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      Virulence of Vibrio alginolyticus Accentuates Apoptosis and Immune Rigor in the Oyster Crassostrea hongkongensis

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          Abstract

          Vibrio species are ubiquitously distributed in marine environments, with important implications for emerging infectious diseases. However, relatively little is known about defensive strategies deployed by hosts against Vibrio pathogens of distinct virulence traits. Being an ecologically relevant host, the oyster Crassostrea hongkongensis can serve as an excellent model for elucidating mechanisms underlying host- Vibrio interactions. We generated a Vibrio alginolyticus mutant strain ( V. alginolyticus vscC ) with attenuated virulence by knocking out the vscC encoding gene, a core component of type III secretion system (T3SS), which led to starkly reduced apoptotic rates in hemocyte hosts compared to the V. alginolyticus WT control. In comparative proteomics, it was revealed that distinct immune responses arose upon encounter with V. alginolyticus strains of different virulence. Quite strikingly, the peroxisomal and apoptotic pathways are activated by V. alginolyticus WT infection, whereas phagocytosis and cell adhesion were enhanced in V. alginolyticus vscC infection. Results for functional studies further show that V. alginolyticus WT strain stimulated respiratory bursts to produce excess superoxide (O2 •−) and hydrogen peroxide (H 2O 2) in oysters, which induced apoptosis regulated by p53 target protein (p53tp). Simultaneously, a drop in sGC content balanced off cGMP accumulation in hemocytes and repressed the occurrence of apoptosis to a certain extent during V. alginolyticus vscC infection. We have thus provided the first direct evidence for a mechanistic link between virulence of Vibrio spp. and its immunomodulation effects on apoptosis in the oyster. Collectively, we conclude that adaptive responses in host defenses are partially determined by pathogen virulence, in order to safeguard efficiency and timeliness in bacterial clearance.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            TBtools - an integrative toolkit developed for interactive analyses of big biological data

            The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
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              The PRIDE database and related tools and resources in 2019: improving support for quantification data

              Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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                Author and article information

                Contributors
                Journal
                Front Immunol
                Front Immunol
                Front. Immunol.
                Frontiers in Immunology
                Frontiers Media S.A.
                1664-3224
                21 September 2021
                2021
                : 12
                : 746017
                Affiliations
                [1] 1Chinese Academy of Sciences Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science , Guangzhou, China
                [2] 2Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou, China
                [3] 3College of Earth and Planetary Sciences, University of Chinese Academy of Sciences , Beijing, China
                [4] 4Department of Pharmacology, Shantou University Medical College , Shantou, China
                Author notes

                Edited by: Jun Li, Lake Superior State University, United States

                Reviewed by: Yishan Lu, Guangdong Ocean University, China; Shihao Li, Institute of Oceanology (CAS), China; Lingling Wang, Dalian Ocean University, China

                *Correspondence: Yang Zhang, yzhang@ 123456scsio.ac.cn ; Ziniu Yu, carlzyu@ 123456scsio.ac.cn

                †These authors have contributed equally to this work

                This article was submitted to Comparative Immunology, a section of the journal Frontiers in Immunology

                Article
                10.3389/fimmu.2021.746017
                8490866
                34621277
                a8c3d0ad-c5dc-4b78-adb8-7f8b885e9d41
                Copyright © 2021 Mao, Liu, Wong, Zhang, Yi, Xiang, Xiao, Yu and Zhang

                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
                : 23 July 2021
                : 31 August 2021
                Page count
                Figures: 7, Tables: 0, Equations: 0, References: 95, Pages: 16, Words: 8185
                Categories
                Immunology
                Original Research

                Immunology
                vibrio alginolyticus,oyster,virulence,host-pathogen interactions,proteomics
                Immunology
                vibrio alginolyticus, oyster, virulence, host-pathogen interactions, proteomics

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