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Bas E Dutilh Cristiane C Thompson Ana CP Vicente Michel A Marin Clarence Lee Genivaldo GZ Silva Robert Schmieder Bruno GN Andrade Luciane Chimetto Daniel Cuevas Daniel R Garza Iruka N Okeke Aaron Oladipo Aboderin Jessica Spangler Tristen Ross Elizabeth A Dinsdale Fabiano L Thompson Timothy T Harkins Robert A Edwards 《BMC genomics》2014,15(1)
Background
Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.Results
Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.Conclusions
Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users. 相似文献52.
Role of STAT6 in IgE receptor/FcepsilonRI-mediated late phase allergic responses of mast cells. 总被引:1,自引:0,他引:1
In this study we show that IgE receptor engagement triggers activation of STAT6 in mast cells. We sought to determine the role of STAT6 activation in IgE receptor-mediated mast cell responses using STAT6 knockout mice. After IgE receptor engagement, bone marrow mast cells from STAT6(-/-) mice exhibited normal histamine and leukotriene C(4) release, but their cytokine release was markedly reduced. In accordance with these in vitro data, IgE/Ag-challenged STAT6(-/-) mice showed normal early phase, but severely impaired late phase, allergic reactions. These findings provide unprecedented evidence that STAT6 plays a pivotal role in mast cell responses to IgE/Ag stimulation. 相似文献
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Manoj V. Parakhia Rukam S. Tomar Bipin J. Malaviya Rashmin M. Dhingani Visha M. Rathod Jalpa R. Thakkar B. A. Golakiya 《Indian journal of microbiology》2014,54(1):118-119
Enterobacter sp. MR1 an endophytic plant growth promoting bacterium was isolated from the roots of Butea monosperma, a drought tolerant plant. Genome sequencing of Enterobacter spp. MR1 was carried out in Ion Torrent (PGM), Next Generation Sequencer. The data obtained revealed 640 contigs with genome size of 4.58 Mb and G+C content of 52.8 %. This bacterium may contain genes responsible for inducing drought tolerance in plant, including genes for phosphate solubilization, growth hormones and other useful genes for plant growth. 相似文献
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Chakrapani H Goodblatt MM Udupi V Malaviya S Shami PJ Keefer LK Saavedra JE 《Bioorganic & medicinal chemistry letters》2008,18(3):950-953
Structural analogues of JS-K, an anti-cancer lead compound, were prepared and their in vitro anti-leukemic activity was determined. The rate of nitric oxide release from the corresponding diazeniumdiolate anions did not appear to affect the anti-leukemic activity of the prodrug forms. Two compounds with potent inhibitory activity and a potentially favorable toxicological profile were identified. 相似文献
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Dewald DB Ozaki S Malaviya S Shope JC Manabe K Crosby L Neilsen P Johnston D Harihar S Prestwich GD 《Cell calcium》2005,38(2):59-72
Intracellular calcium [Ca(2+)](i) is mobilized in many cell types in response to activation of phosphoinositide (PIP(n)) signaling pathways involving PtdIns(4,5)P(2) or PtdIns(3,4,5)P(3). To further explore the relationship between increases in intracellular PIP(n) concentrations and mobilization of [Ca(2+)](i), each of the seven phosphorylated phosphoinositides (PIP(n)s) were delivered into cells and the metabolism and physiological effects of the exogenously administered PIP(n)s were determined. The efficient cellular delivery of fluorophore-tagged and native PIP(n)s was accomplished using histone protein, neomycin, and dendrimeric polyamines. PtdIns(4,5)P(2) fluorophore-tagged analogs with short- and long-acyl chains were substrates for cellular enzymes in vitro and for phospholipases in stimulated fibroblasts. PtdIns(4)P, PtdIns(3,4)P(2) and PtdIns(4,5)P(2), each induced calcium mobilization rapidly after exogenous addition to fibroblasts. PtdIns(3,4,5)P(3) induced a significant, but smaller increase in intracellular calcium. These observations suggest that PIP(n)s other than PtdIns(4,5)P(2) or PtdIns(3,4,5)P(3) may have direct roles in signaling involving [Ca(2+)](i). 相似文献
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Alterations in immunological response before and after chemotherapy were investigated in hamsters infected with A. ceylanicum. Four reference anthelmintics mebendazole, albendazole, levamisole and pyrantel pamoate and one newly synthesized anthelmintic compound 81-470 were used. Drugs in curative doses were administered on day 30 post infection and the humoral response was assessed by counter immunoelectrophoresis and ELISA and cell mediated immunity by delayed type of hypersensitivity reaction. In infected untreated animals the precipitins appeared on day 30 and remained prominent till day 250 post infection. However with ELISA the antibodies could be demonstrated as early as day 3 post infection and peaked on day 40. Delayed type of hypersensitivity could not be demonstrated during the course of infection. All the drugs including Comp. 81-470 were effective in removing the parasites. Precipitin antibodies were only demonstrable till day 60 post treatment. ELISA depicted gradual depletion of antibody titre following treatment with mebendazole, albendazole and pyrantel pamoate. In levamisole treated hamsters the initial fall in serum antibody was restored by day 20 post treatment. With Compound 81-470, immediately after the treatment there was sharp rise in antibodies concentration followed by gradual fall and on day 60 post treatment the titre was still higher than the pretreated titre. Thus the study denotes that effective therapy will bring down immune responses of the host if the drug possess no immunopotentiating action. Therefore the immune parameters may be used as supportive indicator to successful therapy particularly in systemic parasites where parasitic forms are nondemonstrable in excreta or blood. 相似文献
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