Vibrio sinensis strain:BEI233
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PROVIDER: PRJNA486078 | ENA |
REPOSITORIES: ENA
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Project description:Vibrio sinensis strain:BEI233 Raw sequence reads
| PRJNA493561 | ENA
Project description:Background: Liver cancer is the third deadliest type of cancer, posing a serious threat to human health. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. C. sinensis, classified as a definite group I carcinogen by the IARC (International Agency for Research on Cancer), is an important risk factor for HCC. Although many studies have shown that C. sinensis infection affects the prognosis of HCC patients, the specific mechanisms are still unclear, especially the dynamics and regulatory roles of chromatin accessibility. Results: In this study, we integrated ATAC-seq, RNA-seq, and ChIP-seq data to elucidate changes in the epigenetics of HCC after the C. sinensis infection. Many different accessibility regions (DARs) were identified both in tumors and adjacent tissue after the C. sinensis infection. Meanwhile, top TFs whose motifs were enriched in DAR were found, such as HNF4a, FOXI1, etc. Although there were slight deviations, epigenetic changes were found to be consistent with gene expression levels. We also revealed that H3K9ac, H3K4me2, H3K4me3, H3K27ac, and H3K4me1 were associated with chromatin accessibility. Importantly, we also found potential evidence that C. sinensis infection would alter the spatial structure of the HCC genome. Finally, both molecular experimental results and clinical data certified that C. sinensis infection would promote the metastasis of HCC. Conclusions: C. sinensis infection will remodel the chromatin accessibility of HCC, leading to changes in gene expression levels. This study provides conclusive evidence that C. sinensis infection alters the epigenetics of HCC.
2024-11-26 | GSE276855 | GEO
Project description:Bacterial strains within a species can differ in traits that shape host–microbe interactions. Using the squid–vibrio symbiosis, we examined how strain-level variation influences host responses. Strains from squid and fish light organs were compared for their effects on Euprymna scolopes gene expression and development. Non-native strains showed reduced colonization success and delayed host phenotypes. Transcriptomic responses were most similar with native isolates and most divergent with a fish-derived strain. These findings demonstrate that fine-scale strain differences shape host compatibility and underscore the importance of strain-level diversity in the establishment of beneficial symbioses.
2025-11-05 | GSE306269 | GEO
Project description:Investigation of whole genome gene expression level changes in a Vibrio cholerae O395N1 delta-nqrA-F mutant, compared to the wild-type strain.
2014-04-01 | GSE56387 | GEO
Project description:The transcriptome of the wild type strain and ΔcueR of Vibrio parahaemolyticus was compared by RNA sequencing analysis.
2025-06-14 | GSE299205 | GEO
Project description:Environmental isolates of Vibrio cholerae from California coastal water compared to reference strain N16961. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design; array CGH
2007-07-17 | GSE8499 | GEO
Project description:Vibrio campbellii BB120 (ATCC BAA-1116, previously designated as Vibrio harveyi) is a fundamental model strain for studying population density-based cell-to-cell communication, known as quorum sensing, among gram-negative bacteria. In V. campbellii BB120, sensing of autoinducers at high cell densities activates the expression of the master transcriptional regulator, LuxR, which controls the expression of genes involved in group behaviors. Unlike BB120, the Vibrio campbellii environmental isolate DS40M4 was recently shown to be capable of natural transformation, a process by which bacteria take up exogenous DNA and incorporate it into their genome via homologous recombination. Here, we compare other phenotypes between DS40M4 and BB120. We find that DS40M4 has a faster growth rate and stronger type VI secretion-mediated cell killing, whereas BB120 forms more robust biofilms and is bioluminescent. We exploited the power of natural transformation to rapidly generate >30 mutant strains to explore the function of DS40M4-encoded homologs of the BB120 quorum-sensing system. Our results show that DS40M4 has a similar quorum-sensing circuit to BB120 but with three distinct differences: 1) DS40M4 lacks the canonical HAI-1 autoinducer LuxM synthase but has an active LuxN receptor, 2) the quorum regulatory small RNAs (Qrrs) are not solely regulated by autoinducer signaling through the response regulator LuxO, and 3) the DS40M4 LuxR regulon is <100 genes, which is relatively small compared to the >400 genes regulated in BB120. This work illustrates that DS40M4 is a tractable and relevant model strain for studying quorum-sensing phenotypes in Vibrio campbellii.
2021-06-28 | GSE147616 | GEO
Project description:Supplementary proteome data of Vibrio alginolyticus strain: ZJ-T, the Wild-type raw files are in another project (ProteomeXchange ID: PXD035385).
2023-09-22 | PXD045577 |
Project description:Background The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome level assembled lycophyte genomes, has hindered our understanding of evolution and environmental adaption of lycophytes. Findings We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and the diploid I. taiwanensis revealed of genomic features and polyploid of lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provides insights into environmental adaption of lycophytes. Conclusions The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic research and the conservation of not only I. sinensis but also other lycophytes.
2023-08-21 | GSE198196 | GEO