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      Transcriptome Analysis of the Innate Immunity-Related Complement System in Spleen Tissue of Ctenopharyngodon idella Infected with Aeromonas hydrophila

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          Abstract

          The grass carp ( Ctenopharyngodon idella) is an important commercial farmed herbivorous fish species in China, but is susceptible to Aeromonas hydrophila infections. In the present study, we performed de novo RNA-Seq sequencing of spleen tissue from specimens of a disease-resistant family, which were given intra-peritoneal injections containing PBS with or without a dose of A. hydrophila. The fish were sampled from the control group at 0 h, and from the experimental group at 4, 8, 12, 24, 48 and 72 h. 122.18 million clean reads were obtained from the normalized cDNA libraries; these were assembled into 425,260 contigs and then 191,795 transcripts. Of those, 52,668 transcripts were annotated with the NCBI Nr database, and 41,347 of the annotated transcripts were assigned into 90 functional groups. 20,569 unigenes were classified into six main categories, including 38 secondary KEGG pathways. 2,992 unigenes were used in the analysis of differentially expressed genes (DEGs). 89 of the putative DEGs were related to the immune system and 41 of them were involved in the complement and coagulation cascades pathway. This study provides insights into the complement and complement-related pathways involved in innate immunity, through expression profile analysis of the genomic resources in C. idella. We conclude that complement and complement-related genes play important roles during defense against A. hydrophila infection. The immune response is activated at 4 h after the bacterial injections, indicating that the complement pathways are activated at the early stage of bacterial infection. The study has improved our understanding of the immune response mechanisms in C. idella to bacterial pathogens.

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          Performance comparison of benchtop high-throughput sequencing platforms.

          Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. We compared the performance of these instruments by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011. The MiSeq had the highest throughput per run (1.6 Gb/run, 60 Mb/h) and lowest error rates. The 454 GS Junior generated the longest reads (up to 600 bases) and most contiguous assemblies but had the lowest throughput (70 Mb/run, 9 Mb/h). Run in 100-bp mode, the Ion Torrent PGM had the highest throughput (80–100 Mb/h). Unlike the MiSeq, the Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors (1.5 and 0.38 errors per 100 bases, respectively).
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            Chemokines in innate and adaptive host defense: basic chemokinese grammar for immune cells.

            Chemokines compose a sophisticated communication system used by all our cell types, including immune cells. Chemokine messages are decoded by specific receptors that initiate signal transduction events leading to a multitude of cellular responses, leukocyte chemotaxis and adhesion in particular. Critical determinants of the in vivo activities of chemokines in the immune system include their presentation by endothelial cells and extracellular matrix molecules, as well as their cellular uptake via "silent" chemokine receptors (interceptors) leading either to their transcytosis or to degradation. These regulatory mechanisms of chemokine histotopography, as well as the promiscuous and overlapping receptor specificities of inflammation-induced chemokines, shape innate responses to infections and tissue damage. Conversely, the specific patterns of homeostatic chemokines, where each chemokine is perceived by a single receptor, are charting lymphocyte navigation routes for immune surveillance. This review presents our current understanding of the mechanisms that regulate the cellular perception and pathophysiologic meaning of chemokines.
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              RNA-Seq analysis in MeV

              Summary: RNA-Seq is an exciting methodology that leverages the power of high-throughput sequencing to measure RNA transcript counts at an unprecedented accuracy. However, the data generated from this process are extremely large and biologist-friendly tools with which to analyze it are sorely lacking. MultiExperiment Viewer (MeV) is a Java-based desktop application that allows advanced analysis of gene expression data through an intuitive graphical user interface. Here, we report a significant enhancement to MeV that allows analysis of RNA-Seq data with these familiar, powerful tools. We also report the addition to MeV of several RNA-Seq-specific functions, addressing the differences in analysis requirements between this data type and traditional gene expression data. These tools include automatic conversion functions from raw count data to processed RPKM or FPKM values and differential expression detection and functional annotation enrichment detection based on published methods. Availability: MeV version 4.7 is written in Java and is freely available for download under the terms of the open-source Artistic License version 2.0. The website (http://mev.tm4.org/) hosts a full user manual as well as a short quick-start guide suitable for new users. Contact: johnq@jimmy.harvard.edu
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                6 July 2016
                2016
                : 11
                : 7
                : e0157413
                Affiliations
                [1 ]Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
                [2 ]National Pathogen Collection Center for Aquatic Animals, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, PR China
                Chinese Academy of Fishery Sciences, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: YFD JLL LQL. Performed the experiments: YFD XYX. Analyzed the data: YFD. Contributed reagents/materials/analysis tools: YFD YBS MYH MZ LSL. Wrote the paper: YFD JLL.

                Article
                PONE-D-16-13569
                10.1371/journal.pone.0157413
                4934786
                27383749
                5372f8e9-2c04-453b-9d02-53ebcf6f77be
                © 2016 Dang et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 April 2016
                : 27 May 2016
                Page count
                Figures: 9, Tables: 5, Pages: 22
                Funding
                Funded by: The China's Agricultural Reseach System
                Award ID: CARS-46-04
                Award Recipient :
                Funded by: The National Key Technology R and D Program of China
                Award ID: 2012BAD26B02
                Award Recipient :
                The work was supported by the following: the China's Agricultural Research System (CARS-46-04), Jiale Li; and the National Key Technology R&D Program of China (2012BAD26B02), Jiale Li.
                Categories
                Research Article
                Biology and Life Sciences
                Physiology
                Immune Physiology
                Complement System
                Medicine and Health Sciences
                Physiology
                Immune Physiology
                Complement System
                Biology and Life Sciences
                Immunology
                Immune System
                Complement System
                Medicine and Health Sciences
                Immunology
                Immune System
                Complement System
                Biology and Life Sciences
                Immunology
                Immune System Proteins
                Complement System
                Medicine and Health Sciences
                Immunology
                Immune System Proteins
                Complement System
                Biology and Life Sciences
                Biochemistry
                Proteins
                Immune System Proteins
                Complement System
                Biology and Life Sciences
                Immunology
                Immune System
                Medicine and Health Sciences
                Immunology
                Immune System
                Biology and Life Sciences
                Organisms
                Bacteria
                Aeromonas
                Aeromonas Hydrophila
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Aeromonas Hydrophila
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Aeromonas Hydrophila
                Biology and Life Sciences
                Organisms
                Animals
                Vertebrates
                Fishes
                Osteichthyes
                Carps
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Organisms
                Plants
                Grasses
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Sequence Databases
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Databases
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Databases
                Research and analysis methods
                Extraction techniques
                RNA extraction
                Custom metadata
                All transcriptome data files are available from the NCBI Sequence Read Archive database (accession number SRP060308).

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