM 16107(T)).
not annotated - annotated - LINNAEUS only
Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.
A Gram-staining-positive, coccoid to rod-shaped bacterium, designated strain YC6903(T), was isolated from a halophytic plant (Carex scabrifolia Steud.) collected from sand dunes at Namhae Island, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC6903(T) grew optimally at 30 ^0C and at pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6903(T) belongs to the genus Nocardioides in the family Nocardioidaceae. Strain YC6903(T) was related most closely to Nocardioides pyridinolyticus OS4(T) (97.0 % 16S rRNA gene sequence similarity), Nocardioides dokdonensis FR1436(T) (96.6 %), Nocardioides aquiterrae GW-9(T) (96.6 %) and Nocardioides hankookensis DS-30(T) (96.6 %). The cell-wall peptidoglycan contained LL-diaminopimelic acid and MK-8(H(4)) was the major respiratory quinone. The mean (+/-SD) level of DNA-DNA relatedness between strain YC6903(T) and N. pyridinolyticus OS4(T) was 53.5+/-5.5 %. The predominant cellular fatty acid of strain YC6903(T) was iso-C(16 : 0) (28.9 %). The DNA G+C content was 71.7 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YC6903(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides caricicola sp. nov. is proposed. The type strain is YC6903(T) (=KACC 13778(T) =DSM 22177(T)).
not annotated - annotated - LINNAEUS only
Radionuclide and hybrid imaging of recurrent prostate cancer.
Prostate cancer is one of the most common cancers in men, leading to substantial morbidity and mortality. After definitive therapy with surgery or radiation, many patients have biochemical relapse of disease--ie, an increase in their prostate-specific antigen level--which often precedes clinically apparent disease by months or even years. Therefore, imaging of the site and extent of tumour recurrence (local, regional, distant, or a combination) is of great interest. Conventional morphological imaging methods showed limited accuracy for assessment of recurrent prostate cancer; however, in recent years, functional and molecular imaging have offered the possibility of imaging molecular or cellular processes of individual tumours, often with more accuracy than morphological imaging. Hybrid imaging modalities (PET-CT, and single-photon emission CT [SPECT]-CT) have been introduced that combine functional and morphological data and allow whole-body imaging. Here, we review the contribution of radionuclide imaging and hybrid imaging for assessment of recurrent prostate cancer (local vs regional vs distant disease). We discuss available data on PET-CT and SPECT-CT, and provide an overview of experimental tracers and their preclinical and clinical development. Finally, we present a perspective on the potential of future hybrid magnetic resonance-PET imaging.
not annotated - annotated - LINNAEUS only
Fertility-sparing surgery in patients with cervical cancer.
There are several types of fertility saving procedures that can be done in patients with cervical cancer, which differ in terms of surgical approach and extent of paracervical resection. This review assesses oncological and pregnancy results after different procedures. The oncological results of vaginal radical trachelectomies (VRT) and abdominal radical trachelectomies (ART) are similar for tumours less than 2 cm in size, and are now considered safe surgical procedures. Oncological outcomes of VRT and ART in tumours larger than 2 cm are also identical, but the results cannot be considered satisfactory. Preliminary findings of less radical procedures (ie, deep cone and simple trachelectomy) in patients with tumours less than 2 cm, and negative sentinel and other pelvic lymph nodes, are comparable with the results of VRT and ART. Downstaging tumours larger than 2 cm by neoadjuvant chemotherapy is still an experimental procedure and will need multicentre cooperation to verify its oncological safety. Pregnancy results vary statistically with the different methods.
not annotated - annotated - LINNAEUS only
Morphology and ultrastructure of multiple life cycle stages of the photosynthetic relative of apicomplexa, Chromera velia.
Chromera velia is a photosynthetic alga with a secondary plastid that represents the closest known photosynthetic relative of the apicomplexan parasites. The original description of this organism was based on brownish, immotile coccoid cells, which is the predominating stage of C. velia in the culture. Here we provide a detailed light and electron microscopy description of coccoid cells of C. velia and a previously undocumented bi-flagellated stage that is highly motile and moves in a characteristic zig-zag pattern. Transformation from a coccoid into a flagellate stage occurs in exponentially growing cultures, and is accelerated by exposure to light. The C. velia cells contain a pseudoconoid, which is likely homologous to the corresponding structure in the apical complex of Apicomplexa, cortical alveoli subtended by subpellicular microtubules, mitochondrion with tubular cristae, a micropyle, and a distinctive chromerosome, an apparently novel type of extrusion organelle. Ultrastructural analysis of the flagellate supports its close association with colpodellids and apicomplexans and provides important insight into their evolution.
not annotated - annotated - LINNAEUS only
Introns, alternative splicing, spliced leader trans-splicing and differential expression of pcna and cyclin in Perkinsus marinus.
To gain understanding on the structure and regulation of growth-related genes of the parasitic alveolate Perkinsus marinus, we analyzed genes encoding proliferating cell nuclear antigen (pcna) and cyclins (cyclin). Comparison of the full-length cDNAs with the corresponding genomic sequences revealedtrans-splicing of the mRNAs of these genes with a conserved 21-22 nt spliced leader. Over 10 copies of pcna were detected, with identical gene structures and similar nucleotide (nt) sequences (88-99%), encoding largely identical amino acid sequences (aa). Two distinct types ofcyclin (Pmacyclin1 and Pmacyclin2) were identified, with 66-69% nt and 81-85% aa similarities.Pmacyclin2 was organized in tandem repeats, and was alternatively spliced, giving rise to five subtypes of transcripts. For both pcna and cyclin genes, 6-10 introns were found. Quantitative RT-PCR assays showed that pcna and Pmacyclin2 expression levels were low with small variations during a 28-h time course, whereas Pmacyclin1 transcript abundance was 10-100 times higher, and increased markedly during active cell division, suggesting that it is a mitoticcyclinand can be a useful growth marker for this species. The gene structure and expression features along with phylogenetic results position this organism between dinoflagellates and apicomplexans, but its definitive affiliation among alveolates requires further studies.
not annotated - annotated - LINNAEUS only
Highly diverse and seasonally dynamic protist community in a pristine peat bog.
Culture-independent molecular methods based on the amplification, cloning and sequencing of small-subunit ribosomal RNA genes (SSU rDNAs) are powerful tools to study the diversity of microorganisms. Despite so, the eukaryotic microbial diversity of many ecosystems, including peatlands has not yet received much attention. We analysed the eukaryotic diversity by molecular surveys in water from the centre of a pristine Sphagnum-dominated peatland in the Jura Mountains of Switzerland during a complete seasonal cycle. The clone libraries constructed from five different temporal samplings revealed a high diversity of protists with representatives of all major eukaryotic phyla. In addition, four sequence types could not be assigned to any known high-level eukaryotic taxon but branched together with a rather good statistic support, raising the possibility of a novel, deep branching eukaryotic clade. The analysis of seasonal patterns of phylotypes showed a clear change in the eukaryotic communities between the warm period (late spring and summer) and the cold period (autumn and winter). Chrysophytes dominated the samples in the cold period while testate amoebae (Arcellinida and Euglyphida) and a few other groups peaked in summer. A few phylotypes (such as a cryptomonad and a perkinsid) were abundant at given sampling times and then almost disappeared, suggesting bloom-like dynamics.
not annotated - annotated - LINNAEUS only
Comparing potential COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida).
The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barcode" for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses has yet to be tested within the Rhizaria. Accordingly, we analysed mitochondrial COI gene sequences and nuclear small subunit rDNA (SSU) sequences from several morphospecies of euglyphid testate amoebae (Cercozoa, Rhizaria) in order to evaluate the utility of these DNA markers for species discrimination and phylogenetic reconstructions. Sequences were obtained from eleven populations belonging to six Cyphoderia morphospecies that were isolated from field samples in North America and Europe. Mean inter-population COI sequence dissimilarities were on average 2.9 times greater than in the SSU, while the intra-population sequence dissimilarities were higher in the SSU (0-0.95%) than in the COI (0%); this suggests that the COI fragment is valuable for discriminating Cyphoderiidae isolates. Our study also demonstrated that COI sequences are useful for inferring phylogenetic relationships among Cyphoderiidae isolates. COI and SSU tree topologies were very similar even though the COI fragment used in these analyses (500bp) was much shorter than the SSU sequences (1600bp). Altogether, these results demonstrate the utility of the COI as a potential taxonomic DNA barcode for assessing cyphoderiid species diversity and for inferring phylogenetic relationships within the group.
not annotated - annotated - LINNAEUS only
Expanding character sampling for ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker.
Molecular systematics of ciliates, particularly at deep nodes, has largely focused on increasing taxon sampling using the nuclear small subunit rDNA (nSSU-rDNA) locus. These previous analyses have generally been congruent with morphologically-based classifications, although there is extensive non-monophyly at many levels. However, caution is needed in interpreting these results as nSSU-rDNA is just a single molecular marker. Here the mitochondrial small subunit rDNA (mtSSU-rDNA) is evaluated for deep ciliate nodes using the Colpodea as an example. Overall, well-supported nodes in the mtSSU-rDNA and concatenated topologies are well supported in the nSSU-rDNA topology; e.g., the non-monophyly of the Cyrtolophosidida. The two moderately- to well-supported incongruences between the loci are the placement of the Sorogenida and Colpoda aspera.Our analyses of mtSSU-rDNA support the conclusion, originally derived from nSSU-rDNA, that the morphological characters used in taxonomic circumscriptions of the Colpodea represent a mixture of ancestral and derived states. This demonstration of the efficacy of the mtSSU-rDNA will enable phylogenetic reconstructions of deep nodes in the ciliate tree of life to move from a single-locus to a multi-locus approach.
not annotated - annotated - LINNAEUS only
Diversification and evolution of the avirulence gene AVR-Pita1 in field isolates of Magnaporthe oryzae.
Rice blast disease is the single most destructive plant disease that threatens stable rice production worldwide. Race-specific resistance to the rice blast pathogen has not been durable and the mechanism by which the resistance is overcome remains largely unknown. Here we report the molecular mechanisms of diversification and the instability of the avirulence gene AVR-Pita1 in field strains of Magnaporthe oryzae interacting with the host resistance gene Pi-ta and triggering race-specific resistance. Two-base-pair insertions resulting in frame-shift mutations and partial and complete deletions of AVR-Pita1 were identified in virulent isolates. Moreover, a total of 38 AVR-Pita1 haplotypes encoding 27 AVR-Pita1 variants were identified among 151 avirulent isolates. Most DNA sequence variation was found to occur in the exon region resulting in amino acid substitution. These findings demonstrate that AVR-Pita1 is under positive selection and mutations of AVR-Pita1 are responsible for defeating race-specific resistance in nature.
not annotated - annotated - LINNAEUS only
Analysis of spatial niche structure in coexisting tidepool fishes: null models based on multi-scale experiments.
1. Fundamental and realized spatial niches were investigated through a combination of laboratory and mesocosm experiments, field observations and null model analysis in three intertidal gobiid species (Bathygobius fuscus, Chaenogobius annularis and C. gulosus). Null models based on the results of single-species experiments were used to assess interspecific spatial use and coexistence on two different scales: (i) microhabitats within a tidepool ('microhabitat' scale); and (ii) distribution among a set of tidepools ('habitat-wide' scale). 2. Patterns of microhabitat use varied from single to paired treatments, depending on paired species. Realized overlap of microhabitat use was smaller than would be expected from single-individual situations for intraspecific combinations, but not for interspecific ones. 3. Patterns of tidepool occupancy (a measure of spatial niche breadth) in the mesocosm were influenced by interspecific interactions. Two Chaenogobius species, but not B. fuscus, decreased tidepool occupancy in the hetero-specific treatments compared with the mono-specific ones. For all interspecific combinations, spatial overlap (habitat-wide scale) was significantly lower than the values expected from mono-specific situations. The results also indicated a possible trade-off between competitiveness and growth efficiency in these fishes. 4. Interspecific spatial overlap in the field was similar to that in the mesocosm experiment and the pattern of coexistence of gobiids can be explained by the results of our experiments. 5. This study demonstrates that niches of intertidal fishes may experience modifications under the influence of species interactions and that null models based on controlled experiments can greatly facilitate the deciphering of such changes in niche structure.
not annotated - annotated - LINNAEUS only
Linking disease and community ecology through behavioural indicators: immunochallenge of white-footed mice and its ecological impacts.
1. Pathogens and immune challenges can induce changes in host phenotype in ways that indirectly impact important community interactions, including those that affect host-pathogen interactions. 2. To explore host behavioural response to immune challenge, we exposed wild white-footed mice (Peromyscus leucopus) to an immunogen from an endemic, zoonotic pathogen, the spirochete Borrelia burgdorferi. White-footed mice are a major reservoir host of Lyme disease (LD) spirochetes in northeastern USA and an abundant member of forest communities. The activity patterns, foraging behaviour, and space use of white-footed mice have implications for population growth rates of community members upon which mice incidentally prey (i.e. gypsy moths and native thrushes), as well as potentially determining host-vector encounter rates and human risk of LD. 3. Immunochallenge led to specific humoral (antibody) and cellular (i.e. elevated neutrophils and eosinophils) immune responses, supporting use of the immunogen as a surrogate for pathogenic infection. 4. Immunochallenged mice had reduced wheel-running activity early in the night when measured in the lab. However, mouse activity, as measured by track plates in natural field experiments, did not differ between mice exposed to the immunogen and unexposed mice. 5. Foraging behaviour of wild mice in the field - assessed with giving-up densities of seed at artificial feeding stations - was affected by exposure to the immunogen. Whereas immunochallenge did not influence whether foraging mice gained information on patch quality while foraging, it led to reductions in predator avoidance during foraging, suggesting that the proportion of space used by foraging mice may be greater as a result of immunochallenge. This increased space use is predicted to increase encounter rates with patchily distributed LD vectors (ticks) and with incidental prey items. 6. Thus, immunochallenge in white-footed mice, and potentially pathogenic infection, have the potential to indirectly impact community interactions, including those important for pathogen transmission.
not annotated - annotated - LINNAEUS only
Amino acid divergence between the CHS domain contributes to the different intracellular behaviour of Family II fungal chitin synthases in Saccharomyces cerevisiae.
Family II chitin synthases (CS), including classes IV and V enzymes, share conserved catalytic domains flanked by transmembrane regions. Here we addressed the characterization of Family II fungal CSs by heterologous expression in Saccharomyces cerevisiae. Full-length CSs from classes V or IV were not functional when expressed in S. cerevisiae and accumulated in different intracellular compartments. However, the exchange between different class IV, but not of class V, CHS domains resulted in functional proteins both in vivo and in vitro. The different domains afford the chimeric proteins distinct intracellular behaviours, ranging from endoplasmic reticulum retention to reduced endocytic turnover at the plasma membrane. These results allow a role in chitin synthesis to be assigned to all class IV enzymes, but they also highlight the involvement of the intracellular globular domain of these CSs, not only in enzymatic activity but also in the regulation of their intracellular turnover.
not annotated - annotated - LINNAEUS only
Activation of the heat shock transcription factor Hsf1 is essential for the full virulence of the fungal pathogen Candida albicans.
The evolutionarily conserved heat shock transcription factor Hsf1 plays a central role in thermal adaptation in the major fungal pathogen of humans, Candida albicans. Hsf1 becomes hyperphosphorylated in response to heat shock and activates the transcription of genes with heat shock elements (HSEs) in their promoters, these genes contributing to thermal adaptation. However, the relevance of Hsf1 activation to C. albicans virulence is not clear as this pathogen is thought to be obligately associated with warm blooded animals, and this issue has not been tested because HSF1 is essential for viability in C. albicans. In this study, we demonstrate that the HSE regulon is active in C. albicans cells infecting the kidney. We also show the CE2 region of Hsf1 is required for activation and that the phosphorylation of specific residues in this domain contributes to Hsf1 activation. C. albicans HSF1 mutants that lack this CE2 region are viable. However, they are unable to activate HSE-containing genes in response to heat shock, and they are thermosensitive. Using this HSF1 CE2 deletion mutant we demonstrate that Hsf1 activation, and hence thermal adaptation, contributes significantly to the virulence of C. albicans.
not annotated - annotated - LINNAEUS only
Early response of plant cell to carbon deprivation: in vivo 31P-NMR spectroscopy shows a quasi-instantaneous disruption on cytosolic sugars, phosphorylated intermediates of energy metabolism, phosphate partitioning, and intracellular pHs.
* In plant cells, sugar starvation triggers a cascade of effects at the scale of 1-2 days. However, very early metabolic response has not yet been investigated. * Soluble phosphorus (P) compounds and intracellular pHs were analysed each 2.5 min intervals in heterotrophic sycamore (Acer pseudoplatanus) cells using in vivo phosphorus nuclear magnetic resonance ((31)P-NMR). * Upon external-sugar withdrawal, the glucose 6-P concentration dropped in the cytosol, but not in plastids. The released inorganic phosphate (Pi) accumulated transiently in the cytosol before influx into the vacuole; nucleotide triphosphate concentration doubled, intracellular pH increased and cell respiration decreased. It was deduced that the cytosolic free-sugar concentration was low, corresponding to only 0.5 mM sucrose in sugar-supplied cells. * The release of sugar from the vacuole and from plastids is insufficient to fully sustain the cell metabolism during starvation, particularly in the very short term. Similarly to Pi-starvation, the cell's first response to sugar starvation occurs in the cytosol and is of a metabolic nature. Unlike the cytoplasm, cytosolic homeostasis is not maintained during starvation. The important metabolic changes following cytosolic sugar exhaustion deliver early endogenous signals that may contribute to trigger rescue metabolism.
not annotated - annotated - LINNAEUS only
Habitat contrasts reveal a shift in the trophic position of ant assemblages.
1. Trophic structure within a guild can be influenced by factors such as resource availability and competition. While ants occupy a wide range of positions in food webs, and ant community composition changes with habitat, it is not well understood if ant genera tend to maintain their position in the trophic structure, or if trophic position varies across habitats. 2. We used ratios of stable isotopes of carbon and nitrogen to test for differences in the trophic structure and position of assemblages of ants among habitat types. We tested for differences between assemblages in replicate sites of the land use categories: (i) pastures with old large trees; (ii) recently revegetated pastures with small young trees; and (iii) remnant woodlands. Known insect herbivores and predatory spiders provided baselines for herbivorous and predaceous arthropods. Soil samples were used to correct for the base level of isotopic enrichment at each site. 3. We found no significant interactions between land use and ant genus for isotope enrichment, indicating that trophic structure is conserved across land use categories. The fixed relative positions of genera in the trophic structure might be re-enforced by competition or some other factor. However, the entire ant assemblage had significantly lower delta(15) N values in revegetated sites, suggesting that ants feed lower down in the food chain i.e. they are more 'herbivorous' in revegetated sites. This may be a result of the high availability of plant sugars, honeydew and herbivorous arthropod prey. 4. Surprisingly, ants in remnants and pastures with trees displayed similar isotopic compositions. Interactions within ant assemblages are thus likely to be resilient to changes in land use, but ant diets in early successional habitats may reflect the simplicity of communities, which may have comparatively lower rates of saprophagy and predation.
not annotated - annotated - LINNAEUS only
Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability.
* Reduced oxygen availability is not only associated with flooding, but occurs also during growth and development. It is largely unknown how hypoxia is perceived and what signaling cascade is involved in activating adaptive responses. * We analysed the expression of over 1900 transcription factors (TFs) and 180 microRNA primary transcripts (pri-miRNAs) in Arabidopsis roots exposed to different hypoxic conditions by means of quantitative PCR. We also analysed the promoters of genes induced by hypoxia with respect to over-represented DNA elements that can act as potential TF binding sites and their in vivo interaction was verified. * We identified various subsets of TFs that responded differentially through time and in an oxygen concentration-dependent manner. The regulatory potential of selected TFs and their predicted DNA binding elements was validated. Although the expression of pri-miRNAs was differentially regulated under hypoxia, only one corresponding mature miRNA changed accordingly. Putative target transcripts of the miRNAs were not significantly affected. * Our results show that the regulation of hypoxia-induced genes is controlled via simultaneous interaction of various combinations of TFs. Under anoxic conditions, an additional set of TFs is induced. Regulation of gene expression via miRNAs appears to play a minor role during hypoxia.
not annotated - annotated - LINNAEUS only
Rarity, life history and scaling of the dynamics in time and space of British birds.
1. Many patterns in macroecology are closely related to the total abundance of a species in a region. Here we show that interspecific differences in the pattern of population fluctuations of British bird species can be predicted from knowledge of their overall abundance and some basic life-history characteristics. 2. We identify a rarity syndrome that arises through an increased stochastic influence on population fluctuations with decreasing population size, mainly resulting from an inverse density-dependent effect of demographic stochasticity. This syndrome involves an increase in the annual changes in population size with increasing rarity in the United Kingdom. 3. The relationship between the magnitude of temporal variation and local mean population size differs between species dependent on their life history, i.e. species with larger clutch size and lower survival tended to have larger annual changes in population size than low-reproducing long-lived species. 4. The probability of local disappearance from a study plot depended on the population size and was hence closely related to the overall abundance of the species in UK. For a given population size, this probability was also related to species-specific life-history characteristics, being higher in species with larger clutch sizes and smaller survival rates. 5. Rareness results in a spatial decoupling of the temporal variation in population size. 6. These patterns show that once a species has become rare, e.g. due to human activities, key population dynamical characteristics will change because of density-dependent stochastic effects, which in turn are dependent on species-specific life-history characteristics.
not annotated - annotated - LINNAEUS only
Mannitol permeation and radial flow of water in maize roots.
* The postulated nonselective hydraulic route through the root apoplast has not yet been supported by experimental findings on solvent drag. * Therefore, mannitol transport from the medium to the shoot of young maize plants was studied at different rates of transpiration in hydroculture. The concentration of mannitol was determined by gas chromatography. * Mannitol utilization in shoot metabolism was not detectable. Experiments with exuding roots showed that the radial transport of mannitol was mainly apoplastic. The ratio alpha between the mannitol concentration in xylem vessels and that of the external medium was calculated from mannitol translocation to the shoot or measurement of the mannitol concentration in the root exudate, where it reached c. 0.07 in the steady state. In transpiring plants, alpha decreased with increasing water flux from 0.04 to values below 0.01. These findings demonstrate that the root reflection coefficient for mannitol is above 0.99. * It is concluded that the radial movement of water to the vessels is under complete protoplastic control, whereas solutes can diffuse on an apoplastic path. The absence of a significant volume flux through the root apoplast is of physiological importance as it prevents the coupling of the apoplastic permeation of ballast solutes, such as NaCl, to transpiration.
not annotated - annotated - LINNAEUS only
Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes.
The genomes of 49 filamentous ascomycetes (subphylum Pezizomycotina) were examined by two independent methods for evidence of multiple C->T transitions typical of RIP. At least one transposable element or other repeat family was identified in each genome, and members were assessed for transition and transversion mutations relative to a model of their intact progenitor. Occurrence of RIP was indicated where family members differed by excess of directional transitions over transversions. Transition mutations were quantified by an algorithm taking double mutations in CpG and CpC dinucleotides into account. A second method assessed dinucleotide frequency distribution anomalies in whole genomes, a procedure that allowed quantification of fractions of the non-coding genome that had been subject to extensive directional mutation. The results of both methods revealed that RIP-like activity varied greatly, both in extent of mutation and in dinucleotide context for C->T transitions. In the most extreme case, 75% of a Blastomyces dermatitidis genome had suffered conspicuous GC-depletion, all of it in the non-coding fraction. Many genomes carried both intact repeats as well as others that had suffered heavily from transitions. Only one species, Chaetomium globosum, showed no evidence of directional mutation.
not annotated - annotated - LINNAEUS only
Accelerometry estimates field metabolic rate in giant Australian cuttlefish Sepia apama during breeding.
1. Estimating the metabolic rate of animals in nature is central to understanding the physiological, behavioural and evolutionary ecology of animals. Doubly labelled water and heart-rate methods are the most commonly used approaches, but both have limitations that preclude their application to some systems. 2. Accelerometry has emerged as a powerful tool for estimating energy expenditure in a range of animals, but is yet to be used to estimate field metabolic rate in aquatic taxa. We combined two-dimensional accelerometry and swim-tunnel respirometry to estimate patterns of energy expenditure in giant Australian cuttlefish Sepia apama during breeding. 3. Both oxygen consumption rate (Vo2) and swimming speed showed strong positive associations with body acceleration, with coefficients of determination comparable to those using similar accelerometers on terrestrial vertebrates. Despite increased activity during the day, field metabolic rate rarely approached Vo2, and night-time Vo2 was similar to that at rest. 4. These results are consistent with the life-history strategy of this species, which has a poor capacity to exercise anaerobically, and a mating strategy that is visually based. With the logistical difficulties associated with observation in aquatic environments, accelerometry is likely to prove a valuable tool for estimating energy expenditure in aquatic animals.
not annotated - annotated - LINNAEUS only
Generation of Se-fortified broccoli as functional food: impact of Se fertilization on S metabolism.
Selenium (Se)-fortified broccoli (Brassica oleracea var. italica) has been proposed as a functional food for cancer prevention, based on its high glucosinolate (GSL) content and capacity for Se accumulation. However, as selenate and sulphate share the initial assimilation route, Se fertilization could interfere with sulphur metabolism and plant growth. Consequently, GSL accumulation could be compromised. To evaluate these potentially adverse effects of Se fertilization, we performed a comprehensive study on sand-grown young broccoli plants (weekly selenate applications of 0.8 mumol plant(-1) via the root) and field-grown adult broccoli plants during head formation (single foliar selenate application: 25.3 or 253 mumol plant(-1) ). The results show that under these conditions, Se application does not affect plant growth, contents of cysteine, glutathione, total GSL, glucoraphanin (major aliphatic GSL) or the expression of BoMYB28 (encoding a functionally confirmed master regulator for aliphatic GSL biosynthesis). Conversely, due to the changed expression of sulphate transporters (BoSULTR1;1, 1;2, 2;1, and 2;2), sulphate and total S contents increased in the shoot of young plants while decreasing in the root. We conclude that broccoli can be fertilized with Se without reduction in GSL content, even with Se accumulation exceeding the level recommended for human consumption.
not annotated - annotated - LINNAEUS only
Arbuscular mycorrhizal hyphopodia and germinated spore exudates trigger Ca2+ spiking in the legume and nonlegume root epidermis.
* The aim of this study was to investigate Ca(2+) responses to endosymbiotic arbuscular mycorrhizal (AM) fungi in the host root epidermis following pre-infection hyphopodium formation in both legumes and nonlegumes, and to determine to what extent these responses could be mimicked by germinated fungal spore exudate. * Root organ cultures of both Medicago truncatula and Daucus carota, expressing the nuclear-localized cameleon reporter NupYC2.1, were used to monitor AM-elicited Ca(2+) responses in host root tissues. * Ca(2+) spiking was observed in cells contacted by AM hyphopodia for both hosts, with highest frequencies correlating with the epidermal nucleus positioned facing the fungal contact site. Treatment with AM spore exudate also elicited Ca(2+) spiking within the AM-responsive zone of the root and, in both cases, spiking was dependent on the M. truncatula common SYM genes DMI1/2, but not on the rhizobial Nod factor perception gene NFP. * These findings support the conclusion that AM fungal root penetration is preceded by a SYM pathway-dependent oscillatory Ca(2+) response, whose evolutionary origin predates the divergence between asterid and rosid clades. Our results further show that fungal symbiotic signals are already generated during spore germination, and that cameleon-expressing root organ cultures represent a novel AM-specific bio-assay for such signals.
not annotated - annotated - LINNAEUS only
The Perigord black truffle responds to cold temperature with an extensive reprogramming of its transcriptional activity.
The Tuber melanosporum genome has been analysed with the aim of identifying and characterizing the genes involved in the environmental stress response. A whole genome array (7496 genes/probe) was used to verify the fungal transcriptional profiling upon a cold temperature period (7 days at 4 ^0C). A total of 423 genes resulted to be differentially expressed in a significant manner (>2.5-fold; p-value<0.05) in the mycelia exposed to cold, compared to the control ones: 187 of these genes were up-regulated, while 236 were down-regulated. Sixty-six and fifty-one percent, respectively, of the up- or down-regulated transcripts had no KOG classification and were clustered as unclassified proteins, which was the most abundant category in the both up- and down-regulated genes. A gene subset, containing a range of biological functions, was chosen to validate the microarray experiment through quantitative real time PCR (qRT-PCR). The analysis confirmed the array data for 16 out of 22 of the considered genes, confirming that a cold temperature period influences the truffle global gene expression. The expressed genes, which mostly resulted to be genes for heat shock proteins (HSPs) and genes involved in cell wall and lipid metabolism, could be involved in mechanisms, which are responsible for fungal adaptation. Since truffle ascomata develop during the winter period, we hypothesize that these differentially expressed genes may help the truffle to adapt to low temperatures and/or perceive environmental signals that regulate the fructification.
not annotated - annotated - LINNAEUS only
The rapid production of high-titer porcine endogenous retrovirus(PERV)-B env pseudotype and construction of an EGFP-expressing replication competent PERV-A vector.
Porcine endogenous retroviruses (PERVs) present a unique concern associated with xenotransplantation because they have been shown to infect certain human cells in vitro and it is also difficult to generate herds of pigs free of PERVs. A simple system for the production of high-titer MoMLV-PERV pseudotypes is reported; an EGFP-expressing replication-competent molecular clone that allows direct measurement of titer was also constructed. To improve the MLV-based retroviral vector system, a 2.1-kb PERV-B env product was amplified from PK-15 genomic DNA and cloned into the pCL-Eco retroviral vector. The titer of lacZ (PERV-B) from the 293 cells was about 1.0x10(4) CFU/ml. In contrast, the titer of lacZ (PERV-B) from a conventional murine retroviral vector (split genome) was found to be 1.2x10(2) CFU/ml when the PERV-B env expression vector was transfected into TELCeB6 cells, which harbor MFGnlslacZ and the gag-pol-expressing vector. In addition, an infectious PERV-A clone containing enhanced GFP (EGFP) by using a PCR-based method was developed. This EGFP-expressing PERV-A-IRES-EGFP molecular clone was found to be stable genetically on transfection in 293 cells.
not annotated - annotated - LINNAEUS only
Rhizomastix biflagellata sp. nov., a new amoeboflagellate of uncertain phylogenetic position isolated from frogs.
The genus Rhizomastix contains five species of amoeboflagellates with a single anterior flagellum, which live as intestinal symbionts of insects and amphibians. Though established in 1911, Rhizomastix has been neglected for decades and its phylogenetic position is uncertain. This paper describes the morphology of the first cultivated strain of Rhizomastix. The organism was isolated from an argentine horned frog and differs from the known Rhizomastix species by the presence of biflagellate cells. The isolate is described as Rhizomastix biflagellata sp. nov. A possible relationship of Rhizomastix to Archamoebae is discussed.
not annotated - annotated - LINNAEUS only
Whole-genome sequences of thirteen isolates of Borrelia burgdorferi.
Borrelia burgdorferi is a causative agent of Lyme disease in North America and Eurasia. The first complete genome sequence of B. burgdorferi strain 31, available for more than a decade, has assisted research on the pathogenesis of Lyme disease. Because a single genome sequence is not sufficient to understand the relationship between genotypic and geographic variation and disease phenotype, we determined the whole-genome sequences of 13 additional B. burgdorferi isolates that span the range of natural variation. These sequences should allow improved understanding of pathogenesis and provide a foundation for novel detection, diagnosis, and prevention strategies.
not annotated - annotated - LINNAEUS only
Association between nonsynonymous mutations of starch synthase IIa and starch quality in rice (Oryza sativa).
Starch quality is one of the most important agronomic traits in Asian rice, Oryza sativa. Starch synthase IIa (SsIIa) is a major candidate gene for starch quality variation. Within SsIIa, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in Escherichia coli. To search for the variation in SsIIa that is responsible for starch quality variation in rice, we sequenced the SsIIa exon 8 region and measured starch quality as starch disintegration in alkali for 289 accessions of cultivated rice and 57 accessions of its wild ancestor, Oryza rufipogon. A general linear model and nested clade analysis were used to identify the associations between the three nonsynonymous single nucleotide polymorphisms (SNPs) and starch quality. Among the three nonsynonymous SNPs, we found strong evidence of association at one nucleotide site ('SNP 3'), corresponding to a Leu/Phe replacement at codon 781. A second SNP, corresponding to a Val/Met replacement at codon 737, could potentially show an association with increased sample sizes. Variation in SsIIa enzyme activity is associated with the cohesiveness of rice grains when cooked, and our findings are consistent with selection for more cohesive grains during the domestication of tropical japonica rice.
not annotated - annotated - LINNAEUS only
Ecological differentiation in xylem cavitation resistance is associated with stem and leaf structural traits.
Cavitation resistance is a critical determinant of drought tolerance in tropical tree species, but little is known of its association with life history strategies, particularly for seasonal dry forests, a system critically driven by variation in water availability. We analysed vulnerability curves for saplings of 13 tropical dry forest tree species differing in life history and leaf phenology. We examined how vulnerability to cavitation (P50) related to dry season leaf water potentials and stem and leaf traits. P50-values ranged from -0.8 to -6.2 MPa, with pioneers on average 38% more vulnerable to cavitation than shade-tolerants. Vulnerability to cavitation was related to structural traits conferring tissue stress vulnerability, being negatively correlated with wood density, and surprisingly maximum vessel length. Vulnerability to cavitation was negatively related to the Huber-value and leaf dry matter content, and positively with leaf size. It was not related to SLA. We found a strong trade-off between cavitation resistance and hydraulic efficiency. Most species in the field were operating at leaf water potentials well above their P50, but pioneers and deciduous species had smaller hydraulic safety margins than shade-tolerants and evergreens. A trade-off between hydraulic safety and efficiency underlies ecological differentiation across these tropical dry forest tree species.
not annotated - annotated - LINNAEUS only
Genetics of lung-cancer susceptibility.
Lung cancer is the most common form of cancer death worldwide. Although reduction of tobacco consumption remains the most appropriate strategy to reduce lung-cancer burden, identification of genes involved in the cause of disease could contribute to further understanding of the underlying mechanisms, and eventually lead to additional prevention strategies and targeted treatments. Common gene variants involved in lung cancer have been recently identified through large, collaborative, genome-wide association studies. These studies identified three separate loci that are associated with lung cancer (5p15, 6p21, and 15q25) and include genes that regulate acetylcholine nicotinic receptors and telomerase production. However, much about genetic risk remains to be discovered, and rarer gene variants, such as those of the CHEK2 gene, likely account for most of the remaining risk. There is also a need for studies that investigate how genetic susceptibility is associated with clinical outcome measures, including treatment response and tumour relapse.
not annotated - annotated - LINNAEUS only
The validation of a real-time RT-PCR assay which detects influenza A and types simultaneously for influenza A H1N1 (2009) and oseltamivir-resistant (H275Y) influenza A H1N1 (2009).
Influenza A H1N1 (2009) was declared by the World Health Organisation (WHO) as the first influenza pandemic of the 21st century. Rapid detection of influenza A and differentiation of influenza A H1N1 (2009) and seasonal influenza A is beneficial. In addition the rapid detection of antiviral resistant strains of influenza A H1N1 (2009) would be useful for clinicians to allow for change to an effective treatment at a much earlier stage if resistance is found. It was the aim of this study to develop a real-time RT-PCR that can detect all influenza A viruses and type simultaneously for influenza A H1N1 (2009) and oseltamivir resistant (H275Y) influenza A H1N1 (2009). This multiplex assay will allow laboratories to screen respiratory samples for all types of influenza A, influenza A H1N1 (2009) virus and oseltamivir resistant (H275Y) influenza A H1N1 (2009) virus in a rapid and cost effective format, ensuring that typing methods for seasonal and avian viruses are used on a smaller subset of samples. Since most virology laboratories already offer a molecular service for influenza A this assay could easily be implemented into most areas at little cost therefore increasing local access to resistance testing.
not annotated - annotated - LINNAEUS only
Comparison of seasonal variations in water-use efficiency calculated from the carbon isotope composition of tree rings and flux data in a temperate forest.
Tree-ring delta(13) C is often interpreted in terms of intrinsic water-use efficiency (WUE) using a carbon isotope discrimination model established at the leaf level. We examined whether intra-ring delta(13) C could be used to assess variations in intrinsic WUE (W(g), the ratio of carbon assimilation and stomatal conductance to water) and variations in ecosystem WUE (W(t) , the ratio of C assimilation and transpiration) at a seasonal scale. Intra-ring delta(13) C was measured in 30- to 60-mum-thick slices in eight oak trees (Quercus petraea). Canopy W(g) was simulated using a physiologically process-based model. High between-tree variability was observed in the seasonal variations of intra-ring delta(13) C. Six trees showed significant positive correlations between W(g) calculated from intra-ring delta(13) C and canopy W(g) averaged over several days during latewood formation. These results suggest that latewood is a seasonal recorder of W(g) trends, with a temporal lag corresponding to the mixing time of sugars in the phloem. These six trees also showed significant negative correlations between photosynthetic discrimination Delta calculated from intra-ring delta(13) C, and ecosystem W(t), during latewood formation. Despite the observed between-tree variability, these results indicate that intra-ring delta(13) C can be used to access seasonal variations in past W(t).
not annotated - annotated - LINNAEUS only
Resistance and recovery of soil microbial communities in the face of Alliaria petiolata invasions.
Invaders can gain ecological advantages because of their evolutionary novelty, but little is known about how these novel advantages will change over time as the invader and invaded community evolve in response to each other. Invasive plants often gain such an advantage through alteration of soil microbial communities. In soil communities sampled from sites along a gradient of invasion history with Alliaria petiolata, microbial richness tended to decline, but the community's resistance to A. petiolata's effects generally increased with increasing history of invasion. However, sensitive microbial taxa appeared to recover in the two oldest sites, leading to an increase in richness, but consequent decrease in resistance. This may be because of evolutionary changes in the A. petiolata populations, which tend to reduce their investment to allelopathic compounds over time. These results show that, over time, microbial communities can develop resistance to an invasive plant but at the cost of lower richness. However, over longer time-scales evolution in the invasive species may allow for the recovery of soil microbial communities.
not annotated - annotated - LINNAEUS only
Differentiating between effects of invasion and diversity: impacts of aboveground plant communities on belowground fungal communities.
Exotic plant species can affect soil microbial communities with the potential for community and ecosystem feedbacks. Yet, separating the effects of exotics from confounded changes in plant community diversity still remains a challenge. We focused on how plant diversity and native or exotic life history affected root fungi because of their significant roles in community and ecosystem processes. Specifically, we examined how fungi colonizing plant roots were affected by plant richness (one, two or four species) replicated across a range of plant community mixtures (natives, exotics, native-exotic mixtures). Fungal biomass inside roots was affected independently by plant richness and mixture, while root fungal community composition was affected only by plant richness. Extraradical networks also increased in size with plant richness. By contrast, plant biomass was a function of plant mixture, with natives consistently smaller than exotics and native-exotic mixtures intermediate. Plant invasions may have an impact on the belowground community primarily through their effects on diversity, at least in the short-term. Disentangling the effects of diversity and invasion on belowground microbial communities can help us to understand both the controllers of belowground resilience and mechanisms of successful colonization and spread of exotic plants.
not annotated - annotated - LINNAEUS only
Neuropeptide precursor gene discovery in the Chagas disease vector Rhodnius prolixus.
We show a straightforward workflow combining homology search in Rhodnius prolixus genome sequence with cloning by rapid amplification of cDNA ends and mass spectrometry. We have identified 32 genes and their transcripts that encode a number of neuropeptide precursors leading to 194 putative peptides. We validated by mass spectrometry 82 of those predicted neuropeptides in the brain of R. prolixus to achieve the first comprehensive genomic, transcriptomic and neuropeptidomic analysis of an insect disease vector. Comparisons of available insect neuropeptide sequences revealed that the R. prolixus genome contains most of the conserved neuropeptides in insects, many of them displaying specific features at the sequence level. Some gene families reported here are identified for the first time in the order Hemiptera, a highly biodiverse group of insects that includes many human, animal and plant disease agents.
not annotated - annotated - LINNAEUS only
The alphaherpesvirus US3/ORF66 protein kinases direct phosphorylation of the nuclear matrix protein matrin 3.
The protein kinase found in the short region of alphaherpesviruses, termed US3 in herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV) and ORF66 in varicella-zoster virus (VZV), affects several viral and host cell processes, and its specific targets remain an area of active investigation. Reports suggesting that HSV-1 US3 substrates overlap with those of cellular protein kinase A (PKA) prompted the use of an antibody specific for phosphorylated PKA substrates to identify US3/ORF66 targets. HSV-1, VZV, and PRV induced very different substrate profiles that were US3/ORF66 kinase dependent. The predominant VZV-phosphorylated 125-kDa species was identified as matrin 3, one of the major nuclear matrix proteins. Matrin 3 was also phosphorylated by HSV-1 and PRV in a US3 kinase-dependent manner and by VZV ORF66 kinase at a novel residue (KRRRT150EE). Since VZV-directed T150 phosphorylation was not blocked by PKA inhibitors and was not induced by PKA activation, and since PKA predominantly targeted matrin 3 S188, it was concluded that phosphorylation by VZV was PKA independent. However, purified VZV ORF66 kinase did not phosphorylate matrin 3 in vitro, suggesting that additional cellular factors were required. In VZV-infected cells in the absence of the ORF66 kinase, matrin 3 displayed intranuclear changes, while matrin 3 showed a pronounced cytoplasmic distribution in late-stage cells infected with US3-negative HSV-1 or PRV. This work identifies phosphorylation of the nuclear matrix protein matrin 3 as a new conserved target of this kinase group.
not annotated - annotated - LINNAEUS only
Small-molecule inhibition of human immunodeficiency virus type 1 infection by virus capsid destabilization.
Human immunodeficiency virus type 1 (HIV-1) infection is dependent on the proper disassembly of the viral capsid, or "uncoating," in target cells. The HIV-1 capsid consists of a conical multimeric complex of the viral capsid protein (CA) arranged in a hexagonal lattice. Mutations in CA that destabilize the viral capsid result in impaired infection owing to defects in reverse transcription in target cells. We describe here the mechanism of action of a small molecule HIV-1 inhibitor, PF-3450074 (PF74), which targets CA. PF74 acts at an early stage of HIV-1 infection and inhibits reverse transcription in target cells. We show that PF74 binds specifically to HIV-1 particles, and substitutions in CA that confer resistance to the compound prevent binding. A single point mutation in CA that stabilizes the HIV-1 core also conferred strong resistance to the virus without inhibiting compound binding. Treatment of HIV-1 particles or purified cores with PF74 destabilized the viral capsid in vitro. Furthermore, the compound induced the rapid dissolution of the HIV-1 capsid in target cells. PF74 antiviral activity was promoted by binding of the host protein cyclophilin A to the HIV-1 capsid, and PF74 and cyclosporine exhibited mutual antagonism. Our data suggest that PF74 triggers premature HIV-1 uncoating in target cells, thereby mimicking the activity of the retrovirus restriction factor TRIM5alpha. This study highlights uncoating as a step in the HIV-1 life cycle that is susceptible to small molecule intervention.
not annotated - annotated - LINNAEUS only
PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice.
Influenza A viruses are human and animal pathogens that cause morbidity and mortality, which range from mild to severe. The 2009 H1N1 pandemic was caused by the emergence of a reassortant H1N1 subtype (H1N1pdm) influenza A virus containing gene segments that originally circulated in human, avian, and swine virus reservoirs. The molecular determinants of replication and pathogenesis of H1N1pdm viruses in humans and other mammals are poorly understood. Therefore, we set out to elucidate viral determinants critical to the pathogenesis of this novel reassortant using a mouse model. We found that a glutamate-to-glycine substitution at residue 158 of the PB2 gene (PB2-E158G) increased the morbidity and mortality of the parental H1N1pdm virus. Results from mini-genome replication assays in human cells and virus titration in mouse tissues demonstrated that PB2-E158G is a pathogenic determinant, because it significantly increases viral replication rates. The virus load in PB2-E158G-infected mouse lungs was 1,300-fold higher than that of the wild-type virus. Our data also show that PB2-E158G had a much stronger influence on the RNA replication and pathogenesis of H1N1pdm viruses than PB2-E627K, which is a known pathogenic determinant. Remarkably, PB2-E158G substitutions also altered the pathotypes of two avian H5 viruses in mice, indicating that this residue impacts genetically divergent influenza A viruses and suggesting that this region of PB2 could be a new antiviral target. Collectively, the data presented in this study demonstrate that PB2-E158G is a novel pathogenic determinant of influenza A viruses in the mouse model. We speculate that PB2-E158G may be important in the adaptation of avian PB2 genes to other mammals, and BLAST sequence analysis identified a naturally occurring human H1N1pdm isolate that has this substitution. Therefore, future surveillance efforts should include scrutiny of this region of PB2 because of its potential impact on pathogenesis.
not annotated - annotated - LINNAEUS only
Hepatitis C virus NS2 protein serves as a scaffold for virus assembly by interacting with both structural and nonstructural proteins.
Many aspects of the assembly of hepatitis C virus (HCV) remain incompletely understood. To characterize the role of NS2 in the production of infectious virus, we determined NS2 interaction partners among other HCV proteins during productive infection. Pulldown assays showed that NS2 forms complexes with both structural and nonstructural proteins, including E1, E2, p7, NS3, and NS5A. Confocal microscopy also demonstrated that NS2 colocalizes with E1, E2, and NS5A in dot-like structures near lipid droplets. However, NS5A did not coprecipitate with E2 and interacted only weakly with NS3 in pulldown assays. Also, there was no demonstrable interaction between p7 and E2 or NS3 in such assays. Therefore, NS2 is uniquely capable of interacting with both structural and nonstructural proteins. Among mutations in p7, NS2, and NS3 that prevent production of infectious virus, only p7 mutations significantly reduced NS2-mediated protein interactions. These p7 mutations altered the intracellular distribution of NS2 and E2 and appeared to modulate the membrane topology of the C-terminal domain of NS2. These results suggest that NS2 acts to coordinate virus assembly by mediating interactions between envelope proteins and NS3 and NS5A within replication complexes adjacent to lipid droplets, where virus particle assembly is thought to occur. p7 may play an accessory role by regulating NS2 membrane topology, which is important for NS2-mediated protein interactions and therefore NS2 function.
not annotated - annotated - LINNAEUS only
Alcohol dehydrogenase and hydrogenase transcript fluctuations during a day-night cycle in Chlamydomonas reinhardtii: the role of anoxia.
* The unicellular green alga Chlamydomonas reinhardtii contains two iron (Fe)-hydrogenases which are responsible for hydrogen production under anoxia. In the present work the patterns of expression of alcohol dehydrogenase, a typical anaerobic gene in plants, of the hydrogenases genes (HYD1, HYD2) and of the genes responsible for their maturation (HYDEF, HYDG), were analysed. * The expression patterns were analysed by real-time reverse-transcription polymerase chain reaction in Chlamydomonas cultures during the day-night cycle, as well as in response to oxygen availability. * The results indicated that ADH1, HYD1, HYD2, HYDEF and HYDG were expressed following precise day-night fluctuations. ADH1 and HYD2 were modulated by the day-night cycle. Low oxygen plays an important role for the induction of HYD1, HYDEF and HYDG, while ADH1 and HYD2 expression was relatively insensitive to oxygen availability. * The regulation of the anaerobic gene expression in Chlamydomonas is only partly explained by responses to anoxia. The cell cycle and light-dark cycles are equally important elements in the regulatory network modulating the anaerobic response in Chlamydomonas.
not annotated - annotated - LINNAEUS only
Evaluation of the Virus Counter(R) for rapid baculovirus quantitation.
The utility of a new instrument for rapid virus quantitation, the Virus Counter, was evaluated in a blind study conducted at three sites. This instrument is a substantially improved version of the original academic research instrument described previously by Stoffel and Rowlen (2005a). The addition of hydrodynamic focusing, a self-contained fluidics system and customized software for system control and data analysis has resulted in a commercially viable and available design. Baculovirus samples were provided by Protein Sciences Corporation and blinded to InDevR and Baylor College of Medicine. Protein Sciences Corporation and Baylor College of Medicine analyzed the samples by plaque assay and InDevR analyzed the samples using the Virus Counter. Serial dilution of stock viruses into growth media and buffer allowed for comparison of measured versus intended concentrations. Direct log-scale comparison between pooled Virus Counter results and pooled plaque assay results indicated a linear relationship (slope=1.1+/-0.2, R(2)=0.86) with statistically significant Pearson correlation (r=0.93, p<0.001).
not annotated - annotated - LINNAEUS only
Applied biotechnology for production of immunoglobulin Y specific to hepatitis A virus.
A new protocol for producing polyclonal antibody against hepatitis A virus (HAV) is described. Twenty hens were immunized three times with a commercial HAV vaccine and HAV from a cell culture with three types of adjuvants: CpG oligodeoxynucleotides (CpG-ODN), incomplete Freund's adjuvant and an alum adjuvant. In each of the last two booster inoculations, blood from the birds was collected and tested for HAV antibodies. Egg yolk was separated from egg white and immunoglobulin Y (IgY) antibody was then purified by polyethylene glycol 6000. The mean yield of total protein in yolk was 22.62 mg/mL. Specific activity of the antibody was tested using commercial ELISA, Western blotting, and in vitro neutralization assay demonstrating that anti-HAV IgY bound specifically. After the first immunization, birds immunized with HAV from cell culture plus incomplete Freund's adjuvant with/without CpG-ODN showed highest levels of anti-HAV IgY in serum (p<0.05). Viral combination with CpG-ODN resulted in early response of anti-HAV serum in hens, reflecting the amount of IgY transferred to the egg yolk (p<0.05). The results suggest that egg yolk may be a large scale source of specific antibodies against hepatitis A virus. Further applications of this method have yet to be tested.
not annotated - annotated - LINNAEUS only
Cotterillia bromelicola nov. gen., nov. spec., a gonostomatid ciliate (Ciliophora, Hypotricha) from tank bromeliads (Bromeliaceae) with de novo originating dorsal kineties.
Cotterillia bromelicola nov. gen., nov. spec. was discovered in the tanks of the Mexican bromeliad Tillandsia heterophylla. Its morphology, ontogenesis, and 18S rDNA were studied with standard methods. Cotterillia has many cirral rows on both sides of the body. Uniquely, and thus used to diagnose the new genus Cotterillia, it has dorsal kineties originating de novo, producing neokinetal waves where the parental dorsal kineties reorganize to "combined rows", consisting of dorsal bristles anteriorly and of cirri posteriorly. Thus, up to four generations of bristles and cirri occur on the dorsal body surface. Cotterillia bromelicola has a gonostomatid body and adoral zone of membranelles, while the dense ciliature and the neokinetal waves resemble kahliellid hypotrichs. However, the de novo origin of anlage 1 and the molecular analyses show convincingly that Cotterillia belongs to the Gonostomatidae Small and Lynn, 1985, for which an improved diagnosis is provided. Thus, neokinetal waves originated several times independently. The molecular differences between Trachelostyla, Gonostomum, and Cotterillia are small (=< 5%) compared to their distinct morphologies and ontogeneses, suggesting that the 18S rDNA underestimates generic diversity. Our study emphasizes the need of combined morphological, ontogenetic, and molecular investigations to unravel the complex phylogeny and evolution of hypotrich ciliates.
not annotated - annotated - LINNAEUS only
The nodulation of alfalfa by the acid-tolerant Rhizobium sp. strain LPU83 does not require sulfated forms of lipochitooligosaccharide nodulation signals.
The induction of root nodules by the majority of rhizobia has a strict requirement for the secretion of symbiosis-specific lipochitooligosaccharides (nodulation factors [NFs]). The nature of the chemical substitution on the NFs depends on the particular rhizobium and contributes to the host specificity imparted by the NFs. We present here a description of the genetic organization of the nod gene cluster and the characterization of the chemical structure of the NFs associated with the broad-host-range Rhizobium sp. strain LPU83, a bacterium capable of nodulating at least alfalfa, bean, and Leucena leucocephala. The nod gene cluster was located on the plasmid pLPU83b. The organization of the cluster showed synteny with those of the alfalfa-nodulating rhizobia, Sinorhizobium meliloti and Sinorhizobium medicae. Interestingly, the strongest sequence similarity observed was between the partial nod sequences of Rhizobium mongolense USDA 1844 and the corresponding LPU83 nod genes sequences. The phylogenetic analysis of the intergenic region nodEG positions strain LPU83 and the type strain R. mongolense 1844 in the same branch, which indicates that Rhizobium sp. strain LPU83 might represent an early alfalfa-nodulating genotype. The NF chemical structures obtained for the wild-type strain consist of a trimeric, tetrameric, and pentameric chitin backbone that shares some substitutions with both alfalfa- and bean-nodulating rhizobia. Remarkably, while in strain LPU83 most of the NFs were sulfated in their reducing terminal residue, none of the NFs isolated from the nodH mutant LPU83-H were sulfated. The evidence obtained supports the notion that the sulfate decoration of NFs in LPU83 is not necessary for alfalfa nodulation.
not annotated - annotated - LINNAEUS only
The Rcs signal transduction pathway is triggered by enterobacterial common antigen structure alterations in Serratia marcescens.
The enterobacterial common antigen (ECA) is a highly conserved exopolysaccharide in Gram-negative bacteria whose role remains largely uncharacterized. In a previous work, we have demonstrated that disrupting the integrity of the ECA biosynthetic pathway imposed severe deficiencies to the Serratia marcescens motile (swimming and swarming) capacity. In this work, we show that alterations in the ECA structure activate the Rcs phosphorelay, which results in the repression of the flagellar biogenesis regulatory cascade. In addition, a detailed analysis of wec cluster mutant strains, which provoke the disruption of the ECA biosynthesis at different levels of the pathway, suggests that the absence of the periplasmic ECA cyclic structure could constitute a potential signal detected by the RcsF-RcsCDB phosphorelay. We also identify SMA1167 as a member of the S. marcescens Rcs regulon and show that high osmolarity induces Rcs activity in this bacterium. These results provide a new perspective from which to understand the phylogenetic conservation of ECA among enterobacteria and the basis for the virulence attenuation detected in wec mutant strains in other pathogenic bacteria.
not annotated - annotated - LINNAEUS only
A cis-encoded antisense small RNA regulated by the HP0165-HP0166 two-component system controls expression of ureB in Helicobacter pylori.
Expression of urease is essential for gastric colonization by Helicobacter pylori. The increased level of urease in gastric acidity is due, in part, to acid activation of the two-component system (TCS) consisting of the membrane sensor HP0165 and its response regulator, HP0166, which regulates transcription of the seven genes of the urease gene cluster. We now find that there are two major ureAB transcripts: a 2.7-kb full-length ureAB transcript and a 1.4-kb truncated transcript lacking 3' ureB. Acidic pH (pH 4.5) results in a significant increase in transcription of ureAB, while neutral pH (pH 7.4) increases the truncated 1.4-kb transcript. Northern blot analysis with sense RNA and strand-specific oligonucleotide probes followed by 5' rapid amplification of cDNA ends detects an antisense small RNA (sRNA) encoded by the 5' ureB noncoding strand consisting of -290 nucleotides (5'ureB-sRNA). Deletion of HP0165 elevates the level of the truncated 1.4-kb transcript along with that of the 5'ureB-sRNA at both pH 7.4 and pH 4.5. Overexpression of 5'ureB-sRNA increases the 1.4-kb transcript, decreases the 2.7-kb transcript, and decreases urease activity. Electrophoretic mobility shift assay shows that unphosphorylated HP0166 binds specifically to the 5'ureB-sRNA promoter. The ability of the HP0165-HP0166 TCS to both increase and decrease ureB expression at low and high pHs, respectively, facilitates gastric habitation and colonization over the wide range of intragastric pHs experienced by the organism.
not annotated - annotated - LINNAEUS only
Non-structural protein 1 (NS1) antibody-based assays to differentiate West Nile (WN) virus from Japanese encephalitis virus infections in horses: effects of WN virus NS1 antibodies induced by inactivated WN vaccine.
Antibodies to non-structural protein 1 (NS1) of West Nile virus (WNV) have been used to differentiate WNV infection from infection by serologically cross-reactive flaviviruses, including Japanese encephalitis virus (JEV), in horses. However, since the inactivated West Nile (WN) vaccine has been reported to induce NS1 antibodies, there is concern about the reliability of using NS1-based assays for testing vaccinated horses. Therefore, the effect of inactivated WN vaccine-induced antibodies on an epitope-blocking ELISA and complement-dependent cytotoxicity (CDC) assay were investigated. Both assays are based on NS1 antibodies and were established previously to differentiate WNV from JEV infections in horses. Groups of three horses were vaccinated with two or three doses of a commercial inactivated WN vaccine and NS1 antibodies were detected by a conventional ELISA after the second vaccination. Vaccine-induced NS1 antibodies were also detected by blocking ELISA and a CDC assay and affected the ability of these assays to differentiate WNV from JEV infections. However, the effect was less significant in the CDC assay, where use of a low serum concentration ensured effective differentiation. The more efficient detection of infection-induced antibodies over vaccine-induced antibodies by the CDC assay was potentially attributable to the different IgG isotype profiles of these antibodies.
not annotated - annotated - LINNAEUS only
The B cell response is redundant and highly focused on V1V2 during early subtype C infection in a Zambian seroconverter.
High-titer autologous neutralizing antibody responses have been demonstrated during early subtype C human immunodeficiency virus type 1 (HIV-1) infection. However, characterization of this response against autologous virus at the monoclonal antibody (MAb) level has only recently begun to be elucidated. Here we describe five monoclonal antibodies derived from a subtype C-infected seroconverter and their neutralizing activities against pseudoviruses that carry envelope glycoproteins from 48 days (0 month), 2 months, and 8 months after the estimated time of infection. Sequence analysis indicated that the MAbs arose from three distinct B cell clones, and their pattern of neutralization compared to that in patient plasma suggested that they circulated between 2 and 8 months after infection. Neutralization by MAbs representative of each B cell clone was mapped to two residues: position 134 in V1 and position 189 in V2. Mutational analysis revealed cooperative effects between glycans and residues at these two positions, arguing that they contribute to a single epitope. Analysis of the cognate gp120 sequence through homology modeling places this potential epitope near the interface between the V1 and V2 loops. Additionally, the escape mutation R189S in V2, which conferred resistance against all three MAbs, had no detrimental effect on virus replication in vitro. Taken together, our data demonstrate that independent B cells repeatedly targeted a single structure in V1V2 during early infection. Despite this assault, a single amino acid change was sufficient to confer complete escape with minimal impact on replication fitness.
not annotated - annotated - LINNAEUS only
A nuclear inhibitor of NF-kappaB encoded by a poxvirus.
Poxviruses have evolved various strategies to inhibit cytoplasmic events leading to activation of the nuclear factor kappaB (NF-kappaB) signaling pathway, with individual viruses often encoding multiple NF-kappaB inhibitors. Here, the novel orf virus (ORFV)-encoded protein ORFV002 was shown to inhibit nuclear events regulating NF-kappaB transcriptional activity. ORFV002 expression in cell cultures significantly decreased wild-type-virus-, tumor necrosis factor alpha (TNF-alpha)-, and lipopolysaccharide (LPS)-induced NF-kappaB-mediated gene expression. Expression of ORFV002 in cells, while not affecting phosphorylation or nuclear translocation of NF-kappaB-p65, markedly decreased TNF-alpha- and wild-type-virus-induced acetylation of NF-kappaB-p65, a p300-mediated nuclear modification of NF-kappaB-p65 that regulates its transactivating activity. ORFV002 was shown to colocalize and interact with NF-kappaB-p65, and expression of ORFV002 in cell cultures resulted in a reduced interaction of NF-kappaB-p65 with p300, suggesting that ORFV002 interferes with NF-kappaB-p65/p300 association. Deletion of ORFV002 from the OV-IA82 genome had no significant effect on ORFV pathogenesis in sheep, indicating that ORFV002 is nonessential for virus virulence in the natural host. This represents the first description of a nuclear inhibitor of NF-kappaB encoded by a poxvirus.
not annotated - annotated - LINNAEUS only
Norovirus GII.4 strain antigenic variation.
Noroviruses are the principal cause of epidemic gastroenteritis worldwide. Multiple reports have concluded that the major capsid proteins of GII.4 strains, which cause 80% of norovirus infections worldwide, are evolving rapidly, resulting in new epidemic strains. Surrogate neutralization assays using sera from outbreaks and from immunized mice suggest that, as with influenza virus, antigenic variation maintains GII.4 persistence in the face of human population herd immunity. To test this hypothesis, mice were hyperimmunized with virus-like particles (VLPs) representing an early (GII.4-1987) and a contemporary (GII.4-2006) GII.4 strain. Anti-GII.4-1987 IgG monoclonal antibodies (MAbs) strongly reacted with GII.4 VLPs derived between only 1987 and 2002. Ligand binding blockade was more efficient with GII.4-1987 and GII.4-1997 VLPs than with GII.4-2002. Anti-GII.4-2006 IgG MAbs recognized either a broad panel of GII.4 VLPs (1987 to 2006) or a subset of contemporary (2004 to 2006) VLPs. Most 2006 antibodies did not recognize or only poorly recognized GII.4 VLPs of 2007 or 2008, documenting rapid antigenic evolution of GII.4 capsids. Generally, 2006 MAbs blocked homotypic VLP-ligand binding but were unable to block VLPs representing strains primarily circulating during or earlier than 2002. These analyses demonstrate that both subtle and significant evolutionary change has occurred within antibody epitopes between epidemic strains, providing direct evidence that the GII.4 noroviruses are undergoing antigenic variation, likely in response to herd immunity. As with influenza virus, HIV, and hepatitis C virus, norovirus antigenic variation will significantly influence the design of efficacious vaccines and immunotherapeutics against these important human pathogens.
not annotated - annotated - LINNAEUS only
Dominant inhibition of Akt/protein kinase B signaling by the matrix protein of a negative-strand RNA virus.
Vesicular stomatitis virus (VSV) is a rhabdovirus that alters host nuclear and cytoplasmic function upon infection. We have investigated the effect of VSV infection on cellular signaling through the phosphatidylinositol-3 kinase (PI3k)/Akt signaling pathway. Akt phosphorylation at both threonine 308 (Thr308) and serine 473 (Ser473) was inhibited in cells infected with VSV. This inhibition was rapid (beginning within the first 2 to 3 h postinfection) and correlated with the dephosphorylation of downstream effectors of Akt, such as glycogen synthase kinase 3Beta (GSK3Beta) and mammalian target of rapamycin (mTOR). The dephosphorylation of Akt occurred in the presence of growth factor stimulation and was not overcome through constitutive membrane targeting of Akt or high levels of phosphatidylinositol-3,4,5-triphosphate (PIP3) accumulation in the membrane. Akt dephosphorylation was not a result of alterations in PDK1 phosphorylation or activity, changes in phosphatase and tensin homologue deleted on chromosome 10 (PTEN) levels, or the downregulation of PI3k signaling. Inactivation of Akt was caused by the expression of the viral M protein in the absence of other viral components, and an M protein mutant that does not inhibit RNA polymerase II (Pol II) transcription and nuclear/cytoplasmic transport was also defective in inhibiting Akt phosphorylation. These data illustrate that VSV utilizes a novel mechanism to alter this central player in cell signaling and oncogenesis. It also suggests an inside-out model of signal transduction where VSV interruption of nuclear events has a rapid and significant effect on membrane signaling events.
not annotated - annotated - LINNAEUS only
Activation of plasmacytoid dendritic cells by Kaposi's sarcoma-associated herpesvirus.
Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with multiple human malignancies, including Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. Following primary infection, KSHV typically goes through a brief period of lytic replication prior to the establishment of latency. Plasmacytoid dendritic cells (pDCs) are the major producers of type 1 interferon (IFN), primarily in response to virus infection. Toll-like receptors (TLRs) are key components of the innate immune system, and they serve as pathogen recognition receptors that stimulate the host antiviral response. pDCs express exclusively TLR7 and TLR9, and it is through these TLRs that the type 1 interferon response is activated in pDCs. Currently, it is not known whether KSHV is recognized by pDCs and whether activation of pDCs occurs in response to KSHV infection. We now report evidence that KSHV can infect human pDCs and that pDCs are activated upon KSHV infection, as measured by upregulation of CD83 and CD86 and by IFN-alpha secretion. We further show that induction of IFN-alpha occurs through activation of TLR9 signaling and that a TLR9 inhibitor diminishes the production and secretion of IFN-alpha by KSHV-infected pDCs.
not annotated - annotated - LINNAEUS only
An in-depth analysis of original antigenic sin in dengue virus infection.
The evolution of dengue viruses has resulted in four antigenically similar yet distinct serotypes. Infection with one serotype likely elicits lifelong immunity to that serotype, but generally not against the other three. Secondary or sequential infections are common, as multiple viral serotypes frequently cocirculate. Dengue infection, although frequently mild, can lead to dengue hemorrhagic fever (DHF) which can be life threatening. DHF is more common in secondary dengue infections, implying a role for the adaptive immune response in the disease. There is currently much effort toward the design and implementation of a dengue vaccine but these efforts are made more difficult by the challenge of inducing durable neutralizing immunity to all four viruses. Domain 3 of the dengue virus envelope protein (ED3) has been suggested as one such candidate because it contains neutralizing epitopes and it was originally thought that relatively few cross-reactive antibodies are directed to this domain. In this study, we performed a detailed analysis of the anti-ED3 response in a cohort of patients suffering either primary or secondary dengue infections. The results show dramatic evidence of original antigenic sin in secondary infections both in terms of binding and enhancement activity. This has important implications for dengue vaccine design because heterologous boosting is likely to maintain the immunological footprint of the first vaccination. On the basis of these findings, we propose a simple in vitro enzyme-linked immunosorbent assay (ELISA) to diagnose the original dengue infection in secondary dengue cases.
not annotated - annotated - LINNAEUS only
When it is too hot for photosynthesis: heat-induced instability of photosynthesis in relation to respiratory burst, cell permeability changes and H2O2 formation.
Photosynthesis rate (A(n)) becomes unstable above a threshold temperature, and the recovery upon return to low temperature varies because of reasons not fully understood. We investigated responses of A(n), dark respiration and chlorophyll fluorescence to supraoptimal temperatures of varying duration and kinetics in Phaseolus vulgaris asking whether the instability of photosynthesis under severe heat stress is associated with cellular damage. Cellular damage was assessed by Evans blue penetration (enhanced membrane permeability) and by H2O2 generation [3,3'-diaminobenzidine 4HCl (DAB)-staining]. Critical temperature for dark fluorescence (F(0) ) rise (T(F)) was at 46-48 ^0C, and a burst of respiration was observed near T(F). However, A(n) was strongly inhibited already before T(F) was reached. Membrane permeability increased with temperature according to a switch-type response, with enhanced permeability observed above 48 ^0C. Experiments with varying heat pulse lengths and intensities underscored the threshold-type loss of photosynthetic function, and indicated that the degree of photosynthetic deterioration and cellular damage depended on accumulated heat-dose. Beyond the 'point of no return', propagation of cellular damage and reduction of photosynthesis continued upon transfer to lower temperatures and photosynthetic recovery was slow or absent. We conclude that instability of photosynthesis under severe heat stress is associated with time-dependent propagation of cellular lesions.
not annotated - annotated - LINNAEUS only
A fluorescence resonance energy transfer-based fluorometer assay for screening anti-coxsackievirus B3 compounds.
In view of the need to develop a simple and rapid method to screen for antiviral therapeutic agents, a fluorescence resonance energy transfer (FRET)-based reporter system consisting of engineered mammalian cells expressing a cyan fluorescent protein-yellow fluorescent protein (CFP-YFP) pair linked by a short peptide containing the cleavage site of viral protease 2A (2A(pro)) was developed. By detecting the 2A(pro) produced early during the virus infection cycle, the CFP-YFP pair effectively identifies infectious coxsackievirus B3 (CVB3), a picornavirus that causes viral myocarditis in humans. The reporter system was used to screen a library of 2000 drugs and natural products for potential antiviral compounds. The reporter cells were treated with the test compounds, challenged with CVB3, and then examined using a fluorometer at 24h post-infection. Sixty-four compounds, mostly therapeutic drugs, antimicrobial compounds and compounds with unknown functions, caused at least 50% inhibition of 2A(pro) activity. Three known antiviral compounds, cosmosiin, ribavirin and baicalein, were also identified in the screening. The developed method is an effective strategy for rapid screening, and identifies compounds that inhibit CVB3 2A(pro). This method should be a valuable aid in the antiviral drug discovery effort.
not annotated - annotated - LINNAEUS only
One-step real-time reverse transcription-PCR assays for detecting and subtyping pandemic influenza A/H1N1 2009, seasonal influenza A/H1N1, and seasonal influenza A/H3N2 viruses.
Pandemic influenza A/H1N1 2009 (A/H1N1pdm) virus has caused significant outbreaks worldwide. A previous one-step real-time reverse transcription-PCR (rRT-PCR) assay for detecting A/H1N1pdm virus (H1pdm rRT-PCR assay) was improved since the former probe had a low melting temperature and low tolerance to viral mutation. To help with the screening of the A/H1N1pdm virus, rRT-PCR assays were also developed for detecting human seasonal A/H1N1 (H1 rRT-PCR assay) and A/H3N2 influenza viruses (H3 rRT-PCR assay). H1pdm, H1, and H3 rRT-PCR assays were evaluated using in vitro-transcribed control RNA, isolated viruses, and other respiratory pathogenic viruses, and were shown to have high sensitivity, good linearity (R(2)=0.99), and high specificity. In addition, the improved H1pdm rRT-PCR assay could detect two viral strains of A/H1N1pdm, namely, A/Aichi/472/2009 (H1N1)pdm and A/Sakai/89/2009 (H1N1)pdm, which have mutation(s) in the probe-binding region of the hemagglutinin gene, without loss of sensitivity. Using the three rRT-PCR assays developed, 90 clinical specimens collected between May and October 2009 were then tested. Of these, 26, 20, and 2 samples were identified as positive for A/H1pdm, A/H3, and A/H1, respectively, while 42 samples were negative for influenza A viruses. The present results suggest that these highly sensitive and specific H1pdm, H1, and H3 rRT-PCR assays are useful not only for diagnosing influenza viruses, but also for the surveillance of influenza viruses.
not annotated - annotated - LINNAEUS only
Comparison of commercial systems for extraction of nucleic acids from DNA/RNA respiratory pathogens.
This study compared six automated nucleic acid extraction systems and one manual kit for their ability to recover nucleic acids from human nasal wash specimens spiked with five respiratory pathogens, representing Gram-positive bacteria (Streptococcus pyogenes), Gram-negative bacteria (Legionella pneumophila), DNA viruses (adenovirus), segmented RNA viruses (human influenza virus A), and non-segmented RNA viruses (respiratory syncytial virus). The robots and kit evaluated represent major commercially available methods that are capable of simultaneous extraction of DNA and RNA from respiratory specimens, and included platforms based on magnetic-bead technology (KingFisher mL, Biorobot EZ1, easyMAG, KingFisher Flex, and MagNA Pure Compact) or glass fiber filter technology (Biorobot MDX and the manual kit Allprep). All methods yielded extracts free of cross-contamination and RT-PCR inhibition. All automated systems recovered L. pneumophila and adenovirus DNA equivalently. However, the MagNA Pure protocol demonstrated more than 4-fold higher DNA recovery from the S. pyogenes than other methods. The KingFisher mL and easyMAG protocols provided 1- to 3-log wider linearity and extracted 3- to 4-fold more RNA from the human influenza virus and respiratory syncytial virus. These findings suggest that systems differed in nucleic acid recovery, reproducibility, and linearity in a pathogen specific manner.
not annotated - annotated - LINNAEUS only
Aerosol drug delivery: developments in device design and clinical use.
Aerosolised drugs are prescribed for use in a range of inhaler devices and systems. Delivering drugs by inhalation requires a formulation that can be successfully aerosolised and a delivery system that produces a useful aerosol of the drug; the particles or droplets need to be of sufficient size and mass to be carried to the distal lung or deposited on proximal airways to give rise to a therapeutic effect. Patients and caregivers must use and maintain these aerosol drug delivery devices correctly. In recent years, several technical innovations have led to aerosol drug delivery devices with efficient drug delivery and with novel features that take into account factors such as dose tracking, portability, materials of manufacture, breath actuation, the interface with the patient, combination therapies, and systemic delivery. These changes have improved performance in all four categories of devices: metered dose inhalers, spacers and holding chambers, dry powder inhalers, and nebulisers. Additionally, several therapies usually given by injection are now prescribed as aerosols for use in a range of drug delivery devices. In this Review, we discuss recent developments in the design and clinical use of aerosol devices over the past 10-15 years with an emphasis on the treatment of respiratory disorders.
not annotated - annotated - LINNAEUS only
Regulation of horizontal gene transfer in Bacillus subtilis by activation of a conserved site-specific protease.
The mobile genetic element ICEBs1 is an integrative and conjugative element (a conjugative transposon) found in Bacillus subtilis. The RecA-dependent SOS response and the RapI-PhrI cell sensory system activate ICEBs1 gene expression by stimulating cleavage of ImmR, the ICEBs1 immunity repressor, by the protease ImmA. We found that increasing the amount of wild-type ImmA in vivo caused partial derepression of ICEBs1 gene expression. However, during RapI-mediated derepression of ICEBs1 gene expression, ImmA levels did not detectably increase, indicating that RapI likely activates the protease ImmA by increasing its specific activity. We also isolated and characterized mutations in immA (immA(h)) that cause partial derepression of ICEBs1 gene expression in the absence of inducing signals. We obtained two types of immA(h) mutations: one type caused increased amounts of the mutant proteins in vivo but no detectable effect on specific activity in vitro; the other type had no detectable effect on the amount of the mutant protein in vivo but caused increased specific activity of the protein (as measured in vitro). Together, these findings indicate that derepression of ICEBs1 gene expression is likely caused by an increase in the specific activity of ImmA. Homologs of ImmA and ImmR are found in many mobile genetic elements, so the mechanisms that regulate ImmA-mediated cleavage of ImmR may be widely conserved.
not annotated - annotated - LINNAEUS only
Orientation of SecA and SecB in complex, derived from disulfide cross-linking.
SecA is the ATPase that acts as the motor for protein export in the general secretory, or Sec, system of Escherichia coli. The tetrameric cytoplasmic chaperone SecB binds to precursors of exported proteins before they can become stably folded and delivers them to SecA. During this delivery step, SecB binds to SecA. The complex between SecA and SecB that is maximally active in translocation contains two protomers of SecA bound to a tetramer of SecB. The aminoacyl residues on each protein that are involved in binding the other have previously been identified by site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy; however, that study provided no information concerning the relative orientation of the proteins within the complex. Here we used our extensive collection of single-cysteine variants of the two proteins and subjected pairwise combinations of SecA and SecB to brief oxidation to identify residues in close proximity. These data were used to generate a model for the orientation of the two proteins within the complex.
not annotated - annotated - LINNAEUS only
Inactivation of the RluD pseudouridine synthase has minimal effects on growth and ribosome function in wild-type Escherichia coli and Salmonella enterica.
The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the pseudouridine (Psi) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion of rluD in K-12 strains of E. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50S ribosomal subunit assembly and 30S-50S subunit association. Suppressor mutations in the prfB and prfC genes encoding release factor 2 (RF2) and RF3 that restore the wild type-growth rate and also correct the ribosomal defects have now been isolated. These suppressors link helix 69 Psi residues with the termination phase of protein synthesis. However, further genetic analysis reported here also reveals that the slow growth and other defects associated with inactivation of rluD in E. coli K-12 strains are due to a defective RF2 protein, with a threonine at position 246, which is present in all K-12 strains. This is in contrast to the more typical alanine found at this position in most bacterial RF2s, including those of other E. coli strains. Inactivation of rluD in E. coli strains containing the prfB allele from E. coli B or in Salmonella enterica, both carrying an RF2 with Ala246, has negligible effects on growth, termination, or ribosome function. The results indicate that, in contrast to those in wild bacteria, termination functions in E. coli K-12 strains carrying a partially defective RF2 protein are especially susceptible to perturbation of ribosome-RF interactions, such as that caused by loss of h69 Psi modifications.
not annotated - annotated - LINNAEUS only
Effect of energetic constraints on distribution and winter survival of weasel males.
1. The absolute energy needs of small animals are generally lower than those of larger animals. This should drive higher mortality of larger animals, when the environmental conditions deteriorate. However, demonstration of the effect of energy constraints on survivals proved difficult, because the range of body mass within species is generally too small to produce enough variation for studying such an effect. An opportunity for an intraspecific study comes from weasels inhabiting the Bialowieza Forest (north-eastern Poland), which are characterized by a threefold variation in body mass. 2. We assumed that in summer larger weasel males are favoured by sexual selection, because they are more successful when competing for mates. We then tested whether they suffer higher mortality in winter, because they have difficulty finding sufficient food to satisfy their energy needs and/or because the additional foraging time would result in increased exposure to predation. 3. We measured daily energy expenditures (DEE) of overwintering weasel males using the doubly labelled water (DLW) technique. We constructed an energetic model predicting how individuals of different size are able to balance their energy budgets feeding on large and small prey while minimizing time spent hunting, thereby reducing their own exposure to predation. 4. The range of body mass in overwintering weasels predicted by our model corresponded very well with the distribution of prey body mass in three different habitats within our study area. Larger individuals were able to compensate for higher food requirements by using habitats with larger prey species than those available to smaller male weasels. This effectively offset the expected negative association between body mass and winter survival predicted from considerations of energy balance. 5. Our results show how energetic constraints affect body mass and spatial segregation of a species at the intra-specific level not only across large geographical ranges, but also within a relatively small area.
not annotated - annotated - LINNAEUS only
Bud set in poplar--genetic dissection of a complex trait in natural and hybrid populations.
* The seasonal timing of growth events is crucial to tree distribution and conservation. The seasonal growth cycle is strongly adapted to the local climate that is changing because of global warming. We studied bud set as one cornerstone of the seasonal growth cycle in an integrative approach. * Bud set was dissected at the phenotypic level into several components, and phenotypic components with most genetic variation were identified. While phenotypic variation resided in the timing of growth cessation, and even so more in the duration from growth cessation to bud set, the timing of growth cessation had a stronger genetic component in both natural and hybrid populations. * Quantitative trait loci (QTL) were identified for the most discriminative phenotypic bud-set components across four poplar pedigrees. The QTL from different pedigrees were recurrently detected in six regions of the poplar genome. * These regions of 1.83-4.25 Mbp in size, containing between 202 and 394 genes, form the basis for further molecular-genetic dissection of bud set.
not annotated - annotated - LINNAEUS only
Alphacoronavirus transmissible gastroenteritis virus nsp1 protein suppresses protein translation in mammalian cells and in cell-free HeLa cell extracts but not in rabbit reticulocyte lysate.
The nsp1 protein of transmissible gastroenteritis virus (TGEV), an alphacoronavirus, efficiently suppressed protein synthesis in mammalian cells. Unlike the nsp1 protein of severe acute respiratory syndrome coronavirus, a betacoronavirus, the TGEV nsp1 protein was unable to bind 40S ribosomal subunits or promote host mRNA degradation. TGEV nsp1 also suppressed protein translation in cell-free HeLa cell extract; however, it did not affect translation in rabbit reticulocyte lysate (RRL). Our data suggested that HeLa cell extracts and cultured host cells, but not RRL, contain a host factor(s) that is essential for TGEV nsp1-induced translational suppression.
not annotated - annotated - LINNAEUS only
Modification of nonstructural protein 1 of influenza A virus by SUMO1.
Nonstructural protein 1 (NS1) is one of the major factors resulting in the efficient infection rate and high level of virulence of influenza A virus. Although consisting of only approximately 230 amino acids, NS1 has the ability to interfere with several systems of the host viral defense. In the present study, we demonstrate that NS1 of the highly pathogenic avian influenza A/Duck/Hubei/L-1/2004 (H5N1) virus interacts with human Ubc9, which is the E2 conjugating enzyme for sumoylation, and we show that SUMO1 is conjugated to H5N1 NS1 in both transfected and infected cells. Furthermore, two lysine residues in the C terminus of NS1 were identified as SUMO1 acceptor sites. When the SUMO1 acceptor sites were removed by mutation, NS1 underwent rapid degradation. Studies of different influenza A virus strains of human and avian origin showed that the majority of viruses possess an NS1 protein that is modified by SUMO1, except for the recently emerged swine-origin influenza A virus (S-OIV) (H1N1). Interestingly, growth of a sumoylation-deficient WSN virus mutant was retarded compared to that of wild-type virus. Together, these results indicate that sumoylation enhances NS1 stability and thus promotes rapid growth of influenza A virus.
not annotated - annotated - LINNAEUS only
Acclimation to high CO2 in maize is related to water status and dependent on leaf rank.
The responses of C(3) plants to rising atmospheric CO(2) levels are considered to be largely dependent on effects exerted through altered photosynthesis. In contrast, the nature of the responses of C(4) plants to high CO(2) remains controversial because of the absence of CO(2) -dependent effects on photosynthesis. In this study, the effects of atmospheric CO(2) availability on the transcriptome, proteome and metabolome profiles of two ranks of source leaves in maize (Zea mays L.) were studied in plants grown under ambient CO(2) conditions (350 +/- 20 muL L(-1) CO(2) ) or with CO(2) enrichment (700 +/- 20 muL L(-1) CO(2) ). Growth at high CO(2) had no effect on photosynthesis, photorespiration, leaf C/N ratios or anthocyanin contents. However, leaf transpiration rates, carbohydrate metabolism and protein carbonyl accumulation were altered at high CO(2) in a leaf-rank specific manner. Although no significant CO(2) -dependent changes in the leaf transcriptome were observed, qPCR analysis revealed that the abundance of transcripts encoding a Bowman-Birk protease inhibitor and a serpin were changed by the growth CO(2) level in a leaf rank specific manner. Moreover, CO(2) -dependent changes in the leaf proteome were most evident in the oldest source leaves. Small changes in water status may be responsible for the observed responses to high CO(2,) particularly in the older leaf ranks.
not annotated - annotated - LINNAEUS only
Seasonal dynamics in the stable carbon isotope composition delta^1^3C from non-leafy branch, trunk and coarse root CO2 efflux of adult deciduous (Fagus sylvatica) and evergreen (Picea abies) trees.
Respiration is a substantial driver of carbon (C) flux in forest ecosystems and stable C isotopes provide an excellent tool for its investigation. We studied seasonal dynamics in delta^1^3C of CO2 efflux (delta^1^3C(E)) from non-leafy branches, upper and lower trunks and coarse roots of adult trees, comparing deciduous Fagus sylvatica (European beech) with evergreen Picea abies (Norway spruce). In both species, we observed strong and similar seasonal dynamics in the delta^1^3C(E) of above-ground plant components, whereas delta^1^3C(E) of coarse roots was rather stable. During summer, delta^1^3C(E) of trunks was about -28.2% (Beech) and -26.8% (Spruce). During winter dormancy, delta^1^3C(E) increased by 5.6-9.1%. The observed dynamics are likely related to a switch from growth to starch accumulation during fall and remobilization of starch, low TCA cycle activity and accumulation of malate by PEPc during winter. The seasonal delta^1^3C(E) pattern of branches of Beech and upper trunks of Spruce was less variable, probably because these organs were additionally supplied by winter photosynthesis. In view of our results and pervious studies, we conclude that the pronounced increases in delta^1^3C(E) of trunks during the winter results from interrupted access to recent photosynthates.
not annotated - annotated - LINNAEUS only
The atypical OmpR/PhoB response regulator ChxR from Chlamydia trachomatis forms homodimers in vivo and binds a direct repeat of nucleotide sequences.
Two-component signal transduction systems are widespread in bacteria and are essential regulatory mechanisms for many biological processes. These systems predominantly rely on a sensor kinase to phosphorylate a response regulator for controlling activity, which is frequently transcriptional regulation. In recent years, an increasing number of atypical response regulators have been discovered in phylogenetically diverse bacteria. These atypical response regulators are not controlled by phosphorylation and exhibit transcriptional activity in their wild-type form. Relatively little is known regarding the mechanisms utilized by these atypical response regulators and the conserved characteristics of these atypical response regulators. Chlamydia spp. are medically important bacteria and encode an atypical OmpR/PhoB subfamily response regulator termed ChxR. In this study, protein expression analysis supports that ChxR is likely exerting its effect during the middle and late stages of the chlamydial developmental cycle, stages that include the formation of infectious elementary bodies. In the absence of detectable phosphorylation, ChxR formed homodimers in vitro and in vivo, similar to a phosphorylated OmpR/PhoB subfamily response regulator. ChxR was demonstrated to bind to its own promoter in vivo, supporting the role of ChxR as an autoactivator. Detailed analysis of the ChxR binding sites within its own promoter revealed a conserved cis-acting motif that includes a tandem repeat sequence. ChxR binds specifically to each of the individual sites and exhibits a relatively large spectrum of differential affinity. Taken together, these observations support the conclusion that ChxR, in the absence of phosphorylation, exhibits many of the characteristics of a phosphorylated (active) OmpR/PhoB subfamily response regulator.
not annotated - annotated - LINNAEUS only
Cold stress contributes to aberrant cytokinesis during male meiosis I in a wheat thermosensitive genic male sterile line.
The male sterility of a wheat thermosensitive genic male sterile (TGMS) line is strictly controlled by temperature. When the TGMS line BS366 was exposed to 10 ^0C from the pollen mother cell stage to the meiosis stage, a few pollen grains were formed and devoid of starch. We report here a large-scale transcriptomic study using the Affymetrix wheat GeneChip to follow gene expression in BS366 line anthers in response to cold stress. Notably, many cytoskeletal signaling components were gradually induced in response to cold stress in BS366 line anthers. However, the cytoskeleton-associated genes that play key roles in the dynamic organization of the cytoskeleton were dramatically repressed. Histological studies revealed that the separation of dyads occurred abnormally during male meiosis I, indicating defective male meiotic cytokinesis. Fluorescence labelling and subcellular histological observations revealed that the phragmoplast was defectively formed and the cell plate was abnormally assembled during meiosis I under cold stress. Based on the transcriptomic analysis and observations of characterized histological changes, our results suggest that cold stress repressed transcription of cytoskeleton dynamic factors and subsequently caused the defective cytokinesis during meiosis I. The results may explain the male sterility caused by low temperature in wheat TGMS lines.
not annotated - annotated - LINNAEUS only
Characterizing the role of RNA silencing components in Cryptococcus neoformans.
The RNA interference (RNAi) mediated by homology-dependent degradation of the target mRNA with small RNA molecules plays a key role in controlling transcription and translation processes in a number of eukaryotic organisms. The RNAi machinery is also evolutionarily conserved in a wide variety of fungal species, including pathogenic fungi. To elucidate the physiological functions of the RNAi pathway in Cryptococcus neoformans that causes fungal meningitis, here we performed genetic analyses for genes encoding Argonaute (AGO1 and AGO2), RNA-dependent RNA polymerase (RDP1), and Dicers (DCR1 and DCR2) in both serotype Aserotype A and D C. neoformans. The present study shows that Ago1, Rdp1, and Dcr2 are the major components of the RNAi process occurring in C. neoformans. However, the RNAi machinery is not involved in regulation of production of two virulence factors (capsule and melanin), sexual differentiation, and diverse stress response. Comparative transcriptome analysis of the serotype A and D RNAi mutants revealed that only modest changes occur in the genome-wide transcriptome profiles when the RNAi process was perturbed. Notably, the serotype D rdp1Delta mutants showed an increase in transcript abundance of active retrotransposons and transposons, such as T2 and T3, the latter of which is a novel serotype D-specific transposon of C. neoformans. In a wild type background both T2 and T3 were found to be weakly active mobile elements, although we found no evidence of Cnl1 retrotransposon mobility. In contrast, all three transposable elements exhibited enhanced mobility in the rdp1Delta mutant strain. In conclusion, the RNAi pathway plays an important role in controlling transposon activity and genome integrity of C. neoformans.
not annotated - annotated - LINNAEUS only
Fur negatively regulates hns and is required for the expression of HilA and virulence in Salmonella enterica serovar Typhimurium.
Iron is an essential element for the survival of living cells. However, excess iron is toxic, and its uptake is exquisitely regulated by the ferric uptake regulator, Fur. In Salmonella, the Salmonella pathogenicity island 1 (SPI-1) encodes a type three secretion system, which is required for invasion of host epithelial cells in the small intestine. A major activator of SPI-1 is HilA, which is encoded within SPI-1. One known regulator of hilA is Fur. The mechanism of hilA regulation by Fur is unknown. We report here that Fur is required for virulence in Salmonella enterica serovar Typhimurium and that Fur is required for the activation of hilA, as well as of other HilA-dependent genes, invF and sipC. The Fur-dependent regulation of hilA was independent of PhoP, a known repressor of hilA. Instead, the expression of the gene coding for the histone-like protein, hns, was significantly derepressed in the fur mutant. Indeed, the activation of hilA by Fur was dependent on 28 nucleotides located upstream of hns. Moreover, we used chromatin immunoprecipitation to show that Fur bound, in vivo, to the upstream region of hns in a metal-dependent fashion. Finally, deletion of fur in an hns mutant resulted in Fur-independent activation of hilA. In conclusion, Fur activates hilA by repressing the expression of hns.
not annotated - annotated - LINNAEUS only
MexT regulates the type III secretion system through MexS and PtrC in Pseudomonas aeruginosa.
The type III secretion system (T3SS) is the most important virulence factor in Pseudomonas aeruginosa, and its expression level varies in different isolates. We studied the molecular basis for such differences in two laboratory strains, PAK and PAO1. A chromosomal clone library from the high-T3SS-producer strain PAK was introduced into the low-producer strain PAO1, and we found that a mexS gene from PAK confers high T3SS expression in the PAO1 background. Further tests demonstrated that both mexS and its neighboring mexT gene are required for the repression of the T3SS in PAO1, while the PAK genome encodes a defective MexS, accounting for the derepression of the T3SS in PAK and the dominant negative effect when it is introduced into PAO1. MexS is a probable oxidoreductase whose expression is dependent on MexT, a LysR-type transcriptional regulator. Various genetic data support the idea that MexS modulates the transcriptional regulator function of MexT. In searching for the MexT-dependent repressor of the T3SS, a small gene product of PA2486 (ptrC) was found effective in suppressing the T3SS upon overexpression. However, deletion of ptrC in the PAO1 background did not result in derepression of the T3SS, indicating the presence of another repressor for the T3SS. Interestingly, overexpression of functional mexS alone was sufficient to repress T3SS even in the absence of MexT, suggesting that MexS is another mediator of MexT-dependent T3SS repression. Overexpression of mexS alone had no effect on the well-known MexT-dependent genes, including those encoding MexEF efflux pump, elastase, and pyocyanin, indicating alternative regulatory mechanisms. A model has been proposed for the MexS/MexT-mediated regulation of the T3SS, the MexEF efflux pump, and the production of elastase and pyocyanin.
not annotated - annotated - LINNAEUS only
Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8.
Achromobacter xylosoxidans strain A8 was isolated from soil contaminated with polychlorinated biphenyls. It can use 2-chlorobenzoate and 2,5-dichlorobenzoate as sole sources of carbon and energy. This property makes it a good starting microorganism for further development toward a bioremediation tool. The genome of A. xylosoxidans consists of a 7-Mb chromosome and two large plasmids (98 kb and 248 kb). Besides genes for the utilization of xenobiotic organic substrates, it contains genes associated with pathogenesis, toxin production, and resistance. Here, we report the complete genome sequence.
not annotated - annotated - LINNAEUS only
Complete genome sequences of three Erwinia amylovora phages isolated in north america and a bacteriophage induced from an Erwinia tasmaniensis strain.
Fire blight, a plant disease of economic importance caused by Erwinia amylovora, may be controlled by the application of bacteriophages. Here, we provide the complete genome sequences and the annotation of three E. amylovora-specific phages isolated in North America and genomic information about a bacteriophage induced by mitomycin C treatment of an Erwinia tasmaniensis strain that is antagonistic for E. amylovora. The American phages resemble two already-described viral genomes, whereas the E. tasmaniensis phage displays a singular genomic sequence in BLAST searches.
not annotated - annotated - LINNAEUS only
Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli.
Three paralogous transcriptional activators MarA, SoxS, and Rob, activate > 40 Escherichia coli promoters. To understand why MarA does not activate certain promoters as strongly as SoxS, we compared MarA, MarA mutants, and SoxS for their abilities to activate 16 promoters and to bind their cognate marbox binding sites. Replacement of the MarA glutamic acid residue 89 with alanine greatly increased the marbox binding and activation of many class I promoters. Like cells constitutive for SoxS, cells expressing the MarA with the E89A mutation were more resistant to superoxides than those harboring WT MarA. The activities of several other E89 substitutions ranked as follows: E89A > E89G > E89V > WT > E89D. Increased binding and activation occurred only at class I promoters when the 12th base of the promoter's marbox (a position at which there is no known interaction between the marbox and MarA) was not a T residue. Furthermore, WT MarA binding to a synthetic marbox in vitro was enhanced when the phosphate group between positions 12 and 13 was eliminated on one strand. The results demonstrate that relatively minor changes in a single amino acid side chain (e.g., alanine to valine or glutamic acid to aspartic acid) can strongly influence activity despite any evidence that the side chain is involved in positive interactions with either DNA or RNA polymerase. We present a model which attributes the differences in binding and activation to the interference between the Beta- and gamma-carbons of the amino acid at position 89 and the phosphate group between positions 12 and 13.
not annotated - annotated - LINNAEUS only
A model-driven approach to quantify migration patterns: individual, regional and yearly differences.
1. Animal migration has long intrigued scientists and wildlife managers alike, yet migratory species face increasing challenges because of habitat fragmentation, climate change and over-exploitation. Central to the understanding migratory species is the objective discrimination between migratory and nonmigratory individuals in a given population, quantifying the timing, duration and distance of migration and the ability to predict migratory movements. 2. Here, we propose a uniform statistical framework to (i) separate migration from other movement behaviours, (ii) quantify migration parameters without the need for arbitrary cut-off criteria and (iii) test predictability across individuals, time and space. 3. We first validated our novel approach by simulating data based on established theoretical movement patterns. We then formulated the expected shapes of squared displacement patterns as nonlinear models for a suite of movement behaviours to test the ability of our method to distinguish between migratory movement and other movement types. 4. We then tested our approached empirically using 108 wild Global Positioning System (GPS)-collared moose Alces alces in Scandinavia as a study system because they exhibit a wide range of movement behaviours, including resident, migrating and dispersing individuals, within the same population. Applying our approach showed that 87% and 67% of our Swedish and Norwegian subpopulations, respectively, can be classified as migratory. 5. Using nonlinear mixed effects models for all migratory individuals we showed that the distance, timing and duration of migration differed between the sexes and between years, with additional individual differences accounting for a large part of the variation in the distance of migration but not in the timing or duration. Overall, the model explained most of the variation (92%) and also had high predictive power for the same individuals over time (69%) as well as between study populations (74%). 6. The high predictive ability of the approach suggests that it can help increase our understanding of the drivers of migration and could provide key quantitative information for understanding and managing a broad range of migratory species.
not annotated - annotated - LINNAEUS only
Citrate uptake in exchange with intermediates in the citrate metabolic pathway in Lactococcus lactis IL1403.
Carbohydrate/citrate cometabolism in Lactococcus lactis results in the formation of the flavor compound acetoin. Resting cells of strain IL1403(pFL3) rapidly consumed citrate while producing acetoin when substoichiometric concentrations of glucose or l-lactate were present. A proton motive force was generated by electrogenic exchange of citrate and lactate catalyzed by the citrate transporter CitP and proton consumption in decarboxylation reactions in the pathway. In the absence of glucose or l-lactate, citrate consumption was biphasic. During the first phase, hardly any citrate was consumed. In the second phase, citrate was converted rapidly, but without the formation of acetoin. Instead, significant amounts of the intermediates pyruvate and alpha-acetolactate, and the end product acetate, were excreted from the cells. It is shown that the intermediates and acetate are excreted in exchange with the uptake of citrate catalyzed by CitP. The availability of exchangeable substrates in the cytoplasm determines both the rate of citrate consumption and the end product profile. It follows that citrate metabolism in L. lactis IL1403(pFL3) splits up in two routes after the formation of pyruvate, one the well-characterized route yielding acetoin and the other a new route yielding acetate. The flux distribution between the two branches changes from 85:15 in the presence of l-lactate to 30:70 in the presence of pyruvate. The proton motive force generated was greatest in the presence of l-lactate and zero in the presence of pyruvate, suggesting that the pathway to acetate does not generate proton motive force.
not annotated - annotated - LINNAEUS only
Interbacterial macromolecular transfer by the Campylobacter fetus subsp. venerealis type IV secretion system.
We report here the first demonstration of intra- and interspecies conjugative plasmid DNA transfer for Campylobacter fetus. Gene regions carried by a Campylobacter coli plasmid were identified that are sufficient for conjugative mobilization to Escherichia coli and C. fetus recipients. A broader functional range is predicted. Efficient DNA transfer involves the virB9 and virD4 genes of the type IV bacterial secretion system encoded by a pathogenicity island of C. fetus subsp. venerealis. Complementation of these phenotypes from expression constructions based on the promoter of the C. fetus surface antigen protein (sap) locus was temperature dependent, and a temperature regulation of the sap promoter was subsequently confirmed under laboratory conditions. Gene transfer was sensitive to surface or entry exclusion functions in potential recipient cells carrying IncPalpha plasmid RP4 implying functional relatedness to C. fetus proteins. The virB/virD4 locus is also known to be involved in bacterial invasion and killing of cultured human cells in vitro. Whether specifically secreted effector proteins contribute to host colonization and infection activities is currently unknown. Two putative effector proteins carrying an FIC domain conserved in a few bacterial type III and type IV secreted proteins of pathogens were analyzed for secretion by the C. fetus or heterologous conjugative systems. No evidence for interbacterial translocation of the Fic proteins was found.
not annotated - annotated - LINNAEUS only
Canopy connectivity and the availability of diverse nesting resources affect species coexistence in arboreal ants.
1. Arboreal ants are both diverse and ecologically dominant in the tropics. Such ecologically important groups are likely to be particularly useful in ongoing empirical efforts to understand the processes that regulate species diversity and coexistence. 2. Our study addresses how access to tree-based resources and the diversity of pre-existing nesting cavities affect species diversity and coexistence in tropical arboreal ant assemblages. We focus on assemblage-level responses to these variables at local scales. We first surveyed arboreal ant diversity across three naturally occurring levels of canopy connectivity and a gradient of tree size. We then conducted whole-tree experimental manipulations of canopy connectivity and the diversity of cavity entrance sizes. All work was conducted in the Brazilian savanna or 'cerrado'. 3. Our survey suggested that species richness was equivalent among levels of connectivity. However, there was a consistent trend of lower species density with low canopy connectivity. This was confirmed at the scale of individual trees, with low-connectivity trees having significantly fewer species across all tree sizes. Our experiment demonstrated directly that low canopy connectivity results in significantly fewer species coexisting per tree. 4. A diverse array of cavity entrance sizes did not significantly increase overall species per tree. Nevertheless, cavity diversity did significantly increase the species using new cavities on each tree, the species per tree unique to new cavities, total species using new cavities, and total cavity use. The populations of occupied cavities were consistent with newly founded colonies and new nests of established colonies from other trees. Cavity diversity thus appears to greatly affect new colony founding and colony growth. 5. These results contribute strong evidence that greater resource access and greater cavity diversity have positive effects on species coexistence in local arboreal ant assemblages. More generally, these positive effects are broadly consistent with niche differentiation promoting local species coexistence in diverse arboreal ant assemblages. The contributions of this study to the understanding of the processes of species coexistence are discussed, along with the potential of the focal system for future work on this issue.
not annotated - annotated - LINNAEUS only
Ontogeny and leaf gas exchange mediate the carbon isotopic signature of herbaceous plants.
Values (Delta(i)) predicted by a simplified photosynthetic discrimination model, based only on diffusion through air followed by carboxylation, are often used to infer ecological conditions from the ^1^3C signature of plant organs (delta^1^3C(p)). Recent studies showed that additional isotope discrimination (d that includes mesophyll conductance, photorespiration and day respiration, and post-carboxylation discrimination) can strongly affect delta^1^3C(p); however, little is known about its variability during plant ontogeny for different species. Effect of ontogeny on leaf gas exchange rates, Delta(i) , observed discrimination (Delta(p)) and d in leaf, phloem and root of seven herbaceous species at three ontogenetic stages were investigated under controlled conditions. Functional group identity and ontogeny significantly affected Delta(i) and Delta(p). However, predicted Delta(i) did not match Delta(p). d, strongly affected by functional group identity and ontogeny, varied by up to 14 %. d scaled tightly with stomatal conductance, suggesting complex controls including changes in mesophyll conductance. The magnitude of the changes in delta^1^3C(p) due to ontogeny was similar to that due to environmental factors reported in other studies. d and ontogeny should, therefore, be considered in ecosystem studies, integrated in ecosystem models using delta^1^3C(p) and limit the applicability of delta^1^3C(leaf) as a proxy for water-use efficiency in herbaceous plants.
not annotated - annotated - LINNAEUS only
The pH regulatory factor Pac1 regulates Tri gene expression and trichothecene production in Fusarium graminearum.
Fungi manage the adaptation to extra-cellular pH through the PacC transcription factor, a key component of the pH regulatory system. PacC regulates the production of various secondary metabolites in filamentous fungi. In the important cereal pathogen Fusarium graminearum, the production of trichothecene is induced only under acidic pH conditions. Here, we examined the role of the PacC homologue from F. graminearum, FgPac1, on the regulation of trichothecene production. An FgDeltaPac1 deletion mutant was constructed in F. graminearum which showed a reduced development under neutral and alkaline pH, increased sensitivity to H(2)O(2) and an earlier Tri gene induction and toxin accumulation at acidic pH. A strain expressing the FgPac1(c) constitutively active form of Pac1 exhibited a strongly repressed Tri gene expression and reduced toxin accumulation at acidic pH. These results demonstrate that Pac1 negatively regulates Tri gene expression and toxin production in F. graminearum.
not annotated - annotated - LINNAEUS only
Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease.
Since the isolation of HIV, multiple transmissions are thought to have occurred between man and other old-world primates. Assessment of samples from apes and human beings with African equatorial forest ancestry has traced the origin of HIV-1 to chimpanzees, and dated its most recent common ancestor to 1908. The evolution of HIV-1 has been rapid, which has resulted in a complex classification, worldwide spread, and intermixing of strains; at least 48 circulating recombinant forms are currently identified. In addition to posing a nearly insurmountable challenge for diagnosis, treatment, vaccine development, and prevention, this extreme and divergent evolution has led to differences in virulence between HIV-1 groups, subtypes, or both. Coincidental changes in human migration in the Congo river basin also affected spread of disease. Research over the past 25 years and advances in genomic sequencing methods, such as deep DNA sequencing, have greatly improved understanding and analysis of the thousands to millions of full infectious HIV-1 genomes.
not annotated - annotated - LINNAEUS only
A caffeyl-coenzyme A synthetase initiates caffeate activation prior to caffeate reduction in the acetogenic bacterium Acetobacterium woodii.
The anaerobic acetogenic bacterium Acetobacterium woodii couples the reduction of caffeate with electrons derived from hydrogen to the synthesis of ATP by a chemiosmotic mechanism using sodium ions as coupling ions, but the enzymes involved remain to be established. Previously, the electron transfer flavoproteins EtfA and EtfB were found to be involved in caffeate respiration. By inverse PCR, we identified three genes upstream of etfA and etfB: carA, carB, and carC. carA encodes a potential coenzyme A (CoA) transferase, carB an acyl-CoA synthetase, and carC an acyl-CoA dehydrogenase. carA, -B, and -C are located together with etfA/carE and etfB/carD on one polycistronic message, indicating that CarA, CarB, and CarC are also part of the caffeate respiration pathway. The genetic data suggest an initial ATP-dependent activation of caffeate by CarB. To prove the proposed function of CarB, the protein was overproduced in Escherichia coli, and the recombinant protein was purified. Purified CarB activates caffeate to caffeyl-CoA in an ATP- and CoA-dependent reaction. The enzyme has broad pH and temperature optima and requires K(+) for activity. In addition to caffeate, it can use p-coumarate, ferulate, and cinnamate as substrates, with 50, 15, and 9%, respectively, of the activity obtained with caffeate. Expression of the car operon is induced not only by caffeate, p-coumarate, ferulate, and cinnamate but also by sinapate. There is no induction by p-hydroxybenzoate or syringate.
not annotated - annotated - LINNAEUS only
Complete genome sequence of Burkholderia rhizoxinica, an Endosymbiont of Rhizopus microsporus.
Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic fungus Rhizopus microsporus. The vertically transmitted endosymbiont not only delivers the antimitotic macrolide rhizoxin to its host but is also essential for vegetative spore formation of the fungus. To shed light on the genetic equipment of this model organism, we sequenced the whole genome of B. rhizoxinica HKI 0454, thus providing the first genomic insight into an intracellular mutualist of a fungal species. The 3.75-Mb genome consists of a chromosome and two strain-specific plasmids. The primary metabolism appears to be specialized for the uptake of fungal metabolites. Besides the rhizoxin biosynthesis gene cluster, there are 14 loci coding for nonribosomal peptide synthetase (NRPS) assembly lines, which represent novel targets for genomic mining of cryptic natural products. Furthermore, the endosymbionts are equipped with a repertoire of virulence-related factors, which can now be studied to elucidate molecular mechanisms underlying bacterial-fungal interaction.
not annotated - annotated - LINNAEUS only
Network topology: patterns and mechanisms in plant-herbivore and host-parasitoid food webs.
1. Biological communities are organized in complex interaction networks such as food webs, which topology appears to be non-random. Gradients, compartments, nested subsets and even combinations of these structures have been shown in bipartite networks. However, in most studies only one pattern is tested against randomness and mechanistic hypotheses are generally lacking. 2. Here we examined the topology of regional, coexisting plant-herbivore and host-parasitoid food webs to discriminate between the mentioned network patterns. We also evaluated the role of species body size, local abundance, regional frequency and phylogeny as determinants of network topology. 3. We found both food webs to be compartmented, with interaction range boundaries imposed by host phylogeny. Species degree within compartments was mostly related to their regional frequency and local abundance. Only one compartment showed an internal nested structure in the distribution of interactions between species, but species position within this compartment was unrelated to species size or abundance. 4. These results suggest that compartmentalization may be more common than previously considered, and that network structure is a result of multiple, hierarchical, non-exclusive processes.
not annotated - annotated - LINNAEUS only
Gel-based mass spectrometric and computational approaches to the mitochondrial proteome of Neurospora.
We have used gel electrophoretic techniques including isoelectric focusing, blue native, acid-urea, 16-benzyldimethyl-n-hexadecylammonium chloride or SDS first dimensions and SDS Laemmli or tricine second dimensions to separate the proteins from highly-purified Neurospora mitochondria and sub-mitochondrial fractions (membrane, soluble, protein complexes and ribonucleoproteins). The products of 260 genes, many of them in multiple processed or modified forms, were identified by MALDI-TOF mass spectrometry. This work confirms the existence, expression, and mitochondrial localization of the products of 55 Neurospora genes previously annotated only as predicted or hypothetical, and of 101 genes not identified in previous mass spectrometry studies. Combined with previous mass spectrometry studies, and re-evaluation of genome annotations, we have compiled a curated list of 358 proteins identified in proteomic studies that are likely to be bona fide mitochondrial proteins plus 80 other identified proteins that may be mitochondrial. Literature data mining and computational predictions suggest that Neurospora mitochondria also contain another 299 proteins not yet identified in proteomics projects. Taken together, these data suggest that the products of at least 738 genes comprise the Neurospora mitochondrial proteome.
not annotated - annotated - LINNAEUS only
Sequenced dermatophyte strains: growth rate, conidiation, drug susceptibilities, and virulence in an invertebrate model.
Although dermatophytes are the most common cause of fungal infections in the world, their basic biology is not well understood. The recent sequencing and annotation of the genomes of five representative dermatophyte species allows for the creation of hypotheses as to how they cause disease and have adapted to their distinct environments. An understanding of the microbiology of these strains will be essential for testing these hypotheses. This study is the first to generally characterize these five sequenced strains of dermatophytes for their microbiological aspects. We measured the growth rate on solid medium and found differences between species, with Microsporum gypseum CBS118893 having the fastest growth and Trichophyton rubrum CBS118892 the slowest. We also compared different media for conidia production and found that the highest numbers of conidia were produced when dermatophytes were grown on MAT agar. We determined the Minimum Inhibitory Concentration (MIC) of nine antifungal agents and confirmed susceptibility to antifungals commonly used as selectable markers. Finally, we tested virulence in the Galleria mellonella (wax moth) larvae model but found the results variable. These results increase our understanding of the microbiology and molecular biology of these dermatophyte strains and will be of use in advancing hypothesis-driven research about dermatophytes.
not annotated - annotated - LINNAEUS only
Relating the physical properties of Pseudomonas aeruginosa lipopolysaccharides to virulence by atomic force microscopy.
Lipopolysaccharides (LPS) are an important class of macromolecules that are components of the outer membrane of Gram-negative bacteria such as Pseudomonas aeruginosa. P. aeruginosa contains two different sugar chains, the homopolymer common antigen (A band) and the heteropolymer O antigen (B band), which impart serospecificity. The characteristics of LPS are generally assessed after isolation rather than in the context of whole bacteria. Here we used atomic force microscopy (AFM) to probe the physical properties of the LPS of P. aeruginosa strain PA103 (serogroup O11) in situ. This strain contains a mixture of long and very long polymers of O antigen, regulated by two different genes. For this analysis, we studied the wild-type strain and four mutants, DeltaWzz1 (producing only very long LPS), DeltaWzz2 (producing only long LPS), DDeltaM (with both the wzz1 and wzz2 genes deleted), and Wzy::GM (producing an LPS core oligosaccharide plus one unit of O antigen). Forces of adhesion between the LPS on these strains and the silicon nitride AFM tip were measured, and the Alexander and de Gennes model of steric repulsion between a flat surface and a polymer brush was used to calculate the LPS layer thickness (which we refer to as length), compressibility, and spacing between the individual molecules. LPS chains were longest for the wild-type strain and DeltaWzz1, at 170.6 and 212.4 nm, respectively, and these values were not statistically significantly different from one another. Wzy::GM and DDeltaM have reduced LPS lengths, at 34.6 and 37.7 nm, respectively. Adhesion forces were not correlated with LPS length, but a relationship between adhesion force and bacterial pathogenicity was found in a mouse acute pneumonia model of infection. The adhesion forces with the AFM probe were lower for strains with LPS mutations, suggesting that the wild-type strain is optimized for maximal adhesion. Our research contributes to further understanding of the role of LPS in the adhesion and virulence of P. aeruginosa.
not annotated - annotated - LINNAEUS only
The minor pilin subunit Sgp2 is necessary for assembly of the pilus encoded by the srtG cluster of Streptococcus suis.
Gram-positive pili are composed of covalently bound pilin subunits whose assembly is mediated via a pilus-specific sortase(s). Major subunits constitute the pilus backbone and are therefore essential for pilus formation. Minor subunits are also incorporated into the pilus, but they are considered to be dispensable for backbone formation. The srtG cluster is one of the putative pilus gene clusters identified in the major swine pathogen Streptococcus suis. It consists of one sortase gene (srtG) and two putative pilin subunit genes (sgp1 and sgp2). In this study, by constructing mutants for each of the genes in the cluster and by both immunoblotting and immunogold electron microscopic analysis with antibodies against Sgp1 and Sgp2, we found that the srtG cluster mediates the expression of pilus-like structures in S. suis strain 89/1591. In this pilus, Sgp1 forms the backbone, whereas Sgp2 is incorporated as the minor subunit. In accordance with the current model of pilus assembly by Gram-positive organisms, the major subunit Sgp1 was indispensable for backbone formation and the cognate sortase SrtG mediated the polymerization of both subunits. However, unlike other well-characterized Gram-positive bacterial pili, the minor subunit Sgp2 was required for polymerization of the major subunit Sgp1. Because Sgp2 homologues are encoded in several other Gram-positive bacterial pilus gene clusters, in some types of pili, minor pilin subunits may contribute to backbone formation by a novel mechanism.
not annotated - annotated - LINNAEUS only
Growth and reproductive costs of larval defence in the aposematic lepidopteran Pieris brassicae.
1. Utilization of plant secondary compounds for antipredator defence is common in immature herbivorous insects. Such defences may incur a cost to the animal, either in terms of survival, growth rate or in the reproductive success. 2. A common defence in lepidopterans is the regurgitation of semi-digested material containing the defensive compounds of the food plant, a defence which has led to gut specialization in this order. Regurgitation is often swift in response to cuticular stimulation and deters predators from consuming or parasitizing the larva. The loss of food and other gut material seems likely to impact on fitness, but evidence is lacking. 3. Here, we raised larvae of the common crop pest Pieris brassicae on commercial cabbage leaves, simulated predator attacks throughout the larval period, and measured life-history responses. 4. We found that the probability of survival to pupation decreased with increasing frequency of attacks, but this was because of regurgitation rather than the stimulation itself. There was a growth cost to the defence such that the more regurgitant that individuals produced over the growth period, the smaller they were at pupation. 5. The number of mature eggs in adult females was positively related to pupal mass, but this relationship was only found when individuals were not subjected to a high frequency of predator simulation. This suggests that there might be cryptic fitness costs to common defensive responses that are paid despite apparent growth rate being maintained. 6. Our results demonstrate a clear life-history cost of an antipredator defence in a model pest species and show that under certain conditions, such as high predation threat, the expected relationship between female body size and potential fecundity can be disrupted.
not annotated - annotated - LINNAEUS only
Huntington's disease: from molecular pathogenesis to clinical treatment.
Huntington's disease is a progressive, fatal, neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin gene, which encodes an abnormally long polyglutamine repeat in the huntingtin protein. Huntington's disease has served as a model for the study of other more common neurodegenerative disorders, such as Alzheimer's disease and Parkinson's disease. These disorders all share features including: delayed onset; selective neuronal vulnerability, despite widespread expression of disease-related proteins during the whole lifetime; abnormal protein processing and aggregation; and cellular toxic effects involving both cell autonomous and cell-cell interaction mechanisms. Pathogenic pathways of Huntington's disease are beginning to be unravelled, offering targets for treatments. Additionally, predictive genetic testing and findings of neuroimaging studies show that, as in some other neurodegenerative disorders, neurodegeneration in affected individuals begins many years before onset of diagnosable signs and symptoms of Huntington's disease, and it is accompanied by subtle cognitive, motor, and psychiatric changes (so-called prodromal disease). Thus, Huntington's disease is also emerging as a model for strategies to develop therapeutic interventions, not only to slow progression of manifest disease but also to delay, or ideally prevent, its onset.
not annotated - annotated - LINNAEUS only
Natural history and intragenomic dynamics of the Transib transposon Hztransib in the cotton bollworm Helicoverpa zea.
Hztransib, recently identified from Helicoverpa zea, represents the first intact and transcriptionally active Transib element. Its open reading frame was detected in Helicoverpa armigera, from which H. zea evolved, and in Helicoverpa assulta, the common ancestor of H. zea and H. armigera, but its remaining parts were found only in H. armigera. Thirty-nine Hztransib insertion sites, all of which are polymorphic, were detected from eight populations of H. zea. Out of the 39 insertion sites, 35 were not frequently occupied, with 1-33 occurrences in a total of 128 individuals from the eight populations (16 larvae per population). Its copy number ranged from 5.8 to 14.2 per individual, with putative intact copies always more abundant than internally deleted ones. Taking this evidence together, Hztransib probably transferred to H. zea from H. armigera and most likely still retains its capacity to maintain structural integrity, increase copy number and remobilize in H. zea.
not annotated - annotated - LINNAEUS only
Identification of an extracellular polysaccharide network essential for cytochrome anchoring and biofilm formation in Geobacter sulfurreducens.
Transposon insertions in Geobacter sulfurreducens GSU1501, part of an ATP-dependent exporter within an operon of polysaccharide biosynthesis genes, were previously shown to eliminate insoluble Fe(III) reduction and use of an electrode as an electron acceptor. Replacement of GSU1501 with a kanamycin resistance cassette produced a similarly defective mutant, which could be partially complemented by expression of GSU1500 to GSU1505 in trans. The Delta1501 mutant demonstrated limited cell-cell agglutination, enhanced attachment to negatively charged surfaces, and poor attachment to positively charged poly-d-lysine- or Fe(III)-coated surfaces. Wild-type and mutant cells attached to graphite electrodes, but when electrodes were poised at an oxidizing potential inducing a positive surface charge (+0.24 V versus the standard hydrogen electrode [SHE]), Delta1501 mutant cells detached. Scanning electron microscopy revealed fibrils surrounding wild-type G. sulfurreducens which were absent from the Delta1501 mutant. Similar amounts of type IV pili and pilus-associated cytochromes were detected on both cell types, but shearing released a stable matrix of c-type cytochromes and other proteins bound to polysaccharides. The matrix from the mutant contained 60% less sugar and was nearly devoid of c-type cytochromes such as OmcZ. The addition of wild-type extracellular matrix to Delta1501 cultures restored agglutination and Fe(III) reduction. The polysaccharide binding dye Congo red preferentially bound wild-type cells and extracellular matrix material over mutant cells, and Congo red inhibited agglutination and Fe(III) reduction by wild-type cells. These results demonstrate a crucial role for the xap (extracellular anchoring polysaccharide) locus in metal oxide attachment, cell-cell agglutination, and localization of essential cytochromes beyond the Geobacter outer membrane.
not annotated - annotated - LINNAEUS only
Hyphal and cytoskeleton polarization in Tuber melanosporum: a genomic and cellular analysis.
Filamentous polarized growth involves a series of events including polarization of the cytoskeleton to selected growth sites, and the transport of secretory vesicles containing the components required for growth. The availability of fungal genome sequences has recently led to the identification of a large number of proteins involved in these processes. We have explored the Tuber melanosporum genome sequence by searching for homologs of genes known to play crucial roles in the morphogenesis and cell polarity of yeasts and filamentous fungi. One hundred and forty-nine genes have been identified and functionally grouped according to the deduced amino acid sequences (44 genes involved in cell polarity/morphogenesis, 39 belonging to the actin cytoskeleton and 66 involved in membrane dynamics, septation and exocytosis). A detailed gene annotation has shown that most components of the cell polarity machinery, morphogenesis and cytoskeleton found in yeasts and filamentous fungi are conserved, although the degree of similarity varies from strong to weak. Microscopic analysis of quick-frozen truffle hyphae detected the characteristic subcellular components of the hyphal tip in septate filamentous fungi, while transcript profiles revealed a moderately variable pattern during the biological cycle.
not annotated - annotated - LINNAEUS only
Proteomics of cryoprotective dehydration in Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola).
The Arctic springtail, Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola), is one of the few organisms known to survive the extreme stresses of its environment by using cryoprotective dehydration. We have undertaken a proteomics study comparing M. arctica, acclimated at -2^0C, the temperature known to induce the production of the anhydroprotectant trehalose in this species, and -6^0C, the temperature at which trehalose expression plateaus, against control animals acclimated at +5^0C. Using difference gel electrophoresis, and liquid chromatography tandem mass spectrometry, we identified three categories of differentially expressed proteins with specific functions, up-regulated in both the -2^0C and -6^0C animals, that were involved in metabolism, membrane transport and protein folding. Proteins involved in cytoskeleton organisation were only up-regulated in the -6^0C animals.
not annotated - annotated - LINNAEUS only
The pyrokinin/ pheromone biosynthesis-activating neuropeptide (PBAN) family of peptides and their receptors in Insecta: evolutionary trace indicates potential receptor ligand-binding domains.
The pyrokinin/pheromone biosynthesis-activating neuropeptide (PBAN) family of G-protein-coupled receptors and their ligands have been identified in various insects. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates, among other functions, pheromone production in moths which indicates the pleiotropic nature of these peptides. Based on the alignment of annotated genomic sequences, the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors of vertebrates. In our study, evolutionary trace (ET) analysis on the insect receptor sequences was conducted to predict the putative ligand recognition and binding sites. The ET analysis of four class-specific receptors indicated several amino acid residues that are conserved in the transmembrane domains. The receptor extracellular domains exhibit several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding.
not annotated - annotated - LINNAEUS only
acon-3, the Neurospora crassa ortholog of the developmental modifier, medA, complements the conidiation defect of the Aspergillus nidulans mutant.
Aspergillus nidulans and Neurospora crassa are ascomycetes that produce asexual spores through morphologically distinct processes. MedA, a protein with unknown function, is required for normal asexual and sexual development in A. nidulans. We determined that the N. crassa ortholog of medA is acon-3, a gene required for early conidiophore development and female fertility. To test hypotheses about the evolutionary origins of asexual development in distinct fungal lineages it is important to understand the degree of conservation of developmental regulators. The amino acid sequences of A. nidulans MedA and N. crassa ACON-3 shared 37% identity and 51% similarity. acon-3 is induced at late time points of conidiation. In contrast, medA is constitutively expressed and MedA protein localizes to nuclei in all tissue types. Nonetheless, expression of acon-3 using its native promoter complemented the conidiation defects of the A. nidulans DeltamedA and medA15 mutants. We conclude that the biochemical activity of the medA orthologs is conserved for conidiation.
not annotated - annotated - LINNAEUS only
Towards achievement of universal health care in India by 2020: a call to action.
To sustain the positive economic trajectory that India has had during the past decade, and to honour the fundamental right of all citizens to adequate health care, the health of all Indian people has to be given the highest priority in public policy. We propose the creation of the Integrated National Health System in India through provision of universal health insurance, establishment of autonomous organisations to enable accountable and evidence-based good-quality health-care practices and development of appropriately trained human resources, the restructuring of health governance to make it coordinated and decentralised, and legislation of health entitlement for all Indian people. The key characteristics of our proposal are to strengthen the public health system as the primary provider of promotive, preventive, and curative health services in India, to improve quality and reduce the out-of-pocket expenditure on health care through a well regulated integration of the private sector within the national health-care system. Dialogue and consensus building among the stakeholders in the government, civil society, and private sector are the next steps to formalise the actions needed and to monitor their achievement. In our call to action, we propose that India must achieve health care for all by 2020.
not annotated - annotated - LINNAEUS only
Financing health care for all: challenges and opportunities.
India's health financing system is a cause of and an exacerbating factor in the challenges of health inequity, inadequate availability and reach, unequal access, and poor-quality and costly health-care services. Low per person spending on health and insufficient public expenditure result in one of the highest proportions of private out-of-pocket expenses in the world. Citizens receive low value for money in the public and the private sectors. Financial protection against medical expenditures is far from universal with only 10% of the population having medical insurance. The Government of India has made a commitment to increase public spending on health from less than 1% to 3% of the gross domestic product during the next few years. Increased public funding combined with flexibility of financial transfers from centre to state can greatly improve the performance of state-operated public systems. Enhanced public spending can be used to introduce universal medical insurance that can help to substantially reduce the burden of private out-of-pocket expenditures on health. Increased public spending can also contribute to quality assurance in the public and private sectors through effective regulation and oversight. In addition to an increase in public expenditures on health, the Government of India will, however, need to introduce specific methods to contain costs, improve the efficiency of spending, increase accountability, and monitor the effect of expenditures on health.
not annotated - annotated - LINNAEUS only
Continuing challenge of infectious diseases in India.
In India, the range and burden of infectious diseases are enormous. The administrative responsibilities of the health system are shared between the central (federal) and state governments. Control of diseases and outbreaks is the responsibility of the central Ministry of Health, which lacks a formal public health department for this purpose. Tuberculosis, malaria, filariasis, visceral leishmaniasis, leprosy, HIV infection, and childhood cluster of vaccine-preventable diseases are given priority for control through centrally managed vertical programmes. Control of HIV infection and leprosy, but not of tuberculosis, seems to be on track. Early success of malaria control was not sustained, and visceral leishmaniasis prevalence has increased. Inadequate containment of the vector has resulted in recurrent outbreaks of dengue fever and re-emergence of Chikungunya virus disease and typhus fever. Other infectious diseases caused by faecally transmitted pathogens (enteric fevers, cholera, hepatitis Ahepatitis A and E viruses) and zoonoses (rabies, leptospirosis, anthrax) are not in the process of being systematically controlled. Big gaps in the surveillance and response system for infectious diseases need to be addressed. Replication of the model of vertical single-disease control for all infectious diseases will not be efficient or viable. India needs to rethink and revise its health policy to broaden the agenda of disease control. A comprehensive review and redesign of the health system is needed urgently to ensure equity and quality in health care. We recommend the creation of a functional public health infrastructure that is shared between central and state governments, with professional leadership and a formally trained public health cadre of personnel who manage an integrated control mechanism of diseases in districts that includes infectious and non-infectious diseases, and injuries.
not annotated - annotated - LINNAEUS only
ATP citrate lyase is required for normal sexual and asexual development in Gibberella zeae.
Adenosine triphosphate (ATP) citrate lyase (ACL) is a key enzyme in the production of cytosolic acetyl-CoA, which is crucial for de novo lipid synthesis and histone acetylation in mammalian cells. In this study, we characterized the mechanistic roles of ACL in the homothallic ascomycete fungus Gibberella zeae, which causes Fusarium head blight in major cereal crops. Deletion of ACL in the fungus resulted in a complete loss of self and female fertility as well as a reduction in asexual reproduction, virulence, and trichothecene production. When the wild-type strain was spermatized with the ACL deletion mutants, they produced viable ascospores, however ascospore delimitation was not properly regulated. Although lipid synthesis was not affected by ACL deletion, histone acetylation was dramatically reduced in the ACL deletion mutants during sexual development, suggesting that the defects in sexual reproduction were caused by the reduction in histone acetylation. This study is the first report demonstrating a link between sexual development and ACL-mediated histone acetylation in fungi.
not annotated - annotated - LINNAEUS only
Expression of a Brassica napus heme oxygenase confers plant tolerance to mercury toxicity.
Plant heme oxygenases (HOs) regulate biosynthesis of phytochrome which accounts for photo-acceptance and -morphogenesis. Recent studies have demonstrated that plant HOs also regulate many other physiological processes including response to environmental stimuli. To elucidate the mechanism by which HOs regulate plant adaptation to heavy metal exposure, three novel HOs genes were isolated from rapeseed (Brassica napus) and their expression patterns were analysed. Alignment of deduced protein sequences revealed that the three BnHOs share high identity with their corresponding orthologos (AtHO1-3) from Arabidopsis. To investigate whether the BnHO regulates plant tolerance to Hg toxicity, we constructed B. napus transgenic plants overexpressing BnHO-1. Under Hg stress, the transgenic plants had 1.41-1.59 folds higher biomass than the untransformants. However, overexpression of BnHO-1 resulted in less accumulation of Hg in some lines of transformants than in untransformants. The transgenic plants show lower abundance of reactive oxygen species and attenuated oxidative injury compared with the untransgenic plants. We cloned the promoter sequences of BnHO-1 from B. napus. Analysis revealed that the 1119 bp fragment contains a conserved Cd responsive element (CdRE) and others responding to multiple environmental stimuli. Transient expression in tobacco leaves showed differential responses to heavy metals (Zn, Cu, Pb, Hg and Cd).
not annotated - annotated - LINNAEUS only
The rate-limiting step for CO(2) assimilation at different temperatures is influenced by the leaf nitrogen content in several C(3) crop species.
Effects of nitrogen (N) supply on the limiting step of CO(2) assimilation rate (A) at 380 mumol mol(-1) CO(2) concentration (A(380) ) at several leaf temperatures were studied in several crops, since N nutrition alters N allocation between photosynthetic components. Contents of leaf N, ribulose 1*5-bisphosphate carboxylase/oxygenase (Rubisco) and cytochrome f (cyt f) increased with increasing N supply, but the cyt f/Rubisco ratio decreased. Large leaf N content was linked to a high stomatal (g(s) ) and mesophyll conductance (g(m) ), but resulted in a lower intercellular (C(i) ) and chloroplast CO(2) concentration (C(c) ) because the increase in g(s) and g(m) was insufficient to compensate for change in A(380) . The A-C(c) response was used to estimate the maximum rate of RuBP carboxylation (V(cmax) ) and chloroplast electron transport (J(max) ). The J(max) /V(cmax) ratio decreased with reductions in leaf N content, which was consistent with the results of the cyt f/Rubisco ratio. Analysis using the C(3) photosynthesis model indicated that A(380) tended to be limited by RuBP carboxylation in plants grown at low N concentration, whereas it was limited by RuBP regeneration in plants grown at high N concentration. We conclude that the limiting step of A(380) depends on leaf N content and is mainly determined by N partitioning between Rubisco and electron transport components.
not annotated - annotated - LINNAEUS only
Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis.
The legume genus Lotus includes glycophytic forage crops and other species adapted to extreme environments, such as saline soils. Understanding salt tolerance mechanisms will contribute to the discovery of new traits which may enhance the breeding efforts towards improved performance of legumes in marginal agricultural environments. Here, we used a combination of ionomic and gas chromatography-mass spectrometry (GC-MS)-based metabolite profilings of complete shoots (pooling leaves, petioles and stems) to compare the extremophile Lotus creticus, adapted to highly saline coastal regions, and two cultivated glycophytic grassland forage species, Lotus corniculatus and Lotus tenuis. L. creticus exhibited better survival after exposure to long-term lethal salinity and was more efficient at excluding Cl- from the shoots than the glycophytes. In contrast, Na+ levels were higher in the extremophile under both control and salt stress, a trait often observed in halophytes. Ionomics demonstrated a differential rearrangement of shoot nutrient levels in the extremophile upon salt exposure. Metabolite profiling showed that responses to NaCl in L. creticus shoots were globally similar to those of the glycophytes, providing little evidence for metabolic pre-adaptation to salinity. This study is the first comparing salt acclimation responses between extremophile and non-extremophile legumes, and challenges the generalization of the metabolic salt pre-adaptation hypothesis.
not annotated - annotated - LINNAEUS only
The rise of chronic non-communicable diseases in southeast Asia: time for action.
Southeast Asia faces an epidemic of chronic non-communicable diseases, now responsible for 60% of deaths in the region. The problem stems from environmental factors that promote tobacco use, unhealthy diet, and inadequate physical activity. Disadvantaged populations are the hardest hit, with death rates inversely proportional to a country's gross national income. Families shoulder the financial burden, but entire economies suffer as well. Although attempts to control non-communicable diseases are increasing, more needs to be done. Health-care systems need to be redesigned to deliver chronic care that is founded on existing primary health-care facilities, but supported by good referral systems. Surveillance of key modifiable risk factors is needed to monitor the magnitude of the problem and to study the effects of interventions. All branches of government and all sectors of society have to get involved in establishing environments that are conducive to healthy living. The Association of Southeast Asian Nations is in a unique position to make a united stand against chronic non-communicable diseases in the region. Inaction will affect millions of lives-often, the lives of those who have the least.
not annotated - annotated - LINNAEUS only
Aberrant genome size and instability of Phytophthora ramorum oospore progenies.
The functionality of the sexual cycle in the heterothallic pathogen Phytophthora ramorum, causal agent of Sudden Oak Death, has recently been demonstrated. Sexual reproduction could create genotypic variation and increase the pathogen's ability to adapt to other host plants or changing environments. Genetic characterization using co-dominant microsatellite markers and flow cytometry of single-oospore progeny of crosses between a European A1 isolate and North American or European A2 isolates revealed a considerable number of non-Mendelian inheritance events. This includes inheritance of more than two alleles at a locus and non-inheritance of alleles from one parent at another locus. The progenies were mitotically unstable: zoospore and hyphal tip derivatives of the progenies showed genotypic rearrangements and phenotypic variation. Flow cytometry confirmed variation and instability in DNA content of the single-oospore progenies. This indicates that single-oospore progenies not only display aberrant genomic and phenotypic variation due to meiotic irregularities, but also extra variation as a result of post-meiotic genomic rearrangements.
not annotated - annotated - LINNAEUS only
Independent duplications of alpha-amylase in different strains of Aspergillus oryzae.
Aspergillus oryzae is a filamentous fungus that has arisen through the ancient domestication of Aspergillus flavus for making traditional oriental foods and beverages. In the many centuries A. oryzae has been used for fermenting the starch in rice to simple sugars, it has undergone selection for increased secretion of starch-degrading enzymes. In particular, all A. oryzae strains investigated thus far have two or more copies of a gene encoding alpha-amylase, whereas A. flavus has only one. Here we investigate the duplications leading to these copies in three A. oryzae strains. We find evidence of at least three separate duplications of alpha-amylase, an example of parallel evolution in a micro-organism under artificial selection. At least two of these duplications appear to be associated with activity of transposable elements of the Tc1/mariner class. Both involve a 9.1 kb element that terminates in inverted repeats, encodes a putative transposase and another putative protein of unknown function, and contains an unusual arrangement of four short internal imperfect repeats. Although "unusual Mariners" of this size have previously been identified in A. oryzae, Aspergillus fumigatus and Aspergillus nidulans, this is the first evidence we know of that at least some of them are active in modern times and that their activity can contribute to beneficial genetic changes.
not annotated - annotated - LINNAEUS only
Response of ecosystems to realistic extinction sequences.
Recent research suggests that effects of species loss on the structure and functioning of ecosystems will critically depend on the order with which species go extinct. However, there are few studies of the response of natural ecosystems to realistic extinction sequences. Using an extinction scenario based on the International Union for Conservation of Nature (IUCN) Red List, de Visser et al. sequentially deleted species from a topological model of the Serengeti food web. Under this scenario, large-bodied species like top predators and mega-herbivores go extinct first. The resulting changes in the trophic structure of the food web might affect the robustness of the ecosystem to future disturbances.
not annotated - annotated - LINNAEUS only
Host characteristics and environmental factors differentially drive the burden and pathogenicity of an ectoparasite: a multilevel causal analysis.
1. Understanding the ecological factors driving the burden and pathogenicity of parasites is challenging. Indeed, the dynamics of host-parasite interactions is driven by factors organized across nested hierarchical levels (e.g. hosts, localities), and indirect effects are expected owing to interactions between levels. 2. In this study, we combined Bayesian multilevel models, path analyses and a model selection procedure to account for these complexities and to decipher the relative effects of host- and environment-related factors on the burden and the pathogenicity of an ectoparasite (Tracheliastes polycolpus) on its fish host (Leuciscus leuciscus). We also tested the year-to-year consistency of the relationships linking these factors to the burden and the pathogenic effects of T. polycolpus. 3. We found significant relationships between the parasite burden and host-related factors: body length and age were positively related to parasite burden and heterozygous hosts displayed a higher parasite burden. In contrast, both host- and environment-related factors were linked to pathogenic effects. Pathogenicity was correlated negatively with host body length and positively with age; this illustrates that some factors (e.g. body length) showed inverse relationships with parasite burden and pathogenicity. Pathogenic effects were stronger in cooler upstream sites and where host density was lower. Path analyses revealed that these relationships between environment-related factors and pathogenic effects were direct and were not indirect relationships mediated by the host characteristics. Finally, we found that the strength and the shape of certain relationships were consistent across years, while they were clearly not for some others. 4. Our study illustrates that considering conjointly causal relationships among factors and the hierarchical structure of host-parasite interactions is appropriate for dissecting the complex links between hosts, parasites and their common environment.
not annotated - annotated - LINNAEUS only
Experimental evidence for emergent facilitation: promoting the existence of an invertebrate predator by killing its prey.
1. Recent theoretical insights have shown that predator species may help each other to persist by size-selective foraging on a shared prey. By feeding on a certain prey stage, a predator may induce a compensatory response in another stage of the same prey species, thereby favouring other predators; a phenomenon referred to as emergent facilitation. 2. To test whether emergent facilitation may occur in a natural system, we performed an enclosure experiment where we mimicked fish predation by selectively removing large zooplankton and subsequently following the response of the invertebrate predator Bythotrephes longimanus. 3. Positive responses to harvest were observed in the biomass of juvenile individuals of the dominant zooplankton Holopedium gibberum and in Bythotrephes densities. Hence, by removing large prey, we increased the biomass of small prey, i.e. stage-specific biomass overcompensation was present in the juvenile stage of Holopedium. This favoured Bythotrephes, which preferentially feed on small Holopedium. 4. We argue that the stage-specific overcompensation occurred as a result of increased per capita fecundity of adult Holopedium and as a result of competitive release following harvest. If shown to be common, emergent facilitation may be a major mechanism behind observed predator extinctions and patterns of predator invasions.
not annotated - annotated - LINNAEUS only
A clone-based transcriptomics approach for the identification of genes relevant for itaconic acid production in Aspergillus.
Several Aspergillus species are well-known for the production of a variety of organic acids. In this study, a cloned based transcriptomics approach was used to identify genes crucial in the biosynthesis pathway for one of these acids, itaconic acid. From a number of different Aspergillus terreus controlled batch fermentations, those cultures with the largest difference in itaconic acid titer and productivity were selected for mRNA isolation. cDNAs derived from these mRNA samples were used for subsequent hybridization of glass slide arrays based on a collection of 5000 cDNA clones. A selection of 13 cDNA clones resulting in the strongest (>10-fold) differential hybridization signals were identified and subsequently the inserts of these clones were sequenced. Sequence analysis revealed the presence of in total five different gene inserts among the sequenced clones. From one of these sequences, encoding a gene of the MmgE-PrpD family, the full length coding region was shown to encode one of the crucial itaconic acid pathway enzymes cis-aconitate decarboxylase, by heterologous expression in Escherichia coli. Expression of this gene in Aspergillus niger, which is a natural citric acid producer, resulted in itaconate production. Genome analysis suggests that in A. terreus the cis-aconitate decarboxylase gene is part of an itaconate acid related gene cluster including genes encoding two pathway specific transporters and a Zinc finger protein. Interestingly, this cluster is directly linked to the large lovastatin gene cluster.
not annotated - annotated - LINNAEUS only
The outcome of competition between the two chrysomonads Ochromonas sp. and Poterioochromonas malhamensis depends on pH.
We investigated the effect of pH on the competition of two closely related chrysomonad species, Poterioochromonas malhamensis originating from circumneutral Lake Constance, and Ochromonas sp. isolated from a highly acidic mining lake in Austria (pH -2.6). We performed pairwise growth experiments between these two species at four different pH ranging from 2.5 to 7.0. Heterotrophic bacteria served as food for both flagellates. Results were compared to growth rates measured earlier in single species experiments over the same pH range. We tested the hypothesis that the acidotolerant species benefits from competitive release under conditions of acid stress. The neutrophilic strain numerically dominated over the acidotolerant strain at pH 7.0, but was the inferior competitor at pH 2.5. At pH 3.5 and 5.0 both strains coexisted. Surprisingly, P. malhamensis prevailed over Ochromonas sp. under moderately acidic conditions, i.e. at the pH where growth rates of the latter peaked when grown alone. Since bacterial food was not limiting, resource competition is improbable. It appears more likely that P. malhamensis ingested cells of its slightly smaller competitor. Adverse effects mediated via allelopathy, either directly on the competing flagellate or indirectly by affecting its bacterial food, might also have affected the outcome of competition.
not annotated - annotated - LINNAEUS only
Differentially expressed genes in silkworm cell cultures in response to infection by Wolbachia and Cardinium endosymbionts.
Wolbachia and Cardinium are bacterial endosymbionts that are widely distributed amongst arthropods. Both cause reproductive alterations, such as cytoplasmic incompatibility, parthenogenesis and feminization. Here we studied differentially expressed genes in Wolbachia- and Cardinium-infected Bm-aff3 silkworm cells using a silkworm microarray. Wolbachia infection did not alter gene expression or induce or suppress immune responses. In contrast, Cardinium infection induced many immune-related genes, including antimicrobial peptides, pattern recognition receptors and a serine protease. Host immune responses differed, possibly because of the different cell wall structures of Wolbachia and Cardinium because the former lacks genes encoding lipopolysaccharide components and two racemases for peptidoglycan formation. A few possibly non-immune-related genes were differentially expressed, but their involvement in host reproductive alteration was unclear.
not annotated - annotated - LINNAEUS only
Neuropeptide Y-like signalling and nutritionally mediated gene expression and behaviour in the honey bee.
Previous research has led to the idea that derived traits can arise through the evolution of novel roles for conserved genes. We explored whether neuropeptide Y (NPY)-like signalling, a conserved pathway that regulates food-related behaviour, is involved in a derived, nutritionally-related trait, the division of labour in worker honey bees. Transcripts encoding two NPY-like peptides were expressed in separate populations of brain neurosecretory cells, consistent with endocrine functions. NPY-related genes were upregulated in the brains of older foragers compared with younger bees performing brood care ('nurses'). A subset of these changes can be attributed to nutrition, but neuropeptide F peptide treatments did not influence sugar intake. These results contrast with recent reports of more robust associations between division of labour and the related insulin-signalling pathway and suggest that some elements of molecular pathways associated with feeding behaviour may be more evolutionarily labile than others.
not annotated - annotated - LINNAEUS only
Apolipoprotein E in Alzheimer's disease and other neurological disorders.
Apolipoprotein E (APOE) is a 299-aminoacid protein encoded by the APOE gene. Three common polymorphisms in the APOE gene, epsilo2, epsilo3, and epsilo4, result in a single aminoacid change in the APOE protein. APOE epsilo2, epsilo3, and epsilo4 alleles strongly alter, in a dose-dependent manner, the likelihood of developing Alzheimer's disease and cerebral amyloid angiopathy. In particular, APOE epsilo4 is associated with increased risk for Alzheimer's disease whereas APOE epsilo2 is associated with decreased risk. The effects of APOE genotype on risk of these diseases are likely to be mediated by differential effects of APOE on amyloid-Beta accumulation in the brain and its vasculature. Response to treatment for Alzheimer's disease might differ according to APOE genotype. Because convincing evidence ties the APOE genotype to risk of Alzheimer's disease and cerebral amyloid angiopathy, APOE has been studied in other neurological diseases. APOE epsilo4 is associated with poor outcome after traumatic brain injury and brain haemorrhage, although the mechanisms underlying these associations are unclear. The possibility that APOE has a role in these and other neurological diseases has been of great interest, but convincing associations have not yet emerged.
not annotated - annotated - LINNAEUS only
Titrating the cost of plant toxins against predators: determining the tipping point for foraging herbivores.
1. Foraging herbivores must deal with plant characteristics that inhibit feeding and they must avoid being eaten. Principally, toxins limit food intake, while predation risk alters how long animals are prepared to harvest resources. Each of these factors strongly affects how herbivores use food patches, and both constraints can pose immediate proximate costs and long-term consequences to fitness. 2. Using a generalist mammalian herbivore, the common brushtail possum (Trichosurus vulpecula), our aim was to quantitatively compare the influence of plant toxin and predation risk on foraging decisions. 3. We performed a titration experiment by offering animals a choice between non-toxic food at a risky patch paired with food with one of five toxin concentrations at a safe patch. This allowed us to identify the tipping point, where the cost of toxin in the safe food patch was equivalent to the perceived predation risk in the alternative patch. 4. At low toxin concentration, animals ate more from the safe than the risky patch. As toxin concentration increased at the safe patch, intake shifted until animals ate mainly from the risky patch. This shift was associated with behavioural changes: animals spent more time and fed longer at the risky patch, while vigilance increased at both risky and safe patches. 5. Our results demonstrate that the variation in toxin concentration, which occurs intraspecifically among plants, can critically influence the relative cost of predation risk on foraging. We show that herbivores quantify, compare and balance these two different but proximate costs, altering their foraging patterns in the process. This has potential ecological and evolutionary implications for the production of plant defence compounds in relation to spatial variation in predation risk to herbivores.
not annotated - annotated - LINNAEUS only
What determines variation in home range size across spatiotemporal scales in a large browsing herbivore?
1. Most studies of intraspecific variation in home range size have investigated only a single or a few factors and often at one specific scale. However, considering multiple spatial and temporal scales when defining a home range is important as mechanisms that affect variation in home range size may differ depending on the scale under investigation. 2. We aim to quantify the relative effect of various individual, forage and climatic determinants of variation in home range size across multiple spatiotemporal scales in a large browsing herbivore, the moose (Alces alces), living at the southern limit of its distribution in Norway. 3. Total home range size and core home range areas were estimated for daily to monthly scales in summer and winter using both local convex hull (LoCoH) and fixed kernel home range methods. Variance in home range size was analysed using linear mixed-effects models for repeated measurements. 4. Reproductive status was the most influential individual-level factor explaining variance in moose home range size, with females accompanied by a calf having smaller summer ranges across all scales. Variation in home range size was strongly correlated with spatiotemporal changes in quantity and quality of natural food resources. Home range size decreased with increasing browse density at daily scales, but the relationship changed to positive at longer temporal scales. In contrast, browse quality was consistently negatively correlated with home range size except at the monthly scale during winter when depletion of high-quality forage occurs. Local climate affected total home range size more than core areas. Temperature, precipitation and snow depth influenced home range size directly at short temporal scales. 5. The relative effects of intrinsic and extrinsic determinants of variation in home range size differed with spatiotemporal scale, providing clear evidence that home range size is scale dependent in this large browser. Insight into the behavioural responses of populations to climatic stochasticity and forage variability is essential in view of current and future climate change, especially for populations with thermoregulatory restrictions living at the southern limit of their distribution.
not annotated - annotated - LINNAEUS only
Npc1 is involved in sterol trafficking in the filamentous fungus Fusarium graminearum.
The ortholog of the human gene NPC1 was identified in the plant pathogenic, filamentous fungus Fusarium graminearum by shared amino acid sequence, protein domain structure and cellular localization of the mature fungal protein. The FusariumNpc1 gene shares 34% amino acid sequence identity and 51% similarity to the human gene, has similar domain structure and is constitutively expressed, although up-regulated in ungerminated macroconidia and ascospores. GFP-tagged Npc1p localizes to the fungal vacuolar membrane. Cultures derived from a Deltanpc1 mutant strain contain significantly more ergosterol than cultures of the wildtype. Staining with the fluorescent, sterol binding dye filipin, shows that ergosterol accumulates in vacuoles of the Deltanpc1 mutant but not the wildtype strain. The Deltanpc1 mutant has a temperature dependent reduction in growth and greater sensitivity to the ergosterol synthesis inhibiting fungicide tebuconazole compared with the wildtype strain or the mutant complemented with wildtype Npc1. The mutant also is significantly reduced in pathogenicity to wheat. Our results are consistent with the interpretation that Npc1p is important for normal transport of ergosterol from the vacuole and is essential for proper membrane function under particular environmental conditions.
not annotated - annotated - LINNAEUS only
Genetic diversity and phylogenetic position of the subclass Astomatia (Ciliophora) based on a sampling of six genera from West African oligochaetes (Glossoscolecidae, Megascolecidae), including description of the new genus Paraclausilocola n. gen.
To more confidently assess phylogenetic relationships among astome ciliates, we obtained small subunit (SSU) rRNA sequences from nine species distributed in six genera and three families: Almophrya bivacuolata, Eudrilophrya complanata, Metaracoelophrya sp. 1, Metaracoelophrya sp. 2, Metaracoelophrya intermedia, Metaradiophrya sp., Njinella prolifera, Paraclausilocola constricta n. gen., n. sp., and Paraclausilocola elongata n. sp. The two new species in the proposed new clausilocolid genus Paraclausilocola n. gen. are astomes with no attachment apparatus, two files of contractile vacuoles, and an arc-like anterior suture that has differentiations of thigmotactic ciliature on the anterior ends of the left kineties of the upper surface. Phylogenetic analyses were undertaken using neighbor-joining, Bayesian inference, maximum likelihood, and maximum parsimony. The nine species of astomes formed a strongly supported clade, showing the subclass Astomatia to be monophyletic and a weakly supported sister clade to the scuticociliates. There were two strongly supported clades within the astomes. However, genera assigned to the same family were found in different clades, and genera assigned to the same order were found in both clades. Thus, astome taxa appear to be paraphyletic when morphology is used to assign species to genera.
not annotated - annotated - LINNAEUS only
Negotiating a noisy, information-rich environment in search of cryptic prey: olfactory predators need patchiness in prey cues.
1. Olfactory predator search processes differ fundamentally to those based on vision, particularly when odour cues are deposited rather than airborne or emanating from a point source. When searching for visually cryptic prey that may have moved some distance from a deposited odour cue, cue context and spatial variability are the most likely sources of information about prey location available to an olfactory predator. 2. We tested whether the house mouse (Mus domesticus), a model olfactory predator, would use cue context and spatial variability when searching for buried food items; specifically, we tested the effect of varying cue patchiness, odour strength, and cue-prey association on mouse foraging success. 3. Within mouse- and predator-proof enclosures, we created grids of 100 sand-filled Petri dishes and buried peanut pieces in a set number of these patches to represent visually cryptic 'prey'. By adding peanut oil to selected dishes, we varied the spatial distribution of prey odour relative to the distribution of prey patches in each grid, to reflect different levels of cue patchiness (Experiment 1), odour strength (Experiment 2) and cue-prey association (Experiment 3). We measured the overnight foraging success of individual mice (percentage of searched patches containing prey), as well as their foraging activity (percentage of patches searched), and prey survival (percentage of unsearched prey patches). 4. Mouse foraging success was highest where odour cues were patchy rather than uniform (Experiment 1), and where cues were tightly associated with prey location, rather than randomly or uniformly distributed (Experiment 3). However, when cues at prey patches were ten times stronger than a uniformly distributed weak background odour, mice did not improve their foraging success over that experienced when cues were of uniform strength and distribution (Experiment 2). 5. These results suggest that spatial variability and cue context are important means by which olfactory predators can use deposited odour cues to locate visually cryptic prey. They also indicate that chemical crypsis can disrupt these search processes as effectively as background matching in visually based predator-prey systems.
not annotated - annotated - LINNAEUS only
Behaviour during elevated water temperatures: can physiology explain movement of juvenile Atlantic salmon to cool water?
1. Temperature governs most physiological processes in animals. Ectotherms behaviourally thermoregulate by selecting habitats with temperatures regulating their body temperature for optimal physiological functioning. However, ectotherms can experience temperature extremes forcing the organisms to seek temperature refuge. 2. Fish actively avoid potentially lethal temperatures by moving to cool-water sites created by inflowing tributaries and groundwater seeps. Juvenile Atlantic salmon (Salmo salar) of different age classes exhibit different behavioural responses to elevated temperatures (>23 ^0C). Yearling (1+) and 2-year-old (2+) Atlantic salmon often cease feeding, abandon territorial behaviour and swim continuously in aggregations in cool-water sites; whereas young-of-the-year (0+) fish continue defending territories and foraging. 3. This study determined whether the behavioural shift in older individuals (2+) occurred when basal metabolic rate, driven by increasing water temperature, reached the maximum metabolic rate such that anaerobic pathways were recruited to provide energy to support vital processes. Behaviour (feeding and stress responses), oxygen consumption, muscle lactate and glycogen, and circulating blood lactate and glucose concentrations were measured in wild 0+ and 2+ Atlantic salmon acclimated to water temperatures between 16 and 28 ^0C. 4. Results indicate that oxygen consumption of the 2+ fish increased with temperature and reached a plateau at 24 ^0C, a temperature that corresponded to cessation of feeding and a significant increase in muscle and blood lactate levels. By contrast, oxygen consumption in 0+ fish did not reach a plateau, feeding continued and muscle lactate did not increase, even at the highest temperatures tested (28 ^0C). 5. To conclude, the experiment demonstrated that the 0+ and 2+ fish had different physiological responses to the elevated water temperatures. The results suggest that wild 2+ Atlantic salmon employ behavioural responses (e.g. movement to cool-water sites) at elevated temperatures in an effort to mitigate physiological imbalances associated with an inability to support basal metabolism through aerobic metabolic processes.
not annotated - annotated - LINNAEUS only
Food web complexity and allometric scaling relationships in stream mesocosms: implications for experimentation.
1. Mesocosms are used extensively by ecologists to gain a mechanistic understanding of ecosystems based on the often untested assumption that these systems can replicate the key attributes of natural assemblages. 2. Previous investigations of stream mesocosm utility have explored community composition, but here for the first time, we extend the approach to consider the replicability and realism of food webs in four outdoor channels (4 m(2)). 3. The four food webs were similarly complex, consisting of diverse assemblages (61-71 taxa) with dense feeding interactions (directed connectance 0.09-0.11). Mesocosm food web structural attributes were within the range reported for 82 well-characterized food webs from natural streams and rivers. When compared with 112 additional food webs from standing freshwater, marine, estuarine and terrestrial environments, stream food webs (including mesocosms) had similar characteristic path lengths, but typically lower mean food chain length and exponents for the species-link relationship. 4. Body size (M) abundance (N) allometric scaling coefficients for trivariate taxonomic mesocosm food webs (-0.53 to -0.49) and individual size distributions (-0.60 to -0.58) were consistent and similar to those from natural systems, suggesting that patterns of energy flux between mesocosm consumers and resources were realistic approximations. 5. These results suggest that stream mesocosms of this scale can support replicate food webs with a degree of biocomplexity that is comparable to 'natural' streams. The findings highlight the potential value of mesocosms as model systems for performing experimental manipulations to test ecological theories, at spatiotemporal scales of relevance to natural ecosystems.
not annotated - annotated - LINNAEUS only
Tuberculosis.
Tuberculosis results in an estimated 1*7 million deaths each year and the worldwide number of new cases (more than 9 million) is higher than at any other time in history. 22 low-income and middle-income countries account for more than 80% of the active cases in the world. Due to the devastating effect of HIV on susceptibility to tuberculosis, sub-Saharan Africa has been disproportionately affected and accounts for four of every five cases of HIV-associated tuberculosis. In many regions highly endemic for tuberculosis, diagnosis continues to rely on century-old sputum microscopy; there is no vaccine with adequate effectiveness and tuberculosis treatment regimens are protracted and have a risk of toxic effects. Increasing rates of drug-resistant tuberculosis in eastern Europe, Asia, and sub-Saharan Africa now threaten to undermine the gains made by worldwide tuberculosis control programmes. Moreover, our fundamental understanding of the pathogenesis of this disease is inadequate. However, increased investment has allowed basic science and translational and applied research to produce new data, leading to promising progress in the development of improved tuberculosis diagnostics, biomarkers of disease activity, drugs, and vaccines. The growing scientific momentum must be accompanied by much greater investment and political commitment to meet this huge persisting challenge to public health. Our Seminar presents current perspectives on the scale of the epidemic, the pathogen and the host response, present and emerging methods for disease control (including diagnostics, drugs, biomarkers, and vaccines), and the ongoing challenge of tuberculosis control in adults in the 21st century.
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Characterization of an omega-class glutathione S-transferase in the stress response of the silkmoth.
The glutathione S-transferase (GST) superfamily is involved in detoxification of various xenobiotics. Using real-time PCR, mRNA encoding an omega-class GST of Bombyx mori (bmGSTO) was shown to be induced after exposure to various environmental stresses. A soluble form of recombinant protein (rbmGSTO) was functionally overexpressed in Escherichia coli cells and purified to homogeneity. Cys 38 and Pro 39 were found to be highly conserved in omega-class GSTs, and their roles were investigated by site-directed mutagenesis/kinetic analysis. Mutations of Cys 38 and Pro 39 residues affected the catalytic efficiency of enzymes, indicating that the presence of Cys 38 and Pro 39 residues is important for bmGSTO activity. Thus, bmGSTO could contribute to increasing the environmental stress resistance of lepidopteran insects.
not annotated - annotated - LINNAEUS only
Treatment advances in neonatal neuroprotection and neurointensive care.
Knowledge of the nature, prognosis, and ways to treat brain lesions in neonatal infants has increased remarkably. Neonatal hypoxic-ischaemic encephalopathy (HIE) in term infants, mirrors a progressive cascade of excito-oxidative events that unfold in the brain after an asphyxial insult. In the laboratory, this cascade can be blocked to protect brain tissue through the process of neuroprotection. However, proof of a clinical effect was lacking until the publication of three positive randomised controlled trials of moderate hypothermia for term infants with HIE. These results have greatly improved treatment prospects for babies with asphyxia and altered understanding of the theory of neuroprotection. The studies show that moderate hypothermia within 6 h of asphyxia improves survival without cerebral palsy or other disability by about 40% and reduces death or neurological disability by nearly 30%. The search is on to discover adjuvant treatments that can further enhance the effects of hypothermia.
not annotated - annotated - LINNAEUS only
Origin and evolution of the canal raphe system in diatoms.
One lineage of pennate diatoms has a slit through the siliceous cell wall, called a "raphe," that functions in motility. Raphid pennate diatoms number in the perhaps tens of thousands of species, with the diversity of raphe forms potentially matching this number. Three lineages-the Bacillariales, Rhopalodiales, and Surirellales-possess a complex and presumably highly derived raphe that is physically separated from the cell interior, most often by a set of siliceous braces. Because the relationship among these three lineages is unclear, the number of origins of the canal raphe system and the homology of it and its constitutive parts among these lineages, is equally unclear. We reconstructed the phylogeny of raphid pennate diatoms and included, for the first time, members of all three canal raphid diatom lineages, and used the phylogeny to test specific hypotheses about the origin of the canal raphe. The canal raphe appears to have evolved twice, once in the common ancestor of Bacillariales and once in the common ancestor of Rhopalodiales and Surirellales, which form a monophyletic group in our analyses. These results recommend careful follow-up morphogenesis studies of the canal raphe in these two lineages to determine the underlying developmental basis for this remarkable case of parallel evolution.
not annotated - annotated - LINNAEUS only
Osteoporosis: now and the future.
Osteoporosis is a common disease characterised by a systemic impairment of bone mass and microarchitecture that results in fragility fractures. With an ageing population, the medical and socioeconomic effect of osteoporosis, particularly postmenopausal osteoporosis, will increase further. A detailed knowledge of bone biology with molecular insights into the communication between bone-forming osteoblasts and bone-resorbing osteoclasts and the orchestrating signalling network has led to the identification of novel therapeutic targets. Novel treatment strategies have been developed that aim to inhibit excessive bone resorption and increase bone formation. The most promising novel treatments include: denosumab, a monoclonal antibody for receptor activator of NF-kappaB ligand, a key osteoclast cytokine; odanacatib, a specific inhibitor of the osteoclast protease cathepsin K; and antibodies against the proteins sclerostin and dickkopf-1, two endogenous inhibitors of bone formation. This overview discusses these novel therapies and explains their underlying physiology.
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Increasing burden of liver disease in patients with HIV infection.
Introduction of effective combined antiretroviral therapy has made HIV infection a chronic illness. Substantial reductions in the number of AIDS-related deaths have been accompanied by an increase in liver-related morbidity and mortality due to co-infection with chronic hepatitis B and C viruses. Increases in non-alcoholic fatty liver disease and drug-induced hepatotoxicity, together with development of hepatocellular carcinoma, also potentiate the burden of liver disease in individuals with HIV infection. We provide an overview of the key causes, disease mechanisms of pathogenesis, and recommendations for treatment options including the evolving role of liver transplantation.
not annotated - annotated - LINNAEUS only
Adaptive trade-offs in juvenile salmonid metabolism associated with habitat partitioning between coho salmon and steelhead trout in coastal streams.
1. Adaptive trade-offs are fundamental to the evolution of diversity and the coexistence of similar taxa and occur when complimentary combinations of traits maximize efficiency of resource exploitation or survival at different points on environmental gradients. 2. Standard metabolic rate (SMR) is a key physiological trait that reflects adaptations to baseline metabolic performance, whereas active metabolism reflects adaptations to variable metabolic output associated with performance related to foraging, predator avoidance, aggressive interactions or migratory movements. Benefits of high SMR and active metabolism may change along a resource (productivity) gradient, indicating that a trade-off exists among active metabolism, resting metabolism and energy intake. 3. We measured and compared SMR, maximal metabolic rate (MMR), aerobic scope (AS), swim performance (UCrit) and growth of juvenile hatchery and wild steelhead and coho salmon held on high- and low-food rations in order to better understand the potential significance of variation in SMR to growth, differentiation between species, and patterns of habitat use along a productivity gradient. 4. We found that differences in SMR, MMR, AS, swim performance and growth rate between steelhead trout and coho salmon were reduced in hatchery-reared fish compared with wild fish. Wild steelhead had a higher MMR, AS, swim performance and growth rate than wild coho, but adaptations between species do not appear to involve differences in SMR or to trade-off increased growth rate against lower swim performance, as commonly observed for high-growth strains. Instead, we hypothesize that wild steelhead may be trading off higher growth rate for lower food consumption efficiency, similar to strategies adopted by anadromous vs. resident brook trout and Atlantic salmon vs. brook trout. This highlights potential differences in food consumption and digestion strategies as cryptic adaptations ecologically differentiating salmonid species. 5. We hypothesize that divergent digestive strategies, which are common and well documented among terrestrial vertebrates, may be an important but overlooked aspect of adaptive strategies of juvenile salmonids, and fish in general.
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Natal conditions alter age-specific reproduction but not survival or senescence in a long-lived bird of prey.
1. Natal conditions and senescence are two major factors shaping life-history traits of wild animals. However, such factors have rarely been investigated together, and it remains largely unknown whether they interact to affect age-specific performance. 2. We used 27 years of longitudinal data collected on tawny owls with estimates of prey density (field voles) from Kielder Forest (UK) to investigate how prey density at birth affects ageing patterns in reproduction and survival. 3. Natal conditions experienced by tawny owls, measured in terms of vole density, dramatically varied among cohorts and explained 87% of the deviance in first-year apparent survival (annual estimates ranging from 0*07 to 0*33). 4. We found evidence for senescence in survival for females as well as for males. Model-averaged estimates showed that adult survival probability declined linearly with age for females from age 1. In contrast, male survival probability, lower on average than for female, declined after a plateau at age 1-3. 5. We also found evidence for reproductive senescence (number of offspring). For females, reproductive performance increased until age 9 then declined. Males showed an earlier decline in reproductive performance with an onset of senescence at age 3. 6. Long-lasting effects of natal environmental conditions were sex specific. Female reproductive performance was substantially related to natal conditions (difference of 0*24 fledgling per breeding event between females born in the first or third quartile of vole density), whereas male performance was not. We found no evidence for tawny owls born in years with low prey density having accelerated rates of senescence. 7. Our results, combined with previous findings, suggest the way natal environmental conditions affect senescence varies not only across species but also within species according to gender and the demographic trait considered.
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Post-splenectomy and hyposplenic states.
The spleen is crucial in regulating immune homoeostasis through its ability to link innate and adaptive immunity and in protecting against infections. The impairment of splenic function is defined as hyposplenism, an acquired disorder caused by several haematological and immunological diseases. The term asplenia refers to the absence of the spleen, a condition that is rarely congenital and mostly post-surgical. Although hyposplenism and asplenia might predispose individuals to thromboembolic events, in this Review we focus on infectious complications, which are the most widely recognised consequences of these states. Because of the high mortality, the fulminant course, and the refractoriness to common treatment of overwhelming infections caused by encapsulated bacteria, prevention through vaccination and antibiotic prophylaxis is the basis of the management of patients who have had splenectomy or have hyposplenism. In this Review, we critically assess clinical and diagnostic aspects of splenic dysfunction and highlight new perspectives in the prevention of overwhelming post-splenectomy infections.
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Priority actions for the non-communicable disease crisis.
The UN High-Level Meeting on Non-Communicable Diseases (NCDs) in September, 2011, is an unprecedented opportunity to create a sustained global movement against premature death and preventable morbidity and disability from NCDs, mainly heart disease, stroke, cancer, diabetes, and chronic respiratory disease. The increasing global crisis in NCDs is a barrier to development goals including poverty reduction, health equity, economic stability, and human security. The Lancet NCD Action Group and the NCD Alliance propose five overarching priority actions for the response to the crisis--leadership, prevention, treatment, international cooperation, and monitoring and accountability--and the delivery of five priority interventions--tobacco control, salt reduction, improved diets and physical activity, reduction in hazardous alcohol intake, and essential drugs and technologies. The priority interventions were chosen for their health effects, cost-effectiveness, low costs of implementation, and political and financial feasibility. The most urgent and immediate priority is tobacco control. We propose as a goal for 2040, a world essentially free from tobacco where less than 5% of people use tobacco. Implementation of the priority interventions, at an estimated global commitment of about US$9 billion per year, will bring enormous benefits to social and economic development and to the health sector. If widely adopted, these interventions will achieve the global goal of reducing NCD death rates by 2% per year, averting tens of millions of premature deaths in this decade.
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Serotype replacement in disease after pneumococcal vaccination.
Vaccination with heptavalent pneumococcal conjugate vaccine (PCV7) has significantly reduced the burden of pneumococcal disease and has had an important public health benefit. Because this vaccine targets only seven of the more than 92 pneumococcal serotypes, concerns have been raised that non-vaccine serotypes (NVTs) could increase in prevalence and reduce the benefits of vaccination. Indeed, among asymptomatic carriers, the prevalence of NVTs has increased substantially, and consequently, there has been little or no net change in the bacterial carriage prevalence. In many populations, pneumococcal disease caused by NVT has increased, but in most cases this increase has been less than the increase in NVT carriage. We review the evidence for serotype replacement in carriage and disease, and address the surveillance biases that might affect these findings. We then discuss possible reasons for the discrepancy between near-complete replacement in carriage and partial replacement for disease, including differences in invasiveness between vaccine serotypes. We contend that the magnitude of serotype replacement in disease can be attributed, in part, to a combination of lower invasiveness of the replacing serotypes, biases in the pre-vaccine carriage data (unmasking), and biases in the disease surveillance systems that could underestimate the true amount of replacement. We conclude by discussing the future potential for serotype replacement in disease and the need for continuing surveillance.
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Stillbirths: how can health systems deliver for mothers and babies?
The causes of stillbirths are inseparable from the causes of maternal and neonatal deaths. This report focuses on prevention of stillbirths by scale-up of care for mothers and babies at the health-system level, with consideration for effects and cost. In countries with high mortality rates, emergency obstetric care has the greatest effect on maternal and neonatal deaths, and on stillbirths. Syphilis detection and treatment is of moderate effect but of lower cost and is highly feasible. Advanced antenatal care, including induction for post-term pregnancies, and detection and management of hypertensive disease, fetal growth restriction, and gestational diabetes, will further reduce mortality, but at higher cost. These interventions are best packaged and provided through linked service delivery methods tailored to suit existing health-care systems. If 99% coverage is reached in 68 priority countries by 2015, up to 1*1 million (45%) third-trimester stillbirths, 201 000 (54%) maternal deaths, and 1*4 million (43%) neonatal deaths could be saved per year at an additional total cost of US$10*9 billion or $2*32 per person, which is in the range of $0*96-2*32 for other ingredients-based intervention packages with only recurrent costs.
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The contribution of the S-phase checkpoint genes MEC1 and SGS1 to genome stability maintenance in Candida albicans.
Genome rearrangements, a common feature of Candida albicans isolates, are often associated with the acquisition of antifungal drug resistance. In Saccharomyces cerevisiae, perturbations in the S-phase checkpoints result in the same sort of Gross Chromosomal Rearrangements (GCRs) observed in C. albicans. Several proteins are involved in the S. cerevisiae cell cycle checkpoints, including Mec1p, a protein kinase of the PIKK (phosphatidyl inositol 3-kinase-like kinase) family and the central player in the DNA damage checkpoint. Sgs1p, the ortholog of BLM, the Bloom's syndrome gene, is a RecQ-related DNA helicase; cells from BLM patients are characterized by an increase in genome instability. Yeast strains bearing deletions in MEC1 or SGS1 are viable (in contrast to the inviability seen with loss of MEC1 in S. cerevisiae) but the different deletion mutants have significantly different phenotypes. The mec1Delta/Delta colonies have a wild-type colony morphology, while the sgs1Delta/Delta mutants are slow-growing, producing wrinkled colonies with pseudohyphal-like cells. The mec1Delta/Delta mutants are only sensitive to ethylmethane sulfonate (EMS), methylmethane sulfonate (MMS), and hydroxyurea (HU) but the sgs1Delta/Delta mutants exhibit a high sensitivity to all DNA-damaging agents tested. In an assay for chromosome 1 integrity, the mec1Delta/Delta mutants exhibit an increase in genome instability; no change was observed in the sgs1Delta/Delta mutants. Finally, loss of MEC1 does not affect sensitivity to the antifungal drug fluconazole, while loss of SGS1 leads to an increased susceptibility to fluconazole. Neither deletion elevated the level of antifungal drug resistance acquisition.
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Postural deformities in Parkinson's disease.
Postural deformities are frequent and disabling complications of Parkinson's disease (PD) and atypical parkinsonism. These deformities include camptocormia, antecollis, Pisa syndrome, and scoliosis. Recognition of specific postural syndromes might have differential diagnostic value in patients presenting with parkinsonism. The evidence to date suggests that postural deformities have a multifactorial pathophysiology. Contributing factors include muscular rigidity; axial dystonia; weakness caused by myopathy; body scheme defects due to centrally impaired proprioception; and structural changes in the spine. The relative contribution of these different factors varies between patients and across specific syndromes. Improved understanding of the mechanisms underlying postural deformities in PD might ultimately lead us to more effective management strategies for these disabling and drug-refractory complications.
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Tortricid moths reared from the invasive weed Mexican palo verde, Parkinsonia aculeata, with comments on their host specificity, biology, geographic distribution, and systematics.
As part of efforts to identify native herbivores of Mexican palo verde, Parkinsonia aculeata L. (Leguminosae: Caesalpinioideae), as potential biological control agents against this invasive weed in Australia, ten species of Tortricidae (Lepidoptera) were reared from Guatemala, Mexico, Nicaragua, and Venezuela: Amorbia concavana (Zeller), Platynota rostrana (Walker), Platynota helianthes (Meyrick), Platynota stultana Walsingham (all Tortricinae: Sparganothini), Rudenia leguminana (Busck), Cochylis sp. (both Tortricinae: Cochylini), Ofatulena duodecemstriata (Walsingham), O. luminosa Heinrich, Ofatulena sp. (all Olethreutinae: Grapholitini), and Crocidosema lantana Busck (Olethreutinae: Eucosmini). Significant geographic range extensions are provided for O. duodecemstriata and R. leguminana. These are the first documented records of P. aculeata as a host plant for all but O. luminosa. The four species of Sparganothini are polyphagous; in contrast, the two Cochylini and three Grapholitini likely are specialists on Leguminosae. Ofatulena luminosa is possibly host specific on P. aculeata. Host trials with Rudenia leguminana also provide some evidence of specificity, in contrast to historical rearing records. To examine the possibility that R. leguminana is a complex of species, two data sets of molecular markers were examined: (1) a combined data set of two mitochondrial markers (a 781-basepair region of cytochrome c oxidase I (COI) and a 685-basepair region of cytochrome c oxidase II) and one nuclear marker (a 531-basepair region of the 28S domain 2); and (2) the 650-basepair "barcode" region of COI. Analyses of both data sets strongly suggest that individuals examined in this study belong to more than one species.
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Evidence for the higher importance of signal size over body size in aposematic signaling in insects.
To understand the evolution of warning coloration, it is important to distinguish between different aspects of conspicuous color patterns. As an example, both pattern element size and body size of prey have been shown to enhance the effectiveness of warning signals. However, it is unclear whether the effect of body size is merely a side effect of proportionally increasing pattern elements, or if there is an effect of body size per se. These possibilities were evaluated by offering different sized artificial caterpillars with either fixed or proportionally increasing aposematic color signal elements to wild great tits, Parus major L. (Passeriformes: Paridae). The birds' hesitation time to attack each "caterpillar" was used as a measure of the warning effect. The hesitation time showed a significant, positive size-dependence with the caterpillars whose pattern elements increased proportionally with their body size. In contrast, no size dependence was found in the larvae with fixed-size signal elements. Such a difference in mortality curves is consistent with the idea that pattern element size is a more important aspect than body size in enhancing a warning signal. Since no evidence of an effect of body size per se on signal efficiency was found, this study does not support the hypothesis that aposematic insects gain more from large size than cryptic ones.
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Wolbachia wSinvictaA infections in natural populations of the fire ant Solenopsis invicta: testing for phenotypic effects.
Wolbachia are intracellular bacteria that commonly infect many arthropods and some nematodes. In arthropods, these maternally transmitted bacteria often induce a variety of phenotypic effects to enhance their own spread within host populations. Wolbachia phenotypic effects generally either provide benefits to infected host females (cytoplasmic incompatibility, positive fitness effects) or bias host sex ratio in favor of females (male-killing, parthenogenesis, feminization), all of which increase the relative production of infected females in host populations. Wolbachia surveys have found infections to be exceedingly common in ants, but little is known at this juncture as to what phenotypic effects, if any, they induce in this group. Previous studies have demonstrated that individuals from native populations of the invasive fire ant Solenopsis invicta commonly harbor one or more of three Wolbachia variants. One of the variants, wSinvictaA, typically occurs at low prevalence in S. invicta populations, appears to have been transmitted horizontally into S. invicta three or more times, and has been lost repeatedly from host lineages over time. In order to determine the phenotypic effects and likely population dynamics of wSinvictaA infections in these ants, brood production patterns of newly mated fire ant queens were studied during simulated claustral founding and measured wSinvictaA transmission fidelity within mature single-queen families. No clear evidence was found for Wolbachia-induced cytoplasmic incompatibility, significant fitness effects, or male-killing. Maternal transmission was perfect to both virgin queens and males. Possible mechanisms for how this variant could be maintained in host populations are discussed.
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Growth inhibition of Beauveria bassiana by bacteria isolated from the cuticular surface of the corn leafhopper, Dalbulus maidis and the planthopper, Delphacodes kuscheli, two important vectors of maize pathogens.
The phytosanitary importance of the corn leafhopper, Dalbulus maidis (De Long and Wolcott) (Hemiptera: Cicadellidae) and the planthopper, Delphacodes kuscheli Fennah (Hemiptera: Delphacidae) lies in their ability to transmit phloem-associated plant pathogens, mainly viruses and mollicutes, and to cause considerable mechanical damage to corn plants during feeding and oviposition. Fungi, particularly some members of the Ascomycota, are likely candidates for biocontrol agents against these insect pests, but several studies revealed their failure to invade the insect cuticle possibly because of the presence of inhibitory compounds such as phenols, quinones, and lipids and also by the antibiosis effect of the microbiota living on the cuticular surface of the host. The present work aims to understand interactions between the entomopathogenic fungus Beauveria bassiana (Balsamao-Crivelli) Vuillemin (Hypocreales: Cordycipitaceae) and bacterial antagonists isolated from the cuticular surface of D. maidis and D. kuscheli. A total of 155 bacterial isolates were recovered from the insect's cuticle and tested against B. bassiana. Ninety-one out of 155 strains inhibited the growth of B. bassiana. Bacterial strains isolated from D. maidis were significantly more antagonistic against B. bassiana than those isolates from D. kuscheli. Among the most effective antagonistic strains, six isolates of Bacillus thuringiensis Berliner (Bacillales: Bacillaeae (after B. subtilis)), one isolate of B. mycoides Flugge, eight isolates of B. megaterium de Bary, five isolates of B.pumilus Meyer and Gottheil, one isolate of B. licheniformis (Weigmann) Chester, and four isolates of B. subtilis (Ehrenberg) Cohn were identified.
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Mig1 is involved in mycelial formation and expression of the genes encoding extracellular enzymes in Saccharomycopsis fibuligera A11.
The MIG1 gene of Saccharomycopsis fibuligera A11 was cloned from its genomic DNA using the degenerated primers and inverse PCR. The MIG1 gene (1152bp, accession number: HM450676) encoded a 384-amino acid protein very similar to Mig1s from other fungi. Besides their highly conserved zinc fingers, the Mig1 proteins displayed short conserved motifs of possible significance in glucose repression. The MIG1 gene in S. fibuligera A11 was disrupted by integrating the HPT (hygromycin B phosphotransferase) gene into ORF (Open Reading Frame) of the MIG1 gene. The disruptant A11-c obtained could grow in the media containing hygromycin and 2-deoxy-d-glucose, respectively. alpha-Amylase, glucoamylse, acid protease and Beta-glucosidase production by the disruptant and expression of their genes in the disruptant were greatly enhanced. This confirms that Mig1, the transcriptional repressor, indeed regulates expression of the genes and production of the extracellular enzymes in S. fibuligera A11. At the same time, it was found that cell budding was enhanced and mycelial formation was reduced in the disruptant.
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Morphological differences and molecular phylogeny of freshwater blooming species, Peridiniopsis spp. (Dinophyceae) from China.
In 2008-2010, several freshwater dinoflagellate blooms caused by Peridiniopsis spp. were observed in China. P. penardii and P. niei sampled from various geographical localities were examined by means of light and scanning electron microscopy. After comparing morphological and molecular differences, the new freshwater variety Peridiniopsis penardii var. robusta var. nov. (Peridiniales, Dinophyceae) found in Manwan Reservoir, Yunnan Province was described. The new variety differed from P. penardii since it possessed numerous robust antapical spines and a conspicuous apical spine. Molecular phylogenetic analyses based on SSU, LSU and ITS indicated P. niei, P. penardii and P. penardii var. robusta were closely related with P. kevei, and clustered into a monophyletic clade. The new variety possessed an endosymbiotic diatom which was similar to P. penardii and P. kevei, whereas the endosymbiont was not present in cells of P. niei. The endosymbiont SSU and ITS phylogenies showed that the endosymbionts of these three dinoflagellates were closely related to members of Thalassiosirales. Furthermore it was concluded that the endosymbionts might originate from Discostella-like species.
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Beta-Thymosin is upregulated by the steroid hormone 20-hydroxyecdysone and microorganisms.
Thymosins have diverse biological activities including actin-sequestering and tissue repair in vertebrates, however, there is little information about the function of thymosins in invertebrates. We isolated a Beta-thymosin gene in Helicoverpa armigera. It has two transcript variants, HaTHY1 and HaTHY2, encoding 19.0 kDa and 14.5 kDa peptides, respectively. HaTHY1 was mainly transcribed in the integument and midgut, while HaTHY2 was principally presented in the fat body and haemocytes. The transcript levels of HaTHY2 showed some fluctuation; there was an obvious increase at the metamorphic stage in the integument or fat body. HaTHY was able to be upregulated by 20-hydroxyecdysone or by bacterial and viral challenge. These data suggest that HaTHY is upregulated by the steroid hormone and by responses to microorganism infection.
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The cell cycle gene MoCDC15 regulates hyphal growth, asexual development and plant infection in the rice blast pathogen Magnaporthe oryzae.
Rice blast, caused by the pathogen Magnaporthe oryzae, is a serious hindrance to rice production and has emerged as an important model for the characterization of molecular mechanisms relevant to pathogenic development in plants. Similar to other pathogenic fungi, conidiation plays a central role in initiation of M.oryzae infection and spread over a large area. However, relatively little is known regarding the molecular mechanisms that underlie conidiation in M. oryzae. To better characterize these mechanisms, we identified a conidiation-defective mutant, ATMT0225B6 (MoCDC15(T-DNA)), in which a T-DNA insertion disrupted a gene that encodes a homolog of fission yeast cdc15, and generated a second strain containing a disruption in the same allele (DeltaMoCDC15(T-DNA)). The cdc15 gene has been shown to act as a coordinator of the cell cycle in yeast. Functional analysis of the MoCDC15(T-DNA) and DeltaMoCDC15(T-DNA) mutants revealed that MoCDC15 is required for conidiation, preinfection development and pathogenicity in M. oryzae. Conidia from these mutants were viable, but failed to adhere to hydrophobic surface, a crucial step required for subsequent pathogenic development. All phenotypic defects observed in mutants were rescued in a strain complemented with wild type MoCDC15. Together, these data indicate that MoCDC15 functions as a coordinator of several biological processes important for pathogenic development in M. oryzae.
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Inactivation of a macronuclear intra-S-phase checkpoint in Tetrahymena thermophila with caffeine affects the integrity of the micronuclear genome.
Aphidicolin (APH), an inhibitor of DNA polymerase alpha, arrested cell divisions in Tetrahymena thermophila. Surprisingly, low concentrations of APH induced an increase of macronuclear DNA content and cell size in non-dividing cells. In spite of the cell size increase, most proliferation of basal bodies, ciliogenesis and development of new oral primordia were prevented by the APH treatment. The division arrest induced by APH was partly overridden by caffeine (CAF) treatment, which caused the fragmentation ("pulverization") of the chromosomes in G2 micronuclei. Somatic progeny of dividers with pulverized micronuclei (APH+CAF strains) contained aneuploid and amicronucleate cells. The amicronucleate cells, after losing their oral structures and most of their cilia, and undergoing progressive disorganization of cortical structures, assumed an irregular shape ("crinkled") and were nonviable. "Crinkled" cells were not formed after APH + CAF treatment of the amicronuclear BI3840 strain, which contains some mic-specific sequences in its macronucleus. Most of the APH +CAF strains had a typical "*"- like conjugation phenotype: they did not produce pronuclei, but received them unilaterally from their mates and retained old macronuclei. However, 4 among 100 APH+CAF clones induced arrest at meiotic metaphase I in their wt mates. It is likely that the origin of such clones was enhanced by chromosome pulverization.
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Analysis of the Fusarium graminearum species complex from wheat, barley and maize in South Africa provides evidence of species-specific differences in host preference.
Species identity and trichothecene toxin potential of 560 members of the Fusarium graminearum species complex (FGSC) collected from diseased wheat, barley and maize in South Africa was determined using a microsphere-based multilocus genotyping assay. Although three trichothecene types (3-ADON, 15-ADON and NIV) were represented among these isolates, strains with the 15-ADON type predominated on all three hosts. A significant difference, however, was identified in the composition of FGSC pathogens associated with Gibberella ear rot (GER) of maize as compared to Fusarium head blight (FHB) of wheat or barley (P<0.001). F. graminearum accounted for more than 85% of the FGSC isolates associated with FHB of wheat and barley (N=425), and was also the dominant species among isolates from maize roots (N=35). However, with the exception of a single isolate identified as an interspecific hybrid between Fusariumboothii and F. graminearum, GER of maize (N=100) was exclusively associated with F. boothii. The predominance of F. graminearum among FHB isolates, and the near exclusivity of F. boothii among GER isolates, was observed across all cultivars, collection dates, and provinces sampled. Because these results suggest a difference in host preference among species of the FGSC, we hypothesize that F. graminearum may be less well adapted to infect maize ears than other members of the FGSC.
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Suitability of different media for in vitro cultivation of the ruminal protozoa species Entodinium caudatum, Eudiplodinium maggii, and Epidinium ecaudatum.
Three protozoal cultivation media were tested to determine the medium which best facilitated growth and viability of key B-type ciliates isolated from the sheep rumen. Entodinium caudatum and Eudiplodinium maggii were grown anaerobically in 50-ml flasks for 32 days in Caudatum-type (C), Kisidayova (K) or Dehority (M) medium. On day 32, in media K and M, E. caudatum cell counts were high with 5.6x10(3) and 7.8x10(3) mL(-1), respectively, and the proportion of dead cells was low with 0.6 and 1.4%, respectively. E. maggii concentrations when grown in medium M and C were 2.7x10(3) and 2.4x10(3) mL(-1), respectively, with 3.9 and 14.1% dead cells. Medium M, which favoured growth of both protozoa species, was tested again and Epidinium ecaudatum was included. Protozoa were grown for a 4-month period and samples were taken in the last two months on days 1, 7, 35 and 57. Average cell concentrations were 10.0, 0.8 and 0.5x10(3) mL(-1) for E. caudatum, E. maggii, and E. ecaudatum, respectively. In conclusion, medium M would appear to be the best choice for cultivating these three species in one medium.
not annotated - annotated - LINNAEUS only
Synganglion transcriptome and developmental global gene expression in adult females of the American dog tick, Dermacentor variabilis (Acari: Ixodidae).
454 Pyrosequencing was used to characterize the expressed genes from the synganglion and associated neurosecretory organs of unfed and partially fed virgin and mated replete females of the American dog tick, Dermacentor variabilis. A total of 14,881 contiguous sequences (contigs) was assembled, with an average size of 229 bp. Gene ontology terms for Level 2 biological processes were assigned to 4366 contigs. Seven acetylcholinesterases, a muscarinic acetylcholine (ACh) receptor, two nicotinic ACh receptor Beta-subunits, two ACh unc-18 regulators, two dopamine receptors, two gamma aminobutyric acid (GABA) receptors, two GABA transporters, two norepinephrine transporters and an octopamine receptor are described. Microarrays were conducted to examine global gene expression and quantitative real-time polymerase chain reaction was used to verify expression of selected neuropeptides. Hierarchical clustering of all differentially expressed transcripts grouped part-fed and replete ticks as being more similar in terms of differentially expressed genes with unfed ticks as the outgroup. Nine putative neuropeptides (allatostatin, bursicon-Beta, preprocorazonin, glycoprotein hormone alpha, insulin-like peptide, three orcokinins, preprosulphakinin) and a gonadotropin releasing hormone receptor were differentially expressed, and their developmental expression and role in reproduction was investigated. The presence of eclosion hormone, corazonin and bursicon in the synganglion, which in insects regulate behaviour and cuticle development associated with moulting, suggest that this system may be used in ticks to regulate blood feeding, cuticle expansion and development related to female reproduction; adult ticks do not moult.
not annotated - annotated - LINNAEUS only
Endogenous regulation of the growth-rate responses of a spring-dwelling strain of the freshwater alga, Chlorella minutissima, to light and temperature.
The paper presents a laboratory investigation of the temperature- and light- dependence of autotrophic growth of the alga Chlorella minutissima. It was isolated from the storage basin of a spring in the mountains of the Massif Central, France. The alga was grown at temperatures between (10 and 35 ^0C) and under irradiances from 30 to 550 mumol m(-2) s(-1), under a light/dark cycle. The results were fitted to selected descriptive models, seeking to express, as far as possible, the observed physiological behaviour of the strain and the minimum irradiance required to sustain net growth. At all temperatures, the maximum rates of growth observed are strikingly slower than those of other Chlorella strains and of other small algae, reported in the literature, even when correction is made for continuous light. The Q10 statistic for growth at temperatures>20 ^0C rates is also noticeably lower than in other species, while the apparent threshold of any growth is about 8 ^0C. Growth rates are readily light-saturated at all temperatures but with little evidence of adaptation of photosynthesis to low photon-flux rates. No short-term flexibility in these properties (over a time-scale of days) was demonstrated during the course of our experiments. We deduce that the algal strain had become genetically adapted to the relatively constant, even-temperature and low-light conditions of the spring-water habitat whence it was originally isolated.
not annotated - annotated - LINNAEUS only
Characterization of the oxysterol-binding protein gene family in the yellow fever mosquito, Aedes aegypti.
The oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) are sterol-binding proteins that may be involved in cellular sterol transportation, sterol metabolism and signal transduction pathways. Four ORP genes were cloned from Aedes aegypti. Based on amino acid sequence homology to human proteins, they are AeOSBP, AeORP1, AeORP8 and AeORP9. Splicing variants of AeOSBP and AeORP8 were identified. The temporal and spatial transcription patterns of members of the AeOSBP gene family through developmental stages and the gonotrophic cycle were profiled. AeORP1 transcription seemed to be head tissue-specific, whereas AeOSBP and AeORP9 expression was induced by a bloodmeal. Furthermore, over-expression of AeORPs facilitated [(3)H]-cholesterol uptake in Ae. aegypti cultured Aag -2 cells.
not annotated - annotated - LINNAEUS only
Identification and expression analysis of nervous wreck, which is preferentially expressed in the brain of the male silkworm moth, Bombyx mori.
Sexually dimorphic neural circuits are essential for reproductive behaviour. The molecular basis of sexual dimorphism in the silkworm moth (Bombyx mori) brain, however, is unclear. We conducted cDNA subtraction screening and identified nervous wreck (Bmnwk), a synaptic growth regulatory gene, whose expression is higher in the male brain than in the female brain of the silkworm. Bmnwk was preferentially expressed in the brain at the late pupae and adult stages. In situ hybridization revealed that Bmnwk is highly expressed in the optic lobe of the male moth brain. These findings suggest that Bmnwk has a role in the development and/or maintenance of the optic lobe in the male silkworm brain.
not annotated - annotated - LINNAEUS only
Infraciliature of eight Triplumaria species (Ciliophora, Entodiniomorphida) from Asian elephants with the description of six new species.
Intestinal ciliates excreted in the feces of Asian elephants were surveyed. Fourteen species in the order Entodiniomorphida were detected. Nine Triplumaria species in the family Cycloposthiidae were found. Using the silver impregnation, two known species, T. antis and T. dvoinosi, were redescribed and six new species, T. sukuna n. sp., T. zuze n. sp., T. solea n. sp., T. suwako n. sp., T. fulgora n. sp., and T. harpagonis n. sp., were described. T. sukuna, T. zuze, T. solea, and T. suwako have the perivestibular polybrachykinety along the vestibular opening. The buccal infraciliary bands of T. suwako are similar to those of T. selenica found from elephants and the buccal infraciliary bands of T. sukuna, T. zuze, and T. solea are similar to those of T. grypoclunis described from rhinoceroses. T. antis, T. dvoinosi, T. fulgora, and T. harpagonis have the vestibular polybrachykinety extending down inside the vestibulum as found in rumen ciliates in the family Ophryoscolecidae. The caudalial ciliary zones of T. dvoinosi and T. fulgora were retractable as found in rumen ophryoscolecids. Raabena bella and Pseudoentodinium elephantis showed high composition values over 30%. Ciliate densities in the three fecal samples were 0.15, 1.09, and 2.07x10(4)/ml.
not annotated - annotated - LINNAEUS only
Prolixicin: a novel antimicrobial peptide isolated from Rhodnius prolixus with differential activity against bacteria and Trypanosoma cruzi.
We identified and characterized the activity of prolixicin, a novel antimicrobial peptide (AMP) isolated from the hemipteran insect, Rhodnius prolixus. Sequence analysis reveals one region of prolixicin that may be related to the diptericin/attacin family of AMPs. Prolixicin is an 11-kDa peptide containing a putative 21 amino acid signal peptide, two putative phosphorylation sites and no glycosylation sites. It is produced by both adult fat body and midgut tissues in response to bacterial infection of the haemolymph or the midgut. Unlike most insect antibacterial peptides, the prolixicin gene does not seem to be regulated by NF-kappaB binding sites, but its promoter region contains several GATA sites. Recombinant prolixicin has strong activity against the Gram-negative bacterium Escherichia coli and differential activity against several Gram-negative and Gram-positive bacteria. No significant toxicity was demonstrated against Trypanosoma cruzi, the human parasite transmitted by R. prolixus.
not annotated - annotated - LINNAEUS only
Development Time and Body Size in Eupolyphaga sinensis Along a Latitudinal Gradient From China.
The responses of organisms to temperature variations may be via short term responses of the phenotype (phenotypic plasticity), or they could involve long-term evolutionary change and adaptation (via selection) to the genotype. These could involve changes to the mean size of the animal or to the thermal reaction norm. We examined the effects of various temperatures (of 22, 25, 28, and 31^0C) on development time, adult body size and preadult survivorship in three populations of the cockroach, Eupolyphaga sinensis (Walker), collected at different latitudes. We found substantial temperature-induced plasticity in development time, body size, and preadult survivorship, indicating that developmental temperatures have strong impacts on growth and life history traits of E. sinensis. Genetic differences for development time, body size, and preadult survivorship were detected among populations, and the three traits exhibited highly significant variations in the responses of different populations to various temperature conditions, indicating genetic differences among populations in terms of thermal reaction norms. We also found that two populations seem to support the beneficial acclimation hypothesis whereas the third mid-latitude population does not. The results are likely because of differences in season length and voltinism, indicating that not only temperature regime but also its interactions with generation time (and development time), voltinism, and season length are likely to have considerable effects on insect development time and body size. Overall, changes in development time, body size, and preadult survivorship in E. sinensis can all be regarded as adaptations to changing thermal regimes.
not annotated - annotated - LINNAEUS only
Culture Independent Survey of the Microbiota of the Glassy-Winged Sharpshooter (Homalodisca vitripennis) Using 454 Pyrosequencing.
The glassy-winged sharpshooter, Homalodisca vitripennis (Germar), is an invasive pest that has spread across the southern and western United States. H. vitripennis is highly polyphagous and voracious, feeding on at least 100 plant species and consuming up to 100 times its weight in xylem fluid daily. The insect is a vector of the phytopathogen Xylella fastidiosa (Wells), which is the causative agent of Pierce's disease in grapevines. To evaluate the microbial flora associated with H. vitripennis, total DNA extracts from hemolymph, alimentary canal excretions, and whole insect bodies were subjected to 16S rDNA pyrosequencing using the bTEFAP methodology and the resulting sequences (370-520 bp in length) were compared with a curated high quality 16S database derived from GenBank http://www.ncbi.nlm.nih.gov. Species from the genera Wolbachia, Delftia (formerly Pseudomonas), Pectobacterium, Moraxella, Serratia, Bacillus, and many others were detected and a comprehensive picture of the microbiome associated with H. vitripennis was established. Some of the bacteria identified in this report are initial discoveries; providing a breadth of knowledge to the microbial flora of this insect pest can serve as a reservoir of information for developing biological control strategies.
not annotated - annotated - LINNAEUS only
Infection by Mycorrhizal Fungi Increases Natural Enemy Abundance on Tobacco (Nicotiana rustica).
The presence of arbuscular mycorrhizal fungi (AMF) influences plant nutrient uptake, growth, and plant defensive chemistry, thereby directly influencing multi-trophic interactions. Different fungal isolates (genotypes of the same fungal species) have been shown to differ in nutrient uptake ability. Plants infected with different AMF genotypes may vary in foliar nutrient or defensive chemical levels, potentially influencing multi-trophic interactions. Using a completely randomized design, we compared the effect of two isolates of the mycorrhizal fungus Glomus etunicatum W. N. Becker & Gerdemann on silver leaf whitefly (Bemisia argentifolii Bellows & Perring) (Hemiptera: Aleyrodidae) and parasitic wasp (Eretmocerus eremicus Rose & Zolnerowich) (Hymenoptera: Aphelinidae) abundance. Whitefly populations were not influenced by AMF infection. Parasite populations were higher on plants infected with the isolate collected from Georgia, even after controlling for whitefly abundance and plant architecture. We propose that AMF indirectly influences parasite abundance and parasitism through a change in leaf surface chemicals that affect parasitic wasps. Because of the ubiquity of and genetic variation in AMF, multi-trophic interactions are likely to be strongly influenced by belowground processes.
not annotated - annotated - LINNAEUS only
The ability of selected pupal parasitoids (hymenoptera: pteromalidae) to locate stable fly hosts in a soiled equine bedding substrate.
The ability of Spalangia cameroni Perkins, Spalangia endius Walker, and Muscidifurax raptorellus Kogan and Legner to locate and attack stable fly hosts was evaluated under laboratory conditions. Postfeeding third-instar stable fly larvae were released and allowed to pupate in two arena types: large 4.8 liter chambers containing a field-collected, soiled equine bedding substrate; or 120-ml plastic cups containing wood chips. At the time of fly pupariation, parasitoids were released and permitted 72 h to locate and attack hosts. On average, parasitism rates of freely accessible stable fly pupae in cups were not significantly different between parasitoid species. However, parasitism rates in chambers containing either Spalangia spp. were =50-fold more than M. raptorellus. Additional intraspecies analysis revealed that parasitism rates both by S. cameroni and S. endius were not significantly different when pupae were freely accessible or within bedding, whereas M. raptorellus attacked significantly more pupae in cups than in the larger chambers where hosts were distributed within bedding. These results suggest that Spalangia spp. are more suited to successfully locate and attack hosts in habitats created by equine husbandry in Florida. Therefore, commercially available parasitoid mixtures containing Muscidifurax spp. may be ineffective if used as a control measure at Florida equine facilities.
not annotated - annotated - LINNAEUS only
Flavobacterium sinopsychrotolerans sp. nov., isolated from a glacier.
An aerobic, Gram-negative, yellow-pigmented bacterial strain, designated 0533(T), was isolated from frozen soil from the China No. 1 glacier. Phylogenetic analysis of the 16S rRNA gene sequence demonstrated that strain 0533(T) was a member of the genus Flavobacterium and exhibited 97.1-98.7 % 16S rRNA sequence similarity with its nearest phylogenetic neighbours. Strain 0533(T) exhibited phenotypic and chemotaxonomic characteristics common to the genus Flavobacterium: menaquinone-6 (MK-6) was the predominant quinone and iso-C(15 : 0), C(17 : 1)omega6c, anteiso-C(15 : 0), iso-C(15 : 0) 3-OH, C(15 : 1)omega6c, iso-C(16 : 0) 3-OH, summed feature 3 (comprising C(16 : 1)omega7c and/or C(16 : 1)omega6c), iso-C(15 : 1) G and iso-C(17 : 0) 3-OH were the major fatty acids (>5 %). The DNA G+C content was 32.5 mol%. On the basis of phenotypic and genotypic data, a novel species, Flavobacterium sinopsychrotolerans sp. nov., is proposed. The type strain is 0533(T) (=CGMCC 1.8704(T) =JCM 16398(T)).
not annotated - annotated - LINNAEUS only
Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore.
Two Gram-negative, strictly aerobic, non-motile bacteria designated strains KMM 3851(T) and KMM 3842(T) were respectively isolated from a marine snail specimen (Umbonium costatum) and from surrounding sediments collected simultaneously from the shore of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains KMM 3851(T) and KMM 3842(T) were affiliated with the Roseobacter lineage of the class Alphaproteobacteria as a separate phylogenetic line adjacent to the members of the genus Thalassobacter. These novel isolates shared 98.5 % 16S rRNA gene sequence similarity and 15 % DNA-DNA relatedness. The major isoprenoid quinone of both strains was Q-10 and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and aminophospholipids. In addition, strain KMM 3851(T) contained two unknown lipids, whereas strain KMM 3842(T) contained diphosphatidylglycerol. Fatty acid analysis revealed C(18 : 1)omega7c and C(16 : 0) as major components and small amounts of C(18 : 2). The DNA G+C contents were 60.4 mol% (KMM 3851(T)) and 58.5 mol% (KMM 3842(T)). Based on distinctive phenotypic characteristics, DNA-DNA hybridization data and phylogenetic distance, strains KMM 3851(T) and KMM 3842(T) should be classified as representatives of two novel species in a new genus, Litoreibacter gen. nov., with the type species Litoreibacter albidus sp. nov. (type strain KMM 3851(T) =NRIC 0773(T) =JCM 16493(T)) and a second species Litoreibacter janthinus sp. nov. (type strain KMM 3842(T) =NRIC 0772(T) =JCM 16492(T)).
not annotated - annotated - LINNAEUS only
Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., mesophilic methanogens isolated from salty environments.
Two methane-producing archaea, designated Mic5c12(T) and Mic6c05(T), were isolated from sludge deposited in a crude oil storage tank and a tubercle on the interior of a pipe transporting natural gas-containing brine, respectively. The isolates were Gram-staining-variable, non-motile rods and grew only on H(2)/CO(2). Strain Mic6c05(T) produced methane from some alcohols without showing any growth; strain Mic5c12(T) did not utilize alcohols. The optimum growth conditions for strain Mic5c12(T) were 35 ^0C, pH 6.5 and 0-0.68 M NaCl and for strain Mic6c05(T) were 40 ^0C, pH 6.0-7.5 and 0.34 M NaCl. Strain Mic5c12(T) was halotolerant and strain Mic6c05(T) was halophilic. Comparative 16S rRNA gene sequence analysis revealed that strains Mic5c12(T) and Mic6c05(T) belonged to the genus Methanobacterium and their closest relative was Methanobacterium subterraneum A8p(T) (97.3 and 97.9 % 16S rRNA gene sequence similarity, respectively). The findings from the 16S rRNA gene sequence analyses were supported by analysis of McrA, the alpha subunit of methyl-coenzyme M reductase. On the basis of phylogenetic analyses and phenotypic characteristics, two novel species are proposed, Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., with type strains Mic5c12(T) (=NBRC 105198(T) =DSM 22353(T)) and Mic6c05(T) (=NBRC 105197(T) =DSM 21974(T)), respectively.
not annotated - annotated - LINNAEUS only
Jiangella muralis sp. nov., from an indoor environment.
A Gram-stain-positive, non-spore-forming actinobacterium, designated 15-Je-017(T), was isolated from wall material of an indoor environment. The isolate formed a rudimentary substrate mycelium that fragmented into rod-shaped cells. On the basis of 16S rRNA gene sequence analysis, strain 15-Je-017(T) was shown to belong to the genus Jiangella and was most closely related to Jiangella alba YIM 61503(T) (99.7 % 16S rRNA gene sequence similarity), Jiangella alkaliphila D8-87(T) (99.0 %) and Jiangella gansuensis YIM 002(T) (99.0 %). The predominant menaquinone was MK-9(H(4)). Whole-cell hydrolysates contained ll-diaminopimelic acid as the diagnostic diamino acid in the cell wall and rhamnose and glucose as the main sugars. Mycolic acids were absent. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and seven unknown phospholipids. The fatty acid profile contained major amounts (>5 %) of anteiso-C(15 : 0), iso-C(16 : 0), iso-C(15 : 0), iso-C(17 : 0), anteiso-C(17 : 0) and C(17 : 1)omega8c, which supported the affiliation of strain 15-Je-017(T) to the genus Jiangella. DNA-DNA relatedness and physiological and biochemical tests allowed the differentiation of strain 15-Je-017(T) from the type strains of the three known Jiangella species. Strain 15-Je-017(T) represents a novel Jiangella species, for which we propose the name Jiangella muralis sp. nov., with type strain 15-Je-017(T) (=DSM 45357(T) =CCM 7680(T)).
not annotated - annotated - LINNAEUS only
Surveys of non-ribosomal peptide and polyketide assembly lines in fungi and prospects for their analysis in vitro and in vivo.
With many bioactive non-ribosomal peptides and polyketides produced in fungi, studies of their biosyntheses are an active area of research. Practical limitations of working with mega-dalton synthetases including cell lysis and protein extraction to recombinant gene and pathway expression has slowed understanding of many secondary metabolic processes relative to bacterial counterparts. Recent advances in accessing fungal biosynthetic machinery are beginning to change this. Here we describe the successes of some studies of thiotemplate biosynthesis in fungal systems, along with very recent advances in chemical tagging and mass spectrometric strategies to selectively study biosynthetic conveyer belts in isolation, and within a few years, in endogenous fungal proteomes.
not annotated - annotated - LINNAEUS only
OsEDR1 negatively regulates rice bacterial resistance via activation of ethylene biosynthesis.
Rice OsEDR1 is a sequence ortholog of Arabidopsis EDR1. However, its molecular function is unknown. We show here that OsEDR1-suppressing/knockout (KO) plants, which developed spontaneous lesions on the leaves, have enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo) causing bacterial blight disease. This resistance was associated with increased accumulation of salicylic acid (SA) and jasmonic acid (JA), induced expression of SA- and JA-related genes and suppressed accumulation of 1-aminocyclopropane-1-carboxylic acid (ACC), the direct precursor of ethylene, and expression of ethylene-related genes. OsEDR1-KO plants also showed suppressed production of ethylene. Knockout of OsEDR1 suppressed the ACC synthase (ACS) gene family, which encodes the rate-limiting enzymes of ethylene biosynthesis by catalysing the formation of ACC. The lesion phenotype and enhanced bacterial resistance of the OsEDR1-KO plants was partly complemented by the treatment with ACC. ACC treatment was associated with decreased SA and JA biosynthesis in OsEDR1-KO plants. In contrast, aminoethoxyvinylglycine, the inhibitor of ethylene biosynthesis, promoted expression of SA and JA synthesis-related genes in OsEDR1-KO plants. These results suggest that ethylene is a negative signalling molecule in rice bacterial resistance. In the rice-Xoo interaction, OsEDR1 transcriptionally promotes the synthesis of ethylene that, in turn, suppresses SA- and JA-associated defence signalling.
not annotated - annotated - LINNAEUS only
Characterizing demographic variation and contributions to population growth rate in a declining population.
1. Understanding how demographic variation translates into variation in population growth rate (lambda) is central to understanding population dynamics. Such understanding ideally requires knowledge of the mean, variance and covariance among all demographic rates, allowing the potential and realized contribution of each rate to lambda to be estimated. Such studies require integrated monitoring of all demographic rates across multiple years and are consequently rare, particularly in declining populations and for species with less tractable life histories. 2. We used 12 years of comprehensive demographic data from a declining ring ouzel (Turdus torquatus) population to estimate the mean, variance and covariance in all major demographic rates and estimate potential and realized demographic contributions to lambda. 3. Population size decreased from 39 to 13 breeding pairs (-67%) and mean lambda was 0*91 during 1998-2009. This decrease did not reflect a substantial concurrent decrease in any single key demographic rate, but reflected varying combinations of demographic rates that consistently produced lambda < 1. 4. Basic prospective elasticity analysis indicated that lambda was most sensitive to adult survival, closely followed by early season reproductive success and early brood first-year survival. In contrast, integrated elasticity analysis, accounting for estimated demographic covariance, indicated that lambda was most sensitive to early brood first-year survival, closely followed by re-nesting rate, early season reproductive success, late-brood first-year survival and adult survival. 5. Retrospective decomposition of variance suggested that first-year survival contributed most to observed variation in lambda. 6. However, demographic comparison with other related species suggested that adult survival, but not reproductive success or post-fledging survival, averaged lower than expected throughout the 12-year study. 7. These data demonstrate that multiple approaches, including comprehensive demographic and comparative analyses and due consideration of conflicting answers, may be necessary to accurately diagnose the demographic basis of population change.
not annotated - annotated - LINNAEUS only
Hydraulic constraints limit height growth in trees at high altitude.
* Low temperatures limit the fixation of photosynthates and xylogenesis. Here, we hypothesized that reduced longitudinal growth in trees at high altitude is related to the lower hydraulic efficiency of the transport system. * Apical buds of Norway spruce (Picea abies) trees at high and low elevation were heated during 2006 and 2007. At the end of the experiment, trees were felled. Longitudinal increments and tracheid lumen areas were measured along the stem. Apical hydraulic conductivity (k) was estimated from anatomical data. * Before heating, high-altitude trees showed fewer (P = 0.002) and smaller (P = 0.008) apical conduits, and therefore reduced k (P = 0.016) and stem elongation (P < 0.0001), in comparison with trees at low elevation. After 2 yr of heating, k increased at both high (P = 0.014) and low (P = 0.047) elevation. Only high-altitude trees showed increased stem elongation, which reached the same magnitude as that of controls at low elevation (P = 0.735). Heating around the apical shoots did not appear to induce significant changes in conduit dimension along the rest of the stem. * The total number and size of xylem elements at the stem apex are strongly constrained by low temperatures. Trees at high altitude are therefore prevented from building up an efficient transport system, and their reduced longitudinal growth reflects strong hydraulic limitations.
not annotated - annotated - LINNAEUS only
Physiological performance of an Alaskan shrub (Alnus fruticosa) in response to disease (Valsa melanodiscus) and water stress.
* Following the decades-long warming and drying trend in Alaska, there is mounting evidence that temperature-induced drought stress is associated with disease outbreaks in the boreal forest. Recent evidence of this trend is an outbreak of Cytospora canker disease (fungal pathogen Valsa melanodiscus (anamorph = Cytospora umbrina)) on Alnus species. * For Alnus fruticosa, we examined the effects of water stress on disease predisposition, and the effects of disease and water stress on host physiology. In two trials, we conducted a full-factorial experiment that crossed two levels of water stress with three types of inoculum (two isolates of V. melanodiscus, one control isolate). * Water stress was not required for disease predisposition. However, the effects of water stress and disease on host physiology were greatest near the peak phenological stage of the host and during hot, dry conditions. During this time, water stress and disease reduced light-saturated photosynthesis (-30%), light saturation point (-60%) and stomatal conductance (-40%). * Our results depended on the timing of water stress and disease in relation to host phenology and the environment. These factors should not be overlooked in attempts to generalize predictions about the role of temperature-induced drought stress in this pathosystem.
not annotated - annotated - LINNAEUS only
The novel marine gliding zooflagellate genus Mantamonas (Mantamonadida ord. n.: Apusozoa).
Mantamonas is a novel genus of marine gliding zooflagellates probably related to apusomonad and planomonad Apusozoa. Using phase and differential interference contrast microscopy we describe the type species Mantamonas plastica sp. n. from coastal sediment in Cumbria, England. Cells are -5mum long, -5mum wide, asymmetric, flattened, biciliate, and somewhat plastic. The posterior cilium, on which they glide smoothly over the substratum, is long and highly acronematic. The much thinner, shorter, and almost immobile anterior cilium points forward to the cell's left. These morphological and behavioural traits suggest that Mantamonas is a member of the protozoan phylum Apusozoa. Analyses of 18S and 28S rRNA gene sequences of Mantamonas plastica and a second genetically very different marine species from coastal sediment in Tanzania show Mantamonas as a robustly monophyletic clade, that is very divergent from all other eukaryotes. 18S rRNA trees mostly place Mantamonas within unikonts (opisthokonts, Apusozoa, and Amoebozoa) but its precise position varies with phylogenetic algorithm and/or taxon and nucleotide position sampling; it may group equally weakly as sister to Planomonadida, Apusomonadida or Breviata. On 28S rRNA and joint 18/28S rRNA phylogenies (including 11 other newly obtained apusozoan/amoebozoan 28S rRNA sequences) it consistently strongly groups with Apusomonadida (Apusozoa).
not annotated - annotated - LINNAEUS only
Scaling of swim speed in breath-hold divers.
1. Breath-hold divers are widely assumed to descend and ascend at the speed that minimizes energy expenditure per distance travelled (the cost of transport (COT)) to maximize foraging duration at depth. However, measuring COT with captive animals is difficult, and empirical support for this hypothesis is sparse. 2. We examined the scaling relationship of swim speed in free-ranging diving birds, mammals and turtles (37 species; mass range, 0*5-90,000 kg) with phylogenetically informed statistical methods and derived the theoretical prediction for the allometric exponent under the COT hypothesis by constructing a biomechanical model. 3. Swim speed significantly increased with mass, despite considerable variations around the scaling line. The allometric exponent (0*09) was statistically consistent with the theoretical prediction (0*05) of the COT hypothesis. 4. Our finding suggests a previously unrecognized advantage of size in divers: larger animals swim faster and thus could travel longer distance, search larger volume of water for prey and exploit a greater range of depths during a given dive duration. 5. Furthermore, as predicted from the model, endotherms (birds and mammals) swam faster than ectotherms (turtles) for their size, suggesting that metabolic power production limits swim speed. Among endotherms, birds swam faster than mammals, which cannot be explained by the model. Reynolds numbers of small birds (<2 kg) were close to the lower limit of turbulent flow (- 3 x 10(5) ), and they swam fast possibly to avoid the increased drag associated with flow transition.
not annotated - annotated - LINNAEUS only
Stable isotope labelling and zinc distribution in grains studied by laser ablation ICP-MS in an ear culture system reveals zinc transport barriers during grain filling in wheat.
Zinc (Zn) deficiency has been recognized as a potential risk for human health in many developing regions where staple food with low micronutrient density represents a major proportion of the diet. The success of strategies to increase Zn content in the edible part of crops requires better understanding of Zn transport to, and distribution within, the grains. The transfer of Zn from the growth medium to wheat (Triticum aestivum) grains in an ear culture system was investigated by using the stable Zn isotope (70) Zn, and the spatial distribution of Zn within the grains was studied by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). Zinc was readily transported in the stem up to the rachis. More Zn accumulated in the stem when higher amounts of Zn were supplied to the medium. Once Zn was transported into the grain, Zn accumulated particularly in the crease vascular tissue. The gradient of (70) Zn concentration between crease vascular tissue, aleurone layer and endosperm demonstrates that Zn is distributed within grain through the crease phloem. These results suggest that two barriers of Zn transport into wheat grains may exist: between the stem tissue rachis and the grain, and the maternal and filial tissues in the grain.
not annotated - annotated - LINNAEUS only
Differential expression of odorant receptor genes involved in the sexual isolation of two Heliothis moths.
Moth sexual communication systems are highly diverse, but the mechanisms underlying their evolutionary diversification remain unclear. Recently, genes coding for odorant receptors (ORs) OR6, OR14, OR15 and OR16 have been genetically associated with species-specific male response to female pheromone blends in Heliothis virescens (Hv) and Heliothis subflexa (Hs). Quantitative real-time PCR analysis indicates that expression of HvOR6, HsOR6, HvOR14, HsOR14, HvOR15 and HsOR15 is male biased, which supports the hypothesis that they have a role in mediating female sex pheromone detection. The genes HvOR14, HvOR15 and HvOR16 are expressed at higher levels than their corresponding orthologues HsOR14, HsOR15 and HsOR16 in male antennae, while HvOR6 and HsOR6 transcripts are equally abundant in male antennae. The lack of higher expression of any of the receptor genes in H. subflexa antennae suggests that interspecific sequence differences, rather than gene regulation differences, underly the species-specific male response to pheromone components.
not annotated - annotated - LINNAEUS only
Cryptogein, a fungal elicitor, remodels the phenylpropanoid metabolism of tobacco cell suspension cultures in a calcium-dependent manner.
Plant cells use calcium-based signalling pathways to transduce biotic and/or abiotic stimuli into adaptive responses. However, little is known about the coupling between calcium signalling, transcriptional regulation and the downstream biochemical processes. To understand these relationships better, we challenged tobacco BY-2 cells with cryptogein and evaluated how calcium transients (monitored through the calcium sensor aequorin) impact (1) transcript levels of phenylpropanoid genes (assessed by RT-qPCR); and (2) derived-phenolic compounds (analysed by mass spectrometry). Most genes of the phenylpropanoid pathway were up-regulated by cryptogein and cell wall-bound phenolic compounds accumulated (mainly 5-hydroxyferulic acid). The accumulation of both transcripts and phenolics was calcium-dependent. The transcriptional regulation of phenylpropanoid genes was correlated in a non-linear manner with stimulus intensity and with components of the cryptogein-induced calcium signature. In addition, calmodulin inhibitors increased the sensitivity of cells to low concentrations of cryptogein. These results led us to propose a model of coupling between the cryptogein signal, calcium signalling and the transcriptional response, exerting control of transcription through the coordinated action of two decoding modules exerting opposite effects.
not annotated - annotated - LINNAEUS only
Rapid detection of drug-resistant mutations in hepatitis B virus by the PCR-Invader assay.
Early detection of resistant mutations of hepatitis B virus (HBV) is important for patients on nucleos(t)ide analog therapy. An assay based on the PCR-Invader technology was developed to detect resistant mutations with high sensitivity. The assay specifically detects mutations at codons 180, 181, 184, 202, 204, and 250 of the HBV polymerase reverse transcriptase domain. These mutations result in resistance to lamivudine and entecavir. In mixtures of plasmids containing wild-type and resistant mutants, fold-over-zero values for resistant mutations were detected in 2% of the total. Seventy-five serum samples from patients, whose treatment had been switched from lamivudine to entecavir, were examined by the PCR-Invader assay and direct sequencing. The PCR-Invader assay detected all resistant mutations that were detected by direct sequencing and even detected the presence of mutants that direct sequencing could not. Cloning sequencing confirmed those mutations found by the PCR-Invader assay and not by direct sequencing. The PCR-Invader assay is a useful tool for the early detection of drug-resistant mutations.
not annotated - annotated - LINNAEUS only
Separating parental environment from seed size effects on next generation growth and development in Arabidopsis.
Plant growth and development is profoundly influenced by environmental conditions that laboratory experimentation typically attempts to control. However, growth conditions are not uniform between or even within laboratories and the extent to which these differences influence plant growth and development is unknown. Experiments with wild-type Arabidopsis thaliana were designed to quantify the influences of parental environment and seed size on growth and development in the next generation. A single lot of seed was planted in six environmental chambers and grown to maturity. The seed produced was mechanically sieved into small and large size classes then grown in a common environment and subjected to a set of assays spanning the life cycle. Analysis of variance demonstrated that seed size effects were particularly significant early in development, affecting primary root growth and gravitropism, but also flowering time. Parental environment affected progeny germination time, flowering and weight of seed the progeny produced. In some cases, the parental environment affected the magnitude of (interacted with) the observed seed size effects. These data indicate that life history circumstances of the parental generation can affect growth and development throughout the life cycle of the next generation to an extent that should be considered when performing genetic studies.
not annotated - annotated - LINNAEUS only
The first vitellogenin receptor from a Lepidopteran insect: molecular characterization, expression patterns and RNA interference analysis.
The vitellogenin receptor (VgR) belongs to the low-density lipoprotein receptor (LDLR) superfamily, and is an important carrier for the uptake of vitellogenin (Vg) into developing oocytes of all oviparous species. The first full-length message for a VgR from a Lepidopteran insect was cloned and sequenced from the ovary of Spodoptera litura Fabricius (GenBank accession no. GU983858). The coding region consisted of 5370 bp flanked by a 49 bp 5'-untranslated region (UTR) and a 177 bp 3'-UTR, which encoded a 1798-residue protein with a predicted molecular weight (MW) of 201.69 kDa. S. litura VgR (SlVgR)comprised two ligand binding sites with four LDLR class A repeats in the first domain and seven in the second domain, an epidermal growth factor-like domain containing an LDLR class B repeat and a YWXD motif, a transmembrane domain and a cytoplasmic domain. A phylogenetic relationship placed SlVgR as a separate group from the other insects. SlVgR messenger RNA (mRNA) was specifically expressed in the ovarian tissues. The developmental expression patterns showed that VgR mRNA was first transcribed in 6(th) day female pupae and the maximum level of VgR mRNA appeared in 36-h-old adults. Immunoblot analysis detected an ovary-specific VgR protein with a MW of -200 kDa, whose development profiles were consistent with VgR mRNA expression patterns. RNA inteference (RNAi) specifically disrupted the VgR gene by injection of 3 or 5 mug VgR double-stranded RNA per insect in 4(th) or 6(th) day pupae. RNAi of SlVgR led to a phenotype characterized by high Vg accumulation in the haemolymph, low Vg deposition in the ovary and the failure of insect spawning. These results mean that VgR is critical for binding Vg and transporting it into the oocytes of the insect ovary, thus playing an important role in insect reproduction.
not annotated - annotated - LINNAEUS only
Simian immunodeficiency virus from the sooty mangabey and rhesus macaque is modified with O-linked carbohydrate.
Although stretches of serine and threonine are sometimes sites for O-linked carbohydrate attachment, specific sequence and structural determinants for O-linked attachment remain ill defined. The gp120 envelope protein of SIVmac239 contains a serine-threonine-rich stretch of amino acids at positions 128 to 139. Here we show that lectin protein from jackfruit seed (jacalin), which binds to non- and monosialylated core 1 O-linked carbohydrate, potently inhibited the replication of SIVmac239. Selection of a jacalin-resistant SIVmac239 variant population resulted in virus with specific substitutions within amino acids 128 to 139. Cloned simian immunodeficiency virus (SIV) variants with substitutions in the 128-to-139 region had infectivities equivalent to, or within 1 log unit of, that of SIVmac239 and were resistant to the inhibitory effects of jacalin. Characterization of the SIVmac239 gp120 O-linked glycome showed the presence of core 1 and core 2 O-linked carbohydrate; a 128-to-139-substituted variant gp120 from jacalin-resistant SIV lacked O-linked carbohydrate. Unlike that of SIVmac239, the replication of HIV-1 strain NL4-3 was resistant to inhibition by jacalin. Purified gp120s from four SIVmac and SIVsm strains bound jacalin strongly in an enzyme-linked immunosorbent assay, while nine different HIV-1 gp120s, two SIVcpz gp120s, and 128-to-139-substituted SIVmac239 gp120 did not bind jacalin. The ability or inability to bind jacalin thus correlated with the presence of the serine-threonine-rich stretch in the SIVmac and SIVsm gp120s and the absence of such stretches in the SIVcpz and HIV-1 gp120s. Consistent with sequence predictions, two HIV-2 gp120s bound jacalin, while one did not. These data demonstrate the presence of non- and monosialylated core 1 O-linked carbohydrate on the gp120s of SIVmac and SIVsm and the lack of these modifications on HIV-1 and SIVcpz gp120s.
not annotated - annotated - LINNAEUS only
Varicella-zoster virus glycoprotein E is a critical determinant of virulence in the SCID mouse-human model of neuropathogenesis.
Varicella-zoster virus (VZV) is a neurotropic alphaherpesvirus. VZV infection of human dorsal root ganglion (DRG) xenografts in immunodeficient mice models the infection of sensory ganglia. We examined DRG infection with recombinant VZV (recombinant Oka [rOka]) and the following gE mutants: gEDelta27-90, gEDeltaCys, gE-AYRV, and gE-SSTT. gEDelta27-90, which lacks the gE domain that interacts with a putative receptor insulin-degrading enzyme (IDE), replicated as extensively as rOka, producing infectious virions and significant cytopathic effects within 14 days of inoculation. Since neural cells express IDE, the gE/IDE interaction was dispensable for VZV neurotropism. In contrast, gEDeltaCys, which lacks gE/gI heterodimer formation, was significantly impaired at early times postinfection; viral genome copy numbers increased slowly, and infectious virus production was not detected until day 28. Delayed replication was associated with impaired cell-cell spread in ganglia, similar to the phenotype of a gI deletion mutant (rOkaDeltagI). However, at later time points, infection of satellite cells and other supportive nonneuronal cells resulted in extensive DRG tissue damage and cell loss such that cytopathic changes observed at day 70 were more severe than those for rOka-infected DRG. The replication of gE-AYRV, which is impaired for trans-Golgi network (TGN) localization, and the replication of gE-SSTT, which contains mutations in an acidic cluster, were equivalent to that of rOka, causing significant cytopathic effects and infectious virus production by day 14; genome copy numbers were equivalent to those of rOka. These experiments suggest that the gE interaction with cellular IDE, gE targeting to TGN sites of virion envelopment, and phosphorylation at SSTT are dispensable for VZV DRG infection, whereas the gE/gI interaction is critical for VZV neurovirulence.
not annotated - annotated - LINNAEUS only
Antiviral effects of a transgenic RNA-dependent RNA polymerase.
Transgenic expression of the RNA-dependent RNA polymerase 3D(pol) inhibited infection of Theiler's murine encephalitis virus (TMEV), a picornavirus from which it was derived. Here, we infected 3D(pol) transgenic mice with another picornavirus, as well as an alphaherpesvirus and a rhabdovirus. 3D(pol) transgenic FVB mice had significantly lower viral loads and survived longer after infection with all three types of viruses than nontransgenic FVB mice. Viral inhibition among three different types of virus by transgenic 3D(pol) suggests that the mechanism of action is not the direct interference with picornaviral 3D(pol) but instead may be the changing of host cells to an antiviral state before or after viral infection occurs, as basal interferon levels were higher in 3D(pol) transgenic mice before infection. Further study of this mechanism may open new possibilities for future antiviral therapy.
not annotated - annotated - LINNAEUS only
Parasitoid developmental mortality in the field: patterns, causes and consequences for sex ratio and virginity.
1. Sex ratio theory predicts that developmental mortality can affect sex ratio optima under Local Mate Competition and also lead to 'virgin' broods containing only females with no sibling-mating opportunities on maturity. 2. Estimates of developmental mortality and its sex ratio effects have been laboratory based, and both models and laboratory studies have treated mortality as a phenomenon without identifying its biological causes. 3. We contribute a large set of field data on Metaphycus luteolus Timberlake (Hymenoptera: Encyrtidae), an endoparasitoid of soft scale insects (Hemiptera: Coccidae), which has sex allocation conditional on host quality and female-biased brood sex ratios. Developmental mortality within broods can be both assessed and attributed to distinct causes, including encapsulation by the host and larval-larval competition. 4. Thirty per cent of M. luteolus offspring die during development with 65% of this mortality because of encapsulation and 28% because of larval competition. The distributions of mortality overall and for each cause of mortality separately were overdispersed. 5. The probability of an individual being encapsulated increased with clutch size, while the probability of being killed by a brood mate declined with increasing clutch size and with increasing per capita availability of resources. 6. The sexual compositions of broods at emergence were influenced by both the degree and the type of mortality operating. At higher levels of mortality, single sex broods were more common and sex ratios were less precise. Overall, virginity was more prevalent than predicted and was more greatly affected by the occurrence of competition than by other sources of mortality, almost certainly because competition tended to eliminate males. 7. The reproductive and developmental biology of M. luteolus appears to be influenced by a complex interplay of maternal clutch size and sex allocation strategies, offspring-offspring developmental interactions, host defence mechanisms and postemergence mating behaviour. Despite the great sophistication of sex ratio theory, it has not yet evolved to the point where it is capable of considering all of these influences simultaneously.
not annotated - annotated - LINNAEUS only
The degree of mycoheterotrophic carbon gain in green, variegated and vegetative albino individuals of Cephalanthera damasonium is related to leaf chlorophyll concentrations.
* Achlorophyllous variants of some forest orchids are known to reach almost the same size as their green forms. These vegetative albino forms cover their entire carbon (C) demand through fungi that simultaneously form ectomycorrhizae with trees, while green variants partially draw on C from photosynthesis and C from fungal hosts. Here, we investigate whether the amount of C derived from either source is proportional to leaf chlorophyll concentration. The discovery of two Cephalanthera damasonium populations with variegated leaves enabled a continuous bridging of leaf chlorophyll concentrations between green and albino forms. * Leaves of 27 green, variegated and albino individuals of C. damasonium were compared for chlorophyll concentrations, C sources (as characterized by (13)C abundances) and total C and nitrogen (N) concentrations. * We found a linear relationship between leaf chlorophyll concentrations and the proportional reliance on fungi as a C source. Furthermore, we show that the shift in C gain through mycoheterotrophic means significantly changes leaf total C and N concentrations. * Our results document that partial mycoheterotrophy in C. damasonium is not a static nutritional mode but a flexible mechanism related inter alia to leaf chlorophyll concentrations. The change in proportional reliance on fungi as a C source affects leaf chemical composition.
not annotated - annotated - LINNAEUS only
Assembly of the type II secretion system: identification of ExeA residues critical for peptidoglycan binding and secretin multimerization.
Aeromonas hydrophila secretes a number of protein toxins across the outer membrane via the type II secretion system (T2SS). Assembly of the secretion channel ExeD secretin into the outer membrane is dependent on the peptidoglycan binding domain of ExeA. In this study, the peptidoglycan binding domain PF01471 family members were divided into a prokaryotic group and a eukaryotic group. By comparison of their sequence conservation profiles and their representative crystal structures, we found the prokaryotic members to have a highly conserved pocket(s) that is not present in the eukaryotic members. Substitution mutations of nine amino acids of the pocket were constructed in ExeA. Five of the substitution derivatives showed greatly decreased lipase secretion, accompanied by defects in secretin assembly. In addition, using in vivo cross-linking and in vitro cosedimentation assays, we showed that these mutations decreased ExeA-peptidoglycan interactions. These results suggest that the highly conserved pocket in ExeA is the binding site for its peptidoglycan ligand and identify residues critical for this binding.
not annotated - annotated - LINNAEUS only
Translational control of the abundance of cytoplasmic poly(A) binding protein in human cytomegalovirus-infected cells.
Irrespective of their effects on ongoing host protein synthesis, productive replication of the representative alphaherpesvirus herpes simplex virus type 1, the representative gammaherpesvirus Kaposi's sarcoma herpesvirus, and the representative betaherpesvirus human cytomegalovirus [HCMV] stimulates the assembly of the multisubunit, cap-binding translation factor eIF4F. However, only HCMV replication is associated with an increased abundance of eIF4F core components (eIF4E, eIF4G, eIF4A) and the eIF4F-associated factor poly(A) binding protein (PABP). Here, we demonstrate that the increase in translation factor concentration was readily detected in an asynchronous population of HCMV-infected primary human fibroblasts, abolished by prior UV inactivation of virus, and genetically dependent upon viral immediate-early genes. Strikingly, while increased mRNA steady-state levels accompanied the rise in eIF4E and eIF4G protein levels, the overall abundance of PABP mRNA, together with the half-life of the polypeptide it encodes, remained relatively unchanged by HCMV infection. Instead, HCMV-induced PABP accumulation resulted from new protein synthesis and was sensitive to the mTORC1-selective inhibitor rapamycin, which interferes with phosphorylation of the mTORC1 substrate p70 S6K and the translational repressor 4E-BP1. While virus-induced PABP accumulation did not require p70 S6K, it was inhibited by the expression of a dominant-acting 4E-BP1 variant unable to be inactivated by mTORC1. Finally, unlike the situation in alpha- or gammaherpesvirus-infected cells, where PABP is redistributed to nuclei, PABP accumulated in the cytoplasm of HCMV-infected cells. Thus, cytoplasmic PABP accumulation is translationally controlled in HCMV-infected cells via a mechanism requiring mTORC1-mediated inhibition of the cellular 4E-BP1 translational repressor.
not annotated - annotated - LINNAEUS only
A new model of Epstein-Barr virus infection reveals an important role for earlylytic viral protein expression in the development of lymphomas.
Epstein-Barr virus (EBV) infects cells in latent or lytic forms, but the roleof lytic infection in EBV-induced lymphomas is unclear. Here, we have used anew humanized mouse model, in which both human fetal CD34(+) hematopoietic stemcells and thymus/liver tissue are transplanted, to compare EBV pathogenesis andlymphoma formation following infection with a lytic replication-defectiveBZLF1-deleted (Z-KO) virus or a lytically active BZLF1(+) control. Both thecontrol and Z-KO viruses established long-term viral latency in all infectedanimals. The infection appeared well controlled in some animals, but otherseventually developed CD20(+) diffuse large B cell lymphomas (DLBCL). Animalsinfected with the control virus developed tumors more frequently than Z-KOvirus-infected animals. Specific immune responses against EBV-infected B cellswere generated in mice infected with either the control virus or the Z-KOvirus. In both cases, forms of viral latency (type I and type IIB) wereobserved that are less immunogenic than the highly transforming form (type III)commonly found in tumors of immunocompromised hosts, suggesting that immunepressure contributed to the outcome of the infection. These results point to animportant role for lytic EBV infection in the development of B cell lymphomasin the context of an active host immune response.
not annotated - annotated - LINNAEUS only
Serine-threonine ubiquitination mediates downregulation of BST-2/tetherin and relief of restricted virion release by HIV-1 Vpu.
The HIV-1 protein Vpu counteracts the antiviral activity of the innate restriction factor BST-2/tetherin by a mechanism that partly depends on its interaction with Beta-TrCP, a substrate adaptor for an SCF (Skp-Cullin 1-F box) E3 ubiquitin ligase complex. This suggests that Vpu stimulates the ubiquitination of BST-2 and that this underlies the relief of restriction. Here, we show that Vpu stimulates ubiquitination of BST-2. Mutation of all potential ubiquitination sites in the cytoplasmic domain of BST-2, including lysines, cysteines, serines, and threonines, abrogates Vpu-mediated ubiquitination. However, a serine-threonine-serine sequence specifically mediates the downregulation of BST-2 from the cell surface and the optimal relief of restricted virion release. Serine-threonine ubiquitination of BST-2 is likely part of the mechanism by which Vpu counteracts innate defenses.
not annotated - annotated - LINNAEUS only
R5 HIV env and vesicular stomatitis virus G protein cooperate to mediate fusion to naive CD4+ T Cells.
Naive CD4(4) T cells are resistant to both HIV R5 env and vesicular stomatitis virus G protein (VSV-G)-mediated fusion. However, viral particles carrying both HIV R5 env and VSV-G infect naive cells by an unexplained mechanism. We show that VSV-G-pseudotyped virus cannot fuse to unstimulated cells because the viral particles cannot be endocytosed. However, virions carrying both HIV R5 env and VSV-G can fuse because CD4 binding allows viral uptake. Our findings reveal a unique mechanism by which R5 HIV env and VSV-G cooperate to allow entry to naive CD4(+) T cells, providing a tool to target naive CD4(+) T cells with R5 HIV to study HIV coreceptor signaling and latency.
not annotated - annotated - LINNAEUS only
A recombinant measles virus unable to antagonize STAT1 function cannot control inflammation and is attenuated in rhesus monkeys.
Measles remains a leading cause of death worldwide among children because it suppresses immune function. The measles virus (MV) P gene encodes three proteins (P, V, and C) that interfere with innate immunity, controlling STAT1, STAT2, mda5, and perhaps other key regulators of immune function. We identified here three residues in the shared domain of the P and V proteins-tyrosine 110, valine 112, and histidine 115-that function to retain STAT1 in the cytoplasm and inhibit interferon transcription. This information was used to generate a recombinant measles virus unable to antagonize STAT1 function (STAT1-blind MV) differing only in these three residues from a wild-type strain of well-defined virulence. This virus was used to assess the relevance of P and V interactions with STAT1 for virulence in primates. When a group of six rhesus monkeys (Macaca mulatta) was inoculated intranasally with STAT1-blind MV, viremia was short-lived, and the skin rash and other clinical signs observed with wild-type MV were absent. The STAT1-blind virus less efficiently controlled the inflammatory response, as measured by enhanced transcription of interleukin-6 and tumor necrosis factor alpha in peripheral blood mononuclear cells from infected hosts. Importantly, neutralizing antibody titers and MV-specific T-cell responses were equivalent in hosts infected with either virus. These findings indicate that efficient MV interactions with STAT1 are required to sustain virulence in a natural host by controlling the inflammatory response against the virus. They also suggest that selectively STAT1-blind MV may have utility as vectors for targeted oncolysis and vaccination.
not annotated - annotated - LINNAEUS only
RNA aptamers directed to human immunodeficiency virus type 1 Gag polyprotein bind to the matrix and nucleocapsid domains and inhibit virus production.
Gag orchestrates the assembly and release of human immunodeficiency virus type 1 (HIV-1) particles. We explored here the potential of anti-Gag RNA aptamers to inhibit HIV-1 replication. In vitro, RNA aptamers raised against an HIV-1 Gag protein, lacking the N-terminal myristate and the C-terminal p6 (DP6-Gag), could bind to matrix protein (MA), nucleocapsid protein (NC), or entire DP6-Gag protein. Upon cotransfection with pNL4-3.Luc molecular clone into 293T cells, six of the aptamers caused mild inhibition (2- to 3-fold) in the extracellular capsid levels, and one aptamer displayed 20-fold inhibition. The reduction was not due to a release defect but reflected Gag mRNA levels. We hypothesized that the aptamers influence genomic RNA levels via perturbation of specific Gag-genomic RNA interactions. Binding studies revealed that the "NC-binders" specifically compete with the packaging signal (psi) of HIV-1 for binding to DP6-Gag. Therefore, we tested the ability of two NC-binders to inhibit viruses containing psi-region deletions (DeltaSL1 or DeltaSL3) and found that the NC-binders were no longer able to inhibit Gag synthesis. The inability of these aptamers to inhibit psi-deleted viruses correlated with the absence of competition with the corresponding psi transcripts lacking SL1 or SL3 for binding DP6-Gag in vitro. These results indicate that the NC-binding aptamers disrupt Gag-genomic RNA interaction and negatively affect genomic RNA transcription, processing, or stability. Our results reveal an essential interaction between HIV-1 Gag and the psi-region that may be distinct from that which occurs during the encapsidation of genomic RNA. Thus, anti-Gag aptamers can be an effective tool to perturb Gag-genomic RNA interactions.
not annotated - annotated - LINNAEUS only
Energy metabolism in amyotrophic lateral sclerosis.
Amyotrophic lateral sclerosis (ALS) is characterised by the progressive degeneration of upper and lower motor neurons. Besides motor neuron degeneration, ALS is associated with several defects in energy metabolism, including weight loss, hypermetabolism, and hyperlipidaemia. Most of these abnormalities correlate with duration of survival, and available clinical evidence supports a negative contribution of defective energy metabolism to the overall pathogenic process. Findings from animal models of ALS support this view and provide insights into the underlying mechanisms. Altogether, these results have clinical consequences for the management of defective energy metabolism in patients with ALS and pave the way for future therapeutic interventions.
not annotated - annotated - LINNAEUS only
A small protein required for the switch from {sigma}F to {sigma}G during sporulation in Bacillus subtilis.
A cascade of alternative sigma factors governs the program of developmental gene expression during sporulation in Bacillus subtilis. Little is known, however, about how the early-acting sigma factors are inactivated and replaced by the later-acting factors. Here we identify a small protein, Fin (formerly known as YabK), that is required for efficient switching from sigma(F)- to sigma(G)-directed gene expression in the forespore compartment of the developing sporangium. The fin gene, which is conserved among Bacillus species and species of related genera, is transcribed in the forespore under the control of both sigma(F) and sigma(G). Cells mutant for fin are unable to fully deactivate sigma(F) and, conversely, are unable to fully activate sigma(G). Consistent with their deficiency in sigma(G)-directed gene expression, fin cells are arrested in large numbers following the engulfment stage of sporulation, ultimately forming 50-fold fewer heat-resistant spores than the wild type. Based in part on the similarity of Fin to the anti-sigma(G) factor CsfB (also called Gin), we speculate that Fin is an anti-sigma(F) factor which, by disabling sigma(F), promotes the switch to late developmental gene expression in the forespore.
not annotated - annotated - LINNAEUS only
Activation of the SoxR regulon in Streptomyces coelicolor by the extracellular form of the pigmented antibiotic actinorhodin.
The redox-sensitive transcription factor SoxR in enteric bacteria senses and regulates the cellular response to superoxide and nitric oxide. In other bacterial groups, however, it may respond to redox-active small molecules, as demonstrated for pyocyanin sensing in pseudomonads. The antibiotic-producing soil bacterium Streptomyces coelicolor contains a gene for an SoxR homologue (SCO1697) whose DNA recognition helix is identical to that of Escherichia coli SoxR. Using the E. coli SoxR binding sequence, we predicted five candidate genes of the SoxR regulon and demonstrated that SoxR binds to their promoter regions and activates their expression concurrently with the production of the blue antibiotic actinorhodin (a benzoisochromanequinone). These genes encode a probable NADPH-dependent flavin reductase (SCO2478), an NADPH-dependent quinone reductase (SCO4266), an ABC transporter (SCO7008), a monooxygenase (SCO1909), and a hypothetical protein (SCO1178). Addition of actinorhodin to exponentially growing cells activated the expression of SoxR target genes in an SoxR-dependent manner. The secreted gamma-actinorhodin was over 10-fold more effective in activation than the intracellular form of actinorhodin, suggesting that SoxR is specified to respond more to exogenous signals than to intracellular metabolites. The DeltasoxR mutant was not compromised in resistance against oxidants but was slow in forming aerial mycelium on R2YE medium with reduced sporulation, and its production of actinorhodin and undecylprodigiosin was lowered by about 50% and 30%, respectively, compared to that of the wild type. These results support the proposal that SoxR senses redox-active molecules, such as actinorhodin in S. coelicolor, and induces a protective function against them. It also functions to ensure that cells undergo optimal differentiation and secondary metabolite production.
not annotated - annotated - LINNAEUS only
Ecological trade-offs between jasmonic acid-dependent direct and indirect plant defences in tritrophic interactions.
Recent studies on plants genetically modified in jasmonic acid (JA) signalling support the hypothesis that the jasmonate family of oxylipins plays an important role in mediating direct and indirect plant defences. However, the interaction of two modes of defence in tritrophic systems is largely unknown. In this study, we examined the preference and performance of a herbivorous leafminer (Liriomyza huidobrensis) and its parasitic wasp (Opius dissitus) on three tomato genotypes: a wild-type (WT) plant, a JA biosynthesis (spr2) mutant, and a JA-overexpression 35S::prosys plant. Their proteinase inhibitor production and volatile emission were used as direct and indirect defence factors to evaluate the responses of leafminers and parasitoids. Here, we show that although spr2 mutant plants are compromised in direct defence against the larval leafminers and in attracting parasitoids, they are less attractive to adult flies compared with WT plants. Moreover, in comparison to other genotypes, the 35S::prosys plant displays greater direct and constitutive indirect defences, but reduced success of parasitism by parasitoids. Taken together, these results suggest that there are distinguished ecological trade-offs between JA-dependent direct and indirect defences in genetically modified plants whose fitness should be assessed in tritrophic systems and under natural conditions.
not annotated - annotated - LINNAEUS only
The absence of sex-biased dispersal in the cooperatively breeding grey-crowned babbler.
1. Cooperatively breeding birds are thought to be especially vulnerable to habitat fragmentation, in part because dispersal is typically restricted for one sex, increasing the likelihood of inbreeding. Knowledge of dispersal is essential to conservation efforts, but is often hampered by our inability to measure its frequency and distance when dispersal is infrequent and difficult to observe. 2. Disrupted dispersal is a purported cause of decline in the Australian grey-crowned babbler (Pomatostomus temporalis). Both sexes of offspring delay dispersal for up to several years to help parents raise subsequent broods, yet little else is known about the dispersal of this cooperatively breeding woodland bird. 3. As both sexes appear to help, but only male helpers boost fledgling production, we hypothesized that males would be the more philopatric sex in this species, and that female grey-crowned babblers would disperse over greater distances. 4. To ensure reliable determination of sex and minimize bias towards detecting short-distance dispersal events, we combined molecular-based sexing and analyses of population genetic structure using polymorphic microsatellite loci with observational data obtained over multiple field seasons. 5. Observations of banded birds showed only infrequent fission of groups or short-distance dispersal (mean=854 m), but no apparent sex-bias in these patterns. 6. There was significant genetic differentiation between social groups, but not between the sexes. Spatial genetic autocorrelation analysis of breeders revealed a random distribution of genotypes across the study area for both sexes. Thus, contrary to expectations, we found no genetic evidence for restricted dispersal or for sex-biased dispersal over the 85-km scale of this study, indicating that effective dispersal occurs over greater distances and more frequently than recoveries of banded birds indicated. 7. We conclude that while constraints on independent breeding encourage high rates of philopatry, incest avoidance nonetheless drives high rates of dispersal by both sexes. In fragmented habitat, the dispersal dynamics of this cooperatively breeding species are unlikely to render them particularly vulnerable to genetic consequences such as inbreeding, but may lead to increased group dissolution.
not annotated - annotated - LINNAEUS only
Dual Delta^1^3C/delta^1^8O response to water and nitrogen availability and its relationship with yield in field-grown durum wheat.
The combined use of stable carbon and oxygen isotopes in plant matter is a tool of growing interest in cereal crop management and breeding, owing to its relevance for assessing the photosynthetic and transpirative performance under different growing conditions including water and N regimes. However, this method has not been applied to wheat grown under real field conditions. Here, plant growth, grain yield (GY) and the associated agronomic components, carbon isotope discrimination (Delta^1^3C) plus oxygen isotope composition (delta^1^8O) as well as leaf and canopy gas exchange were measured in field-grown wheat subjected to different water and N availabilities. Water limitation was the main factor affecting yield, leaf and canopy gas exchange and Delta^1^3C and delta^1^8O, whereas N had a smaller effect on such traits. The combination of Delta^1^3C and delta^1^8O gave a clear advantage compared with gas exchange measurements, as it provides information on the instantaneous and the long-term plant photosynthetic and transpirative performance and are less labour intensive than gas exchange measurements. In addition, the combination of plant Delta^1^3C and delta^1^8O predicted differences in GY and related agronomical parameters, providing agronomists and breeders with integrative traits for selecting crop management practices and/or genotypes with better performance under water-limiting and N-limiting conditions.
not annotated - annotated - LINNAEUS only
Climate, history and neutrality as drivers of mammal beta diversity in Europe: insights from multiscale deconstruction.
1. Environmental sorting, historical factors and neutral dynamics may all drive beta diversity (change in species composition across space), but their relative importance remains unresolved. In the case of European mammals, key potential drivers of large-scale beta diversity include current climate, neutral dynamics and two historical factors: Pleistocene glaciations and peninsular dynamics (immigration from extra-regional eastern faunal source areas and inter-linked relictual survival and evolutionary differentiation in isolated areas). 2. We assessed the relative importance of these drivers using a novel analytical framework to deconstruct beta diversity of non-volant mammals in Europe (138 species) into its turnover (change in species composition because of species replacements) and nestedness components (change in species composition because of species richness differences) at continental and regional (250,000 km(2) ) scales. 3. We found continental-scale mammal beta diversity to be mainly caused by spatial turnover (99*9%), with only a small contribution (0*1%) from nestedness. 4. Current climate emerged as an important driver of beta diversity, given the strong continental-scale turnover, particularly in north-south direction, i.e., in line with the latitudinal climate gradient, and, more directly, the strong correlation of climate with spatial turnover at both continental and regional scales. 5. However, there was also evidence for the importance of non-climatic drivers. Notably, the compositional variation purely accounted for by space was greater than that purely accounted for by environment for both the turnover and the nestedness component of beta diversity. Furthermore, the strong longitudinal turnover within Southern Europe is in accordance with the region's long-term climatic stability having allowed multiple refugia and local evolutionary diversification. As expected from peninsular dynamics, there was increasing dissimilarity with geographic distance in an east-west direction because of nestedness, but only in Central and Northern Europe. 6. In conclusion, European mammal beta diversity mainly reflects spatial turnover and only to a limited extent nestedness and is driven by current climate in combination with historical - and perhaps, neutral - dynamics. These findings suggest that a key challenge for climate-change predictive studies will be taking the influence of non-climatic factors into account.
not annotated - annotated - LINNAEUS only
Type I signal peptidase and protein secretion in Staphylococcus epidermidis.
Bacterial protein secretion is a highly orchestrated process that is essential for infection and virulence. Despite extensive efforts to predict or experimentally detect proteins that are secreted, the characterization of the bacterial secretome has remained challenging. A central event in protein secretion is the type I signal peptidase (SPase)-mediated cleavage of the N-terminal signal peptide that targets a protein for secretion via the general secretory pathway, and the arylomycins are a class of natural products that inhibit SPase, suggesting that they may be useful chemical biology tools for characterizing the secretome. Here, using an arylomycin derivative, along with two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identify 11 proteins whose secretion from stationary-phase Staphylococcus epidermidis is dependent on SPase activity, 9 of which are predicted to be translated with canonical N-terminal signal peptides. In addition, we find that the presence of extracellular domains of lipoteichoic acid synthase (LtaS) and the Beta-lactam response sensor BlaR1 in the medium is dependent on SPase activity, suggesting that they are cleaved at noncanonical sites within the protein. In all, the data define the proteins whose stationary-phase secretion depends on SPase and also suggest that the arylomycins should be valuable chemical biology tools for the study of protein secretion in a wide variety of different bacteria.
not annotated - annotated - LINNAEUS only
Aerobic degradation of mercaptosuccinate by the gram-negative bacterium Variovorax paradoxus strain B4.
The Gram-negative bacterium Variovorax paradoxus strain B4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (MS). During growth with MS this strain released significant amounts of sulfate into the medium. Tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using MS as a carbon source. In six of these mutants, Tn5::mob insertions were mapped in a putative gene encoding a molybdenum (Mo) cofactor biosynthesis protein (moeA). In two further mutants the Tn5::mob insertion was mapped in the gene coding for a putative molybdopterin (MPT) oxidoreductase. In contrast to the wild type, these eight mutants also showed no growth on taurine. In another mutant a gene putatively encoding a 3-hydroxyacyl-coenzyme A dehydrogenase (paaH2) was disrupted by transposon insertion. Upon subcellular fractionation of wild-type cells cultivated with MS as sole carbon and sulfur source, MPT oxidoreductase activity was detected in only the cytoplasmic fraction. Cells grown with succinate, taurine, or gluconate as a sole carbon source exhibited no activity or much lower activity. MPT oxidoreductase activity in the cytoplasmic fraction of the Tn5::mob-induced mutant Icr6 was 3-fold lower in comparison to the wild type. Therefore, a new pathway for MS catabolism in V. paradoxus strain B4 is proposed: (i) MPT oxidoreductase catalyzes the conversion of MS first into sulfinosuccinate (a putative organo-sulfur compound composed of succinate and a sulfino group) and then into sulfosuccinate by successive transfer of oxygen atoms, (ii) sulfosuccinate is cleaved into oxaloacetate and sulfite, and (iii) sulfite is oxidized to sulfate.
not annotated - annotated - LINNAEUS only
African 2, a clonal complex of Mycobacterium bovis epidemiologically important in East Africa.
We have identified a clonal complex of Mycobacterium bovis isolated at high frequency from cattle in Uganda, Burundi, Tanzania, and Ethiopia. We have named this related group of M. bovis strains the African 2 (Af2) clonal complex of M. bovis. Af2 strains are defined by a specific chromosomal deletion (RDAf2) and can be identified by the absence of spacers 3 to 7 in their spoligotype patterns. Deletion analysis of M. bovis isolates from Algeria, Mali, Chad, Nigeria, Cameroon, South Africa, and Mozambique did not identify any strains of the Af2 clonal complex, suggesting that this clonal complex of M. bovis is localized in East Africa. The specific spoligotype pattern of the Af2 clonal complex was rarely identified among isolates from outside Africa, and the few isolates that were found and tested were intact at the RDAf2 locus. We conclude that the Af2 clonal complex is localized to cattle in East Africa. We found that strains of the Af2 clonal complex of M. bovis have, in general, four or more copies of the insertion sequence IS6110, in contrast to the majority of M. bovis strains isolated from cattle, which are thought to carry only one or a few copies.
not annotated - annotated - LINNAEUS only
Isolation and characterization of P1 adhesin, a leg protein of the gliding bacterium Mycoplasma pneumoniae.
Mycoplasma pneumoniae, a pathogen causing human pneumonia, binds to solid surfaces at its membrane protrusion and glides by a unique mechanism. In this study, P1 adhesin, which functions as a "leg" in gliding, was isolated from mycoplasma culture and characterized. Using gel filtration, blue-native polyacrylamide gel electrophoresis (BN-PAGE), and chemical cross-linking, the isolated P1 adhesin was shown to form a complex with an accessory protein named P90. The complex included two molecules each of P1 adhesin and P90 (protein B), had a molecular mass of about 480 kDa, and was observed by electron microscopy to form 20-nm-diameter spheres. Partial digestion of isolated P1 adhesin by trypsin showed that the P1 adhesin molecule can be divided into three domains, consistent with the results from trypsin treatment of the cell surface. Sequence analysis of P1 adhesin and its orthologs showed that domain I is well conserved and that a transmembrane segment exists near the link between domains II and III.
not annotated - annotated - LINNAEUS only
The peptidoglycan-binding protein FimV promotes assembly of the Pseudomonas aeruginosa type IV pilus secretin.
The Pseudomonas aeruginosa inner membrane protein FimV is among several proteins of unknown function required for type IV pilus-mediated twitching motility, arising from extension and retraction of pili from their site of assembly in the inner membrane. The pili transit the periplasm and peptidoglycan (PG) layer, ultimately exiting the cell through the PilQ secretin. Although fimV mutants are nonmotile, they are susceptible to killing by pilus-specific bacteriophage, a hallmark of retractable surface pili. Here we show that levels of recoverable surface pili were markedly decreased in fimV pilT retraction-deficient mutants compared with levels in the pilT control, demonstrating that FimV acts at the level of pilus assembly. Levels of inner membrane assembly subcomplex proteins PilM/N/O/P were decreased in fimV mutants, but supplementation of these components in trans did not restore pilus assembly or motility. Loss of FimV dramatically reduced the levels of the PilQ secretin multimer through which pili exit the cell, in part due to decreased levels of PilQ monomers, while PilF pilotin levels were unchanged. Expression of pilQ in trans in the wild type or fimV mutants increased total PilQ monomer levels but did not alter secretin multimer levels or motility. PG pulldown assays showed that the N terminus of FimV bound PG in a LysM motif-dependent manner, and a mutant with an in-frame chromosomal deletion of the LysM motif had reduced motility, secretin levels, and surface piliation. Together, our data show that FimV's role in pilus assembly is to promote secretin formation and that this function depends upon its PG-binding domain.
not annotated - annotated - LINNAEUS only
Three motAB stator gene products in Bdellovibrio bacteriovorus contribute to motility of a single flagellum during predatory and prey-independent growth.
The predatory bacterium Bdellovibrio bacteriovorus uses flagellar motility to locate regions rich in Gram-negative prey bacteria, colliding and attaching to prey and then ceasing flagellar motility. Prey are then invaded to form a "bdelloplast" in a type IV pilus-dependent process, and prey contents are digested, allowing Bdellovibrio growth and septation. After septation, Bdellovibrio flagellar motility resumes inside the prey bdelloplast prior to its lysis and escape of Bdellovibrio progeny. Bdellovibrio can also grow slowly outside prey as long flagellate host-independent (HI) cells, cultured on peptone-rich media. The B. bacteriovorus HD100 genome encodes three pairs of MotAB flagellar motor proteins, each of which could potentially form an inner membrane ion channel, interact with the FliG flagellar rotor ring, and produce flagellar rotation. In 2004, Flannagan and coworkers (R. S. Flannagan, M. A. Valvano, and S. F. Koval, Microbiology 150:649-656, 2004) used antisense RNA and green fluorescent protein (GFP) expression to downregulate a single Bdellovibrio motA gene and reported slowed release from the bdelloplast and altered motility of the progeny. Here we inactivated each pair of motAB genes and found that each pair contributes to motility, both predatorily, inside the bdelloplast and during HI growth; however, each pair was dispensable, and deletion of no pair abolished motility totally. Driving-ion studies with phenamil, carbonyl cyanide m-chlorophenylhydrazone (CCCP), and different pH and sodium conditions indicated that all Mot pairs are proton driven, although the sequence similarities of each Mot pair suggests that some may originate from halophilic species. Thus, Bdellovibrio is a "dedicated motorist," retaining and expressing three pairs of mot genes.
not annotated - annotated - LINNAEUS only
FAD binding by ApbE protein from Salmonella enterica: a new class of FAD-binding proteins.
The periplasmic protein ApbE was identified through the analysis of several mutants defective in thiamine biosynthesis and was implicated as having a role in iron-sulfur cluster biosynthesis or repair. While mutations in apbE cause decreased activity of several iron-sulfur enzymes in vivo, the specific role of ApbE remains unknown. Members of the AbpE family include NosX and RnfF, which have been implicated in oxidation-reduction associated with nitrous oxide and nitrogen metabolism, respectively. In this work, we show that ApbE binds one FAD molecule per monomeric unit. The structure of ApbE in the presence of bound FAD reveals a new FAD-binding motif. Protein variants that are nonfunctional in vivo were generated by random and targeted mutagenesis. Each variant was substituted in the environment of the FAD and analyzed for FAD binding after reconstitution. The variant that altered a key tyrosine residue involved in FAD binding prevented reconstitution of the protein.
not annotated - annotated - LINNAEUS only
The Serengeti food web: empirical quantification and analysis of topological changes under increasing human impact.
1. To address effects of land use and human overexploitation on wildlife populations, it is essential to better understand how human activities have changed species composition, diversity and functioning. Theoretical studies modelled how network properties change under human-induced, non-random species loss. However, we lack data on realistic species-loss sequences in threatened, real-world food webs to parameterize these models. 2. Here, we present a first size-structured topological food web of one of the most pristine terrestrial ecosystems in the world, the Serengeti ecosystem (Tanzania). The food web consists of 95 grouped nodes and includes both invertebrates and vertebrates ranging from body masses between 10(-7) and 10(4) kg. 3. We study the topological changes in this food web that result from the simulated IUCN-based species-loss sequence representing current species vulnerability to human disturbances in and around this savanna ecosystem. We then compare this realistic extinction scenario with other extinction sequences based on body size and connectance and perform an analysis of robustness of this savanna food web. 4. We demonstrate that real-world species loss in this case starts with the biggest (mega) herbivores and top predators, causing higher predator-prey mass ratios. However, unlike theoretically modelled linear species deletion sequences, this causes poor-connected species to be lost first, while more highly connected species become lost as human impact progresses. This food web shows high robustness to decreasing body size and increasing connectance deletion sequences compared with a high sensitivity to the decreasing connectance deletion scenario. 5. Furthermore, based on the current knowledge of the Serengeti ecosystem, we discuss how the focus on food web topology alone, disregarding nontrophic interactions, may lead to an underestimation of human impacts on wildlife communities, with the number of trophic links affected by a factor of two. 6. This study underlines the importance of integrative efforts between the development of food web theory and basic field work approaches in the quantification of the structure of interaction networks to sustain natural ecosystems in a changing world.
not annotated - annotated - LINNAEUS only
The osmosensing signal transduction pathway from Botrytis cinerea regulates cell wall integrity and MAP kinase pathways control melanin biosynthesis with influence of light.
Mitogen activated protein kinase (MAPK) signal transduction pathways are ubiquitous among eukaryotic organisms with evolutionary conserved modules. Although generally classified as osmotic and cell wall integrity pathways, functional divergences have been observed for HOG1- and SLT2-related MAPK pathways. Here we show that the osmotic signal transduction cascade is involved in cell wall integrity in the phytopathogenic ascomycete Botrytis cinerea. The deletion mutants of the upstream histidine kinase Bos1 and of the MAPK Sak1 showed modified tolerance to cell wall degrading enzymes and cell wall interfering agents, as well as increased staining of Beta1-3 glucan and chitin compared to the wild-type. The Sak1 MAPK was phosphorylated upon cell wall challenging. Sak1 interfered with the phosphorylation status of the SLT2 type MAPK Bmp3 hinting to cross talk between both MAPK pathways. All signal transduction components interfered with the expression of melanin biosynthesis genes in dark and bright, suggesting a coordinated control of melanin biosynthesis.
not annotated - annotated - LINNAEUS only
Antimalarial drug resistance of Plasmodium falciparum in India: changes over time and space.
After the launch of the National Malaria Control Programme in 1953, the number of malaria cases reported in India fell to an all-time low of 0*1 million in 1965. However, the initial success could not be maintained and a resurgence of malaria began in the late 1960s. Resistance of Plasmodium falciparum to chloroquine was first reported in 1973 and increases in antimalarial resistance, along with rapid urbanisation and labour migration, complicated the challenge that India's large geographical area and population size already pose for malaria control. Although several institutions have done drug-resistance monitoring in India, a complete analysis of countrywide data across institutions does not exist. We did a systematic review of P falciparum malaria drug-efficacy studies in India to summarise drug-resistance data and describe changes over the past 30 years to inform future policy. Continued use of chloroquine for treatment of P falciparum malaria in India will likely be ineffective. Resistance to sulfa-pyrimethamine should be closely monitored to protect the effectiveness of treatment with artesunate plus sulfadoxine-pyrimethamine, which is the new first-line treatment for P falciparum malaria. Strategies to reduce the emergence and spread of future drug resistance need to be proactive and supported by intensive monitoring.
not annotated - annotated - LINNAEUS only
Endotoxin removal devices for the treatment of sepsis and septic shock.
A substantial body of experimental and clinical evidence suggests that neutralising or removing lipopolysaccharide endotoxin would be an effective adjunctive approach to the management of Gram-negative sepsis. Polymyxins are a group of cyclic cationic polypeptide antibiotics. Although they have useful antimicrobial activity against Gram-negative bacteria, their clinical use has been limited because of toxicity. However, in addition to their antimicrobial property, polymyxins can bind to and neutralise endotoxin. Thus, investigators have explored the possibility of using polymyxin bound to a solid-phase carrier for specific haem-adsorption in patients with sepsis, thereby retaining the lipopolysaccharide-binding properties but minimising systemic toxic effects. This system has been widely used in Japan for many years, but convincing clinical evidence of efficacy is lacking. A recent Italian study has some promising data. Although polymyxin has been the principal agent used to explore this approach, other molecules have the ability to bind endotoxin, and some of these have very recently been proposed as the basis for other endotoxin-removal devices. The available evidence is reviewed to assess the potential use of such devices in clinical practice.
not annotated - annotated - LINNAEUS only
Genomics of biotrophic, plant-infecting plasmodiophorids using in vitro dual cultures.
The plasmodiophorids are a phylogenetically distinct group of parasitic protists that infect plants and stramenopiles, causing several important agricultural diseases. Because of the obligate intracellular part of their lifecycle, none of the plasmodiophorids has been axenically cultured. Further, the molecular biology of the plasmodiophorids is poorly understood because pure cultures are not available from any species. We report on an in-vitro dual culture system of the plasmodiophorids Plasmodiophora brassicae and Spongospora subterranea with their respective plant hosts, Brassica rapa and Solanum tuberosum. We show that these plasmodiophorids are capable of initiating and maintaining stable, long-term plant cell callus cultures in the absence of exogenous plant growth regulators. We show that callus cultures harbouring S. subterranea provide an excellent starting material for gene discovery from this organism by constructing a pilot-scale DNA library. Bioinformatic analysis of the sequences established that almost all of the DNA clones from this library were from S. subterranea rather than the plant host. The Spongospora genome was found to be rich in retrotransposable elements, and Spongospora protein-coding genes were shown to contain introns. The sequence of a near full-length non-LTR retrotransposon was obtained, the first transposable element reported from a cercozoan protist.
not annotated - annotated - LINNAEUS only
Molecular characterization of three genes encoding aminopeptidases N in the poplar leaf beetle Chrysomela tremulae.
Three genes encoding proteins showing sequence similarity and features typical of insect APNs were characterized in C. tremulae and designed as CtAPN1, CtAPN2 and CtAPN3. Expression analysis of the three C. tremulae APN genes showed that CtAPN2 transcript is more abundant in the fat body, whereas both CtAPN1 and CtAPN3 are specifically expressed in the midgut. Despite a similar genomic organization, lepidopteran and coleopteran APNs are phylogenetically distant, suggesting that APN gene duplication events occurred after these two insect orders split. Sequence and expression comparisons of CtAPN1, CtAPN2 and CtAPN3 cDNAs in a C. tremulae Bacillus thuringiensis (Bt)-susceptible and in a Bt-resistant strain did not show any polymorphism at the amino acid level or difference at the transcription level.
not annotated - annotated - LINNAEUS only
Alternative community compositional and dynamical states: the dual consequences of assembly history.
1. Much work on ecological consequences of community assembly history has focused on the formation of history-induced alternative stable equilibria. We hypothesize that assembly history may affect not only community composition but also population dynamics, with assembled communities differing in species composition potentially residing in different dynamical states. 2. We provided an empirical test of the aforementioned hypothesis using a laboratory microcosm experiment that manipulated both the colonization order of three bacterivorous protist species in the presence of a protist predator and environmental productivity. 3. Both priority effects and random divergence emerged, resulting in two different community compositional states: one characterized by the dominance of one prey species and the other by the extinction of the same prey. While communities in the former state exhibited noncyclic dynamics, the majority of communities in the latter state exhibited cyclic dynamics driven by the interaction between another prey and the predator. 4. Temporal variability of total prey community biovolume consequently differed among communities with different histories. 5. Changing productivity altered priority effects on the structure and dynamics of communities experiencing only certain histories. 6. Our results support the dual (compositional and dynamical) consequences of assembly history and emphasize the importance of incorporating the dynamical view into the field of community assembly.
not annotated - annotated - LINNAEUS only
Barcoding diatoms: exploring alternatives to COI-5P.
Diatoms are a diverse lineage with species that can be difficult to identify or cryptic, but DNA barcoding, a molecular technique, can assist identification and facilitate studies of speciation and biogeography. The most common region used for DNA barcoding, COI-5P, can distinguish diatom species, but has not displayed universality (i.e., successful PCR amplification from diverse taxa). Therefore, we have assessed the following alternative markers: -1400bp of rbcL; 748bp at the 3' end of rbcL (rbcL-3P); LSU D2/D3 and UPA. Sellaphora isolates were used to determine each marker's ability to discriminate among closely related species and culture collection material was utilized to explore further marker universality. All of the alternative markers investigated have greater universality than COI-5P. Both full and partial (3P) rbcL regions had the power to discriminate between all species, but rbcL-3P can be sequenced more easily. LSU D2/D3 could distinguish between all but the most closely related species (96%), whereas UPA only distinguished 20% of species. Our observations suggest that rbcL-3P should be used as the primary marker for diatom barcoding, while LSU D2/D3 should be sequenced as a secondary marker to facilitate environmental surveys.
not annotated - annotated - LINNAEUS only
Genetic and molecular characterization of a blue light photoreceptor MGWC-1 in Magnaporth oryzae.
Three key factors involved in successful plant disease development include the presence of a susceptible host, a virulent pathogen, and a disease-conducive environment. Our understanding of how environmental factors influence disease-conducive or disease-suppressive conditions, and how a pathogen advantageously capitalizes on them, is quite limited. Utilizing the model pathosystem Magnaporthe oryzae-Oryza sativa, we found a significant light-dependent disease suppression. Our genetic data suggest that the blue-light receptor MGWC-1 in M. oryzae is involved in light-dependent disease suppression during the dark-phase (disease-conducive light condition) immediately after pathogen-host contact. Sensing "darkness" is accomplished by MGWC-1, a blue-light receptor in M. oryzae. To explore the potential molecular mechanisms of light-dependent disease suppression we performed a genome-wide microarray experiment and identified several groups of gene families that are differentially regulated during the light-to-dark transition. Our genetic and molecular data provide insights into how a fungal pathogen utilizes ambient light signals for successful disease development.
not annotated - annotated - LINNAEUS only
Using tunable diode laser spectroscopy to measure carbon isotope discrimination and mesophyll conductance to CO2 diffusion dynamically at different CO2 concentrations.
In C3 leaves, the mesophyll conductance to CO2 diffusion, g(m) , determines the drawdown in CO2 concentration from intercellular airspace to the chloroplast stroma. Both g(m) and stomatal conductance limit photosynthetic rate and vary in response to the environment. We investigated the response of g(m) to changes in CO2 in two Arabidopsis genotypes (including a mutant with open stomata, ost1), tobacco and wheat. We combined measurements of gas exchange with carbon isotope discrimination using tunable diode laser absorption spectroscopy with a CO2 calibration system specially designed for a range of CO2 and O2 concentrations. CO2 was initially increased from 200 to 1000 ppm and then decreased stepwise to 200 ppm and increased stepwise back to 1000 ppm, or the sequence was reversed. In 2% O2 a step increase from 200 to 1000 ppm significantly decreased g(m) by 26-40% in all three species, whereas following a step decrease from 1000 to 200 ppm, the 26-38% increase in g(m) was not statistically significant. The response of g(m) to CO2 was less in 21% O2. Comparing wild type against the ost1 revealed that mesophyll and stomatal conductance varied independently in response to CO2. We discuss the effects of isotope fractionation factors on estimating g(m) .
not annotated - annotated - LINNAEUS only
Maternal, neonatal, and child health in southeast Asia: towards greater regional collaboration.
Although maternal and child mortality are on the decline in southeast Asia, there are still major disparities, and greater equity is key to achieve the Millennium Development Goals. We used comparable cross-national data sources to document mortality trends from 1990 to 2008 and to assess major causes of maternal and child deaths. We present inequalities in intervention coverage by two common measures of wealth quintiles and rural or urban status. Case studies of reduction in mortality in Thailand and Indonesia indicate the varying extents of success and point to some factors that accelerate progress. We developed a Lives Saved Tool analysis for the region and for country subgroups to estimate deaths averted by cause and intervention. We identified three major patterns of maternal and child mortality reduction: early, rapid downward trends (Brunei, Singapore, Malaysia, and Thailand); initially high declines (sustained by Vietnam but faltering in the Philippines and Indonesia); and high initial rates with a downward trend (Laos, Cambodia, and Myanmar). Economic development seems to provide an important context that should be coupled with broader health-system interventions. Increasing coverage and consideration of the health-system context is needed, and regional support from the Association of Southeast Asian Nations can provide increased policy support to achieve maternal, neonatal, and child health goals.
not annotated - annotated - LINNAEUS only
Cataloging and profiling genes expressed in Lentinula edodes fruiting body by massive cDNA pyrosequencing and LongSAGE.
This study investigated the molecular mechanism of the fruiting body development and sporulation in the cap of the Shiitake mushroom, Lentinula edodes. Although there has been much research into L. edodes, there remain significant gaps in our knowledge of how the species reproduces. In order to provide molecular resources and to understand the molecular mechanism of the fruiting body development in basidiomycete comprehensively, we searched for the genes which are important for fruiting body development and sporulation in the cap of mature fruiting body of L. edodes by using the whole-genome approach. Massive cDNA pyrosequencing was used to generate >7000 sequence contigs from mature fruiting bodies. We used Gene Ontology to categorize the contigs to form the catalog of genes expressed at the stage of the mature fruiting body. We also assigned the contigs into the KEGG pathways. The catalog of expressed genes indicates that the mature fruiting bodies (1) sense the external environment, (2) transmit signals to express genes through regulatory systems, (3) produce many proteins, (4) degrade unwanted proteins, (5) perform extensive biosynthesis, (6) generate energy, (7) regulate the internal environment, (8) transport molecules, (9) carry out cell division, and (10) differentiate and develop. After establishing the catalog of expressed genes in L. edodes, we used the LongSAGE approach to analyze the expression levels of genes found in mature fruiting bodies before (FB) and after (FBS) spores appeared. Gene-expression patterns according to GO categories were similar in these two stages. We have also successfully identified genes differentially expressed in FB and FBS. Fold-changes in expression levels of selected genes based on LongSAGE tag counts were similar to those obtained by real-time RT-PCR. The consistency between real-time RT-PCR and LongSAGE results indicates reliability of the LongSAGE results. Overall, this study provides valuable information on the fruiting processes of L. edodes through a combination of massive cDNA pyrosequencing and LongSAGE sequencing, and the knowledge thereby obtained may provide insight into the improvement of the yield of commercially grown Shiitake mushrooms.
not annotated - annotated - LINNAEUS only
A mutation in the Cc.ubc2 gene affects clamp cell morphogenesis as well as nuclear migration for dikaryosis in Coprinopsis cinerea.
The formation and proliferation of the dikaryon in the agaricomycete Coprinopsis cinerea is controlled by the mating type genes, A and B. The B genes, which encode pheromones and pheromone receptors, control nuclear migration for dikaryosis as well as the fusion of the clamp cell with the subterminal cell while the A genes, which encode two classes of homeodomain proteins, control conjugate nuclear division associated with clamp connection development. We characterized the mutant, B28, which was newly isolated as a strain that fails to form a primary hyphal knot, the first visible sign toward fruiting, from a homokaryotic fruiting strain after REMI mutagenesis. Detailed phenotypic analysis revealed that strain B28 exhibits, in addition to the fruiting defect, a defect in A-regulated clamp cell morphogenesis as well as a defect in B-regulated nuclear migration for dikaryosis. The mutant clamp cells are unique in that they continue growing like branches without fusing with the subterminal cells, in contrast to the unfused pseudoclamp which are normally formed in A-on B-off strains, providing evidence for the existence of an as yet unidentified mechanism for the growth suppression of the clamp cell. Molecular analysis revealed that the gene responsible for the phenotypes, designated Cc.ubc2, encodes a protein similar to Ubc2, an adaptor protein for filamentous growth, pheromone response and virulence in the smut fungus Ustilago maydis. In addition, western blot analysis demonstrated that the Cc.ubc2-1 mutation blocks phosphorylation of a presumptive MAP kinase.
not annotated - annotated - LINNAEUS only
Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection.
To expand the representation for phylogenetic analysis, ten additional complete Entamoeba small-subunit rRNA gene sequences were obtained from humans, non-human primates, cattle and a tortoise. For some novel sequences no corresponding morphological data were available, and we suggest that these organisms should be referred to as ribosomal lineages (RL) rather than being assigned species names at present. To investigate genetic diversity and host specificity of selected Entamoeba species, a total of 91 new partial small subunit rRNA gene sequences were obtained, including 49 from Entamoeba coli, 18 from Entamoeba polecki, and 17 from Entamoeba hartmanni. We propose a new nomenclature for significant variants within established Entamoeba species. Based on current data we propose that the uninucleated-cyst-producing Entamoeba infecting humans is called Entamoeba polecki and divided into four subtypes (ST1-ST4) and that Entamoeba coli is divided into two subtypes (ST1-ST2). New hosts for several species were detected and, while host specificity and genetic diversity of several species remain to be clarified, it is clear that previous reliance on cultivated material has given us a misleading and incomplete picture of variation within the genus Entamoeba.
not annotated - annotated - LINNAEUS only
Definition and classification of cancer cachexia: an international consensus.
To develop a framework for the definition and classification of cancer cachexia a panel of experts participated in a formal consensus process, including focus groups and two Delphi rounds. Cancer cachexia was defined as a multifactorial syndrome defined by an ongoing loss of skeletal muscle mass (with or without loss of fat mass) that cannot be fully reversed by conventional nutritional support and leads to progressive functional impairment. Its pathophysiology is characterised by a negative protein and energy balance driven by a variable combination of reduced food intake and abnormal metabolism. The agreed diagnostic criterion for cachexia was weight loss greater than 5%, or weight loss greater than 2% in individuals already showing depletion according to current bodyweight and height (body-mass index [BMI] <20 kg/m(2)) or skeletal muscle mass (sarcopenia). An agreement was made that the cachexia syndrome can develop progressively through various stages--precachexia to cachexia to refractory cachexia. Severity can be classified according to degree of depletion of energy stores and body protein (BMI) in combination with degree of ongoing weight loss. Assessment for classification and clinical management should include the following domains: anorexia or reduced food intake, catabolic drive, muscle mass and strength, functional and psychosocial impairment. Consensus exists on a framework for the definition and classification of cancer cachexia. After validation, this should aid clinical trial design, development of practice guidelines, and, eventually, routine clinical management.
not annotated - annotated - LINNAEUS only
Neuroinflammation in amyotrophic lateral sclerosis: role of glial activation in motor neuron disease.
Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS) are characterised by the appearance of reactive microglial and astroglial cells, a process referred to as neuroinflammation. In transgenic mouse models of mutant SOD1-associated familial ALS, reactive microglial cells and astrocytes actively contribute to the death of motor neurons. The biological processes that drive this glial reaction are complex and have both beneficial and deleterious effects on motor neurons. Therapeutic interventions targeting these cells are being explored. An improved understanding of the biological processes that cause neuroinflammation will help to define its medical importance and to identify the therapeutic potential of interfering with this reaction.
not annotated - annotated - LINNAEUS only
Potassium and sodium uptake systems in fungi. The transporter diversity of Magnaporthe oryzae.
In this study, we report an inventory of the K(+) uptake systems in 62 fungal species for which the complete genome sequences are available. This inventory reveals that three types of K(+) uptake systems, TRK and HAK transporters and ACU ATPases, are widely present in several combinations across fungal species. PAT ATPases are less frequently present and are exceptional in Ascomycota. The genome of Magnaporthe oryzae contains four TRK, one HAK, and two ACU genes. The study of the expression of these genes at high K(+), K(+) starvation, and in infected rice leaves revealed that the expression of four genes, ACU1, ACU2, HAK1, and TRK1 is much lower than that of TRK2, TRK3, and TRK4, except under K(+) starvation. The two ACU ATPases were cloned and functionally identified as high-affinity K(+) or Na(+) uptake systems. These two ATPases endow Saccharomyces cerevisiae with the capacity to grow for several generations in low Na(+) concentrations when K(+) was absent, which produces a dramatic increase of cellular Na(+)/K(+) ratio.
not annotated - annotated - LINNAEUS only
Soil nutrient status determines how elephant utilize trees and shape environments.
1. Elucidation of the mechanism determining the spatial scale of patch selection by herbivores has been complicated by the way in which resource availability at a specific scale is measured and by vigilance behaviour of the herbivores themselves. To reduce these complications, we studied patch selection by an animal with negligible predation risk, the African elephant. 2. We introduce the concept of nutrient load as the product of patch size, number of patches and local patch nutrient concentration. Nutrient load provides a novel spatially explicit expression of the total available nutrients a herbivore can select from. 3. We hypothesized that elephant would select nutrient-rich patches, based on the nutrient load per 2500 m(2) down to the individual plant scale, and that this selection will depend on the nitrogen and phosphorous contents of plants. 4. We predicted that elephant would cause more adverse impact to trees of lower value to them in order to reach plant parts with higher nutrient concentrations such as bark and root. However, elephant should maintain nutrient-rich trees by inducing coppicing of trees through re-utilization of leaves. 5. Elephant patch selection was measured in a homogenous tree species stand by manipulating the spatial distribution of soil nutrients in a large field experiment using NPK fertilizer. 6. Elephant were able to select nutrient-rich patches and utilized Colophospermum mopane trees inside these patches more than outside, at scales ranging from 2500 down to 100 m(2) . 7. Although both nitrogen and phosphorus contents of leaves from C. mopane trees were higher in fertilized and selected patches, patch choice correlated most strongly with nitrogen content. As predicted, stripping of leaves occurred more in nutrient-rich patches, while adverse impact such as uprooting of trees occurred more in nutrient-poor areas. 8. Our results emphasize the necessity of including scale-dependent selectivity in foraging studies and how elephant foraging behaviour can be used as indicators of change in the availability of nutrients.
not annotated - annotated - LINNAEUS only
Social immunity in honeybees (Apis mellifera): transcriptome analysis of varroa-hygienic behaviour.
Honeybees have evolved a social immunity consisting of the cooperation of individuals to decrease disease in the hive. We identified a set of genes involved in this social immunity by analysing the brain transcriptome of highly varroa-hygienic bees, who efficiently detect and remove brood infected with the Varroa destructor mite. The function of these candidate genes does not seem to support a higher olfactory sensitivity in hygienic bees, as previously hypothesized. However, comparing their genomic profile with those from other behaviours suggests a link with brood care and the highly varroa-hygienic Africanized honeybees. These results represent a first step toward the identification of genes involved in social immunity and thus provide first insights into the evolution of social immunity.
not annotated - annotated - LINNAEUS only
Long-term outcomes of patients with aneurysmal subarachnoid haemorrhage.
More and more patients survive aneurysmal subarachnoid haemorrhage (aSAH), with case fatality decreasing by 17% in absolute terms over the past three decades and incidence remaining relatively stable at nine per 100,000 patient-years. The mean age at which aSAH occurs is reasonably young at 55 years, and people of this age in the general population have a good life expectancy. However, there are few data for life expectancy after aSAH, and the risks of late recurrent aSAH and other vascular diseases are unclear. The course of associated long-term physical and cognitive deficits after aSAH is not well established, leading to questions about potential outcomes to quality of life and working capacity, as well as best clinical practices.
not annotated - annotated - LINNAEUS only
Sporadic and familial hemiplegic migraine: pathophysiological mechanisms, clinical characteristics, diagnosis, and management.
Hemiplegic migraine is a rare form of migraine with aura that involves motor aura (weakness). This type of migraine can occur as a sporadic or a familial disorder. Familial forms of hemiplegic migraine are dominantly inherited. Data from genetic studies have implicated mutations in genes that encode proteins involved in ion transportation. However, at least a quarter of the large families affected and most sporadic cases do not have a mutation in the three genes known to be implicated in this disorder, suggesting that other genes are still to be identified. Results from functional studies indicate that neuronal hyperexcitability has a pivotal role in the pathogenesis of hemiplegic migraine. The clinical manifestations of hemiplegic migraine range from attacks with short-duration hemiparesis to severe forms with recurrent coma and prolonged hemiparesis, permanent cerebellar ataxia, epilepsy, transient blindness, or mental retardation. Diagnosis relies on a careful patient history and exclusion of potential causes of symptomatic attacks. The principles of management are similar to those for common varieties of migraine, except that vasoconstrictors, including triptans, are historically contraindicated but are often used off-label to stop the headache, and prophylactic treatment can include lamotrigine and acetazolamide.
not annotated - annotated - LINNAEUS only
An Antarctic hypotrichous ciliate, Parasterkiella thompsoni (Foissner) nov. gen., nov. comb., recorded in Argentinean peat-bogs: morphology, morphogenesis, and molecular phylogeny.
The ciliate Parasterkiella thompsoni (Foissner, 1996) nov. gen., nov. comb. was originally described from Antarctica. In the present study, we report the morphology, morphogenesis during cell division, and molecular phylogeny inferred from the 18S-rDNA sequence of a population isolated from the Rancho Hambre peat bog, Tierra del Fuego Province (Argentina). The study is based on live and protargol-impregnated specimens. Molecular phylogeny was inferred from trees constructed by means of the maximum parsimony, neighbor joining, and Bayesian analyses. The interphase morphology matches the original description of the species. During the cell division, stomatogenesis begins with the de novo proliferation of two fields of basal bodies, each one left of the postoral ventral cirri and of transverse cirri, which later unify. Primordia IV-VI of the proter develop from disaggregation of cirrus IV/3, while primordium IV of the opisthe develops from cirrus IV/2 and primordia V and VI from cirrus V/4. Dorsal morphogenesis occurs in the Urosomoida pattern-that is, the fragmentation of kinety 3 is lacking. Three macronuclear nodules are generated before cytokinesis. Phylogenetic analyses consistently placed P. thompsoni within the stylonychines. New data on the morphogenesis of the dorsal ciliature justifies the transference of Sterkiella thompsoni to a new genus Parasterkiella.
not annotated - annotated - LINNAEUS only
Multiple environmental gradients affect spatial variation in the productivity of a tropical bird population.
1. Spatial variation in habitat quality and its demographic consequences have important implications for the regulation of animal populations. Theoretically, habitat quality is typically viewed as a single gradient from 'poor' to 'good', but in wild populations it is possible that there are multiple environmental gradients that determine spatial variation in demography. 2. Understanding environmental gradients is important to gain mechanistic insights into important population processes, but also to understand how populations might respond to environmental change. Here, we explore habitat and elevation gradients and their implications for population persistence using detailed long-term data on 600 individuals of the Mauritius kestrel. These data allow us to statistically separate spatial variation in demography from variation arising out of individual or environmental quality and explore its relationships with habitat and topography. 3. Birds that breed earlier in the season have higher reproductive success, and we found that the timing of breeding varies significantly between territories. This variation is primarily driven by elevation, with birds breeding progressively later as elevation increases. 4. Pre-fledging survival from the egg to fledgling stage (independently of timing), and recruitment, also varied significantly between territories. This variation is driven by the habitat surrounding breeding sites with increasing agricultural encroachment causing survival and recruitment to decline. 5. Taken together, our results suggest that there are likely to be multiple environmental gradients affecting spatial variation in productivity in wild populations, and hence multiple and different routes through which environmental change might have consequences for population dynamics by modifying spatial processes.
not annotated - annotated - LINNAEUS only
Optimisation of breast cancer management in low-resource and middle-resource countries: executive summary of the Breast Health Global Initiative consensus, 2010.
The purpose of the Breast Health Global Initiative (BHGI) 2010 summit was to provide a consensus analysis of breast cancer control issues and implementation strategies for low-income and middle-income countries (LMCs), where advanced stages at presentation and poor diagnostic and treatment capacities contribute to lower breast cancer survival rates than in high-income countries. Health system and patient-related barriers were identified that create common clinical scenarios in which women do not present for diagnosis until their cancer has progressed to locally advanced or metastatic stages. As countries progress to higher economic status, the rate of late presentation is expected to decrease, and diagnostic and treatment resources are expected to improve. Health-care systems in LMCs share many challenges including national or regional data collection, programme infrastructure and capacity (including appropriate equipment and drug acquisitions, and professional training and accreditation), the need for qualitative and quantitative research to support decision making, and strategies to improve patient access and compliance as well as public, health-care professional, and policy-maker awareness that breast cancer is a cost-effective, treatable disease. The biggest challenges identified for low-income countries were little community awareness that breast cancer is treatable, inadequate advanced pathology services for diagnosis and staging, and fragmented treatment options, especially for the administration of radiotherapy and the full range of systemic treatments. The biggest challenges identified for middle-resource countries were the establishment and maintenance of data registries, the coordination of multidisciplinary centres of excellence with broad outreach programmes to provide community access to cancer diagnosis and treatment, and the resource-appropriate prioritisation of breast cancer control programmes within the framework of existing, functional health-care systems.
not annotated - annotated - LINNAEUS only
Stillbirths: what difference can we make and at what cost?
Worldwide, 2*65 million (uncertainty range 2*08 million to 3*79 million) stillbirths occur yearly, of which 98% occur in countries of low and middle income. Despite the fact that more than 45% of the global burden of stillbirths occur intrapartum, the perception is that little is known about effective interventions, especially those that can be implemented in low-resource settings. We undertook a systematic review of randomised trials and observational studies of interventions which could reduce the burden of stillbirths, particularly in low-income and middle-income countries. We identified several interventions with sufficient evidence to recommend implementation in health systems, including periconceptional folic acid supplementation or fortification, prevention of malaria, and improved detection and management of syphilis during pregnancy in endemic areas. Basic and comprehensive emergency obstetric care were identified as key effective interventions to reduce intrapartum stillbirths. Broad-scale implementation of intervention packages across 68 countries listed as priorities in the Countdown to 2015 report could avert up to 45% of stillbirths according to a model generated from the Lives Saved Tool. The overall costs for these interventions are within the general estimates of cost-effective interventions for maternal care, especially in view of the effects on outcomes across maternal, fetal, and neonatal health.
not annotated - annotated - LINNAEUS only
New insights into the excystation process and oocyst morphology of rodent Eimeria species.
In this study, the mechanism of excystation of the rodent parasites Eimeria nieschulzi, from rats, and Eimeria falciformis, from mice, was investigated. In vitro, oocysts of both species are susceptible to the protease pepsin, and sporocysts and sporozoites can be excysted in a similar way. Scanning electron microscopy (SEM) revealed a collapse of the oocysts wall at both polar ends after pepsin treatment. This occurs without any visible damage of the outer wall. Using fluorescence and transmission electron microscopy (TEM) we observed that pepsin enters sporulated oocysts at both polar ends and causes degradation of the inner oocyst wall. Using scanning electron microscopy we could identify two polar caps in both investigated rodent Eimeria species, but only one is harbouring the micropyle. Thus the polar caps are the entry site for the pepsin. Furthermore, we provide evidence that the oocyst cap and micropyle are functionally different structures. This study complements the morphological description of both Eimeria species and is of relevance for other coccidian species.
not annotated - annotated - LINNAEUS only
First description of the early stage biology of the genus Mygona: the natural history of the satyrine butterfly, Mygona irmina in eastern Ecuador.
The immature stages and natural history of Mygona irmina Doubleday (Lepidoptera: Nymphalidae: Satyrinae: Pronophilina) from northeastern Ecuadorian cloud forests are described based on 17 rearings. The dwarf bamboo, Chusquea c.f. scandens Kunth (Poaceae, Bambusoidea) is the larval food plant. Eggs are laid singly on the bottom side of mature host plant leaves. Larvae take 102-109 days to mature from egg to adult. Adults are encountered most frequently on sunny days, flying rapidly over areas dominated by their food plant or feeding on the ground at mammal feces. Males are often encountered inside large forest gaps near patches of bamboo guarding perches in the mid-canopy.
not annotated - annotated - LINNAEUS only
One size does not fit all: flexible models are required to understand animal movement across scales.
1. Large data sets containing precise movement data from free-roaming animals are now becoming commonplace. One means of analysing individual movement data is through discrete, random walk-based models. 2. Random walk models are easily modified to incorporate common features of animal movement, and the ways that these modifications affect the scaling of net displacement are well studied. Recently, ecologists have begun to explore more complex statistical models with multiple latent states, each of which are characterized by a distribution of step lengths and have their own unimodal distribution of turning angles centred on one type of turn (e.g. reversals). 3. Here, we introduce the compound wrapped Cauchy distribution, which allows for multimodal distributions of turning angles within a single state. When used as a single state model, the parameters provide a straightforward summary of the relative contributions of different turn types. The compound wrapped Cauchy distribution can also be used to build multiple state models. 4. We hypothesize that a multiple state model with unimodal distributions of turning angles will best describe movement at finer resolutions, while a multiple state model using our multimodal distribution will better describe movement at intermediate temporal resolutions. At coarser temporal resolutions, a single state model using our multimodal distribution should be sufficient. We parameterize and compare the performance of these models at four different temporal resolutions (1, 4, 12 and 24 h) using data from eight individuals of Loxodonta cyclotis and find support for our hypotheses. 5. We assess the efficacy of the different models in extrapolating to coarser temporal resolution by comparing properties of data simulated from the different models to the properties of the observed data. At coarser resolutions, simulated data sets recreate many aspects of the observed data; however, only one of the models accurately predicts step length, and all models underestimate the frequency of reversals. 6. The single state model we introduce may be adequate to describe movement data at many resolutions and can be interpreted easily. Multiscalar analyses of movement such as the ones presented here are a useful means of identifying inconsistencies in our understanding of movement.
not annotated - annotated - LINNAEUS only
Effects of temperature on the development and population growth of the sycamore lace bug, Corythucha ciliata.
The sycamore lace bug, Corythucha ciliata (Say) (Hemiptera: Tingidae), is an important invasive exotic pest of Platanus (Proteales: Platanaceae) trees in China. The objective of this study was to determine the effects of temperature on C. ciliata in the laboratory so that forecasting models based on heat accumulation units could be developed for the pest. Development and fecundity of C. ciliata reared on leaves of London plane tree (Platanus x acerifolia) were investigated at seven constant temperatures (16, 19, 22, 26, 30, 33, and 36^0 C) and at a relative humidity of 80% with a photoperiod of 14:10 (L:D). The developmental time was found to significantly decrease with increasing temperature. The developmental time from egg hatching to adult emergence was respectively 47.6, 35.0, 24.1, 20.0, and 17.1 days at the temperatures of 19, 22, 26, 30, and 33^0 C. C. ciliata could not complete full development at 16^0 and 36^0 C. The developmental threshold temperature (C) estimated for egg-to-adult was 11.17^0 C, with a thermal constant of (K) 370.57 degree-days. Longevity of females was found to be the shortest, 17.7 days at 33^0 C and the longest, 58.9 days at 16^0 C, and that of males was the shortest, 19.7 days at 33^0 C and the longest, 59.7 days at 16^0 C. Fecundity was the highest at 30^0 C, being 286.8 eggs per female over an oviposition period of 8.9 days. Female lifetime fecundity was reduced at other temperatures, being the lowest (87.7 eggs per female) at 19^0 C. The population trend index (I) of C. ciliata was the highest (130.1) at 30^0 C and the lowest (24.9) at 19^0 C. Therefore, the optimal developmental temperature for C. ciliata was determined to be 30^0 C.
not annotated - annotated - LINNAEUS only
Parasitism of lepidopterous stem borers in cultivated and natural habitats.
Plant infestation, stem borer density, parasitism, and parasitoid abundance were assessed during two years in two host plants, Zea mays (L.) (Cyperales: Poaceae) and Sorghum bicolor (L.) (Cyperales: Poaceae), in cultivated habitats. The four major host plants (Cyperus spp., Panicum spp., Pennisetum spp., and Sorghum spp.) found in natural habitats were also assessed, and both the cultivated and natural habitat species occurred in four agroecological zones in Kenya. Across habitats, plant infestation (23.2%), stem borer density (2.2 per plant), and larval parasitism (15.0%) were highest in maize in cultivated habitats. Pupal parasitism was not higher than 4.7% in both habitats, and did not vary with locality during each season or with host plant between each season. Cotesia sesamiae (Cameron) and C. flavipes Cameron (Hymenoptera: Braconidae) were the key parasitoids in cultivated habitats (both species accounted for 76.4% of parasitized stem borers in cereal crops), but not in natural habitats (the two Cotesia species accounted for 14.5% of parasitized stem borers in wild host plants). No single parasitoid species exerted high parasitism rates on stem borer populations in wild host plants. Low stem borer densities across seasons in natural habitats indicate that cereal stem borer pests do not necessarily survive the non-cropping season feeding actively in wild host plants. Although natural habitats provided refuges for some parasitoid species, stem borer parasitism was generally low in wild host plants. Overall, because parasitoids contribute little in reducing cereal stem borer pest populations in cultivated habitats, there is need to further enhance their effectiveness in the field to regulate these pests.
not annotated - annotated - LINNAEUS only
DNA methylation in insects: on the brink of the epigenomic era.
DNA methylation plays an important role in gene regulation in animals. However, the evolution and function of DNA methylation has only recently emerged as the subject of widespread study in insects. In this review we profile the known distribution of DNA methylation systems across insect taxa and synthesize functional inferences from studies of DNA methylation in insects and vertebrates. Unlike vertebrate genomes, which tend to be globally methylated, DNA methylation is primarily targeted to genes in insects. Nevertheless, mounting evidence suggests that a specialized role exists for genic methylation in the regulation of transcription, and possibly mRNA splicing, in both insects and mammals. Investigations in several insect taxa further reveal that DNA methylation is preferentially targeted to ubiquitously expressed genes and may play a key role in the regulation of phenotypic plasticity. We suggest that insects are particularly amenable to advancing our understanding of the biological functions of DNA methylation, because insects are evolutionarily diverse, display several lineage-specific losses of DNA methylation and possess tractable patterns of DNA methylation in moderately sized genomes.
not annotated - annotated - LINNAEUS only
The small GTPase BcCdc42 affects nuclear division, germination and virulence of the gray mold fungus Botrytis cinerea.
The small GTPase Cdc42 plays a central role in various processes in eukaryotic cells including growth, differentiation and cytoskeleton organization. Whereas it is essential in the yeast Saccharomyces cerevisiae, its role in filamentous fungi differs, due to the complementing, partly overlapping function of Rac. We analyzed the role of the Cdc42 homologue in the necrotrophic, broad host range pathogen Botrytis cinerea. Deletion mutants of bccdc42 showed various growth abnormalities; the mutants had reduced growth rate and hyphal branching, they produced fewer conidia, which were enlarged and misshapen and had germination defects. Additionally, the mutants were impaired in sclerotia development. Cytological studies indicate that at least part of this phenotype could be attributed to disturbed control of nuclear division: conidia and hyphae of the mutant showed twofold higher nucleus/cytoplasm ratio compared to wild type cells. Apart from these effects on vegetative growth and differentiation, Deltabccdc42 strains were attenuated in penetration and colonization of host tissue, confirming that BcCdc42 - though being not essential like in yeast - is involved in important developmental processes in B. cinerea.
not annotated - annotated - LINNAEUS only
GintAMT2, a new member of the ammonium transporter family in the arbuscular mycorrhizal fungus Glomus intraradices.
In the symbiotic association of plants and arbuscular mycorrhizal (AM) fungi, the fungus delivers mineral nutrients, such as phosphate and nitrogen, to the plant while receiving carbon. Previously, we identified an NH(4)(+) transporter in the AM fungus Glomus intraradices (GintAMT1) involved in NH(4)(+) uptake from the soil when preset at low concentrations. Here, we report the isolation and characterization of a new G. intraradicesNH(4)(+) transporter gene (GintAMT2). Yeast mutant complementation assays showed that GintAMT2 encodes a functional NH(4)(+) transporter. The use of an anti-GintAMT2 polyclonal antibody revealed a plasma membrane location of GintAMT2. GintAMT1 and GintAMT2 were differentially expressed during the fungal life cycle and in response to N. In contrast to GintAMT1, GintAMT2 transcript levels were higher in the intraradical than in the extraradical fungal structures. However, transcripts of both genes were detected in arbuscule-colonized cortical cells. GintAMT1 expression was induced under low N conditions. Constitutive expression of GintAMT2 in N-limiting conditions and transitory induction after N re-supply suggests a role for GintAMT2 to retrieve NH(4)(+) leaked out during fungal metabolism.
not annotated - annotated - LINNAEUS only
Modulation of fungal sensitivity to staurosporine by targeting proteins identified by transcriptional profiling.
An analysis of the time-dependent genetic response to the death-inducer staurosporine was performed in Neurospora crassa by transcriptional profiling. Staurosporine induced two major genes encoding an ABC transporter and a protein with similarity to regulatory subunits of potassium channels. The transcriptional response is dependent on the activity of a novel transcription factor. Deletion mutants in differentially expressed genes displayed altered sensitivity to staurosporine, underscoring significant proteins involved in the response to the drug. A null-mutant of the ABC transporter (abc3) is extremely sensitive to staurosporine, accumulates more staurosporine than the wild type strain and is defective in energy-dependent export of the drug, indicating that the ABC3 protein is the first described staurosporine transporter. It was located in the plasma membrane by immunofluorescence microscopy. The combination of inhibitors of ABC transporters or of potassium channels with staurosporine leads to an enhanced activity against N. crassa and pathogenic fungi paving the way to the development of more potent and specific antifungals. Our results highlight the general use of transcriptional profiling for the identification of novel proteins involved in cell death and their potential use as drug targets.
not annotated - annotated - LINNAEUS only
Novel Fusarium head blight pathogens from Nepal and Louisiana revealed by multilocus genealogical concordance.
This study was conducted to assess evolutionary relationships, species diversity and trichothecene toxin potential of five Fusarium graminearum complex (FGSC) isolates identified as genetically novel during prior Fusarium head blight (FHB) surveys in Nepal and Louisiana. Results of a multilocus genotyping (MLGT) assay for B-trichothecene species determination indicated these isolates might represent novel species within the FGSC. GCPSR-based phylogenetic analyses of a 12-gene dataset, comprising portions of seven loci totaling 13.1kb of aligned DNA sequence data, provided strong support for the genealogical exclusivity of the Nepalese and Louisianan isolates. Accordingly, both species are formally recognized herein as novel FGSC species. Fusarium nepalense was resolved as the sister lineage of Fusarium ussurianum+Fusarium asiaticum within an Asian subclade of the FGSC. Fusarium louisianense was strongly supported as a reciprocally monophyletic sister of Fusarium gerlachii+F. graminearum, suggesting that this subclade might be endemic to North America. Multilocus Bayesian species tree analyses augment these results and provide evidence for a distinct lineage within F. graminearum predominately from the Gulf Coast of Louisiana. As predicted by the MLGT assay, mycotoxin analyses demonstrated that F. nepalense and F. louisianense could produce 15ADON and nivalenol, respectively, in planta. In addition, both species were only able to induce mild FHB symptoms on wheat in pathogenicity experiments.
not annotated - annotated - LINNAEUS only
Comparative Impact of Artificial Selection for Fungicide Resistance on Beauveria bassiana and Metarhizium brunneum.
Hypocreales fungi such as Beauveria bassiana (Balsamo) Vuillemin and Metarhizium brunneum Petch can be negatively affected by fungicides thereby reducing their biocontrol potential. In a previous study, we demonstrated enhanced fungicide resistance in B. bassiana through artificial selection. However, it is not clear if the enhanced resistance was because of improved germination, vegetative growth, or both. Additionally, the enhanced fungicide resistance has only been demonstrated in B. bassiana, and therefore it is of interest to investigate the potential to enhance resistance in other fungi. Thus, the objectives in this study were to determine the potential to enhance fungicide resistance in M. brunneum through artificial selection, and investigate if selection is based on germination, vegetative growth, or both in B. bassiana and M. brunneum. Selection for resistance to fenbuconazole, and triphenyltin hydroxide was assessed through inhibition evaluations on solid media, and germination and mycelial growth in liquid media. Increased resistance after selection was observed for all fungicide-fungus combinations on solid and or liquid media. Selection resulted in increased resistance to fenbuconazole in both fungi in solid and liquid media; in liquid culture fungicide resistance in B. bassiana was manifested by increased germination and mycelial growth, whereas in M. brunneum fungicide resistance concerned only mycelial growth. Selection for resistance to triphenyltin hydroxide varied in the different media. For B. bassiana, triphenyltin hydroxide resistance was enhanced on solid media but not in liquid, whereas enhanced resistance of M. brunneum was detected in both media. Fungicide sensitivity and selection potential differs based on the medium and fungal species. Selection for fungicide resistance, had negative effects on other beneficial traits when fungicide pressure was removed, for example, some selected populations showed decreased germination or growth, relative to their nonselected control populations. Additionally, reduced virulence to the greater wax moth, Galleria mellonella (L.), was observed in all fungal populations that were exposed to fungicide resistance regimes. We conclude that it is possible to use genetic selection to enhance fungicide resistance in B. bassiana and M. brunneum, but before use the resulting populations should be screened for inadvertent negative impacts on beneficial traits.
not annotated - annotated - LINNAEUS only
Dispersion Models and Sampling of Cacao Mirid Bug Sahlbergella singularis (Hemiptera: Miridae) on Theobroma Cacao in Southern Cameroon.
The spatio-temporal distribution of Sahlbergella singularis Haglung, a major pest of cacao trees (Theobroma cacao) (Malvaceae), was studied for 2 yr in traditional cacao forest gardens in the humid forest area of southern Cameroon. The first objective was to analyze the dispersion of this insect on cacao trees. The second objective was to develop sampling plans based on fixed levels of precision for estimating S. singularis populations. The following models were used to analyze the data: Taylor's power law, Iwao's patchiness regression, the Nachman model, and the negative binomial distribution. Our results document that Taylor's power law was a better fit for the data than the Iwao and Nachman models. Taylor's b and Iwao's Beta were both significantly >1, indicating that S. singularis aggregated on specific trees. This result was further supported by the calculated common k of 1.75444. Iwao's alpha was significantly <0, indicating that the basic distribution component of S. singularis was the individual insect. Comparison of negative binomial (NBD) and Nachman models indicated that the NBD model was appropriate for studying S. singularis distribution. Optimal sample sizes for fixed precision levels of 0.10, 0.15, and 0.25 were estimated with Taylor's regression coefficients. Required sample sizes increased dramatically with increasing levels of precision. This is the first study on S. singularis dispersion in cacao plantations. Sampling plans, presented here, should be a tool for research on population dynamics and pest management decisions of mirid bugs on cacao.