E.coli感染的奶牛乳房的差异表达基因与奶牛/水牛AKT3基因序列差异及其功能的研究
发布时间：2021-05-23 11:44
本论文研究奶牛和水牛乳腺炎相关的重要基因及其变异,分析乳腺炎遗传机理。本论文由四个部分组成,第一部分介绍了奶牛乳腺炎的研究进展;第二部分利用多种生物学分析技术和基因差异表达数据库中数据比较分析了E.coli感染的奶牛乳房四个不同部位的基因的表达谱、筛选出了差异表达基因、研究了重要差异表达基因互作和信号通路;第三部分利用生物信息学分析技术探讨了奶牛和水牛的AKT3基因序列的差异,预测了这些序列差异的生物学功能;第四部分利用分子生物技术研究了奶牛和水牛AKT3基因序列差异及其功能,并分析了AKT3基因在脂多糖（LPS）刺激诱导的奶牛乳腺上皮细胞乳腺炎中表达特征与免疫功能。主要研究结果如下:1、分析了大肠杆菌E.coli感染引起的乳腺炎的遗传调控机理,即引起奶牛乳房炎的主要遗传因子:利用基因表达数据库中数据（http://www.ncbi.nlm.nih.gov/geo/,数据编号为GSE15441和GSE15020）和生物信息学分析技术对由大肠杆菌E.coli感染的奶牛乳房四个不同部位（乳头池,腺乳池,小叶肺泡和佛氏玫瑰型支管）中基因表达谱,在乳房四个不同部位中分别筛选出了453、597、...
【文章来源】：华中农业大学湖北省 211工程院校 教育部直属院校
【文章页数】：171 页
【学位级别】：博士
【文章目录】：
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
【参考文献】：
期刊论文
[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:基因结构显示系统[J]. 郭安源,朱其慧,陈新,罗静初. 遗传. 2007(08)
本文编号：3202460
【文章来源】：华中农业大学湖北省 211工程院校 教育部直属院校
【文章页数】：171 页
【学位级别】：博士
【文章目录】：
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
【参考文献】：
期刊论文
[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:基因结构显示系统[J]. 郭安源,朱其慧,陈新,罗静初. 遗传. 2007(08)
本文编号：3202460
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