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      The effect of environmental calcium on gene expression, biofilm formation and virulence of Vibrio parahaemolyticus

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          Abstract

          Calcium (Ca 2+) can regulate the swarming motility and virulence of Vibrio parahaemolyticus BB22. However, the effects of Ca 2+ on the physiology of V. parahaemolyticus RIMD2210633, whose genomic composition is quite different with that of BB22, have not been investigated. In this study, the results of phenotypic assays showed that the biofilm formation, c-di-GMP production, swimming motility, zebrafish survival rate, cytoxicity against HeLa cells, and adherence activity to HeLa cells of V. parahaemolyticus RIMD2210633 were significantly enhanced by Ca 2+. However, Ca 2+ had no effect on the growth, swarming motility, capsular polysaccharide (CPS) phase variation and hemolytic activity. The RNA sequencing (RNA-seq) assay disclosed 459 significantly differentially expressed genes (DEGs) in response to Ca 2+, including biofilm formation-associated genes and those encode virulence factors and putative regulators. DEGs involved in polar flagellum and T3SS1 were upregulated, whereas majority of those involved in regulatory functions and c-di-GMP metabolism were downregulated. The work helps us understand how Ca 2+ affects the behavior and gene expression of V. parahaemolyticus RIMD2210633.

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          Most cited references65

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            KEGG: kyoto encyclopedia of genes and genomes.

            M Kanehisa (2000)
            KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
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              HTSeq—a Python framework to work with high-throughput sequencing data

              Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. Contact: sanders@fs.tum.de
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                Author and article information

                Contributors
                Role: Role: Role:
                Role: Role:
                Role: Role:
                Role: Role:
                Role: Role:
                URI : https://loop.frontiersin.org/people/196964/overviewRole: Role: Role: Role: Role: Role:
                URI : https://loop.frontiersin.org/people/1762508/overviewRole: Role: Role: Role: Role: Role:
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                31 May 2024
                2024
                : 15
                : 1340429
                Affiliations
                [1] 1Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People’s Hospital , Nantong, China
                [2] 2School of Medicine, Jiangsu University , Zhenjiang, China
                Author notes

                Edited by: Nidia León-Sicairos, Autonomous University of Sinaloa, Mexico

                Reviewed by: Uriel Alberto Angulo-Zamudio, Autonomous University of Sinaloa, Mexico

                Jorge Velazquez-Roman, Autonomous University of Sinaloa, Mexico

                Gabriela Tapia-Pastrana, Hospital Regional de Alta Especialidad de Oaxaca, Mexico

                *Correspondence: Yiquan Zhang, zhangyiquanq@ 123456163.com
                Article
                10.3389/fmicb.2024.1340429
                11176486
                38881663
                c96bba42-0330-4c12-b466-901104552762
                Copyright © 2024 Li, Chang, Zhang, Zhou, Zhang, Zhang and Lu.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 17 November 2023
                : 20 May 2024
                Page count
                Figures: 7, Tables: 1, Equations: 0, References: 65, Pages: 12, Words: 8703
                Funding
                Funded by: Special Project on Clinical Medicine of Nantong University
                Award ID: 2022JZ010
                Funded by: Research Project of Nantong Health Commission
                Award ID: QN2022044
                The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Research Project of Nantong Health Commission (MS2023069 and QN2023032) and the Special Project on Clinical Medicine of Nantong University (2022JZ010).
                Categories
                Microbiology
                Original Research
                Custom metadata
                Food Microbiology

                Microbiology & Virology
                vibrio parahaemolyticus,calcium,biofilm,virulence,gene expression
                Microbiology & Virology
                vibrio parahaemolyticus, calcium, biofilm, virulence, gene expression

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