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      Dynamic immune response characteristics of piglets infected with Actinobacillus pleuropneumoniae through omic

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          Abstract

          Porcine infectious pleuropneumonia is characterized by a high-rate of carriage and mixed infection with other pathogens. The host immune response induced by Actinobacillus pleuropneumoniae (APP) is the basis for elucidating pathogenesis and controlling disease. However, there is currently no comprehensive and dynamic data characterising the host immune response. In this study, piglets were infected with APP and differentially expressed proteins of bronchoalveolar lavage fluid (BALF) and peripheral serum were identified by iTRAQ-LC-MS/MS, and differentially expressed genes of peripheral blood mononuclear cells (PBMC) by RNA-seq. The results of the integrated analysis of serum, BALF and PBMC showed significant metabolism and local immune responses in BALF, the general immune response in PBMC mainly involves cytokines, while that in serum mainly involves biosynthesis, phagosome, and complement and coagulation cascades. Furthermore, immune responses in PBMCs and serum were rapid and maintained compared to the lung where metabolism and cell adhesion activities were enriched. Some innate immunity pathways of the cellular response to ROS, neutrophil mediated immunity, granulocyte activation and leukocyte cell-cell adhesion were identified as central points, connecting multiple signaling pathways to form an integrated large network. At 24 h post-infection, 14 molecules were up regulated in BALF, 10 of which were shared with PBMC, but at 120 h, 20 down-regulated molecules were identified in BALF, 11 of them still up- regulated in PBMC. We conclude that, the immune response in the lung is different from that in blood, but there is a similarity in response in PBMC and serum.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s13568-021-01336-z.

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          Gene Ontology: tool for the unification of biology

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            Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

            A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
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              Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

              Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
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                Author and article information

                Contributors
                fylee1987@outlook.com
                leiliancheng@163.com
                Journal
                AMB Express
                AMB Express
                AMB Express
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                2191-0855
                24 December 2021
                24 December 2021
                2021
                : 11
                Affiliations
                [1 ]GRID grid.64924.3d, ISNI 0000 0004 1760 5735, College of Veterinary Medicine, , Jilin University, ; Xi’an Road, Changchun, 5333 People’s Republic of China
                [2 ]GRID grid.412264.7, ISNI 0000 0001 0108 3408, College of Life Science and Engineering, , Northwest Minzu University, ; Lanzhou, People’s Republic of China
                [3 ]GRID grid.410654.2, ISNI 0000 0000 8880 6009, College of Animal Science, , Yangtze University, ; Jingzhou, 434023 Hubei People’s Republic of China
                Article
                1336
                10.1186/s13568-021-01336-z
                8709809
                34952961
                a3b590e3-43ed-46d9-9501-1d9721541f29
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100010896, international cooperation and exchange programme;
                Award ID: No. 31520103917
                Award Recipient :
                Categories
                Original Article
                Custom metadata
                © The Author(s) 2021

                Biotechnology

                actinobacillus pleuropneumoniae, porcine pleuropneumonia, omics, immune response

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