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Immunology and Evolution of Infectious Disease
Steven A. Frank

Book Description | Reviews

TABLE OF CONTENTS:

Acknowledgments xi
1. Introduction 3
PART I: BACKGROUND
2. Vertebrate Immunity 13
2.1 Nonspecific Immunity 14
2.2 Specific Immunity: Antigens and Epitopes 15
2.3 B Cells and Antibodies 16
2.4 T Cells and MHC 19
2.5 Summary 20
3. Benefits of Antigenic Variation 22
3.1 Extend Length of Infection 23
3.2 Infect Hosts with Prior Exposure 24
3.3 Infect Hosts with Genetically
Variable Resistance 26
3.4 Vary Attachment Characters 26
3.5 Antigenic Interference 28
3.6 Problems for Future Research 29
PART II: MOLECULAR PROCESSES
4. Specificity and Cross-Reactivity 33
4.1 Antigens and Antibody Epitopes 35
4.2 Antibody Paratopes 36
4.3 Antibody Affinity Maturation 38
4.4 Natural Antibodies-Low-Affinity Binding to Diverse Antigens 39
4.5 Affinity versus Specificity 40
4.6 Cross-Reaction of Polyclonal Antibodies to Divergent Antigens 42
4.7 T Cell Epitopes 44
4.8 Every Host Differs 52
4.9 Problems for Future Research 54
5. Generative Mechanisms 57
5.1 Mutation and Hypermutation 58
5.2 Stochastic Switching between Archival Copies 61
5.3 New Variants by Intragenomic Recombination 66
5.4 Mixing between Genomes 67
5.5 Problems for Future Research 68
PART III: INDIVIDUAL INTERACTIONS
6. Immunodominance within Hosts 73
6.1 Antibody Immunodominance 74
6.2 CTL Immunodominance 79
6.3 Sequence of Exposure to Antigens: Original Antigenic Sin 87
6.4 Problems for Future Research 89
7. Parasite Escape within Hosts 93
7.1 Natural Selection of Antigenic Variants 94
7.2 Pathogen Manipulation of Host Immune Dynamics 97
7.3 Sequence of Variants in Active Switching from Archives 98
7.4 Ecological Coexistence of Variants within a Host 102
7.5 Problems for Future Research 106
PART IV: POPULATION CONSEQUENCES
8. Genetic Variability of Hosts 111
8.1 Polymorphisms in Specificity 112
8.2 Polymorphisms in Immune Regulation 115
8.3 Problems for Future Research 121
9. Immunological Variability of Hosts 124
9.1 Immunological Memory 125
9.2 Kinds of Parasites 129
9.3 Immunodominance of Memory 132
9.4 Cross-Reactivity and Interference 135
9.5 Distribution of Immune Profiles among Hosts 136
9.6 Problems for Future Research 144
10. Genetic Structure of Parasite Populations 148
10.1 Kinds of Genetic Structure 149
10.2 Pattern and Process 151
10.3 Genome-wide Linkage Disequilibrium 153
10.4 Antigenic Linkage Disequilibrium 164
10.5 Population Structure: Hosts as Islands 166
10.6 Problems for Future Research 168
PART V: STUDYING EVOLUTION
11. Classifications by Antigenicity and Phylogeny 175
11.1 Immunological Measures of Antigenicity 176
11.2 Phylogeny 178
11.3 Hypothetical Relations between Immunology and Phylogeny 179
11.4 Immunology Matches Phylogeny over Long Genetic Distances 181
11.5 Immunology-Phylogeny Mismatch with Radiations into New Hosts 181
11.6 Short-Term Phylogenetic Diversification Driven by Immunological Selection 183
11.7 Discordant Patterns of Phylogeny and Antigenicity Created by Within-Host Immune Pressure 183
11.8 Problems for Future Research 186
12. Experimental Evolution: Foot-and-Mouth Disease Virus 188
12.1 Overview of Antigenicity and Structure 189
12.2 Antibody Escape Mutants 192
12.3 Cell Binding and Tropism 196
12.4 Fitness Consequences of Substitutions 200
12.5 Problems for Future Research 202
13. Experimental Evolution: Influenza 205
13.1 Overview of Antigenicity and Structure 206
13.2 Antibody Escape Mutants 214
13.3 Cell Binding and Tropism 216
13.4 Fitness Consequences of Substitutions 218
13.5 Experimental Evolution of Other Pathogens 224
13.6 Problems for Future Research 227
14. Experimental Evolution: CTL Escape 230
14.1 Cleavage and Transport of Peptides 231
14.2 MHC Binding 232
14.3 TCR Binding 237
14.4 Functional Consequences of Escape 239
14.5 Kinetics of Escape 240
14.6 Problems for Future Research 243
15. Measuring Selection with Population Samples 246
15.1 Kinds of Natural Selection 247
15.2 Positive Selection to Avoid Host Recognition 249
15.3 Phylogenetic Analysis of Nucleotide Substitutions 251
15.4 Predicting Evolution 255
15.5 Problems for Future Research 260
16. Recap of Some Interesting Problems 265
16.1 Population-Level Explanation for Low Molecular Variability 265
16.2 Molecular-Level Explanation for Population Dynamics 266
16.3 Binding Kinetics and the Dynamics of Immunodominance 266
16.4 Diversity and Regulation of Archival Repertoires 267
16.5 Final Note 268
References 269
Author Index 313
Subject Index 337

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File created: 4/17/2014

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