Project description:Transcriptional profiling of Mycobacterium smegmatis comparing strains undergoing I-SceI generated DNA damage at a single genomic locus Gene designations are the updated annotation

2011-07-15 | GSE30635 | GEO

Genomic comparison in Vibrio parahaemolyticus strains by comparative genomic hybridization.

Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Almost all of the clinical V. parahaemolyticus isolates exhibit a beta-type hemolysis on Wagatsuma agar, known as the Kanagawa phenomenon (KP). KP is induced by the thermostable direct hemolysin (TDH) produced by the organism, and has been considered a crucial marker to distinguish pathogenic strains from non-pathogenic ones. Since 1996, so-called “pandemic clones”, the majority of which belong to serotype O3:K6, have caused worldwide outbreaks of gastroenteritis. In this study, we used a DNA microarray constructed based on the genome sequence of a pandemic V. parahaemolyticus strain RIMD2210633 to examin the genomic composition of 22 strains of V. parahaemolyticus, including both pathogenic (pandemic as well as non-pandemic) and non-pathogenic strains. Over 85% of the RIMD2210633 genes were conserved in all the strains tested. Many of variably present genes formed gene clusters on the genome of RIMD2210633 and were probably acquired through lateral gene transfer. At least 70 genes over 10 loci were specifically present in the pandemic strains when compared with any of the non-pandemic strains, suggesting that the difference between pandemic and non-pandemic strains is not due to a simple genetic event. Only the genes in the 80-kb pathogenicity island (Vp-PAI) on chromosome II, including two tdh genes and a set of genes for the Type III secretion system, were detected only in the KP-positive pathogenic strains. These results strongly suggest that acquisition of this Vp-PAI was crucial for the emergence of V. parahaemolyticus strains that are pathogenic for humans. Keywords: comparative genomic hybridization, CGH

2008-03-31 | GSE10020 | GEO

TAU - Ben-Jacob - P. vortex - Gene Prediction Validation - 105k

Project description:Validation of the de-novo sequenced Paenibacillus vortex annotation using microarray.

2010-11-29 | E-MEXP-3019 | biostudies-arrayexpress

Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains

Project description:Nowadays proteomics is the one of the major instruments for editing and correct decryption of genomic information. Genomic correction of socially significant pathogens, like Mycobacterium tuberculosis, is by far the most relevant. We conducted proteogenomic analysis of W-148 strain, which belong to the Beijing B0/W148 cluster. Strains of this cluster possess unique pathogenic properties and have a unique genome organization. Taking into account a high similarity of cluster strains at the genomic level we analysed MS/MS datasets obtained for 63 clinical isolates of Beijing B0/W148. Based on H37Rv and W-148 annotations we identified 2,546 proteins, representing more than 60 % of total proteome. A set of peptides (n=404), specific for W-148 was found in comparison with H37Rv. Start sites for 32 genes were corrected based on combination of LC-MS/MS proteomic data with genomic six frame translation. Additionally, presence of peptides for 10 pseudogenes has been confirmed. Thus, the data obtained by us undoubtedly shows the need for conducting genome annotation based on proteomic data. Corrected during the study W-148 genome annotation will allow to use it in studies on Beijing B0/W148 cluster strains.

2018-10-08 | PXD009489 | Pride

Genomic content analysis of Clostridium botulinum type F strains

Project description:The purpose of this study was to determine the level of genomic content similarity among selected strains of Clostridium botuinum type F strains.

2013-12-19 | GSE53456 | GEO

Genomic comparisons of Salmonella enterica sspI strains

Project description:Comparative genomic analysis of the most important S. enterica sspI clinical isolates and respective strains from the SARB collection Keywords: other

2004-05-10 | GSE1035 | GEO

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