Ontology highlight
ABSTRACT:
PROVIDER: PRJNA534103 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8942570_1.fastq.gz | Fastqsanger.gz | |||
| SRR8942570_2.fastq.gz | Fastqsanger.gz | |||
| SRR8942571_1.fastq.gz | Fastqsanger.gz | |||
| SRR8942571_2.fastq.gz | Fastqsanger.gz | |||
| SRR8942572_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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: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: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: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: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:VarS/A is one of the global factors regulating diverse aspects of metabolism and virulence of bacteria including pathogenic Vibrio spp. An experiment to identify VarS/A-regulon in V. vulnificus revealed that a putative LuxR-type transcriptional regulator was down-regulated in ΔvarA mutant. To investigate the roles of this regulatory cascade from VarS/A to a LuxR-type regulator in V. vulnificus, the target gene regulated by a LuxR-regulator was identified and its expression was characterized.
2015-03-25 | GSE67192 | GEO
Project description:In marine Vibrio species, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in two Vibrio campbellii strains, DS40M4 and NBRC 15631, enables high frequencies of natural transformation. Conversely, transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation in V. campbellii DS40M4. This result is in contrast to Vibrio cholerae that requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar to V. cholerae, QstR is necessary for transformation in DS40M4. To investigate the difference in transformation frequencies between BB120 and DS40M4, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional natural transformation in this strain. Comparison of transformation frequencies among Vibrio species indicates a wide disparity among even closely related strains, with Vibrio vulnificus having the lowest functional transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency in Vibrio vulnificus.
2019-11-14 | GSE136941 | GEO
Project description:The pathogenic marine bacterium Vibrio vulnificus is a causative agent of food-borne diseases such as life-threatening septicemia and gastroenteritis in individuals with underlying predisposed conditions.Because most infection cases of V. vulnificus are caused by ingestion of contaminated seafood, the pathogen has to encounter host cells in the gut at the early stage of infection and alters its gene expression patters to adapt the gut environment of host. To identify differentially expressed genes when V. vulnificus cells are exposed to host cells, a transcriptome analysis of V. vulnificus cells that were either exposed to HT29-methotrexate intestinal epithelial cells or grown in basal medium eagle (Sigma) (as a negative control) was performed using Illumina GAIIx system. 16S and 23S rRNA were depleted using MICROBExpress kit (Ambion) from the total RNAs of each sample. Strand-specific cDNA libraries of the samples were constructed using Truseq stranded mRNA prep. kit (Illumina). Single-end and 36 cycle sequencing were performed using Iluumina GAIIx sequencer by ChunLab (http://www.chunlab.com) and Raw sequence data were analyzed by CLC Genomics Workbench 5. 5. 1 (CLC Bio)
2017-08-29 | E-MTAB-5629 | biostudies-arrayexpress
Project description:Vibrio vulnificus is a marine zoonotic pathogen associated with fish farms that is considered a biomarker of climate change. Zoonotic strains trigger a rapid death of their susceptible hosts (fish or humans) by septicemia that has been linked to a cytokine storm in mice. A toxin called RtxA1 produced by the bacteria might play an important role in bacterial invasion and subsequent death by septic shock since animals infected with a mutant deficient in rtxA1 suffer from septicemia but do not die. The aim of this study was to globally analyze the early eel immune response in blood against V. vulnificus, as well as the role of the RtxA1 toxin on this interaction.
2022-02-18 | GSE196944 | 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