ISBN-10:
3540740406
ISBN-13:
9783540740407
Pub. Date:
12/12/2008
Publisher:
Springer Berlin Heidelberg
Genome Mapping and Genomics in Animal-Associated Microbes / Edition 1

Genome Mapping and Genomics in Animal-Associated Microbes / Edition 1

by Vishvanath Nene, Chittaranjan Kole

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Product Details

ISBN-13: 9783540740407
Publisher: Springer Berlin Heidelberg
Publication date: 12/12/2008
Edition description: 2009
Pages: 237
Product dimensions: 7.50(w) x 10.40(h) x 0.70(d)

Table of Contents

Contributors XIII

Abbreviations XVII

1 Brucella Nammalwar Sirianganathan Mohamed N. Seleem Steven C. Olsen Luis E. Samartino Adrian M. Whatmore Betsy Bricker David O'Callaghan Shirley M. Halling Oswald R. Crasta Rebecca A. Wattam Anjan Purkayastha Bruno W. Sobral Eric E. Snyder Kelley Williams Gong-Xi Yu Thomas A. Ficht C. Marty Roop II Paul deFigueiredo Stephen M. Boyle Oliver He Rene M. Tsolis 1

1.1.1 Discovery of the Brucellae 1

1.1.2 Species Discovery 1

1.1.3 Zoonoses 2

1.1.4 Eradication Program 3

1.1.5 Vaccination 3

1.1.6 Molecular Study and Diagnoses 4

1.2 Economic and Zoonotic Implications of Brucella 4

1.2.1 Distribution of Brucella spp. Worldwide 4

1.2.2 Zoonotic Characteristics of Brucella spp 5

1.2.3 Economic Losses to Producers and Costs for Human Clinical Care 5

1.2.4 Control Programs and Associated Economic Costs 6

1.2.5 Conclusions 7

1.3 Brucella Taxonomy 7

1.3.1 Morphology/Life Cycle 7

1.3.2 Phylogenetic Position of the Genus 7

1.3.3 Brucella Taxonomy 9

1.4 Molecular Epidemiology and Population Dynamics of Brucella 10

1.4.1 Tools for Molecular Epidemiology 10

1.4.2 Population Dynamics and How They Can Impact Molecular Epidemiology 11

1.4.3 Conclusions 13

1.5 Physical and Genetic Map of Genomes 13

1.5.1 Bacterial Genomes and Their Analyses 13

1.5.2 Global Organization-Physical Maps 13

1.5.3 The Brucella Genome is Highly Conserved 14

1.5.4 The Brucella Genome and a-Proteobacteria Evolution 14

1.5.5 Multiple Genomes and Genome Rearrangements 14

1.5.6 Mobile Genetic Elements, Repeat Elements and Genomic Rearrangements 15

1.5.7 Genomic Polymorphisms: Transposons, Phage and Plasmid Associated Sequences 16

1.5.8Genetic Maps: Synteny 16

1.6 Genome Sequencing and Bioinformatics Resources 16

1.6.1 Introduction 16

1.6.2 Genome Sequencing 17

1.6.3 High-Throughput Sequencing Technologies 17

1.6.4 Brucella Genome Sequences 18

1.6.5 Bioinformatics Resources 20

1.6.6 Biological Data Curation in the Age of High-Throughput Technologies 21

1.6.7 Bioinformatics Resources for Brucella 21

1.6.8 The Brucella Bioinformatics Portal 21

1.6.9 The Pathogen Portal 23

1.6.10 The PathoSystems Resource Integration Center 24

1.6.11 Summary 26

1.7 Comparative Genomics of Brucella 26

1.7.1 Introduction 26

1.7.2 Comparative Analysis of Brucella and Related Species 27

1.7.3 Comparative Genomic Analysis of Brucella 29

1.7.4 Summary 35

1.8 Functional Genomics 35

1.8.1 Introduction 35

1.8.2 Genomics: Global Approaches 36

1.8.3 Rational Approaches 38

1.8.4 Transcriptomics 40

1.8.5 Bacterial Microarrays 40

1.8.6 Host Cell Microarrays 41

1.8.7 Proteomics 41

1.8.8 Higher Order (Protein-Protein) Interactions 42

1.8.9 Conclusions 42

1.9 Genome Mapping and Microarray Contributions to Understanding Brucella Pathobiology and Host Responses to Brucella Infections 43

1.9.1 Introduction 43

1.9.2 Biology of a Brucella Infection 43

1.9.3 Genome Mapping for Understanding Brucella Pathobiology 44

1.9.4 Genome Mapping for Understanding Host Response Against Brucella Infections 47

1.10 Future Directions and Prospects 51

References 52

2 Mycobacterium avium subspecies paratuberculosis Ling-Ling Li Sushmita Singh John Bannantine Sagarika Kanjilal Vivek Kapur 65

2.1 Introduction 65

2.1.1 The Pathogen and the Disease It Causes 65

2.1.2 Morphology, Taxonomic Position, Life-Cycle, and Host-Range of Map 67

2.2 The Genome Sequence of Map 68

2.2.1 Characteristics of the Map K-10 Genome 68

2.2.2 Repetitive DNA in Map 68

2.2.3 Protein Encoding Genes 69

2.2.4 Unique Regions and Unique Genes 69

2.2.5 Mycobactin Synthesis 70

2.2.6 Insights into Virulence and Pathogenicity Gleaned from the Map Genome 70

2.2.7 Distinguishing Characteristics of the Map Genome 70

2.2.8 Genomics-Based Insights into Map Metabolism 71

2.3 Population Studies of Map 72

2.3.1 Multi-Locus Enzyme Electrophoresis (MLEE) 73

2.3.2 DNA-Based Tools 73

2.3.3 Multi-Locus Short Sequence Repeats (MLSSR) 75

2.3.4 Variable Number of Tandem Repeats (VNTR) 77

2.4 Concluding Comments 78

References 79

3 Anaplasma Kelly A. Brayton Michael J. Dark Guy H. Palmer 85

3.1 Introduction 85

3.2 History 85

3.3 Impact on Animal Health 87

3.4 Taxonomy 87

3.5 Strains 91

3.5.1 Genotype 91

3.5.2 Strain Diversity 91

3.6 Population Studies 93

3.7 Genome Sequence and Resources 94

3.7.1 Genome Architecture and General Features 94

3.7.2 Metabolism 96

3.7.3 Cell Wall Biogenesis 98

3.7.4 Transporters 99

3.7.5 Paralogous Gene Families 102

3.8 Comparative Genomics 105

3.9 Future Scope 108

References 110

4 Ehrlichia Basil A. Allsopp Jere W. McBride 117

4.1 Introduction 117

4.1.1 History of Ehrlichia 117

4.1.2 Taxonomic Position 117

4.1.3 Ultrastructure 118

4.1.4 Life Cycle 119

4.1.5 Entry and Development in Host Cells 120

4.1.6 Epidemiology 120

4.1.7 Diseases 121

4.1.8 Economic Importance 122

4.1.9 Ehrlichia as Zoonotic Pathogens 123

4.2 Genomics 123

4.2.1 Genetic Variability of Ehrlichia 124

4.2.2 Genome Sequencing 128

4.2.3 Genomic Insights into the Biology of Ehrlichia 140

4.2.4 Molecular Diagnostics 148

4.2.5 Vaccine Development 150

4.2.6 Comparative Genomics of Ehrlichia Species 152

4.3 Future Scope 155

References 156

5 Cryptosporidium Guan Zhu Shinichiro Enomoto Jason M. Fritzler Mitchell S. Abrahamsen Thomas J. Templeton 165

5.1 Cryptosporidium and Cryptosporidiosis 165

5.1.1 Introduction 165

5.1.2 Taxonomic Position 166

5.1.3 Life Cycle 167

5.1.4 Cryptosporidium Genotypes 170

5.1.5 Treatment 170

5.2 Genome Sequencing, Mapping, and Resources 172

5.2.1 History of Genome Sequencing Projects 172

5.2.2 General Features of Cryptosporidium Genomes 172

5.2.3 Comparison Between C. parvum and C. hominis Genomes 174

5.2.4 Genome Databases and Resources 176

5.2.5 Genome Maps 177

5.3 Cryptosporidium Biology: Insights from the Complete Genome 178

5.3.1 Streamlined Metabolism 178

5.3.2 Expanded Families of Transporters 179

5.3.3 Lineage-Specific Expansion of Proteases 180

5.3.4 Cryptosporidium-Specific Amplified Gene Families 180

5.3.5 The Surface Protein Repertoire of Cryptosporidium 180

5.3.6 Mucin-Like Proteins 181

5.3.7 The TRAP Family of Motility and Invasion Proteins 181

5.3.8 The LCCL Domain Family 182

5.3.9 The Oocyst Wall Proteins 182

5.3.10 The Role of Lateral Gene Transfer in the Origin of Apicomplexan Extracellular Proteins 182

5.4 Parasite Targets for New Therapeutics 184

References 185

6 Theileria Richard P. Bishop David O. Odongo David J. Mann Terry W. Pearson Chihiro Sugimoto Lee R. Haines Elizabeth Glass Kirsty Jensen Ulrike Seitzer Jabbar S. Ahmed Simon P. Graham Etienne P. de Villiers 191

6.1 Introduction 191

6.1.1 The Genus Theileria 191

6.1.2 Economic Importance of Theileria 192

6.1.3 Theileria Taxonomy 192

6.1.4 Epidemiology and Pathology of Theileria Infections 193

6.1.5 Theileria Life Cycle and Cell Biology 194

6.2 Physical Mapping of the T. parva Genome 196

6.3 The Theileria parva and T. annulata Genome Sequences 196

6.3.1 Telomere-Associated Sequences 198

6.3.2 Comparative Genomics of T. parva and T. annulata 200

6.3.3 Current Status of the Theileria orientalis Genome Sequencing Project 201

6.4 Population Genetics and Molecular Epidemiology of T. parva and T. annulata 202

6.5 Genetic Recombination in T. parva 203

6.6 The Transcriptome of Theileria parva Schizonts as Revealed Using MPSS 205

6.6.1 Transcription of the Multicopy Tpr and Tar Loci 206

6.7 A Snapshot of the T. parva Proteome 206

6.8 Transcriptional Analyses of Host-Pathogen Interactions of T. annulata Infections in Bovine Macrophages 209

6.9 Application of Genomics to Understand the Biology of Theileria-Mammalian Host Cell Interaction 211

6.9.1 Insights into the Interaction of Theileria with Bovine Leukocytes Derived from Analysis of the Virtual Proteomes of T. parva and T. annulata 211

6.9.2 Analysis of the T. parva Predicted Proteome in Relation to Cell Cycle Regulation and Modulation of Mammalian Host Cell Function 213

6.9.3 Predicted Cyclin-Dependent Kinases in the T. parva Genome 213

6.9.4 Predicted Cyclins in the T. parva Genome 213

6.9.5 Sequence Homologues of Additional Parasite-Encoded Cell Cycle Regulators 219

6.9.6 Potential Modulators of the Host Cell Identified in the Theileria Genomes 219

6.10 Application of Genomics to the Development and Deployment of Vaccines for the Control of Theileria 221

6.10.1 Molecular Tools to Support Live Vaccination Against East Coast Fever 221

6.10.2 Live Attenuated Cell Culture Vaccines for the Control of T. annulata 221

6.10.3 Application of Genomics to Development of Subunit Vaccines for Control of ECF 222

6.11 Initial Investigation of Theileria Interaction with Ixodid Tick Vectors Using Expressed Sequence Tags Derived from R. appendiculatus and A. variegatum Tick Salivary Gland Transcripts 224

6.12 Opportunities for Future Research 224

References 225

Index 233

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