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41 results for “Vibrio parahaemolyticus”
Data on the occurrence of Vibrio spp. of public health importance (i.e. Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae non-O1/non-O139) in seafood in European countries (Jan 2010-Sept 2023)
<p><span>This file contains data on the occurrence of <em><span>Vibrio</span></em><span> spp. of public health importance (<em>i.e</em>. <em>Vibrio parahaemolyticus</em>, <em>Vibrio vulnificus,</em> and <em>Vibrio cholerae </em>non-O1/non-O139) in seafood produced and/or commercialized in Europe, </span>covering studies published between January 2010 and September 2023. </span><span>The systematic review protocol used to identify and extract the information is available at <a href="../doi/10.5281/zenodo.10282513"><span>https://zenodo.org/doi/10.5281/zenodo.10282513</span></a> .</span></p>
Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease
<p>Supplemental File 1: Main genome assemblies (Unpolished Flye assembly, Polished Flye assembly, Unicycler Hybrid Assembly and Unicycler Illumina-only assembly) generated in this study for comparison and their BUSCO output.</p> <p>Supplemental File 2: Phyre2 protein modelling output of the putative MVP1 TcdA toxin</p> <p>Supplemental File 3: Phyre2 protein modelling output of the putative MVP1 TcdB toxin</p> <p>Supplemental File 4: Phyre2 protein modelling output of the putative MVP1 TccC toxin</p> <p>Supplemental File 5: InterProScan output of the NCBI-predicted MVP1 proteome.</p> <p>Supplemental Table 1: NCBI BlastN output using the <em>fuc</em> genes of <em>Vibrio parahaemolyticus</em> MVP1 as the query to search against the Vibrio reference WGS database as of 21 Oct 2019</p>
Screening of AMR-related genes in the genomes of Vibrio parahaemolyticus strains isolated in Europe from clinical, environmental and other sources
<p>The distribution of antimicrobial resistance (AMR) genes for the EU and European Free Trade Association (EFTA) countries data was obtained from the global <em>Vibrio parahaemolyticus</em> genomes based on a collection of nearly 10,000 genomes. Some of the strains are from the collection of prof. Jaime Martinez-Urtaza (Department of Genetics and Microbiology, Universitat Autònoma de Barcelona) or are part of ongoing studies to expand the genome collection; other genomes were retrieved from the European Nucleotide Archive (ENA at <a href="https://www.ebi.ac.uk/ena/browser/home" target="_blank" rel="noopener">https://www.ebi.ac.uk/ena/browser/home</a>) and the National Center for Biotechnology Information (NCBI) [GenBank at <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/genbank/</a>; RefSeq at <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/refseq/</a>; SRA at <a href="https://www.ncbi.nlm.nih.gov/sra" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/sra]</a>. For detection of AMR genes, a resistance genes detection pipeline based on one of the standard databases (CARD database at<a href="https://card.mcmaster.ca/" target="_blank" rel="noopener"> https://card.mcmaster.ca/</a>) was used. The phylogenetic tree was prepared and includes the reference genome from Japan <em>"Osaka" </em>as reference. The RIMD 2210633 strain has been added as the global reference strain which has been historically used for all the phylogenetic analysis of <em>V. parahaemolyticus</em>. The metadata includes the source of the strain, i.e., country, origin (clinical, environmental or unclear), date of isolation, and subtype. The antibiotic-resistant genes are shown as present, absent or not applicable. To build the ARGs European <em>V. parahaemolyticus</em> tree, the Parsnp tool, a fast core-genome multi-aligner and SNP detector, from the Harvest suite was used (Treangen et al., 2014). Parsnp calculates the MUMi distances between the reference genome (RIMD_2210633) and each one of the 152 genomes used in this study. The resulting Newick formatted core genome SNP tree was then uploaded onto the webtool I-Tol (Letunic and Bork, 2021), midpoint rooted and the metadata of the samples was incorporated.</p> <p>The accession IDs for the genomes included in the metadata are accessible in the following databases according to the first characters:<br>* GCA: GenBank (<a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/genbank/</a>)<br>* GCF: RefSeq (<a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/refseq/</a>)<br>* ERR: ENA (<a href="https://www.ebi.ac.uk/ena/browser/home" target="_blank" rel="noopener">https://www.ebi.ac.uk/ena/browser/home</a>)<br>* SRR: SRA (<a href="https://www.ncbi.nlm.nih.gov/sra" target="_blank" rel="noopener">https://www.ncbi.nlm.nih.gov/sra</a>)</p> <p>References</p> <p>Letunic I and Bork P, 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res, 49:W293-w296. doi: 10.1093/nar/gkab301</p> <p>Treangen TJ, Ondov BD, Koren S and Phillippy AM, 2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol, 15:524. doi: 10.1186/s13059-014-0524-x</p>
OpaR Controls a Network of Downstream Transcription Factors in Vibrio parahaemolyticus BB22
GEO Series GSE53639. Vibrio parahaemolyticus. 2 samples. Type: Expression profiling by high throughput sequencing.
Gene expression of Vibrio parahaemolyticus in the early stationary phase
GEO Series GSE65448. Vibrio parahaemolyticus RIMD 2210633. 16 samples. Type: Expression profiling by array.
Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment
GEO Series GSE92847. Vibrio parahaemolyticus. 6 samples. Type: Expression profiling by high throughput sequencing.
Integrative Analyses of mRNA and MicroRNA Expression Profiles Reveals the Innate Immune Mechanism for the Resistance to Vibrio parahaemolyticus Infection in Epinephelus coioides [miRNA-seq]
GEO Series GSE207125. Epinephelus coioides. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The scr circuit in Vibrio parahaemolyticus: output targets and transcriptional regulation by a c-di-GMP responsive protein
GEO Series GSE30508. Vibrio parahaemolyticus RIMD 2210633; Vibrio parahaemolyticus. 4 samples. Type: Expression profiling by array.
Integrative Analyses of mRNA and MicroRNA Expression Profiles Reveals the Innate Immune Mechanism for the Resistance to Vibrio parahaemolyticus Infection in Epinephelus coioides [RNA-seq]
GEO Series GSE207124. Epinephelus coioides. 6 samples. Type: Expression profiling by high throughput sequencing.
Complete genome sequence of Vibrio parahaemolyticus CHN25 and transcriptomic analysis of cold shock proteins of VpaCspA and VpaCspD in the adaptation of low temperature growth
GEO Series GSE65998. Vibrio parahaemolyticus. 4 samples. Type: Expression profiling by high throughput sequencing.
Regulatory mechanism of host cell contact-dependent T3SS gene expression in Vibrio parahaemolyticus
GEO Series GSE266863. Vibrio parahaemolyticus. 15 samples. Type: Expression profiling by high throughput sequencing.
Shrimp transcriptome analysis after exposure to recombinant Vibrio parahaemolyticus PirA and PirB toxins
GEO Series GSE200137. Penaeus vannamei. 30 samples. Type: Expression profiling by high throughput sequencing.
RNA sequencing analysis of the genes regulated by CueR in Vibrio parahaemolyticus.
GEO Series GSE299205. Vibrio parahaemolyticus. 6 samples. Type: Expression profiling by high throughput sequencing.
Deep sequencing of microRNAs in multiple tissues of Scylla paramamosain under Vibrio parahaemolyticus infection
GEO Series GSE39921. Scylla paramamosain. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Integrative Analyses of mRNA and MicroRNA Expression Profiles Reveals the Innate Immune Mechanism for the Resistance to Vibrio parahaemolyticus Infection in Epinephelus coioides
GEO Series GSE207127. Epinephelus coioides. 12 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Transcriptome Analysis of T3SS1 in Vibrio parahaemolyticus
GEO Series GSE51423. Vibrio parahaemolyticus. 20 samples. Type: Expression profiling by high throughput sequencing.
Changes in global gene expression of Vibrio parahaemolyticus viable but non-culturable (VBNC) state
GEO Series GSE65340. Vibrio parahaemolyticus RIMD 2210633. 24 samples. Type: Expression profiling by array.
Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence
GEO Series GSE18763. Vibrio parahaemolyticus; Vibrio parahaemolyticus RIMD 2210633. 15 samples. Type: Expression profiling by array.
Quorum sensing and silencing in Vibrio parahaemolyticus
GEO Series GSE28216. Vibrio parahaemolyticus RIMD 2210633; Vibrio parahaemolyticus. 9 samples. Type: Expression profiling by array.
ChIP-seq identified the regulation of genes by the quorum-sensing regulator OpaR in Vibrio parahaemolyticus
GEO Series GSE122479. Vibrio parahaemolyticus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.