| ABSTRACT | 第9-11页 |
| 摘要 | 第12-14页 |
| Abbreviation | 第14-16页 |
| 1 LITERATURE REVIEW | 第16-31页 |
| 1.1 SIGNIFICANCE OF CATTLE INDUSTRY | 第16页 |
| 1.2 BOVINE MYCOPLASMOSIS | 第16-18页 |
| 1.2.1 Mycoplasma mycoides | 第17-18页 |
| 1.2.2 M. bovis related diseases | 第18页 |
| 1.3 MICROBIOLOGICAL PROPERTIES OF M. BOVIS | 第18-20页 |
| 1.3.1 Taxonomy | 第18-20页 |
| 1.3.2 Morphology and culture | 第20页 |
| 1.4 THE GENOMICS AND PROTEOMICS ASPECTS OF MYCOPLASMA BOVIS HB0801 | 第20-23页 |
| 1.4.1 M. bovis genomics | 第20-21页 |
| 1.4.2 M. bovis proteomics | 第21-23页 |
| 1.5 DISEASES CAUSE BY M. BOVIS | 第23-25页 |
| 1.5.1 Disease patterns | 第23页 |
| 1.5.2 Distribution of M. bovis infection in China | 第23-24页 |
| 1.5.3 Transmission of the diseases | 第24-25页 |
| 1.6 DIAGNOSIS | 第25-26页 |
| 1.6.1 Epidemiological diagnosis | 第25页 |
| 1.6.2 Clinical diagnosis | 第25页 |
| 1.6.3 Macroscopic diagnosis | 第25-26页 |
| 1.6.4 Serological diagnosis | 第26页 |
| 1.7 PATHOGENESIS | 第26-28页 |
| 1.7.1 Adhesion, colonization and invasion | 第26-27页 |
| 1.7.2 Cytotoxicity | 第27页 |
| 1.7.3 Virulence related factors | 第27-28页 |
| 1.8 CONTROL MEASURES | 第28-31页 |
| 1.8.1 Control strategies | 第29页 |
| 1.8.2 Chemotherapy | 第29页 |
| 1.8.3 Vaccination | 第29-31页 |
| 2 AIMS AND OBJECTIVES | 第31-32页 |
| 3 MATERIALS AND METHODS | 第32-49页 |
| 3.1 BIOINFORMATICS ANALYSIS OF DATA | 第32-35页 |
| 3.2 PROTEIN ANNOTATION AND METABOLIC PATHWAYS | 第35-36页 |
| 3.3 SEARCHING CRITERIA TO GET DATA FROM NCBI PUBMED | 第36页 |
| 3.4 SYNONYMOUS/NON-SYNONYMOUS SNPS CONFIRMATION | 第36-37页 |
| 3.4.1 Conversion of nucleotide sequences into amino acids | 第36页 |
| 3.4.2 Searching for SNP location | 第36页 |
| 3.4.3 Checking for the amino acid change | 第36页 |
| 3.4.4 SNPs at active site of the protein | 第36-37页 |
| 3.4.5 SNPs at poly“A”or poly“G”parts of the proteins | 第37页 |
| 3.5 PARALOGUES FINDING | 第37页 |
| 3.7.1 Reference proteins | 第37页 |
| 3.7.2 Whole genome analysis to get paralogues | 第37页 |
| 3.7.3 Fetching sequences of all paralogues | 第37页 |
| 3.7.4 Aligning sequences | 第37页 |
| 3.6 PROTEIN-PROTEIN INTERACTION ANALYSIS | 第37-38页 |
| 3.7 WHOLE GENOME SECRETORY PROTEINS ANALYSIS | 第38页 |
| 3.8 ANALYSIS OF CONSERVED DOMAINS IN PREDICTED SECRETORY PROTEINS | 第38页 |
| 3.9 PROTEIN MODELING FOR STRUCTURES PREDICTION OF THE SECRETORY PROTEINS | 第38-40页 |
| 3.11.1 Template searching by using PDB | 第39页 |
| 3.11.2 Homology modeling | 第39-40页 |
| 3.11.3 Threading (fold detection) | 第40页 |
| 3.11.4 Protein visualization and coloring | 第40页 |
| 3.10 KEGG ENRICHMENT ANALYSIS | 第40-41页 |
| 3.11 GENOMIC AND PATHOGENIC ISLAND ANALYSIS | 第41页 |
| 3.12 WHOLE PROTEOME ANALYSIS OF VIRULENCE FACTORS | 第41-42页 |
| 3.14.1 Virulence factor database (VFDB) | 第41页 |
| 3.14.2 Fetching amino acid sequences of M. bovis HB0801 proteome | 第41页 |
| 3.14.3 Analysis by VFDB | 第41页 |
| 3.14.4 Filtering data on the basis of BLAST score and E value | 第41-42页 |
| 3.13 STATISTICAL ANALYSIS | 第42页 |
| 3.15.1 Description of the formula | 第42页 |
| 3.14 HYDROGEN PEROXIDE PRODUCTION ASSAY | 第42-44页 |
| 3.16.1 Bacterial growth conditions for strains with various passages | 第42页 |
| 3.16.2 Bacterial culture for mutants | 第42-43页 |
| 3.16.3 Confirmation of M. bovis by uvrC primers | 第43页 |
| 3.16.4 Bacterial harvesting | 第43页 |
| 3.16.5 Incubation | 第43页 |
| 3.16.6 Standard curve | 第43页 |
| 3.16.7 Samples in the ELISA plate | 第43页 |
| 3.16.8 Statistical analysis | 第43-44页 |
| 3.15 PCR APPROACH IN ORDER TO FIND THE TARGET MUTANT GENE IN THE MUTANTLIBRARY | 第44-47页 |
| 3.17.1 Making Pool | 第44页 |
| 3.17.2 Target genes primers | 第44-46页 |
| 3.17.3 Samples preparations for PCR | 第46页 |
| 3.17.4 PCR running conditions | 第46页 |
| 3.17.5 Gels preparations | 第46页 |
| 3.17.6 Loading samples in gels and machine running conditions | 第46页 |
| 3.17.7 Taking pictures of the gels | 第46-47页 |
| 3.16 SDS-PAGE TO SEPARATE WHOLE CELL PROTEINS (WCPS) OF THE MUTANTS | 第47-49页 |
| 3.18.1 Extraction of WCPs | 第47页 |
| 3.18.2 Measuring protein concentration | 第47-48页 |
| 3.18.3 Sample preparations for SDS-PAGE | 第48页 |
| 3.18.4 Gel preparations | 第48页 |
| 3.18.5 Sample loading and running conditions | 第48页 |
| 3.18.6 Staining and destaining of the gels | 第48-49页 |
| 4 RESULTS & DISCUSSION | 第49-95页 |
| 4.1 GENES RELATED TO LARGE DELETION OF A 14.2 KB FRAGMENT IN THE GENOME OFTHE THREE ATTENUATED STRAINS | 第49-51页 |
| 4.2 ASSAY OF ASSOCIATION OF NUCLEOTIDE SUBSTITUTIONS (SNPS) TO STRAINATTENUATION | 第51-58页 |
| 4.3 THE MOST SIGNIFICANT DOWN-REGULATED PROTEINS FROM PROTEOMICS DATA | 第58-59页 |
| 4.5 PROTEINS INVOLVED IN ASCORBATE AND ALDARATE METABOLISM PATHWAY | 第59-60页 |
| 4.6 PROTEINS INVOLVED IN GLYCOLYSIS/GLUCONEOGENESIS PATHWAY | 第60-64页 |
| 4.7 PROTEINS INVOLVED IN CARBON METABOLISM PATHWAY | 第64-65页 |
| 4.8 PROTEINS INVOLVED IN PENTOSE PHOSPHATE PATHWAY | 第65-66页 |
| 4.9 OTHER SIGNIFICANT PROTEINS RELATED TO THE VIRULENCE OF THE BACTERIA | 第66-68页 |
| 4.10 PARALOGUES ANALYSIS | 第68-71页 |
| 4.11 MOST SIGNIFICANT PROTEINS PREDICTED BY STRING REGARDING VIRULENCE OFMYCOPLASMA BOVIS | 第71-75页 |
| 4.12 STATISTICAL ANALYSIS OF SNP NUMBERS BETWEEN STRAINS | 第75页 |
| 4.13 KEGG ENRICHMENT ANALYSIS | 第75-77页 |
| 4.14 WHOLE GENOME SECRETORY AND SIGNAL PEPTIDES PROTEINS ANALYSIS | 第77-80页 |
| 4.15 GENOMIC AND PATHOGENIC ISLAND ANALYSIS | 第80-81页 |
| 4.16 ANALYSIS OF THE CONSERVED DOMAINS IN PREDICTED SECRETORY PROTEINS | 第81页 |
| 4.17 PROTEIN MODELING FOR STRUCTURE PREDICTION OF THE SECRETORY PROTEINS | 第81-82页 |
| 4.18 VFDB analysis | 第82-86页 |
| 4.19 HYDROGEN PEROXIDE PRODUCTION ASSAY | 第86-89页 |
| 4.20 SDS-PAGE TO SEPARATE WHOLE CELL PROTEINS (WCPS) | 第89-90页 |
| 4.21 PCR IDENTIFICATION OF THE TARGET MUTANT GENES IN M. BOVIS MUTANTLIBRARY | 第90-95页 |
| 5 CONCLUSION | 第95-96页 |
| 6 REFERENCES | 第96-109页 |
| LIST OF PUBLICATIONS | 第109-110页 |
| ACKNOWLEDGEMENT | 第110-111页 |
