论文说明
声明
摘要
ABSTRACT
ABBREVIATION WORDS
CHAPTER 1
1．1 OVERVIEW
1．2 Mastitis and dairy animals
1．3 Approach of animal selection and breeding
1．4 Research progress of AKT3 gene and mastitis
1．5 Gene function and expression
2．Hyp othesis and objective of this project
CHAPTER 2 BIOINFORMATICS ANALYSIS OF TRANSCRIPTOME PROFILING AND DIFFERENT EXPRESSION GENES OF BOVINE MAMMARY INFECTED WITH E．coli
ABSTRACT
2．1 INTRODUCTION
2．2 MATERIALS AND METHODS
2．2．1 Dataset 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
2．2．6 miRNA-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 CpG 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-miRNA-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 COWAND BUFFALO BASED ON BIOINFORMATICS
ABSTRACT
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，miRNA Prediction，Protein-protein Interaction
3．2．4 Protein Structure and Domains Prediction
3．2．6 Enrichment analysis of AKT3
3．3 RESULTS
3．3．1 Sequences similarity and difference of AKT3 between cow and Bnffalo
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 miRNA 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
ABSTRACT
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／mRNA 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，cDNA，and qPCR
4．2．11 Cloning 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 mRNA 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
Acknowledgment
List of publications
CONFERENCE PAPERS
Author Bibliography
Profile
Worked Experience
