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Transcriptomic Analysis and Determination of Immune-related Genes in Channa Argus Aftyr Challenge with Nocardia Serilae

Abstract第7-8页
摘要第9-11页
Chapter 1 literature review第11-32页
    1.1 Overview of fish immune system第11页
    1.2 Fish immune organs and tissues第11-12页
        1.2.1 Thymus第11-12页
        1.2.2 Kidney第12页
        1.2.3 Spleen第12页
        1.2.4 Mucosa associated lymphoid tissue第12页
    1.3 Overview of non-specific immunity in fish第12-14页
        1.3.1 The importance of non-specific immunity in fish第13-14页
        1.3.2 Non-specific immune factors against bacteria in fish第14页
    1.4 PAMPs and PRRs第14-15页
    1.5 Immune receptor for non-specific immunity in fish第15-19页
        1.5.1 Toll like Receptor (TLR)第15-17页
        1.5.2 Nod like receptor (NLRs)第17-19页
    1.6 Histopathology第19-21页
    1.7 A review of transcriptome studies第21-23页
        1.7.1 Progress in transcriptomic study第21-22页
        1.7.2 High throughput transcriptome sequencing technique第22-23页
            1.7.2.1 Illumina/Solexa sequencing technology第22页
            1.7.2.2 Roche 454 sequencing technology第22页
            1.7.2.3 ABI/SOLiD sequencing technology第22-23页
        1.7.3 Application of transcriptome technology in aquatic animal immunology第23页
    1.8 Overview of research in Nocardia sp第23-28页
        1.8.1 Progress study of Nocardia seriolae第24-25页
        1.8.2 Biochemical profile of Nocardia seriolae第25-26页
        1.8.3 Pathogenicity and histopathological study of Nocardia seriolae第26-28页
        1.8.4 Prevention research of Nocardia seriolae第28页
    1.9 Overview of snakehead fish (Channa argus)第28-30页
        1.9.1 Disease of snakehead fish第29-30页
        1.9.2 Snakehead fish infected by Nocardia seriolae第30页
    1.10 The purpose and significance of the study第30-32页
Chapter 2 Histopathology Analysis第32-40页
    2.1 Materials and methods第32-34页
        2.1.1 Preparation of experimental animals and bacterial第32页
        2.1.2 Artificial infection test and preparation of samples第32-33页
        2.1.3 Histopathology analysis第33-34页
    2.2 Results第34-37页
    2.3 Discussion第37-40页
Chapter 3 Transcriptomic Analysis第40-61页
    3.1 Experimental animals and bacterial第40-46页
        3.1.1 Preparation of experimental animals and bacterial第40页
        3.1.2 Artificial infection test and preparation of samples第40-41页
        3.1.3 RNA Sequencing第41-42页
            3.1.3.1 Nucleotide recognition第41页
            3.1.3.2 Raw data第41页
            3.1.3.3 Mass quality value data removing第41-42页
        3.1.4 Transcriptome data analysis第42-46页
            3.1.4.1 Sequence assembly第42-43页
            3.1.4.2 Simple Sequence Repeat (SSR) annotation第43页
            3.1.4.3 Coding sequence (CDS)第43-44页
            3.1.4.4 Unigene database annotation第44页
            3.1.4.5 KEGG analysis of Unigene第44页
            3.1.4.6 KOG/COG analysis of Unigene第44-45页
            3.1.4.7 GO analysis of Unigene第45页
            3.1.4.8 Differential expression analysis of Unigene第45-46页
    3.2 Results第46-57页
        3.2.1 Statistical sequencing and quality analysis第46-47页
        3.2.2 Sequence assembly第47-48页
        3.2.3 SSR repeat sequence annotation第48-50页
        3.2.4 Coding sequence (CDS)第50页
        3.2.5 Unigene database annotation第50-51页
        3.2.6 KEGG analysis of Unigenes第51页
        3.2.7 KOG/COG analysis of Unigenes第51-54页
        3.2.8 GO analysis of Unigenes第54-56页
        3.2.9 Analysis of differential expression of Unigene第56-57页
    3.3 Discussion第57-61页
Chapter 4 Determination of Non-specific immune receptors (TLR, NLR) based on transcriptomicdata第61-74页
    4.1 qRT-PCR determination of DEGs from TLR and NLR pathway第61-62页
    4.2 Results第62-71页
        4.2.1 Toll like receptors (TLRs) analysis第62-66页
        4.2.2 Nod like Receptors (NLRs) analysis第66-69页
        4.2.3 qRT-PCR determination of DEGs from TLR and NLR pathway第69-71页
    4.3 Discussion第71-74页
References第74-83页
Appendix Ⅰ: Quality evaluation of Raw Data第83-85页
Appendix Ⅱ: Mass quality value data removing第85-88页
Acknowledgement第88页

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