| 摘要 | 第10-12页 |
| ABSTRACT | 第12-13页 |
| ABBREVIATION WORDS | 第14-16页 |
| CHAPTER 1 | 第16-44页 |
| 1 INTRODUCTION | 第16-43页 |
| 1.1 OVERVIEW | 第16-19页 |
| 1.2 Mastitis and dairy animals | 第19-36页 |
| 1.2.1 Probable appliance by which mastitis drops reproduction | 第20页 |
| 1.2.2 Mastitis and embryonic survival | 第20-21页 |
| 1.2.3 In effected mastitis cows the role of cytokines on early embryonic survival | 第21-22页 |
| 1.2.4 Mastitis assimilated endocrine ambiance | 第22-23页 |
| 1.2.5 Mastitis specific pathogen special effects on follicular development and estrous cycle | 第23-24页 |
| 1.2.6 Association of mastitis and conception rate / Mastitis effect conception rate | 第24页 |
| 1.2.7 Mastitis and release of LH and ovulation association | 第24-25页 |
| 1.2.8 Mastitis and effect on oocyte developmental competence | 第25-26页 |
| 1.2.9 Generic effects of mastitis on reproduction | 第26-27页 |
| 1.2.10 precarious era in which mastitis adversely distresses reproduction | 第27-28页 |
| 1.2.11 The Sim Herd classical model | 第28-29页 |
| 1.2.12 Brief overview of worldwide and China Dairy industry | 第29-36页 |
| 1.3 Approach of animal selection and breeding | 第36-37页 |
| 1.4 Research progress of AKT3 gene and mastitis | 第37-42页 |
| 1.5 Gene function and expression | 第42-43页 |
| 2. Hypothesis and objective of this project | 第43-44页 |
| CHAPTER 2 BIOINFORMATICS ANALYSIS OF TRANSCRIPTOME PROFILING AND DIFFERENT EXPRESSION GENES OF BOVINE MAMMARY INFECTED WITH E.coli | 第44-68页 |
| 2.1 INTRODUCTION | 第44-48页 |
| 2.2 MATERILAS AND METHODS | 第48-53页 |
| 2.2.1 Data set and description | 第48-49页 |
| 2.2.2 Data preprocessing and differentially expressed genes (DEGs) screening | 第49-50页 |
| 2.2.3 Hierarchical clustering and comparison analysis of selected DEGs in different region | 第50页 |
| 2.2.4 Enrichment analysis for the overlapping DEGs in the four groups | 第50页 |
| 2.2.5 Protein-Protein interaction network analysis for overlapping DEGs | 第50页 |
| 2.2.6 mi RNA-DEGs-TF regulatory network analysis | 第50-51页 |
| 2.2.7 Validation of the expression level of DEGs | 第51页 |
| 2.2.8 Active site prediction of interested DEGs | 第51页 |
| 2.2.9 Epigenetic analysis, epigenetic modifications and Cp G inland | 第51-52页 |
| 2.2.10 Evolution analysis, phylogenetic analysis | 第52页 |
| 2.2.11 Functional domain identification | 第52页 |
| 2.2.12 Mutation analysis | 第52页 |
| 2.2.13 Protein docking exploration of vibrant immune response genes | 第52页 |
| 2.2.14 Protein sequence based voluntary tree to show the homology with other sequences of different species | 第52-53页 |
| 2.3 RESULTS | 第53-66页 |
| 2.3.1 Processing of data and screening of differential express genes | 第53-55页 |
| 2.3.2 Differential express gene and data interpretation | 第55-56页 |
| 2.3.3 GO and KEGG pathway enrichment analysis for the overlapping DEGs | 第56-58页 |
| 2.3.4 Protein-Protein interaction network analysis for overlapping DEGs | 第58-60页 |
| 2.3.5 TF-mi RNA-target regulatory network analysis | 第60-61页 |
| 2.3.6 Active site prediction of interested DEGs | 第61-64页 |
| 2.3.7 Protein docking exploration of vibrant immune response genes | 第64-66页 |
| 2.4 DISCUSSION | 第66-68页 |
| CHAPTER 3 COMPARATIVE ANALYSIS OF THE SEQUENCE DIFFERENCES AND THEIR FUNCTIONS OF AKT3 GENE BETWEEN COW AND BUFFALO BASED ON BIOINFORMATICS | 第68-92页 |
| 3.1 INTRODUCTION | 第68-71页 |
| 3.2 MATERIALS AND METHODS | 第71-73页 |
| 3.2.1 In Silico and Bioinformatics Analysis | 第71页 |
| 3.2.2 Promoter Prediction, Transcription Starting Sites (TSS) and CPG island prediction | 第71页 |
| 3.2.3 Sequences Similarity, mi RNA Prediction, Protein-protein interaction | 第71-72页 |
| 3.2.4 Protein Structure and Domains Prediction | 第72页 |
| 3.2.5 Alignment, phylogenetic tree, motifs and gene structure, proximal control and core promoters | 第72-73页 |
| 3.2.6 Enrichment analysis of AKT3 | 第73页 |
| 3.3 RESULTS | 第73-90页 |
| 3.3.1 Sequences similarity and difference of AKT3 between cow and buffalo | 第73-76页 |
| 3.3.2 Difference of promoters, core promoters and other sequence motifs | 第76-78页 |
| 3.3.3 Variation of importance of upstream sequences | 第78-81页 |
| 3.3.4 Difference in mi RNA binding in 3’UTR region | 第81-82页 |
| 3.3.5 Difference of Protein-protein interaction, structure and domain | 第82-84页 |
| 3.3.6 Difference in Phylogenetic, alignment, structural and motif | 第84-90页 |
| 3.4 DISCUSSION | 第90-92页 |
| CHAPTER 4 STUDY ON THE FUNCTIONS OF SEQUENCES DIFFERENCES OF AKT3 GENE BETWEEN COW AND BUFFALO | 第92-123页 |
| 4.1 INTRODUCTION | 第93-95页 |
| 4.2 MATERIAL AND METHODS | 第95-102页 |
| 4.2.1 Data Structure and statement of ethics | 第95页 |
| 4.2.2 Animal blood sampling, management and extraction of genomic DNA | 第95-96页 |
| 4.2.3 Primer design and sequencing | 第96页 |
| 4.2.4 Analysis of sequence and SNPs genotyping | 第96页 |
| 4.2.5 Differences in cow and buffalo for CDS/ m RNA region in AKT3 | 第96-97页 |
| 4.2.6 Primers used for various regions of coding sequence regions | 第97页 |
| 4.2.7 Approach to promoter analysis, bioinformatics and soft wares used | 第97页 |
| 4.2.8 Primers used for construction of condensed vectors of cow and buffalo promoters | 第97-98页 |
| 4.2.9 Culture and LPS treatment of the bovine epithelium cell | 第98页 |
| 4.2.10 RNA extraction, c DNA, and q PCR | 第98-99页 |
| 4.2.11Cloning of promoter and generation luciferase reporter constructs | 第99-100页 |
| 4.2.12 Cell line and culture condition | 第100页 |
| 4.2.13 Transient transfection and luciferase reporter essay | 第100-101页 |
| 4.2.14 The Assessment, Association, Evaluation, and comparison of the cow and buffalo AKT3 for functional minimal promoter | 第101页 |
| 4.2.15 Primers used for m RNA expression experiment | 第101页 |
| 4.2.16 Statistical analysis | 第101-102页 |
| 4.3 RESULTS | 第102-120页 |
| 4.3.1 Functions of DNA sequence differences in CDs of AKT3 gene between cow and buffalo | 第102-110页 |
| 4.3.2 Functions of DNA sequence differences in AKT3 core prompter between cow and buffalo | 第110-115页 |
| 4.3.3 Validation of AKT3 promoters in cow and buffalo | 第115-118页 |
| 4.3.4 AKT3 immune response of LPS-induced mastitis | 第118-120页 |
| 4.4 DISCUSSION | 第120-123页 |
| CHAPTER 5 CONCLUSIONS AND FUTURE DIRECTIONS | 第123-124页 |
| References | 第124-146页 |
| LIST OF APPENDIX | 第146-159页 |
| Supplementary Appendix (Table) 2.1 | 第148-151页 |
| Supplementary Appendix (Table) 2.2 | 第151-154页 |
| Supplementary Appendix (Table) 2.3 | 第154-159页 |
| Acknowledgement | 第159-161页 |
| List of publications | 第161-165页 |
| CONFERENCE PAPERS | 第165-169页 |
| Author Bibliography | 第169页 |
| Profile | 第169-170页 |
| Worked Experience | 第170-171页 |
