Vibrio vulnificus
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR015908_1.fastq.gz | Fastqsanger.gz | |||
| DRR015908_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Vibriosis caused by Vibrio vulnificus on eels represents an important threat for this specie under culture conditions. Development of new transcriptomic tools is essential to increase the knowledge of eel biology, that nowadays is scarcer. Therefore, using previous results obtained by 454 sequencing of the eel immune-enriched transcriptome, an eel-specific custom microarray have been designed. Gills transcriptomic pattern were analyzed as a principal portal of entry for pathogens in fish after 1h of bath infection with Vibrio vulnificus to describe gill immune response. Moreover, two different strains were used, vibro vulnificus wild type (R99) and rtx double mutant (CT285), to asses the virulence of these pathogen caused by MARTX.
2013-03-15 | GSE45163 | GEO
Project description:Vibriosis caused by Vibrio vulnificus on eels represents an important threat for this specie under culture conditions. Development of new transcriptomic tools is essential to increase the knowledge of eel biology, that nowadays is scarcer. Therefore, using previous results obtained by 454 sequencing of the eel immune-enriched transcriptome, an eel-specific custom microarray have been designed. Gills transcriptomic pattern were analyzed as a principal portal of entry for pathogens in fish after 1h of bath infection with Vibrio vulnificus to describe gill immune response. Moreover, two different strains were used, vibro vulnificus wild type (R99) and rtx double mutant (CT285), to asses the virulence of these pathogen caused by MARTX. Adult european eels were bath infected with two Vibrio vulnificus strains, the wild type and double Rtx mutant (CT285). After 0, 3, 12h post-infection eel gills were sampled. Three individuals per experimental point were sampled, including a Control group and a Handling control group. Obtaining a total of 24 samples. The transcriptomic profile was described for each individual sample.
2013-03-15 | E-GEOD-45163 | biostudies-arrayexpress
Project description:This is a model of the genome scale reconstruction of the Vibrio vulnificus metabolic network, VvuMBEL943, described in the article:
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery
Hyun Uk Kim, Soo Young Kim, Haeyoung Jeong, Tae Yong Kim, Jae Jong Kim, Hyon E Choy, Kyu Yang Yi, Joon Haeng Rhee, and Sang Yup Lee. Molecular Systems Biology
7:460 Jan 2011 doi: 10.1038/msb.2010.115
Abstract:
Although the genomes of many microbial pathogens have been studied to help identify effective drug targets and novel drugs, such efforts have not yet reached full fruition. In this study, we report a systems biological approach that efficiently utilizes genomic information for drug targeting and discovery, and apply this approach to the opportunistic pathogen Vibrio vulnificus CMCP6. First, we partially re-sequenced and fully re-annotated the V. vulnificus CMCP6 genome, and accordingly reconstructed its genome-scale metabolic network, VvuMBEL943. The validated network model was employed to systematically predict drug targets using the concept of metabolite essentiality, along with additional filtering criteria. Target genes encoding enzymes that interact with the five essential metabolites finally selected were experimentally validated. These five essential metabolites are critical to the survival of the cell, and hence were used to guide the cost-effective selection of chemical analogs, which were then screened for antimicrobial activity in a whole-cell assay. This approach is expected to help fill the existing gap between genomics and drug discovery.
This metabolic network model has been thoroughly validated by the authors. VvuMBEL943 is a stoichiometric model that contains the metabolic information of the microbial pathogen, Vibrio vulnificus CMCP6, at genome-scale. The SBML version was generated by Hyun Uk Kim using MetaFluxNet.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000001064 | BioModels
Project description:Vibrio vulnificus multiply rapidly in host tissues under iron overloaded conditions. To understand the effects of iron in the physiology of this pathogen we performed a genome-wide transcriptional analysis of this bacterium growing under three different iron concentrations. V.vulnificus CMCP6 cells were grown under three different iron concentrations (TSBS + EDDA 50uM, TSBS and TSBS + FAC 250 ug/ml) and samples taken at log phase. Keywords: Response to the iron concentration of the media
2008-08-07 | GSE10633 | GEO
Project description:Dual transcriptome analysis of the V. vulnificus-infected human cells; To understand toxin-stimulated host-pathogen interactions, we set up dual transcriptome sequencing experiments using the human epithelial (HT-29) or immune (differentiated THP-1; dTHP-1) cells infected with the sepsis-causing pathogen Vibrio vulnificus, either in wild-type or the MARTX toxin-deficient backgrounds.
2020-08-03 | GSE136540 | GEO
Project description:Vibrio vulnificus (V. vulnificus) is an opportunistic human pathogen known for causing various illnesses such as gastroenteritis, skin and muscle necrosis, septic shock, and sepsis. This halophilic estuarine bacterium's growth and infection process involves adaptation to both the natural briny environments and the host. OmpR, a response regulator in the EnvZ/OmpR two-component regulatory system (TCS), is crucial for environmental adaptation and pathogenicity. This study focused on investigating the impact of OmpR in V. vulnificus by creating an ompR knockout strain (ΔompR). The ΔompR strain exhibited reduced tolerance to alkaline stress, shorter flagella, and decreased virulence in epithelial cell and mouse models compared to the wild-type (WT) V. vulnificus. RNAseq analysis revealed the downregulation of genes involved in metabolism, flagellum-dependent motility, and transcription factors in the ΔompR strain. OmpR was found to repress the expression of aphB in alkaline conditions, impacting the acid resistance system CadBA, while also positively regulating the transcription of various flagellar genes. These findings suggest that OmpR acts as a global regulator, orchestrating the expression of multiple genes in response to different environments and during host invasion.
2024-11-08 | GSE281430 | GEO
Project description:The profiles of transcripts from the planktonic cells and biofilm cells of V. vulnificus were compared by using a V. vulnificus whole-genome microarray
2014-07-26 | GSE59753 | GEO
Project description:In order to analyze the transcripts of Arabidopsis thaliana (Col-0) and Vibrio vulnificus MO6-24/O simultaneously, Vibrio vulnificus MO6-24/O was infiltrated onto Arabidopsis leaves and then leaves were harvested at 0, 3, 6, 12, 24 and 48 h post-infiltration. A total of 31, 128, 303, 219 and 130 differentially expressed genes (DEGs) of Vibrio were up- and down-regulated at 3, 6, 12, 24 and 48 h post-infiltration (hpi). Meanwhile, differentially expressed genes (DEGs) were monitored at 3, 6, 12, 24 and 48 h post-infiltration. A total of 2,097, 1,839, 1,220, 1,170 and 1,383 genes were characterized at each time points in Arabidopsis. Our data clearly indicate that total transcripts of the marine bacterial pathogen V. vulnificus MO6-24/O are detected and analyzed in plant Arabidopsis and two organisms were inter-communicated at the same time under favorable conditions.
2020-10-06 | GSE159018 | GEO
Project description:IscR is a novel global regulator potentially contributing to the overall success in survival and pathogenesis of V. vulnificus by coordinating the regulation of various virulence factors. The profiles of transcripts from the V. vulnificus iscR mutant and the parental wild type were compared by using a V. vulnificus whole-genome microarray.
2013-02-27 | GSE44679 | GEO
Project description:Vibrio vulnificus multiply rapidly in host tissues under iron overloaded conditions. To understand the effects of iron in the physiology of this pathogen we performed a genome-wide transcriptional analysis of this bacterium growing under three different iron concentrations. V.vulnificus CMCP6 cells were grown under three different iron concentrations (TSBS + EDDA 50uM, TSBS and TSBS + FAC 250 ug/ml) and samples taken at log phase. Keywords: Response to the iron concentration of the media Strains were grown to an OD600nm of 0.6 to 0.8 in TSBS, TSBS with the addition of 250 μg/ml FAC or TSBS with the addition of 50 μM EDDA. Three independent cultures of the V. vulnificus cells grown in each media, were combined and treated as a single sample for the RNA extraction to minimize culture variation. Two samples per condition were used for the microarray analysis. Cells were centrifuged and the pellets resuspended in RNAWiz reagent (Ambion®, Austin, TX). Total RNA was extracted from each strain according to the manufacturerâ??s instructions
2010-05-25 | E-GEOD-10633 | biostudies-arrayexpress