E.coli感染的奶牛乳房的差異表達(dá)基因與奶牛/水牛AKT3基因序列差異及其功能的研究
發(fā)布時間：2021-05-23 11:44
本論文研究奶牛和水牛乳腺炎相關(guān)的重要基因及其變異,分析乳腺炎遺傳機(jī)理。本論文由四個部分組成,第一部分介紹了奶牛乳腺炎的研究進(jìn)展;第二部分利用多種生物學(xué)分析技術(shù)和基因差異表達(dá)數(shù)據(jù)庫中數(shù)據(jù)比較分析了E.coli感染的奶牛乳房四個不同部位的基因的表達(dá)譜、篩選出了差異表達(dá)基因、研究了重要差異表達(dá)基因互作和信號通路;第三部分利用生物信息學(xué)分析技術(shù)探討了奶牛和水牛的AKT3基因序列的差異,預(yù)測了這些序列差異的生物學(xué)功能;第四部分利用分子生物技術(shù)研究了奶牛和水牛AKT3基因序列差異及其功能,并分析了AKT3基因在脂多糖（LPS）刺激誘導(dǎo)的奶牛乳腺上皮細(xì)胞乳腺炎中表達(dá)特征與免疫功能。主要研究結(jié)果如下:1、分析了大腸桿菌E.coli感染引起的乳腺炎的遺傳調(diào)控機(jī)理,即引起奶牛乳房炎的主要遺傳因子:利用基因表達(dá)數(shù)據(jù)庫中數(shù)據(jù)（http://www.ncbi.nlm.nih.gov/geo/,數(shù)據(jù)編號為GSE15441和GSE15020）和生物信息學(xué)分析技術(shù)對由大腸桿菌E.coli感染的奶牛乳房四個不同部位（乳頭池,腺乳池,小葉肺泡和佛氏玫瑰型支管）中基因表達(dá)譜,在乳房四個不同部位中分別篩選出了453、597、...
【文章來源】：華中農(nóng)業(yè)大學(xué)湖北省 211工程院校 教育部直屬院校
【文章頁數(shù)】：171 頁
【學(xué)位級別】：博士
【文章目錄】：
摘要
ABSTRACT
ABBREVIATION WORDS
CHAPTER 1
1 INTRODUCTION
1.1 OVERVIEW
1.2 Mastitis and dairy animals
1.2.1 Probable appliance by which mastitis drops reproduction
1.2.2 Mastitis and embryonic survival
1.2.3 In effected mastitis cows the role of cytokines on early embryonic survival
1.2.4 Mastitis assimilated endocrine ambiance
1.2.5 Mastitis specific pathogen special effects on follicular development and estrous cycle
1.2.6 Association of mastitis and conception rate / Mastitis effect conception rate
1.2.7 Mastitis and release of LH and ovulation association
1.2.8 Mastitis and effect on oocyte developmental competence
1.2.9 Generic effects of mastitis on reproduction
1.2.10 precarious era in which mastitis adversely distresses reproduction
1.2.11 The Sim Herd classical model
1.2.12 Brief overview of worldwide and China Dairy industry
1.3 Approach of animal selection and breeding
1.4 Research progress of AKT3 gene and mastitis
1.5 Gene function and expression
2. Hypothesis and objective of this project
CHAPTER 2 BIOINFORMATICS ANALYSIS OF TRANSCRIPTOME PROFILING AND DIFFERENT EXPRESSION GENES OF BOVINE MAMMARY INFECTED WITH E.coli
2.1 INTRODUCTION
2.2 MATERILAS AND METHODS
2.2.1 Data set and description
2.2.2 Data preprocessing and differentially expressed genes (DEGs) screening
2.2.3 Hierarchical clustering and comparison analysis of selected DEGs in different region
2.2.4 Enrichment analysis for the overlapping DEGs in the four groups
2.2.5 Protein-Protein interaction network analysis for overlapping DEGs
2.2.6 mi RNA-DEGs-TF regulatory network analysis
2.2.7 Validation of the expression level of DEGs
2.2.8 Active site prediction of interested DEGs
2.2.9 Epigenetic analysis, epigenetic modifications and Cp G inland
2.2.10 Evolution analysis, phylogenetic analysis
2.2.11 Functional domain identification
2.2.12 Mutation analysis
2.2.13 Protein docking exploration of vibrant immune response genes
2.2.14 Protein sequence based voluntary tree to show the homology with other sequences of different species
2.3 RESULTS
2.3.1 Processing of data and screening of differential express genes
2.3.2 Differential express gene and data interpretation
2.3.3 GO and KEGG pathway enrichment analysis for the overlapping DEGs
2.3.4 Protein-Protein interaction network analysis for overlapping DEGs
2.3.5 TF-mi RNA-target regulatory network analysis
2.3.6 Active site prediction of interested DEGs
2.3.7 Protein docking exploration of vibrant immune response genes
2.4 DISCUSSION
CHAPTER 3 COMPARATIVE ANALYSIS OF THE SEQUENCE DIFFERENCES AND THEIR FUNCTIONS OF AKT3 GENE BETWEEN COW AND BUFFALO BASED ON BIOINFORMATICS
3.1 INTRODUCTION
3.2 MATERIALS AND METHODS
3.2.1 In Silico and Bioinformatics Analysis
3.2.2 Promoter Prediction, Transcription Starting Sites (TSS) and CPG island prediction
3.2.3 Sequences Similarity, mi RNA Prediction, Protein-protein interaction
3.2.4 Protein Structure and Domains Prediction
3.2.5 Alignment, phylogenetic tree, motifs and gene structure, proximal control and core promoters
3.2.6 Enrichment analysis of AKT3
3.3 RESULTS
3.3.1 Sequences similarity and difference of AKT3 between cow and buffalo
3.3.2 Difference of promoters, core promoters and other sequence motifs
3.3.3 Variation of importance of upstream sequences
3.3.4 Difference in mi RNA binding in 3’UTR region
3.3.5 Difference of Protein-protein interaction, structure and domain
3.3.6 Difference in Phylogenetic, alignment, structural and motif
3.4 DISCUSSION
CHAPTER 4 STUDY ON THE FUNCTIONS OF SEQUENCES DIFFERENCES OF AKT3 GENE BETWEEN COW AND BUFFALO
4.1 INTRODUCTION
4.2 MATERIAL AND METHODS
4.2.1 Data Structure and statement of ethics
4.2.2 Animal blood sampling, management and extraction of genomic DNA
4.2.3 Primer design and sequencing
4.2.4 Analysis of sequence and SNPs genotyping
4.2.5 Differences in cow and buffalo for CDS/ m RNA region in AKT3
4.2.6 Primers used for various regions of coding sequence regions
4.2.7 Approach to promoter analysis, bioinformatics and soft wares used
4.2.8 Primers used for construction of condensed vectors of cow and buffalo promoters
4.2.9 Culture and LPS treatment of the bovine epithelium cell
4.2.10 RNA extraction, c DNA, and q PCR
4.2.11Cloning of promoter and generation luciferase reporter constructs
4.2.12 Cell line and culture condition
4.2.13 Transient transfection and luciferase reporter essay
4.2.14 The Assessment, Association, Evaluation, and comparison of the cow and buffalo AKT3 for functional minimal promoter
4.2.15 Primers used for m RNA expression experiment
4.2.16 Statistical analysis
4.3 RESULTS
4.3.1 Functions of DNA sequence differences in CDs of AKT3 gene between cow and buffalo
4.3.2 Functions of DNA sequence differences in AKT3 core prompter between cow and buffalo
4.3.3 Validation of AKT3 promoters in cow and buffalo
4.3.4 AKT3 immune response of LPS-induced mastitis
4.4 DISCUSSION
CHAPTER 5 CONCLUSIONS AND FUTURE DIRECTIONS
References
LIST OF APPENDIX
Supplementary Appendix (Table) 2.1
Supplementary Appendix (Table) 2.2
Supplementary Appendix (Table) 2.3
Acknowledgement
List of publications
CONFERENCE PAPERS
Author Bibliography
Profile
Worked Experience
【參考文獻(xiàn)】：
期刊論文
[1]Tumor necrosis factor alpha inhibits in vitro bovine embryo development through a prostaglandin mediated mechanism[J]. Lauren R Jackson,Char E Farin,Scott Whisnant. Journal of Animal Science and Biotechnology. 2012(01)
[2]GSDS:基因結(jié)構(gòu)顯示系統(tǒng)[J]. 郭安源,朱其慧,陳新,羅靜初. 遺傳. 2007(08)
本文編號：3202460
【文章來源】：華中農(nóng)業(yè)大學(xué)湖北省 211工程院校 教育部直屬院校
【文章頁數(shù)】：171 頁
【學(xué)位級別】：博士
【文章目錄】：
摘要
ABSTRACT
ABBREVIATION WORDS
CHAPTER 1
1 INTRODUCTION
1.1 OVERVIEW
1.2 Mastitis and dairy animals
1.2.1 Probable appliance by which mastitis drops reproduction
1.2.2 Mastitis and embryonic survival
1.2.3 In effected mastitis cows the role of cytokines on early embryonic survival
1.2.4 Mastitis assimilated endocrine ambiance
1.2.5 Mastitis specific pathogen special effects on follicular development and estrous cycle
1.2.6 Association of mastitis and conception rate / Mastitis effect conception rate
1.2.7 Mastitis and release of LH and ovulation association
1.2.8 Mastitis and effect on oocyte developmental competence
1.2.9 Generic effects of mastitis on reproduction
1.2.10 precarious era in which mastitis adversely distresses reproduction
1.2.11 The Sim Herd classical model
1.2.12 Brief overview of worldwide and China Dairy industry
1.3 Approach of animal selection and breeding
1.4 Research progress of AKT3 gene and mastitis
1.5 Gene function and expression
2. Hypothesis and objective of this project
CHAPTER 2 BIOINFORMATICS ANALYSIS OF TRANSCRIPTOME PROFILING AND DIFFERENT EXPRESSION GENES OF BOVINE MAMMARY INFECTED WITH E.coli
2.1 INTRODUCTION
2.2 MATERILAS AND METHODS
2.2.1 Data set and description
2.2.2 Data preprocessing and differentially expressed genes (DEGs) screening
2.2.3 Hierarchical clustering and comparison analysis of selected DEGs in different region
2.2.4 Enrichment analysis for the overlapping DEGs in the four groups
2.2.5 Protein-Protein interaction network analysis for overlapping DEGs
2.2.6 mi RNA-DEGs-TF regulatory network analysis
2.2.7 Validation of the expression level of DEGs
2.2.8 Active site prediction of interested DEGs
2.2.9 Epigenetic analysis, epigenetic modifications and Cp G inland
2.2.10 Evolution analysis, phylogenetic analysis
2.2.11 Functional domain identification
2.2.12 Mutation analysis
2.2.13 Protein docking exploration of vibrant immune response genes
2.2.14 Protein sequence based voluntary tree to show the homology with other sequences of different species
2.3 RESULTS
2.3.1 Processing of data and screening of differential express genes
2.3.2 Differential express gene and data interpretation
2.3.3 GO and KEGG pathway enrichment analysis for the overlapping DEGs
2.3.4 Protein-Protein interaction network analysis for overlapping DEGs
2.3.5 TF-mi RNA-target regulatory network analysis
2.3.6 Active site prediction of interested DEGs
2.3.7 Protein docking exploration of vibrant immune response genes
2.4 DISCUSSION
CHAPTER 3 COMPARATIVE ANALYSIS OF THE SEQUENCE DIFFERENCES AND THEIR FUNCTIONS OF AKT3 GENE BETWEEN COW AND BUFFALO BASED ON BIOINFORMATICS
3.1 INTRODUCTION
3.2 MATERIALS AND METHODS
3.2.1 In Silico and Bioinformatics Analysis
3.2.2 Promoter Prediction, Transcription Starting Sites (TSS) and CPG island prediction
3.2.3 Sequences Similarity, mi RNA Prediction, Protein-protein interaction
3.2.4 Protein Structure and Domains Prediction
3.2.5 Alignment, phylogenetic tree, motifs and gene structure, proximal control and core promoters
3.2.6 Enrichment analysis of AKT3
3.3 RESULTS
3.3.1 Sequences similarity and difference of AKT3 between cow and buffalo
3.3.2 Difference of promoters, core promoters and other sequence motifs
3.3.3 Variation of importance of upstream sequences
3.3.4 Difference in mi RNA binding in 3’UTR region
3.3.5 Difference of Protein-protein interaction, structure and domain
3.3.6 Difference in Phylogenetic, alignment, structural and motif
3.4 DISCUSSION
CHAPTER 4 STUDY ON THE FUNCTIONS OF SEQUENCES DIFFERENCES OF AKT3 GENE BETWEEN COW AND BUFFALO
4.1 INTRODUCTION
4.2 MATERIAL AND METHODS
4.2.1 Data Structure and statement of ethics
4.2.2 Animal blood sampling, management and extraction of genomic DNA
4.2.3 Primer design and sequencing
4.2.4 Analysis of sequence and SNPs genotyping
4.2.5 Differences in cow and buffalo for CDS/ m RNA region in AKT3
4.2.6 Primers used for various regions of coding sequence regions
4.2.7 Approach to promoter analysis, bioinformatics and soft wares used
4.2.8 Primers used for construction of condensed vectors of cow and buffalo promoters
4.2.9 Culture and LPS treatment of the bovine epithelium cell
4.2.10 RNA extraction, c DNA, and q PCR
4.2.11Cloning of promoter and generation luciferase reporter constructs
4.2.12 Cell line and culture condition
4.2.13 Transient transfection and luciferase reporter essay
4.2.14 The Assessment, Association, Evaluation, and comparison of the cow and buffalo AKT3 for functional minimal promoter
4.2.15 Primers used for m RNA expression experiment
4.2.16 Statistical analysis
4.3 RESULTS
4.3.1 Functions of DNA sequence differences in CDs of AKT3 gene between cow and buffalo
4.3.2 Functions of DNA sequence differences in AKT3 core prompter between cow and buffalo
4.3.3 Validation of AKT3 promoters in cow and buffalo
4.3.4 AKT3 immune response of LPS-induced mastitis
4.4 DISCUSSION
CHAPTER 5 CONCLUSIONS AND FUTURE DIRECTIONS
References
LIST OF APPENDIX
Supplementary Appendix (Table) 2.1
Supplementary Appendix (Table) 2.2
Supplementary Appendix (Table) 2.3
Acknowledgement
List of publications
CONFERENCE PAPERS
Author Bibliography
Profile
Worked Experience
【參考文獻(xiàn)】：
期刊論文
[1]Tumor necrosis factor alpha inhibits in vitro bovine embryo development through a prostaglandin mediated mechanism[J]. Lauren R Jackson,Char E Farin,Scott Whisnant. Journal of Animal Science and Biotechnology. 2012(01)
[2]GSDS:基因結(jié)構(gòu)顯示系統(tǒng)[J]. 郭安源,朱其慧,陳新,羅靜初. 遺傳. 2007(08)
本文編號：3202460
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