Immunology and Evolution
`
`
`of Infectious Disease
`
`Steven A. Frank
`
`Lassen - Exhibit 1055, p. 1
`
`

`

`Immunology
`and Evolution of
`Infectious Disease
`
`STEVEN A. FRANK
`
`Princeton University Press
`Princeton and Oxford
`
`This is a full PDF copy of:(cid:31)
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`(cid:31)F
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`rank, S. A. 2002. Immunology and Evolution of Infectious Disease.
`Princeton University Press.(cid:31)
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`his PDF is a trial version of the book. If you intend to read and use
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`
`Lassen - Exhibit 1055, p. 2
`
`

`

`Copyright © 2002 by Steven A. Frank
`Published by Princeton University Press,
`41 William Street, Princeton, New Jersey 08540
`In the United Kingdom: Princeton University Press,
`3 Market Place, Woodstock, Oxfordshire OX20 1SY
`
`All Rights Reserved
`
`Library of Congress Cataloging-in-Publication Data
`
`Frank, Steven A., 1957–
`Immunology and Evolution of Infectious Disease /
`Steven A. Frank. p. cm.
`Includes bibliographic references and index.
`ISBN 0–691–09594–9 (cloth : alk. paper)
`ISBN 0–691–09595–7 (pbk. : alk. paper)
`1. Immunogenetics. 2. Host-parasite relationships—
`Genetic aspects. 3. Microorganisms—Evolution.
`4. Antigens. 5. Molecular evolution.
`6. Parasite antigens—Variation. I. Title.
`[DNLM: 1. Communicable Diseases—immunology.
`2. Evolution, Molecular. 3. Genetics, Population.
`4. Immunity—genetics. WC 100 F828i 2002]
`QR184 .F73 2002
`(cid:2)
`0479—dc21
`616.9
`
`2002018384
`
`British Library Cataloging-in-Publication Data is available
`
`Typeset by the author with TEX
`Composed in Lucida Bright
`
`Printed on acid-free paper. ∞
`
`www.pupress.princeton.edu
`
`Printed in the United States of America
`
`10 9 8 7 6 5 4 3 2 1
`
`10 9 8 7 6 5 4 3 2 1
`(Pbk.)
`
`Lassen - Exhibit 1055, p. 3
`
`

`

`Contents
`
`Acknowledgments
`
`1 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
`
`xi
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`3
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`13
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`14
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`15
`16
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`Lassen - Exhibit 1055, p. 4
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`

`

`vi
`
`CONTENTS
`
`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
`
`39
`40
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`42
`44
`52
`54
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`57
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`Lassen - Exhibit 1055, p. 5
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`

`

`CONTENTS
`
`vii
`
`7.4 Ecological Coexistence of
`Variants within a Host
`7.5 Problems for Future Research
`
`102
`106
`
`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
`
`111
`
`112
`
`115
`121
`
`9 Immunological Variability of
`Hosts
`124
`125
`9.1 Immunological Memory
`129
`9.2 Kinds of Parasites
`132
`9.3 Immunodominance of Memory
`9.4 Cross-Reactivity and Interference 135
`9.5 Distribution of Immune Profiles
`among Hosts
`9.6 Problems for Future Research
`
`136
`144
`
`10 Genetic Structure of Parasite
`Populations
`
`148
`149
`151
`
`10.1 Kinds of Genetic Structure
`10.2 Pattern and Process
`10.3 Genome-wide Linkage
`153
`Disequilibrium
`10.4 Antigenic Linkage Disequilibrium 164
`10.5 Population Structure: Hosts as
`Islands
`10.6 Problems for Future Research
`
`166
`168
`
`Lassen - Exhibit 1055, p. 6
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`

`

`viii
`
`CONTENTS
`
`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
`
`175
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`176
`178
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`179
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`206
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`216
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`Lassen - Exhibit 1055, p. 7
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`

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`CONTENTS
`
`ix
`
`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
`
`218
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`224
`227
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`230
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`232
`237
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`240
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`Lassen - Exhibit 1055, p. 8
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`

`

`x
`
`CONTENTS
`
`269
`
`313
`
`References
`
`Author Index
`
`Subject Index
`
`Lassen - Exhibit 1055, p. 9
`
`

`

`Acknowledgments
`
`My wife, Robin Bush, read earlier drafts and helped in every way. Camille
`Barr provided comments on the entire manuscript. My department, led
`by Chair Al Bennett, gave me the freedom to read and write over nearly
`two years. The National Science Foundation and the National Institutes
`of Health funded my research. My web pages at http://stevefrank.org/
`provide information and updates for this book.
`
`Lassen - Exhibit 1055, p. 10
`
`

`

`Lassen — Exhibit 1055, p. 11
`
`Lassen - Exhibit 1055, p. 11
`
`

`

`Immunology
`and Evolution of
`Infectious Disease
`
`Lassen - Exhibit 1055, p. 12
`
`

`

`Lassen — Exhibit 1055, p. 13
`
`Lassen - Exhibit 1055, p. 13
`
`

`

`1 Introduction
`
`Multidisciplinary has become the watchword of modern biology. Surely,
`the argument goes, a biologist interested in the biochemical pathways
`by which genetic variants cause disease would also want to understand
`the population processes that determine the distribution of genetic vari-
`ants. And how can one expect to understand the interacting parts of
`complex immune responses without knowing something of the histori-
`cal and adaptive processes that built the immune system?
`Working in the other direction, evolutionary biologists have often
`treated amino acid substitutions within a parasite lineage as simply
`statistical marks to be counted and analyzed by the latest mathemat-
`ical techniques. More interesting work certainly follows when hypothe-
`ses about evolutionary change consider the different selective pressures
`caused by antibody memory, variation among hosts in MHC genotype,
`and the epidemiological contrasts between rapidly and slowly spreading
`infectious diseases.
`Synthesis between the details of molecular biology and the lives of
`organisms in populations will proceed slowly.
`It is now hard enough
`to keep up in one’s own field, and more difficult to follow the foreign
`concepts and language of other subjects. The typical approach to syn-
`thesis uses an academic discipline to focus a biological subject. I use the
`biological problem of parasite variation to tie together many different
`approaches and levels of analysis.
`Why should parasite variation be the touchstone for the integration
`of disciplines in modern biology? On the practical side, infectious dis-
`ease remains a major cause of morbidity and mortality. Consequently,
`great research effort has been devoted to parasites and to host immune
`responses that fight parasites. This has led to rapid progress in under-
`standing the biology of parasites, including the molecular details about
`how parasites invade hosts and escape host immune defenses. Vaccines
`have followed, sometimes with spectacular success.
`But many parasites escape host defense by varying their antigenic
`molecules recognized by host immunity. Put another way, rapid evo-
`lution of antigenic molecules all too often prevents control of parasite
`
`Lassen - Exhibit 1055, p. 14
`
`

`

`4
`
`CHAPTER 1
`
`populations. The challenge has been to link molecular understanding
`of parasite molecules to their evolutionary change and to the antigenic
`variation in populations of parasites.
`On the academic side, the growth of information about antigenic vari-
`ation provides a special opportunity. For example, one can find in the
`literature details about how single amino acid changes in parasite mol-
`ecules allow escape from antibody binding, and how that escape pro-
`motes the spread of variant parasites. Evolutionary studies no longer
`depend on abstractions—one can pinpoint the physical basis for success
`or failure and the consequences for change in populations.
`Molecular understanding of host-parasite recognition leads to a com-
`parative question about the forces that shape variability. Why do some
`viruses escape host immunity by varying so rapidly over a few years,
`whereas other viruses hardly change their antigens? The answer leads
`to the processes that shape genetic variability and evolutionary change.
`The causes of variability and change provide the basis for understanding
`why simple vaccines work well against some viruses, whereas complex
`vaccine strategies achieve only limited success against other viruses.
`I did not start out by seeking a topic for multidisciplinary synthesis.
`Rather, I have long been interested in how the molecular basis of rec-
`ognition between attackers and defenders sets the temporal and spatial
`scale of the battle. Attack and defense occur between insects and the
`plants they eat, between fungi and the crop plants they destroy, between
`viruses and the bacteria they kill, between different chromosomes com-
`peting for transmission through gametes, and between vertebrate hosts
`and their parasites. The battle often comes down to the rates at which
`attacker and defender molecules bind or evade each other. The bio-
`chemical details of binding and recognition set the rules of engagement
`that shape the pacing, scale, and pattern of diversity and the nature of
`evolutionary change.
`Of the many cases of attack and defense across all of biology, the
`major parasites of humans and their domestic animals provide the most
`information ranging from the molecular to the population levels. New
`advances in the conceptual understanding of attack and defense will
`likely rise from the facts and the puzzles of this subject.
`I begin by
`putting the diverse, multidisciplinary facts into a coherent whole. From
`that foundation, I describe new puzzles and define the key problems for
`the future study of parasite variation and escape from host recognition.
`
`Lassen - Exhibit 1055, p. 15
`
`

`

`INTRODU CTION 5
`
`I start at the most basic level, the nature of binding and recognition
`between host and parasite molecules. I summarize the many different
`ways in which parasites generate new variants in order to escape molec-
`ular recognition.
`Next, I build up the individual molecular interactions into the dynam-
`ics of a single infection within a host. The parasites spread in the host,
`triggering immune attack against dominant antigens. The battle within
`the host develops through changes in population numbers—the num-
`bers of parasites with particular antigens and the numbers of immune
`cells that specifically bind to particular antigens.
`I then discuss how the successes and failures of different parasite
`antigens within each host determine the rise and fall of parasite vari-
`ants over space and time. The distribution of parasite variants sets the
`immune memory profiles of different hosts, which in turn shape the
`landscape in which parasite variants succeed or fail. These coevolution-
`ary processes determine the natural selection of antigenic variants and
`the course of evolution in the parasite population.
`Finally, I consider different ways to study the evolution of antigenic
`variation. Experimental evolution of parasites under controlled condi-
`tions provides one way to study the relations between molecular rec-
`ognition, the dynamics of infections within hosts, and the evolution-
`ary changes in parasite antigens. Sampling of parasites from evolving
`populations provides another way to test ideas about what shapes the
`distribution of parasite variants.
`My primary goal is to synthesize across different levels of analysis.
`How do the molecular details of recognition and specificity shape the
`changing patterns of variants in populations? How does the epidemio-
`logical spread of parasites between hosts shape the kinds and amounts
`of molecular variation in parasite antigens?
`I compare different types of parasites because comparative biology
`provides insight into evolutionary process. For example, parasites that
`spread rapidly and widely in host populations create a higher density of
`immune memory in their hosts than do parasites that spread slowly and
`sporadically. Host species that quickly replace their populations with
`offspring decay their population-wide memory of antigens faster than do
`host species that reproduce more slowly. How do these epidemiological
`and demographic processes influence molecular variation of parasite
`antigens?
`
`Lassen - Exhibit 1055, p. 16
`
`

`

`6
`
`CHAPTER 1
`
`I end each chapter with a set of problems for future research. These
`problems emphasize the great opportunities of modern biology. At the
`molecular level, new technologies provide structural data on the three-
`dimensional shape of host antibody molecules bound to parasite anti-
`gens. At the population level, genomic sequencing methods provide
`detailed data on the variations in parasite antigens. One can now map
`the nucleotide variations of antigens and their associated amino acid
`substitutions with regard to the three-dimensional location of antibody
`binding. Thus, the spread of nucleotide variations in populations can
`be directly associated with the changes in molecular binding that allow
`escape from antibody recognition.
`No other subject provides such opportunity for integrating the re-
`cent progress in structural and molecular analysis with the conceptual
`and methodological advances in population dynamics and evolutionary
`biology. My problems for future research at the end of each chapter
`emphasize the new kinds of questions that one can ask by integrating
`different levels of biological analysis.
`
`Part I of the book gives general background. Chapter 2 summarizes
`the main features of vertebrate immunity. I present enough about the
`key cells and molecules so that one can understand how immune recog-
`nition shapes the diversity of parasites.
`Chapter 3 describes various benefits that antigenic variation provides
`to parasites. These benefits explain why parasites vary in certain ways.
`For example, antigenic variation can help to escape host immunity dur-
`ing a single infection, extending the time a parasite can live within a
`particular host. Or antigenic variation may avoid the immunological
`memory of hosts, allowing the variant to spread in a population that
`previously encountered a different variant of that parasite. Different
`benefits favor different patterns of antigenic variation.
`Part II introduces molecular processes. Chapter 4 describes the at-
`tributes of host and parasite molecules that contribute to immune rec-
`ognition. The nature of recognition depends on specificity, the degree
`to which the immune system distinguishes between different antigens.
`Sometimes two different antigens bind to the same immune receptors,
`perhaps with different binding strength. This cross-reactivity protects
`
`Lassen - Exhibit 1055, p. 17
`
`

`

`INTRODU CTION 7
`
`hosts against certain antigenic variants, and sets the molecular dis-
`tance by which antigenic types must vary to escape recognition. Cross-
`reactivity may also interfere with immune recognition when immune
`receptors bind a variant sufficiently to prevent a new response but not
`strongly enough to clear the variant.
`Chapter 5 summarizes the different ways in which parasites gener-
`ate antigenic variants. Many parasites generate variants by the stan-
`dard process of rare mutations during replication. Baseline mutation
`rates vary greatly, from about 10−5 per nucleotide per generation for
`the small genomes of some RNA viruses to about 10−11 for larger ge-
`nomes. Although mutations occur rarely at any particular site during
`replication, large populations generate significant numbers of mutations
`in each generation. Some parasites focus hypermutation directly on
`antigenic loci. Other parasites store within each genome many genetic
`variants for an antigenic molecule. These parasites express only one
`genetic variant at a time and use specialized molecular mechanisms to
`switch gene expression between the variants.
`Part III focuses on the dynamics of a single infection within a par-
`ticular host. Chapter 6 emphasizes the host side, describing how the
`immune response develops strongly against only a few of the many dif-
`ferent antigens that occur in each parasite. This immunodominance
`arises from interactions between the populations of immune cells with
`different recognition specificities and the population of parasites within
`the host. Immunodominance determines which parasite antigens face
`strong pressure from natural selection and therefore which antigens are
`likely to vary over space and time. To understand immunodominance, I
`step through the dynamic processes that regulate an immune response
`and determine which recognition specificities become amplified.
`Chapter 7 considers the ways in which parasites escape recognition
`during an infection and the consequences for antigenic diversity within
`hosts. The chapter begins with the role of escape by mutation in persis-
`tent infections by HIV and hepatitis C virus. I then discuss how other
`parasites extend infection by switching gene expression between vari-
`ants stored within each genome. This switching leads to interesting
`population dynamics within the host. The different variants rise and
`fall in abundance according to the rate of switching between variants,
`the time lag in the expansion of parasite lineages expressing a particular
`variant, and the time lag in the host immune response to each variant.
`
`Lassen - Exhibit 1055, p. 18
`
`

`

`8
`
`CHAPTER 1
`
`Part IV examines variability in hosts and parasites across entire pop-
`ulations. Chapter 8 considers genetic differences among hosts in im-
`mune response. Hosts differ widely in their major histocompatibility
`complex (MHC) alleles, which cause different hosts to recognize and fo-
`cus their immune responses on different parasite antigens. This host
`variability can strongly affect the relative success of antigenic variants
`as they attempt to spread from host to host. Hosts also differ in mi-
`nor ways in other genetic components of specific recognition. Finally,
`host polymorphisms occur in the regulation of the immune response.
`These quantitative differences in the timing and intensity of immune
`reactions provide an interesting model system for studying the genetics
`of regulatory control.
`Chapter 9 describes differences among hosts in their molecular mem-
`ory of antigens. Each host typically retains the ability to respond quickly
`to antigens that it encountered in prior infections. This memory pro-
`tects the host against reinfection by the same antigens, but not against
`antigenic variants that escape recognition. Each host has a particular
`memory profile based on past infections. The distribution of memory
`profiles in the host population determines the ability of particular anti-
`genic variants to spread between hosts. Hosts retain different kinds of
`immunological memory (antibody versus T cell), which affect different
`kinds of parasites in distinct ways.
`Chapter 10 reviews the genetic structure of parasite populations. The
`genetic structure of nonantigenic loci provides information about the
`spatial distribution of genetic variability, the mixing of parasite lineages
`by transmission between hosts, and the mixing of genomes by sexual
`processes. The genetic structure of antigenic loci can additionally be
`affected by the distribution of host immunological memory, because
`parasites must avoid the antigen sets stored in immunological memory.
`Host selection on antigenic sets could potentially structure the parasite
`population into distinct antigenic strains. Finally, each host forms a
`separate island that divides the parasite population from other islands
`(hosts). This island structuring of parasite populations can limit the
`exchange of parasite genes by sexual processes, causing a highly inbred
`structure. Island structuring also means that each host receives a small
`and stochastically variable sample of the parasite population. Stochastic
`fluctuations may play an important role in the spatial distribution of
`antigenic variation.
`
`Lassen - Exhibit 1055, p. 19
`
`

`

`INTRODU CTION 9
`
`Part V considers different methods to study the evolutionary pro-
`cesses that shape antigenic variation. Chapter 11 contrasts two differ-
`ent ways to classify parasite variants sampled from populations.
`Im-
`munological assays compare the binding of parasite isolates to differ-
`ent immune molecules. The reactions of each isolate with each immune
`specificity form a matrix from which one can classify antigenic variants
`according to the degree to which they share recognition by immunity.
`Alternatively, one can classify isolates phylogenetically, that is, by time
`since divergence from a common ancestor. Concordant immunological
`and phylogenetic classifications frequently arise because immunological
`distance often increases with time since a common ancestor, reflecting
`the natural tendency for similarity by common descent. Discordant pat-
`terns of immunological and phylogenetic classifications indicate some
`evolutionary pressure on antigens that distorts immunological similar-
`ity.
`I show how various concordant and discordant relations point to
`particular hypotheses about the natural selection of antigenic proper-
`ties in influenza and HIV.
`Chapter 12 introduces experimental evolution, a controlled method to
`test hypotheses about the natural selection of antigenic diversity. This
`chapter focuses on foot-and-mouth disease virus. This well-studied vi-
`rus illustrates how one can measure multiple selective forces on partic-
`ular amino acids. Selective forces on amino acids in viral surface mole-
`cules include altered binding to host-cell receptors and changed binding
`to host antibodies. The selective forces imposed by antibodies and by at-
`tachment to host-cell receptors can be varied in experimental evolution
`studies to test their effects on amino acid change in the parasite. The
`amino acid substitutions can also be mapped onto three-dimensional
`structural models of the virus to analyze how particular changes alter
`binding properties.
`Chapter 13 continues with experimental evolution of influenza A vi-
`ruses. Experimental evolution has shown how altering the host species
`favors specific amino acid changes in the influenza surface protein that
`binds to host cells. Experimental manipulation of host-cell receptors
`and antibody pressure can be combined with structural data to under-
`stand selection on the viral surface amino acids. These mechanistic
`analyses of selection can be combined with observations on evolution-
`ary change in natural populations to gain a better understanding of how
`selection shapes the observed patterns of antigenic variation.
`
`Lassen - Exhibit 1055, p. 20
`
`

`

`10
`
`CHAPTER 1
`
`Chapter 14 discusses experimental evolution of antigenic escape from
`host T cells. The host T cells can potentially bind to any short peptide
`of an intracellular parasite, whereas antibodies typically bind only to
`the surface molecules of parasites. T cell binding to parasite peptides
`depends on a sequence of steps by which hosts cut up parasite proteins
`and present the resulting peptides on the surfaces of host cells. Para-
`site escape from T cell recognition can occur at any of the processing
`steps, including the digestion of proteins, the transport of peptides, the
`binding of peptides by the highly specific host MHC molecules, and the
`binding of peptide-MHC complexes to receptors on the T cells. One or
`two amino acid substitutions in a parasite protein can often abrogate
`binding to MHC molecules or to the T cell receptors. Experimental evo-
`lution has helped us to understand escape from T cells because many
`of the steps can be controlled, such as the MHC alleles carried by the
`host and the specificities of the T cell receptors. Parasite proteins may
`be shaped by opposing pressures on physiological performance and es-
`cape from recognition.
`Chapter 15 turns to samples of nucleotide sequences from natural
`populations. A phylogenetic classification of sequences provides a his-
`torical reconstruction of evolutionary relatedness and descent. Against
`the backdrop of ancestry, one can measure how natural selection has
`changed particular attributes of parasite antigens. For example, one can
`study whether selection caused particular amino acids to change rapidly
`or slowly. The rates of change for particular amino acids can be com-
`pared with the three-dimensional structural location of the amino acid
`site, the effects on immunological recognition, and the consequences
`for binding to host cells. The changes in natural populations can also
`be compared with patterns of change in experimental evolution, in which
`one controls particular selective forces. Past evolutionary change in pop-
`ulation samples may be used to predict which amino acid variants in
`antigens are likely to spread in the future.
`The last chapter recaps some interesting problems for future research
`that highlight the potential to study parasites across multiple levels of
`analysis.
`
`Lassen - Exhibit 1055, p. 21
`
`

`

`PART I
`
`BACKGROUND
`
`Lassen - Exhibit 1055, p. 22
`
`

`

`Lassen — Exhibit 1055, p. 23
`
`Lassen - Exhibit 1055, p. 23
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`

`

`2 Vertebrate
`
`Immunity
`
`“The CTLs destroy host cells when their TCRs bind matching MHC-pep-
`tide complexes.” This sort of jargon-filled sentence dominates discus-
`sions of the immune response to parasites. I had initially intended this
`book to avoid such jargon, so that any reasonably trained biologist could
`read any chapter without getting caught up in technical terms. I failed—
`the quoted sentence comes from a later section in this chapter.
`The vertebrate immune system has many specialized cells and mole-
`cules that interact in particular ways. One has to talk about those cells
`and molecules, which means that they must be named.
`I could have
`tried a simpler or more logically organized naming system, but then I
`would have created a private language that does not match the rest of
`the literature. Thus, I use the standard technical terms.
`In this chapter, I introduce the major features of immunity shared by
`vertebrates. I present enough about the key cells and molecules so that
`one can understand how immune recognition shapes the diversity of
`parasites. I have not attempted a complete introduction to immunology,
`because many excellent ones already exist. I recommend starting with
`Sompayrac’s (1999) How the Immune System Works, which is a short,
`wonderfully written primer. One should keep a good textbook by one’s
`side—I particularly like Janeway et al. (1999). Mims’s texts also pro-
`vide good background because they describe immunology in relation to
`parasite biology (Mims et al. 1998, 2001).
`The first section of this chapter describes nonspecific components of
`immunity. Nonspecific recognition depends on generic signals of par-
`asites such as common polysaccharides in bacterial cell walls. These
`signals trigger various killing mechanisms, including the complement
`system, which punches holes in the membranes of invading cells, and
`the phagocytes, which engulf invaders.
`The second section introduces specific immunity, the recognition of
`small regions on particular parasite molecules. Specific recognition oc-
`curs when molecules of the host immune system bind to a molecular
`shape on the parasite that is not shared by other parasites. Sometimes
`all parasites of the same species share the specificity, and recognition
`
`Lassen - Exhibit 1055, p. 24
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`

`

`14
`
`CHAPTER 2
`
`differentiates between different kinds of parasites. Other times, differ-
`ent parasite genotypes vary in molecular shape, so that the host mole-
`cules that bind specifically to one parasite molecule do not bind another
`parasite molecule that differs by as little as one amino acid. A parasite
`molecule that stimulates specific recognition is called an antigen. The
`small region of the parasite molecule recognized by the host is called
`an epitope. Antigenic variation occurs when a specific immune response
`against one antigenic molecule fails to recognize a variant antigenic mol-
`ecule.
`The third section presents the B cells, which secrete antibodies. An-
`tibodies are globular proteins that fight infection by binding to small
`regions (epitopes) on the surface molecules of parasites. Different an-
`tibodies bind to different epitopes. An individual can make billions of
`different antibodies, each with different binding specificity. Diverse an-
`tibodies provide recognition and defense against different kinds of par-
`asites, and against particular parasites that vary genetically in the struc-
`ture of their surface molecules. Antibodies bind to surface molecules
`and help to clear parasites outside of host cells.
`The fourth section focuses on specific recognition by the T cells. Host
`cells continually break up intracellular proteins into small peptides. The
`hosts’ major histocompatibility complex (MHC) molecules bind short
`peptides in the cell. The cell then transports the bound peptide-MHC
`pair to the cell surface for presentation to roving T cells. Each T cell
`has receptors that can bind only to particular peptide-MHC combina-
`tions presented on the surface of cells. Different T cell clones produce
`different receptors. When a T cell binds to a peptide-MHC complex on
`the cell surface and also receives stimulatory signals suggesting para-
`site invasion, the T cell can trigger the death of the infected cell. T cells
`bind to parasite peptides digested in infected cells and presented on the
`infected cell’s surface, helping to clear intracellular infections.
`The final section summarizes the roles of antibodies and T cells in
`specific immunity.
`
`2.1 Nonspecific Immunity
`
`Nonspecific immunity recognizes parasites by generic signs that in-
`dicate the parasite is an invader rather than a part of the host. The
`nonspecific complement system consists of different proteins that work
`
`Lassen - Exhibit 1055, p. 25
`
`

`

`VERTEBRATE IMMUNITY
`
`15
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`together to punch holes in the surfaces of cells. Host cells have several
`surface molecules that shut off complement attack, causing complement
`to be directed only against invading cells. Common structural carbo-
`hydrates found on the surfaces of many parasites trigger complement
`attack, whereas the host cells’ carbohydrate molecules do not trigger
`complement.
`Phagocytic cells such as macrophages and neutrophils engulf invad-
`ing parasite cells. Various signals indicate to the phagocytes that nearby
`cells are invaders. For example, certain lipopolysaccharides commonly
`occur in the outer walls of gram-negative bacte