Bibframe Work

Machine generated contents note: Introduction PART I: BACKGROUND 2 Vertebrate Immunity 2.1 Nonspecific Immunity 2.2 Specific Immunity: Antigens and Epitopes 2.3 B Cells and Antibodies 2.4 T Cells and MHC 2.5 Summary 3 Benefits of Antigenic Variation 3.1 Extend Length of Infection 3.2 Infect Hosts with Prior Exposure 3.3 Infect Hosts with Genetically Variable Resistance 3.4 Vary Attachment Characters 3.5 Antigenic Interference 3.6 Problems for Future Research PART II: MOLECULAR PROCESSES 4 Specificity and Cross-Reactivity 4.1 Antigens and Antibody Epitopes 4.2 Antibody Paratopes 4.3 Antibody Affinity Maturation 4.4 Natural Antibodies-Low-Affinity Binding to Diverse Antigens 4.5 Affinity versus Specificity 4.6 Cross-Reaction of Polyclonal Antibodies to Divergent Antigens 4.7 T Cell Epitopes 4.8 Every Host Differs 4.9 Problems for Future Research 5 Generative Mechanisms 5.1 Mutation and Hypermutation 5.2 Stochastic Switching between Archival Copies 5.3 New Variants by Intragenomic Recombination 5.4 Mixing between Genomes 5.5 Problems for Future Research PART III: INDIVIDUAL INTERACTIONS 6 Immunodominance within Hosts 6.1 Antibody Immunodominance 6.2 CTL Immunodominance 6.3 Sequence of Exposure to Antigens: Original Antigenic Sin 6.4 Problems for Future Research 7 Parasite Escape within Hosts 7.1 Natural Selection of Antigenic Variants 7.2 Pathogen Manipulation of Host Immune Dynamics 7.3 Sequence of Variants in Active Switching from Archives 7.4 Ecological Coexistence of Variants within a Host 7.5 Problems for Future Research PART IV: POPULATION CONSEQUENCES 8 Genetic Variability of Hosts 8.1 Polymorphisms in Specificity 8.2 Polymorphisms in Immune Regulation 8.3 Problems for Future Research 9 Immunological Variability of Hosts 9.1 Immunological Memory 9.2 Kinds of Parasites 9.3 Immunodominance of Memory 9.4 Cross-Reactivity and Interference 9.5 Distribution of Immune Profiles among Hosts 9.6 Problems for Future Research 10 Genetic Structure of Parasite Populations 10.1 Kinds of Genetic Structure 10.2 Pattern and Process 10.3 Genome-wide Linkage Disequilibrium 10.4 Antigenic Linkage Disequilibrium 10.5 Population Structure: Hosts as Islands 10.6 Problems for Future Research PART V: STUDYING EVOLUTION 11 Classifications by Antigenicity and Phylogeny 11.1 Immunological Measures of Antigenicity 11.2 Phylogeny 11.3 Hypothetical Relations between Immunology and Phylogeny 11.4 Immunology Matches Phylogeny over Long Genetic Distances 11.5 Immunology-Phylogeny Mismatch with Radiations into New Hosts 11.6 Short-Term Phylogenetic Diversification Driven by Immunological Selection 11.7 Discordant Patterns of Phylogeny and Antigenicity Created by Within-Host Immune Pressure 11.8 Problems for Future Research 12 Experimental Evolution: Foot-and-Mouth Disease Virus 12.1 Overview of Antigenicity and Structure 12.2 Antibody Escape Mutants 12.3 Cell Binding and Tropism 12.4 Fitness Consequences of Substitutions 12.5 Problems for Future Research 13 Experimental Evolution: Influenza 13.1 Overview of Antigenicity and Structure 13.2 Antibody Escape Mutants 13.3 Cell Binding and Tropism 13.4 Fitness Consequences of Substitutions 13.5 Experimental Evolution of Other Pathogens 13.6 Problems for Future Research 14 Experimental Evolution: CTL Escape 14.1 Cleavage and Transport of Peptides 14.2 MHC Binding. 14.3 TCR Binding 14.4 Functional Consequences of Escape 14.5 Kinetics of Escape 14.6 Problems for Future Research 15 Measuring Selection with Population Samples 15.1 Kinds of Natural Selection 15.2 Positive Selection to Avoid Host Recognition 15.3 Phylogenetic Analysis of Nucleotide Substitutions 15.4 Predicting Evolution 15.5 Problems for Future Research 16 Recap of Some Interesting Problems 16.1 Population-Level Explanation for Low Molecular Variability 16.2 Molecular-Level Explanation for Population Dynamics 16.3 Binding Kinetics and the Dynamics of Immunodominance 16.4 Diversity and Regulation of Archival Repertoires 16.5 Final Note.