Whole Genome Sequencing of Vibrio tapetis strains
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PROVIDER: PRJEB22962 | ENA |
REPOSITORIES: ENA
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Project description:In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori(H. pylori) genomes was designed and utilized for comparative genomic profiling of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation were found among these strains, an additional 76 H. pylori stains with different clinical outcomes isolated from various provinces of China were further tested by PCR to demonstrate this distinction. We observed several highly variable regions among strains of gastritis, gastric ulceration and gastric cancer. They are involved in genes associated with bacterial type I, type II and type III R-M system as well as in a virB gene neighboring the well studied cag pathogenic island. Previous studies have reported the diverse genetic characterization of this pathogenic island, but it is conserved in the strains tested by microarray in this study. Moreover, a number of genes involved in the type IV secretion system related to DNA horizontal transfer between H. pylori strains were identified based on the comparative analysis of the strain specific genes. These findings may provide new insights for discovering biomarkers for prediction of gastric diseases.
2013-11-10 | GSE32107 | GEO
Project description:X. oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight of rice. X. oryzae pv. oryzicola (Xoc) is the causal agent of bacterial streak of rice. Fourteen day old rice leaves were inoculated with one of five strains of Xanthomonas oryzae. Seven strains of Xoo were used; three wild type strains (PXO99A, T7174, and PXO86) and strains PXO99AME7, which has a nonfunctional type III secretion system and is non-pathogenic, , PXO99AME1, a pthXo6 and avrXa27 double mutant, PXO99ME2, a pthXo1 mutant, and PXO99ME5, a reduced virulence strain with uncharacterized mutation in a TAL effector. One strain of Xoc (BLS303) was tested. Controls include an inoculation with water (MOCK) and no inoculation. T7174 is our label for the Japanese isolate MAFF311018. Third leaves are inoculated with a needless syringe at adjacent sites along the upper leaf blade. Six leaves from separate plants are pooled. RNA samples were collected 24 h after treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ginny Antony. The equivalent experiment is OS66 at PLEXdb.]
2012-03-06 | GSE36272 | GEO
Project description:Pathogenic bacteria Yersinia enterocolitica injects virulence plasmid-encoded effectors through the type three secretion system into macrophages to modulate gene expression. Here we analyzed the effect on gene expression in primary human macrophages of Y. enterocolitica strains lacking effector YopP (1.5 h infection) or effectors YopP and YopM (1.5 h or 6 h infection) simultaneously using RNA-seq. This is part of a larger sequencing experiment for which other samples can be found in EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-10473 and European Nucleotide Archive (ENA) at http://www.ebi.ac.uk/ena/data/view/PRJEB10086.
2022-06-01 | E-MTAB-10602 | biostudies-arrayexpress
Project description:Pathogenic bacteria Yersinia enterocolitica injects virulence plasmid-encoded effectors through the type three secretion system into macrophages to modulate gene expression. At this point there are no comprehensive gene expression analysis in primary human macrophages analyzing the effect of virulence plasmid-encoded factors on transcription. For this primary human macrophages were infected for 1.5 h and 6 h with mock, WAC (virulence plasmid-cured strain) or WA314 (wild type) and samples were subjected to RNA-seq. The effect of effector protein YopP on gene expression in macrophages was analyzed using a wild type strain lacking YopP.
2021-11-07 | E-MTAB-10473 | biostudies-arrayexpress
Project description:Pathogenic bacteria Yersinia enterocolitica injects virulence plasmid-encoded effectors through the type three secretion system into macrophages to modulate gene expression. At this point it is not known whether epigenetic modifications play a role in Yersinia regulation of gene expression. To answer this question primary human macrophages were infected with mock, WAC (virulence plasmid-cured strain) or WA314 (wild type) and samples were subjected to ChIP-seq for H3K4me3, H3K4me1, H3K27ac and H3K27me3. The effect of effector proteins YopM and YopP on histone modifications in macrophages was analyzed using a wild type strain lacking either YopM or YopP and subsequent ChIP-seq analysis.
2021-11-07 | E-MTAB-10475 | biostudies-arrayexpress
Project description:In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori(H. pylori) genomes was designed and utilized for comparative genomic profiling of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation were found among these strains, an additional 76 H. pylori stains with different clinical outcomes isolated from various provinces of China were further tested by PCR to demonstrate this distinction. We observed several highly variable regions among strains of gastritis, gastric ulceration and gastric cancer. They are involved in genes associated with bacterial type I, type II and type III R-M system as well as in a virB gene neighboring the well studied cag pathogenic island. Previous studies have reported the diverse genetic characterization of this pathogenic island, but it is conserved in the strains tested by microarray in this study. Moreover, a number of genes involved in the type IV secretion system related to DNA horizontal transfer between H. pylori strains were identified based on the comparative analysis of the strain specific genes. These findings may provide new insights for discovering biomarkers for prediction of gastric diseases. Here we describe the design and use of a high-density oligonucleotide microarray covering six sequenced H. pylori genomes as well as several sequenced plasmids. The performance of this microarray is evaluated, and its utility is illustrated for the hybridization of genomic DNA in order to compare eight uncharacterized H. pylori strains which have not been sequenced with the six known, sequenced strains. We utilize this microarray to identify variable genomic region among H. pylori strains isolated from patients with different gastroduodenal diseases in a Chinese patient population. H. pylori isolates from 2 patients with chronic superficial gastritis, 2 patients with atrophic gastritis, 2 patients with gastric ulcer, and 2 patients with gastric cancer were studied. All eight strains were isolated from Heilongjiang province of China. A number of variable regions with high genetic diversity was identified. 26 selected genes were validated by large scale PCR in both microarray tested strains while an additional 76 strains were isolated from eight provinces.
2013-11-10 | E-GEOD-32107 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in leaves of susceptible (MM106) or resistant (ME010) apple genotypes either non-inoculated, inoculated with the wild type strain of Erwinia amylovora (CFBP1430) or the non-pathogenic mutant strain PMV6023. The mutant strain PMV6023 is affected in the biosynthesis of the type 3 secretion system delivering bacterial effectors into apple cells. Leaves were harvested for RNA extraction before inoculation, 6 hours and 24 hours after inoculation.
2021-05-25 | GSE175422 | GEO
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
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 âpandemic clonesâ, 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 Total 66 test samples were analyzed. Genomic DNA from each test strain and a reference strain (RIMD2210633) were labeled with Cy3 and Cy5, respectively, and were cohybridized on a single array. Labeling and hybridization were performed three times independently.
2010-05-25 | E-GEOD-10020 | biostudies-arrayexpress
Project description:IV CRISPR-Cas system displays PAM-dependent interference to vectors without showing nuclease activity to the target
| PRJEB48544 | ENA