Roitt's Essential Immunology E-Book

Peter J. Delves

• Herausgeber: John Wiley & Sons
• Kategorie: Fachliteratur
• Serie: essentials
• Sprache: Englisch

Seitenzahl: 1818

Veröffentlichungsjahr: 2016

Beschreibung

Roitt's Essential Immunology - the textbook of choice for students and instructors of immunology worldwide 

Roitt’s Essential Immunology clearly explains the key principles needed by medical and health sciences students, from the basis of immunity to clinical applications.  A brand new introduction sets the scene to section 1, Fundamentals of Immunology, introducing the microbial world and the strategies the body employs to defend itself. Each chapter then guides the reader through a different part of the immune system, and explains the role of each cell or molecule individually, and then as a whole.  Section 2, Applied Immunology, discusses what happens when things go wrong, and the role the immune system plays alongside the damaging effects of a disease, including cancer, immunodeficiency, allergies and transplantation and the beneficial effects of vaccines.

The 13^th edition continues to be a user-friendly and engaging introduction to the workings of the immune system, whilst supporting those who require a slightly more detailed understanding of the key developments in immunology.  The content has been fully updated throughout and includes:

• An expansion on key clinical topics, including: innate immunity, autoimmune conditions, asthma, primary immunodeficiency, and HIV/AIDS
• Beautifully presented with improved artwork and new illustrations
• A range of learning features, including introduction re-cap boxes, end of chapter and section summaries to aid revision, as well as further reading suggestions, and a glossary to explain the most important immunology terms.

Roitt's Essential Immunology is also supported by a companion website at www.roitt.com including:

• An additional online only chapter on immunological methods and applications 
• Further interactive multiple choice and single best answer questions for each chapter
• Animations and videos showing key concepts
• Fully downloadable figures and illustrations, further reading and useful links
• Updated extracts from the Encyclopaedia of Life Sciences
• Podcasts to reinforce the key principles explained in the text

Leseprobe

Table of Contents

Cover

Title Page

About the authors

Acknowledgments

Preface

Abbreviations

How to use your textbook

About the companion website

Part 1: Fundamentals of immunology

CHAPTER 1: Innate immunity

Introduction

Knowing when to make an immune response

Pattern recognition receptors detect nonself

Immune responses are tailored towards particular types of infection

Innate versus adaptive immunity

External barriers against infection

Cells of the immune system

The beginnings of an immune response

There are several classes of pattern recognition receptors

Phagocytic cells engulf and kill microorganisms

Phagocytes employ an array of killing mechanisms

Complement facilitates phagocytosis and bacterial lysis

Humoral mechanisms provide an additional defensive strategy

Natural killer cells kill virally infected cells

Dealing with large parasites

The innate immune system instigates adaptive immunity

SUMMARY

FURTHER READING

CHAPTER 2: Specific acquired immunity

Just to recap …

Introduction

Antigens – “shapes” recognized by the immune system

Antibody – a specific antigen recognition molecule

Clonal selection

Immunological memory

Antigen specificity

Vaccination produces acquired memory

Cell‐mediated immunity protects against intracellular organisms

Integration of the immune response

Immunopathology

SUMMARY

FURTHER READING

CHAPTER 3: Antibodies

Just to recap …

Introduction

The division of labor

Five classes of immunoglobulin

The IgG molecule

The structure and function of the immunoglobulin classes

Genetics of antibody diversity and function

SUMMARY

FURTHER READING

CHAPTER 4: Membrane receptors for antigen

Just to recap …

Introduction

The B‐cell surface receptor for antigen (BCR)

The T‐cell surface receptor for antigen (TCR)

The generation of diversity for antigen recognition

Invariant natural killer T‐cell receptors bridge innate and adaptive immunity

NK receptors

The major histocompatibility complex (MHC)

Pathogen recognition receptors provide the first line of detection for microbial antigen

SUMMARY

FURTHER READING

CHAPTER 5: Antigen‐specific recognition

Just to recap …

Introduction

What antibodies see

Identifying B‐cell epitopes on a protein

Thermodynamics of antibody–antigen interactions

Specificity and cross‐reactivity of antibodies

What the T‐cell sees

Processing of intracellular antigen for presentation by class I MHC

Processing of extracellular antigen for class II MHC presentation follows a different pathway

Cross‐presentation of antigens

The nature of the “groovy” peptide

The αβ T‐cell receptor binds to a combination of MHC and peptide

T‐cell recognition of non‐protein antigens

Antigen recognition by γδ T‐cells

Superantigens are extremely powerful activators of T‐cells

Why do αβ T‐cells need to recognize antigen in such a complex way?

SUMMARY

FURTHER READING

Chapter 6: The anatomy of the immune response

Just to recap …

Introduction

The location of the immune system

The skin immune system

Mucosal immunity

The blood and lymphatic systems

Organized lymphoid tissue

Lymphocyte homing

Lymph nodes

Spleen

Bone marrow is a major site of antibody synthesis

The liver contains a variety of immune system cells

Immunologically privileged sites

The handling of antigen

SUMMARY

FURTHER READING

Chapter 7: Lymphocyte activation

Just to recap …

Introduction

Clustering of membrane receptors frequently leads to their activation

T‐lymphocytes and antigen‐presenting cells interact through several pairs of accessory molecules

The activation of T‐cells requires two signals

Triggering the T‐cell receptor complex

Protein tyrosine phosphorylation is an early event in T‐cell signaling

Downstream events following TCR signaling

CD28 co‐stimulation amplifies TCR signals and blocks apoptosis

Activated T‐cells exhibit distinct gene expression signatures

Epigenetic control of T‐cell activation

Activated T‐cells undergo an essential metabolic shift

Metabolic control of T‐cell differentiation

Damping T‐cell enthusiasm

Dynamic interactions at the immunological synapse

B‐cells respond to three different types of antigen

The nature of B‐cell activation

Dynamic interactions at the BCR synapse

SUMMARY

FURTHER READING

Chapter 8: The production of effectors

Just to recap …

Introduction

Effector mechanisms of innate and adaptive immunity

Cytokines influence the generation and function of effectors within the adaptive immune system

Cytokines act as intercellular messengers

Chemokines also play important roles in orchestrating immune responses

Cytokines and chemokines act through distinct classes of cell surface receptors

Cytokine receptor signal transduction cascades

Cytokine activities are fine‐tuned through a variety of mechanisms

Activated T‐cells proliferate in response to cytokines

Different T‐cell subsets can make different cytokine patterns

Cells of the innate immune system shape the Th1/Th2/Th17/Tfh response

Policing the adaptive immune system

CD8 T‐cell effectors in cell‐mediated immunity

Proliferation and maturation of B‐cell responses are mediated by cytokines

What is going on in the germinal center?

The synthesis of antibody

Immunoglobulin class switching occurs in individual B‐cells

Factors affecting antibody affinity in the immune response

Memory cells

SUMMARY

FURTHER READING

Chapter 9: The regulation of the immune response

Just to recap …

Introduction

Immunogenetics

Antigenic competition

Complement and antibody help regulate immune responses

Activation‐induced cell death

CD28 superfamily members that negatively regulate the immune response

Immunoregulation by T‐cells

Regulatory immunoneuroendocrine networks

Dietary effects on immunity

The influence of gender and aging

SUMMARY

FURTHER READING

Chapter 10: Development and evolution of the immune response

Just to recap …

Introduction

ONTOGENY

CD antigens

Hematopoietic stem cells

The thymus is required for T‐cell development

T‐cell ontogeny

T‐cell tolerance

B‐cells differentiate in the fetal liver and then in bone marrow

B‐1 and B‐2 cells represent two distinct populations

Development of B‐cell specificity

B‐cell tolerance

Lymphocytes go through antigen‐independent and antigen‐dependent stages of differentiation

Natural killer (NK) cell ontogeny

Neonatal immunity

PHYLOGENY

The evolution of the immune response

The evolution of distinct B‐ and T‐cell lineages was accompanied by the development of separate sites for differentiation

Cellular recognition molecules exploit the immunoglobulin gene superfamily

SUMMARY

FURTHER READING

Part 2: Applied immunology

CHAPTER 11: Adversarial strategies during infection

Just to recap …

Introduction

Infection remains a major healthcare problem

Inflammation revisited

Bacterial survival strategies

The host counterattack against bacteria

The habitat of intracellular bacteria allows avoidance of many of the host defenses

Virus survival strategies

The host counterattack against viruses

Immunity to fungi

Immunity to parasitic infections

Prions

SUMMARY

FURTHER READING

CHAPTER 12: Vaccines

Just to recap …

Introduction

Passively acquired immunity

Principles of vaccination

Killed organisms as vaccines

Live attenuated organisms have many advantages as vaccines

Subunit vaccines

Newer approaches to vaccine development

Current vaccines

Vaccines under development

Vaccines against parasitic diseases have proved particularly difficult to develop: malaria

Vaccines for protection against bioterrorism

Immunization against cancer

Other applications for vaccines

Adjuvants

SUMMARY

FURTHER READING

CHAPTER 13: Immunodeficiency

Just to recap …

Introduction

Deficiencies of pattern recognition receptor signaling

Phagocytic cell defects (Table 13.1)

Primary immunodeficiency affecting other cells of the innate response

Complement system deficiencies (Table 13.2)

Cytokine and cytokine receptor deficiencies

Primary B‐cell deficiency (Table 13.3)

Primary T‐cell deficiency (Table 13.4)

Severe combined immunodeficiency (SCID)

Diagnosis of primary immunodeficiencies

Treatment of primary immunodeficiencies

Secondary immunodeficiency

Acquired immunodeficiency syndrome (AIDS)

SUMMARY

FURTHER READING

CHAPTER 14: Allergy and other hypersensitivities

Just to recap …

Introduction

Type I hypersensitivity – IgE‐mediated mast cell degranulation

Type II hypersensitivity – antibody‐dependent cytotoxicity

Type III hypersensitivity – immune complex‐mediated

Type IV hypersensitivity – cell‐mediated (delayed‐type)

An addition to the original classification – stimulatory hypersensitivity (“type V”)

Innate hypersensitivity reactions

SUMMARY

FURTHER READING

Chapter 15: Transplantation

Just to recap …

Introduction

Types of graft

Types of rejection

Genetic control of transplantation antigens

Some other consequences of MHC incompatibility

Mechanisms of graft rejection

Matching the donor and recipient

Immunosuppression

Is xenografting a practical proposition?

Stem cell therapy

Clinical experience in grafting

The fetus as an allograft

SUMMARY

FURTHER READING

CHAPTER 16: Tumor immunology

Just to recap …

Introduction

Cellular transformation and cancer

Cell‐intrinsic mechanisms of tumor suppression

Cell‐extrinsic mechanisms of tumor suppression

The cancer problem from an immune perspective

Inflammation can enhance tumor initiation, promotion, and progression

Tumor antigens

Classes of tumor antigens

Approaches to cancer immunotherapy

Passive immunotherapy with monoclonal antibodies

Unmasking of latent T‐cell responses

Antigen‐independent cytokine therapy

Vaccination approaches

Ex vivo expanded lymphocytes or dendritic cells

SUMMARY

FURTHER READING

CHAPTER 17: Autoimmune diseases

Just to recap …

Introduction

The spectrum of autoimmune disease

What causes autoimmune disease?

Mechanisms in autoimmune disease

Pathogenic effects of autoantibody

Pathogenic effects of complexes with autoantigens

T‐cell‐mediated hypersensitivity as a pathogenic factor in autoimmune disease

Some other diseases with autoimmune activity

Measurement of autoantibodies

Therapeutic options

SUMMARY

FURTHER READING

Glossary

Index

End User License Agreement

List of Tables

Chapter 01

Table 1.1 Ligands for Toll‐like receptors (TLRs).

Table 1.2 Acute phase proteins.

Chapter 03

Table 3.1 The human immunoglobulins.

Table 3.2 Human leukocyte Fc receptors.

Chapter 04

Table 4.1 Comparison between αβ and γδ T‐cells.

Table 4.2 Calculations of human

V

gene diversity. It is known that the precise number of gene segments varies from one individual to another, perhaps 40 or so in the case of the

V

H

genes for example, so that these calculations represent “typical” numbers. The number of specificities generated by straightforward random combination of germline segments is calculated. These will be increased by the further mechanisms listed: *Minimal assumption of approximately 10 variants for chains lacking

D

segments and 100 for chains with

D

segments. The calculation for the TCR β chain requires further explanation. The first of the two

D

segments,

Dβ1

, can combine with 50 

V

genes and with all 13

Jβ1

and

Jβ2

genes.

Dβ2

behaves similarly but can only combine with the 7 downstream

Jβ2

genes.

Table 4.3 Natural killer (NK) activating and inhibitory receptors in humans. This table is not exhaustive as some receptors have not been included. Note that the killer immunoglobulin‐like receptor (KIR) family is not utilized in the mouse, instead numerous Ly49 family receptors are present.

Table M4.2.1 Identification of H‐2 (antigen II).

Table M4.2.2 Relationship of antigen II to tumor rejection.

Table 4.4 The haplotypes of the

H‐2

complex of some commonly used mouse strains and recombinants derived from them. A/J was derived by interbreeding (

k

 × 

d

) F1 mice, recombination occurring between E (class II) and S (class III) regions*.

Chapter 05

Table 5.1 Natural MHC class I peptide ligands contain two allele‐specific anchor residues.

Chapter 06

Table 6.1 The integrin superfamily. In general, the integrins are concerned with intercellular adhesion and adhesion to extracellular matrix components. Various members are involved in embryogenesis, cell growth, differentiation, motility, programmed cell death, and tissue maintenance. Many of them are also involved in cell signal transduction. They are αβ heterodimers selected from 18 α chains and 8 β chains, which pair to form 24 different combinations. A structure called the I (inserted) domain is present in many integrin subunits and contains the metal ion‐dependent adhesion site (MIDAS) that, in the presence of Mg

2+

, is involved in binding the Arg–Gly–Asp (RGD) motif on many of the ligands essential for cell adhesion. The α

v

β

3

‐ and α

v

β

5

‐integrin ligand MFG‐E8 is expressed by a variety of cell types, including IDC and macrophages in secondary lymphoid tissues where it plays a role in phagocytosis of apoptotic B‐cells. LAP binds to, and thereby inhibits, the activity of TGFβ.

Chapter 08

Table 8.1 Cytokines: their origin and function.

Table 8.2 Chemokines and their receptors.

Chapter 09

Table 9.1 H‐2 haplotype linked to high, low and intermediate immune responses to synthetic peptides.

Table 9.2 Mapping of the MHC gene for (H,G)‐A–L responses by analysis of different recombinant strains.

Chapter 10

Table 10.1 Some of the major clusters of differentiation (CD) markers on human cells.

Table 10.2 Positive and negative selection in SCID transgenic mice bearing the αβ receptors of an H‐2D

b

T‐cell clone cytotoxic for the male antigen H‐Y (i.e., the clone is of

H‐2

b

haplotype and is female anti‐male). (a) The only T‐cells are those bearing the already rearranged transgenic TCR, as SCID mice cannot rearrange their own

V

genes. The clones are only expanded beyond the CD4

+

CD8

+

stage when positively selected by contact with the MHC haplotype (

H‐2

b

) recognized by the original clone from which the transgene was derived. Also, as the TCR recognized class I, only CD8

+

cells were selected. (b) When the anti‐male transgenic clone is expressed on intrathymic T‐cells in a male environment, the strong engagement of the TCR with male antigen‐bearing cells eliminates them.

Table 10.3 Induction of tolerance in bone marrow stem cells by incubation with deoxyguanosine (dGuo)‐sensitive macrophages or dendritic cells in the thymus. Clearly, the bone marrow cells induce tolerance to their own haplotype. Thus the thymic tolerance‐inducing cells can be replaced by progenitors in the bone marrow inoculum (Jenkinson E.J.

et al.

(1985)

Transplantation

39

, 331) or by adult dendritic cells from spleen, showing that it is the stage of differentiation of the immature T‐cell rather than any special nature of the thymic antigen‐presenting cell which leads to tolerance (Matzinger P. and Guerder S. (1989)

Nature

338

, 74).

Chapter 11

Table 11.1 Examples of mechanisms used by bacteria to avoid the host immune response.

Chapter 12

Table 12.1 Examples of passive antibody therapy against infection and toxins.

Table 12.2 Factors required for a successful vaccine.

Table 12.3 Current licensed vaccines for use in the United States and/or Europe.

Table 12.4 Centers for Disease Control and Prevention (CDC) – recommended immunizations schedule for persons aged 0–18 years in the United States, 2014. The recommendations are to be read with many footnotes, which are presented on the CDC website (www.cdc.gov/vaccines/schedules/hcp/imz/child‐adolescent.html).

Table 12.5 Classes of clinically used and tested adjuvants.

Chapter 13

Table 13.1 Some deficiencies of phagocytic cells.

Table 13.2 Some deficiencies of complement pathways.

Table 13.3 Some deficiencies affecting B‐lymphocytes.

Table 13.4 Some deficiencies affecting T‐lymphocytes.

Chapter 14

Table 14.1 Comparison of the two main types of mast cell.

Table 14.2 Some examples of allergens.

Table 14.3 ABO blood groups and serum antibodies.

Table 14.4 Comparison of the main types of hypersensitivity involving acquired responses.

Chapter 15

Table 15.1 The major transplanted organs and tissues.

Table 15.2 The various types of graft rejection.

Chapter 16

Table 16.1 Potential tumor antigens for immunotherapy.

Table 16.2 Selected mAbs approved or in late‐stage clinical trials for cancer therapy.

Chapter 17

Table 17.1 Classification criteria for autoimmune diseases. Not all these criteria will necessarily need to be fulfilled, as clearly it will often not be possible to demonstrate transfer of disease with autoreactive serum and/or autoreactive lymphocytes in humans.

Table 17.2 The major autoimmune diseases. There are a large number of autoimmune diseases. Listed are the most prevalant diseases for which there is strong evidence that the primary cause of the pathology is an autoimmune attack. Other diseases which may also be autoimmune, but for which the pathological contribution of autoimmunity requires further investigation, are discussed later.

Table 17.3 Spontaneous and induced animal models of autoimmune disease. A few examples from among the large number of such models. There are also a very large number of genetically engineered animal models.

Table 17.4 Association of HLA with autoimmune disease. Relative risk refers to the chance of developing the disease compared to an individual who lacks the allele, and are for typical studies in White populations. These will often be different in other ethnic groups.

Table 17.5 Molecular mimicry. Some examples of homologies between microbes and body components as potential cross‐reacting T‐cell epitopes.

List of Illustrations

Chapter 01

Figure 1.1 The formidable range of infectious agents that confront the immune system. Although not normally classified as such because of their lack of a cell wall, the mycoplasmas are included under bacteria for convenience. Fungi adopt many forms and approximate values for some of the smallest forms are given. Square brackets with right arrowheads indicate where a range of sizes is observed for the organism(s); square brackets with left arrowheads indicate list of organisms with a definite size.

Figure 1.2 Pattern recognition receptors (PRRs) detect pathogen‐associated molecular patterns (PAMPs) and initiate immune responses. PRRs can be either soluble or cell‐associated and can instigate a range of responses upon encountering their appropriate ligands.

Figure 1.3 Necrotic cells release danger‐associated molecular patterns (DAMPs), whereas apoptotic cells typically do not. Stimuli that induce necrosis frequently cause severe cellular damage, which leads to rapid cell rupture with consequent release of intracellular DAMPs. DAMPs can then engage cells of the immune system and can promote inflammation. On the other hand, because stimuli that initiate apoptosis are typically physiological and relatively mild, apoptotic cells do not rupture and their removal is coordinated by macrophages and other cells of the innate immune system, before release of DAMPs can occur. For this reason, apoptosis is not typically associated with activation of the immune system.

Figure 1.4 Cytokines and chemokines can have pleiotrophic effects. Stimulation of cells of the innate immune system frequently leads to the production of inflammatory cytokines and chemokines that trigger responses from other cell types, as depicted. Note that the effects of chemokines and cytokines shown are not exhaustive.

Figure 1.5 The vertebrate immune system comprises three levels of defense. The physical barriers of the skin and mucosal surfaces comprise the first level of defense. Infectious agents that successfully penetrate the physical barriers are then engaged by the cells and soluble factors of the innate immune system. The innate immune system is also responsible for triggering activation of the adaptive immune system, as we will discuss later in this chapter. The cells and products of the adaptive immune system reinforce the defense mounted by the innate immune system.

Figure 1.6 The first lines of defense against infection: protection at the external body surfaces.

Figure M1.1.1 Caricature of Professor Metchnikoff.

Figure M1.1.2 Reproductions of some of the illustrations in Metchnikoff’s book,

Comparative Pathology of Inflammation

(1893). (a) Four leukocytes from the frog, enclosing anthrax bacilli; some are alive and unstained, others, which have been killed, have taken up the vesuvine dye and have been colored. (b) Drawing of an anthrax bacillus, stained by vesuvine, in a leukocyte of the frog; the two figures represent two phases of movement of the same frog leukocyte which contains stained anthrax bacilli within its phagocytic vacuole. (c,d) A foreign body (colored) in a starfish larva surrounded by phagocytes that have fused to form a multinucleate plasmodium shown at higher power in (d). (e) This gives a feel for the dynamic attraction of the mobile mesenchymal phagocytes to a foreign intruder within a starfish larva.

Figure 1.7 The cells of the immune system originate in the bone marrow from pluripotent hematopoietic stem cells. Pluripotent hematopoietic stem cells give rise to a common lymphoid progenitor, which gives rise to all of the major lymphoid cell types (T‐cells, B‐cells, and NK cells) or a common myeloid progenitor, which gives rise to all of the major myeloid cell types (neutrophils, eosinophils, basophils, dendritic cells [DCs], mast cells, and monocytes/macrophages) as well as the erythrocytes and megakaryocytes (which generate platelets). See further details of individual cell types in Figure 1.8, Figure 1.9, and Figure 1.11.

Figure 1.8 Macrophages, mast cells, and dendritic cells act as the sentinels of the innate immune system. Macrophages and mast cells play an important role in the initiation of innate immune responses through the liberation of inflammatory mediators and recruitment of additional cells (particularly neutrophils) to the site of infection. Macrophages also serve an important role as phagocytes in engulfing and killing microbes. Dendritic cells act as an important conduit between the innate and adaptive immune systems. Some of the major functions of these cells are shown (see main text for further details). NET, neutrophil extracellular trap.

Figure 1.9 Granulocytes form an important part of the innate immune system. Schematic representations of neutrophil, eosinophil, and basophil granulocytes are depicted along with their major functions. NET, neutrophil extracellular trap.

Figure 1.10 Neutrophils migrate in large numbers to sites of infection. Timelapse microscopy of neutrophils (green) migrating to a wound site.

Figure 1.11 T‐ and B‐lymphocytes comprise the major lymphocytes of the adaptive immune system. Schematic representations of T‐ and B‐lymphocytes are depicted along with their major functions.

Figure 1.12 Activated macrophages secrete a diverse array of cytokines and chemokines. Electron micrograph of an activated macrophage with several bacteria (

Mycobacterium bovi

s) attached to its cell surface. Only a small fraction of the numerous soluble mediators that are liberated from PAMP‐activated macrophages are shown.

Figure 1.13 The acute inflammatory reaction. Bacterial infection initiates a series of responses through activation of the alternative complement pathway, producing C3a and C5a, as well as through stimulation of tissue‐resident macrophages that detect bacterial‐derived PAMPs. The C3b component of complement binds to bacteria, opsonizing the latter for more effective phagocytosis by macrophages and neutrophils. Complement activation can also lead to direct lysis of bacteria through assembly of membrane attack complexes. Activation of macrophages by PAMPs and complement components induces secretion of mediators (i.e., cytokines and chemokines) of the acute inflammatory response that increase vascular permeability and induce neutrophils to migrate from the blood into the tissue. C3a and C5a trigger mast cell activation and secretion of mediators that provoke capillary dilatation and exudation of plasma proteins. Attracted by C3a and C5a, as well as other factors, blood neutrophils stick to the adhesion molecules on the endothelial cell and use this to provide traction as they force their way between the cells, through the basement membrane (with the help of secreted elastase) and up the chemotactic gradient.

Figure 1.14 Mast cell triggering leading to release of mediators by two major pathways. (i) Release of preformed mediators present in the granules; and (ii) the metabolism of arachidonic acid produced through activation of a phospholipase. Intracellular Ca

2+

and cyclic AMP are central to the initiation of these events but details are still unclear. Mast cell triggering may occur through C3a, C5a, and even by some microorganisms that can act directly on cell surface receptors. ECF, eosinophil chemotactic factor; GM‐CSF, granulocyte–macrophage colony‐stimulating factor; NCF, neutrophil chemotactic factor; TNF, tumor necrosis factor. Chemotaxis refers to directed migration of granulocytes up the pathway concentration gradient of the mediator.

Figure 1.15 Neutrophil extravasation. Neutrophils are induced to migrate from blood vessels adjoining sites of infection through changes to the endothelial cells lining the blood vessels that are induced by the products of activated macrophages and mast cells, such as IL‐1, TNF, IL‐8, and histamine. Neutrophils initially loosely attach and roll along the endothelium mediated via sialyl‐Lewis

X

‐mediated interactions with P

‐

and E‐selectins that are upregulated on the activated endothelium. Under the influence of chemokines, such as IL‐8, neutrophils become activated, leading to activation of cell surface integrins (LFA‐1, CR3) that provide firmer attachment to their cognate receptors (ICAMs) on the endothelium. The latter interactions enable neutrophils to arrest on the endothelial wall and to extravasate through the basement membrane of the endothelium and migrate into the tissue towards the source of chemotactic factors (IL‐8, C3a, C5a).

Figure 1.16 A family of Toll‐like receptors (TLRs) act as sensors for pathogen‐associated molecular patterns (PAMPs). TLRs reside within plasma membrane or endosomal membrane compartments, as shown. Upon engagement of the TLR ectodomain with an appropriate PAMP (some examples are shown), signals are propagated into the cell that activate the nuclear factor κB (NFκB) and/or interferon‐regulated factor (IRF) transcription factors, as shown. NFκB and IRF transcription factors then direct the expression of numerous antimicrobial gene products, such as cytokines and chemokines, as well as proteins that are involved in altering the activation state of the cell.

Figure 1.17 Toll‐like receptor (TLR) structure. TLR3 ectodomain structure. (a) Ribbon diagram. Leucine‐rich repeats (LRRs) are colored from blue to red, beginning at LRR1 and proceeding to LRR23, as indicated. NT, N‐terminus; CT, C‐terminus. (b) Electrostatic potential surface shows positive (blue) and negative (red) charges at neutral pH. The

N

‐linked glycans are shown as green ball‐and‐stick.

Figure 1.18 Toll‐like receptors promote NFκB‐dependent transcription through activation of the IkB kinase (IKK) complex. Upon engagement of a TLR dimer (or heterodimer) with its appropriate ligand, a series of adaptor proteins (as shown) are recruited to the TLR receptor Toll and IL‐1 receptor‐like (TIR) domain. Collectively, these proteins activate the IKK complex, which in turn phosphorylates the inhibitor of NFκB (IκB), a protein that binds and tethers NFκB in the cytosol. IκB phosphorylation targets the latter for degradation, liberating NFκB which can then translocate into the nucleus and initiate transcription of multiple genes.

Figure 1.19 Domain organization of the NOD‐like receptor (NLR) family. The four subfamilies of NLRs are depicted, separated primarily on the basis of their usage of different N‐terminal domains (AD, CARD, Pyrin, BIR) that confers unique functional roles on each NLR. All of the NLRs contain a central NACHT domain, which is a motif that permits oligomerization of individual NLRs into supercomplexes. Assembly and activation of NLR complexes is induced through ligand binding to the C‐terminal LRRs that serve as a sensor domain for each of the NLRs. AD, acidic transactivation domain; CARD, caspase recruitment domain; BIR, baculoviral IAP repeat; FIIND, function to find domain; LRR, leucine‐rich repeat.

Figure 1.20 Activation of the NLRP3 inflammasome leads to caspase‐1 activation and IL‐1β processing and release. One example of an NLR complex is illustrated by the NLRP3 inflammasome that is assembled in response to two different signals. Signal 1 is represented by LPS, a PAMP that binds to TLR4 thereby inducing IL‐1β transcriptional upregulation in an NFκB‐dependent manner (not shown). However, a second signal is required for IL‐1β processing and release and this is provided by the cytotoxic actions of bacterial toxins that permit K

+

efflux, through damaging the plasma membrane of an LPS‐primed cell. It is the latter event (i.e., K

+

efflux) that triggers assembly of the NLRP3 inflammasome, leading to caspase‐1 activation, IL‐1β processing, and release of the latter cytokine through death of the injured cell. Thus, the NLRP3 inflammasome acts as a sensor for cell injury‐associated K

+

efflux.

Figure 1.21 Domain organization of the RIG‐I‐like receptors and their common adaptor MAVS. Members of the RIG‐I‐like helicase family that act as cytoplasmic sensors for viral RNA are shown, along with their common adaptor protein MAVS. See also Figure 1.22.

Figure 1.22 RIG‐I is activated by double‐stranded RNA and initiates transcription of antiviral genes via the IRF and NFκB pathways. RIG‐I (retinoic acid inducible gene 1) acts as a cytoplasmic sensor for viral RNA and detects 5

′

‐triphosphate uncapped dsRNA or ssRNA molecules. Upon binding of viral RNA, RIG‐I, which is normally in an autoinhibited conformation, can then bind to MAVS (mitochondrial antiviral signaling protein) via CARD–CARD interactions with the latter to promote activation of IRF and NFκB‐dependent gene transcription, as shown. CARD, caspase recruitment domain.

Figure 1.23 STING acts as a cytoplasmic sensor for DNA and cyclic nucleotides. STING (stimulator of interferon genes) is an endoplasmic reticulum‐associated protein that can sense cytoplasmic DNA either directly, or through DNA binding to cGAS (cyclic GMP–AMP synthase) an enzyme that generates unusual cyclic dinucleotides (cGAMP) that can act as a ligand for STING to activate transcription of IRF and NFκB‐dependent gene transcription. STING may also be able to sense cyclic dinucleotides that are produced by intracellular bacteria.

Figure 1.24 The mononuclear phagocyte system. Promonocyte precursors in the bone marrow develop into circulating blood monocytes that eventually become distributed throughout the body as mature macrophages (Mφ) as shown. The other major phagocytic cell, the polymorphonuclear neutrophil, is largely confined to the bloodstream except when recruited into sites of acute inflammation.

Figure 1.25 Ultrastructure of neutrophil. The multilobed nucleus and two main types of cytoplasmic granules are well displayed. BPI, bactericidal permeability increasing protein.

Figure 1.26 Phagocytosis and killing of a bacterium. Stage c/d, respiratory burst and activation of NADPH oxidase; stage e, damage by reactive oxygen intermediates; stage f/g, damage by peroxidase, cationic proteins, antibiotic peptide defensins, lysozyme, and lactoferrin.

Figure 1.27 Adherence and phagocytosis. (a) Phagocytosis of

Candida albicans

by a polymorphonuclear leukocyte (neutrophil). Adherence to the yeast wall surface mannan initiates enclosure of the fungal particle within arms of cytoplasm. Lysosomal granules are abundant but mitochondria are rare (×15 000). (b) Phagocytosis of

C. albicans

by a monocyte showing near completion of phagosome formation (arrowed) around one organism and complete ingestion of two others (×5000).

Figure 1.28 Phagolysosome formation. (a) Neutrophil 30 minutes after ingestion of

C. albicans

. The cytoplasm is already partly degranulated and two lysosomal granules (arrowed) are fusing with the phagocytic vacuole. Two lobes of the nucleus are evident (×5000). (b) Higher magnification of (a) showing fusing granules discharging their contents into the phagocytic vacuole (arrowed) (×33 000).

Figure 1.29 Microbicidal mechanisms of phagocytic cells. (a) Production of reactive oxygen intermediates. Electrons from NADPH are transferred by the flavocytochrome oxidase enzyme to molecular oxygen to form the microbicidal molecular species shown in the orange boxes. (For the more studious – the phagocytosis‐triggering agent binds to a classic G‐protein‐linked seven transmembrane domain receptor that activates an intracellular guanosine triphosphate (GTP)‐binding protein. This in turn activates an array of enzymes: phosphoinositol‐3 kinase concerned in the cytoskeletal reorganization underlying chemotactic responses, phospholipase‐Cγ2 mediating events leading to lysosome degranulation and phosphorylation of p47

phox

through activation of protein kinase C, and the MEK and MAP kinase systems (see Figure 7.10) that oversee the assembly of the NADPH oxidase. This is composed of the membrane cytochrome

b

558

, consisting of a p21 heme protein linked to gp91 with binding sites for NADPH and FAD on its intracellular aspect, to which phosphorylated p47 and p67 translocate from the cytosol on activation of the oxidase.) (b) Generation of nitric oxide. The enzyme, which structurally resembles the NADPH oxidase, can be inhibited by the arginine analog

N

‐monomethyl‐

L

‐arginine (

L

‐NMMA). The combination of NO· with superoxide anion yields the highly toxic peroxynitrite radical ·ONOO that cleaves on protonation to form reactive ·OH and NO

2

molecules. NO· can form mononuclear iron dithioldinitroso complexes leading to iron depletion and inhibition of several enzymes. (c) The basis of oxygen‐independent antimicrobial systems.

Figure 1.30 Neutrophil activation can lead to the formation of neutrophil extracellular traps (NETs). (a) A

Klebsiella

bacterium (purple) caught in a neutrophil NET (green). (b) Neutrophil NET formation occurs within 1–2 hours after neutrophil activation and involves the liberation of neutrophil DNA, histones, and granule enzymes into the extracellular space where they can ensnare bacteria, yeast, and other extracellular pathogens and kill them

in situ

. (c) Multiple bacteria (red) ensnared on a neutrophil NET.

Figure 1.31 Structural basis for the cleavage of C3 by C3 convertase and its covalent binding to ·OH or ·NH

2

groups at the cell surface through exposure of the internal thiolester bonds. Further cleavage leaves the progressively smaller fragments, C3dg and C3d, attached to the membrane.

Figure 1.32 Microbial activation of the alternative complement pathway by stabilization of the C3 convertase (

) and its control by factors H and I. When bound to the surface of a host cell or in the fluid phase, the C3b in the convertase is said to be “unprotected,” in that its affinity for factor H is much greater than for factor B and is therefore susceptible to breakdown by factors H and I. On a microbial surface, C3b binds factor B more strongly than factor H and is therefore “protected” from or “stabilized” against cleavage – even more so when subsequently bound by properdin. Although in phylogenetic terms this is the oldest complement pathway, it was discovered after a separate pathway to be discussed in the next chapter, and so has the confusing designation “alternative.” Green wiggly arrow represents an activation process. The horizontal bar above a component designates its activation.

Figure 1.33 Post‐C3 pathway generating C5a and the C5b–9 membrane attack complex (MAC). (a) Cartoon of molecular assembly. The conformational change in C9 protein structure that converts it from a hydrophilic to an amphipathic molecule (bearing both hydrophobic and hydrophilic regions) can be interrupted by an antibody raised against linear peptides derived from C9; as the antibody does not react with the soluble or membrane‐bound forms of the molecule, it must be detecting an intermediate structure transiently revealed in a deep‐seated structural rearrangement. (b) Electron micrograph of a membrane C5b–9 complex incorporated into liposomal membranes clearly showing the annular structure. The cylindrical complex is seen from the side inserted into the membrane of the liposome on the left, and end‐on in that on the right. Although in itself a rather splendid structure, formation of the annular C9 cylinder is probably not essential for cytotoxic perturbation of the target cell membrane, as this can be achieved by insertion of amphipathic C9 molecules in numbers too few to form a clearly defined MAC.

Figure 1.34 The mast cell. Transmission electron micrograph of a resting mouse peritoneal mast cell illustrating the copious membrane‐enclosed granules that are filled with inflammatory mediators. Release of the latter mediators may be triggered by direct injury, complement products (C3a, C5a), and through direct stimulation with PAMPs.

Figure 1.35 Structural features of surfacant proteins A and D. Surfactant proteins are composed of collagen‐like and carbohydrate recognition domains (CRD) that are arranged into trimers (middle) and further arranged into higher order multimers of trimers (bottom). Surfactants belong to the collectin family and can recognize nonself carbohydrate moieties on microbes, leading to opsonization followed by phagocytosis.

Figure 1.36 Higher order features of pentraxins. Pentraxins, such as C‐reactive protein (CRP), serum amyloid P (SAP) and pentraxin 3, as depicted, are all composed of five identical subunits with a cyclic structure. Pentraxins act as soluble PRRs and can opsinize bacteria as well as promote complement activation.

Figure 1.37 Structural features of mannose‐binding lectin. Mannose‐binding lectin (MBL) is a multiple of trimeric complexes, each unit of which contains a collagen‐like and lectin‐binding domain (or carbohydrate recognition domain, CRD). MBL can react with a wide variety of bacterial carbohydrates, such as mannose, leading to opsonization of bacteria for uptake through phagocytosis, or can activate the lectin pathway to complement activation (which will be discussed in detail in Chapter 2) through the actions of two associated serine proteases (MASP‐1 and MASP‐2).

Figure 1.38 Structural features of ficolins. Ficolins are composed of collagen‐like and fibrinogen‐like domains (top), that are further arranged into trimers (middle), and then multimerize into higher order structures (bottom). Ficolins can bind to carbohydrate‐based PAMPs to activate the lectin pathway to complement activation, or can opsonize bacteria for uptake through phagocytosis.

Figure 1.39 Cytotoxic lymphocyte killing. In this time‐lapse series, an NK cell (red arrows) is observed to come into close contact with a target cell (green arrows), which is rapidly followed by rounding up and vigorous membrane blebbing within the target cell as it undergoes apoptosis. The interval between each frame is 80 minutes.

Figure 1.40 Natural killer (NK) cells can kill target cells by two major mechanisms: the death receptor and granule‐dependent pathways. In both cases, the target cell dies as a result of the activation of a battery of cytotoxic proteases within the target cell, called caspases. See Figure 1.41 for further details of the molecular mechanisms of killing in either case.

Figure 1.41 Signal transduction events involved in natural killer (NK) cell‐mediated apoptosis. NK cells can kill target cells by two major pathways (I) or (II) as shown. In the cytotoxic granule‐dependent pathway (I), binding of the NK receptors to the surface of the virally infected cell triggers the extracellular release of perforin (a pore‐forming protein) and granzymes (which are a diverse collection of proteases) from the NK cell cytotoxic granules; perforin polymerizes within the target cell membrane to form transmembrane channels that permit entry of granzymes into the target cell. Granzymes induce apoptotic cell death through activation of the caspase protease cascade, either by directly processing and activating caspases, or through release of cytochrome

c

from mitochondria that activates the “apoptosome” pathway to caspase activation. In the second pathway (II) to cell death (called the death receptor pathway), membrane‐bound Fas ligand (FasL) on the NK cell engages and trimerizes surface Fas receptors on the target cell. Engagement of Fas receptors recruits the adaptor protein FADD, followed by caspase‐8, which then becomes activated at the receptor. Caspase‐8 can then promote further caspase activation through directly processing other caspases, or via the mitochondrial apoptosome pathway similar to granzymes. In both pathways, the final common pathway to apoptosis occurs as a result of the activation of several “executioner caspases” that coordinate cell death through restricted proteolysis of hundreds of cellular proteins.

Figure 1.42 Type I interferons, or direct PAMP‐mediated stimulation, activates NK cells leading to IFNγ secretion. Activated macrophages can produce type I interferons, as shown, leading to 100‐fold enhancement of NK killing activity. NK cells can also be activated through direct stimulation with PAMPs. In turn, activated NK cells are an important source of IFNγ, which greatly enhances killing of intracellular microbes by macrophages and also leads to production of IL‐12 by the latter. As we shall see in Chapter 8, IL‐12 is an important T‐cell polarizing cytokine. Production of IFNγ by NK cells also enhances antigen presentation by dendritic cells.

Figure 1.43 Dendritic cell morphology. (a) Phase‐contrast image of an unstained dendritic cell with characteristic “dendron tree. (b) Confocal fluorescence microscopy image of a dendritic cell that has phagocytosed green fluorescent microparticles, followed by staining the plasma membrane with Alexa‐594‐conjugated wheat germ agglutinin (red) to decorate surface carbohydrate.

Figure 1.44 Dendritic cell maturation is induced by PAMPs and other signs of infection. (a) Immature dendritic cells (DCs) undergo maturation and become equipped to present antigen and provide co‐stimulatory signals upon activation by a pathogen‐associated molecular patterns (PAMPs) (or danger‐associated molecular pattern (DAMP)), as this leads to a dramatic increase in the expression of surface MHC and B7 molecules on the DC. The expression of B7 family proteins is controlled by NFkB, which is activated downstream of many PRRs. Whereas immature DCs are relatively nonmotile, mature DCs are highly motile and migrate to secondary lymphoid tissues to present antigen to T‐cells. (b) Mouse epidermal Langerhans cells (i.e., DCs of the skin) were stained for langerin (green) and MHC class II (red) either before (left) or after maturation (right). Note that before DC maturation MHC class II (red) is present intracellularly, whereas after maturation it is readily detected on the cell surface.

Figure 1.45 Dendritic cells (DCs) present antigen to T‐cells of the adaptive immune system. MHC molecules on DCs function as serving platforms for dismembered proteins (i.e., peptides). T‐cells can only “see” antigen when presented within the cleft of an MHC molecule; this represents signal 1. In addition to presenting antigen to T‐cells in the correct format, DCs also give permission for T‐cells to undergo clonal expansion (i.e., proliferation to increase their numbers) by providing co‐stimulatory signals in the form of the membrane ligands, B7–1 and B7–2 (also called CD80/CD86), that engage with CD28 on the surface of the T‐cell; this represents signal 2.

Chapter 02

Figure 2.1 Antibody opsonizes microbes for phagocytosis both directly via Fc receptors and indirectly via complement activation. The Fab (fragment antigen‐binding) part of the antibody binds specific antigen on the microbe and varies from one antibody to another. The Fc (fragment crystallizable) part is identical for all antibodies of the same class/subclass and functionally activates complement (IgM and IgG antibodies, via the classical pathway) and phagocytic cells (IgG antibody, via binding to Fc receptors [FcR] on the surface of the phagocyte). The coating of microbes with substances that are recognized by phagocytic cells is referred to as opsonization and both IgG and complement © components such as C3b, and the products of C3b breakdown iC3b, C3dg, and C3d (all of which are recognized by complement receptors [CR] on the phagocyte) can act as opsonins. In addition, complement activation leads to chemotactic attraction of the phagocytes to the site of the infection and increased vascular permeability in order to facilitate their passage from the blood circulation to the tissues.

Figure 2.2 Activation of the classical complement pathway. The first component, C1, of the classical pathway of complement activation is a complex composed of three subunits: C1q, C1r, and C1s. (a) C1q forms a hexamer arranged in a “bunch of tulips”‐like structure and is associated with the flexible rod‐like Ca

2+

‐dependent complex C1r2–C1s2, which interdigitates with the six arms of C1q. (b) Activation of the complement cascade by the classical pathway requires antibodies to be bound to antigen in order that the globular heads of the C1q hexamer can bind to the Fc part of at least two antibodies. Certain other molecules, such as C‐reactive protein, are also able to coat microbial surfaces and subsequently bind C1q to trigger the classical pathway.

Figure 2.3 Comparison of the classical, lectin, and alternative complement pathways. The classical pathway is activated by antibody, whereas the alternative and lectin pathways are not. The molecules with protease activity are highlighted in light blue. The key central event for all three pathways is the cleavage of C3 by C3 convertase (namely

for the classical and lectin pathways,

for the alternative pathway). Beware confusion with nomenclature: the large C2 fragment that forms the C3 convertase is designated as C2a, but to be consistent with C4b, C3b, and C5b, it would have been more logical to call it C2b. Mannose‐binding lectin (MBL), when combined with microbial surface sugars, associates with the MBL‐associated serine proteases (MASP)‐1 and ‐2, which split C4 and C2.

Figure 2.4 Multiple punctures in the cell wall of

Escherichia coli

bacterium caused by interaction with IgM antibody and complement. Each puncture is caused by a single IgM molecule and shows as a “dark pit” owing to penetration by the “negative stain.” This is somewhat of an illusion as in reality these “pits” are like volcano craters standing proud of the surface, and are each single membrane attack complexes. Comparable results may be obtained in the absence of antibody by using higher concentrations of complement as the cell wall endotoxin can activate the alternative pathway (×400 000).

Figure 2.5 Activities generated by the triggering of the complement cascade. Following the cleavage of C3 by C3 convertase and subsequently of C5 by C5 convertase, various biologically active complement components are generated. Various cells of the immune system possess cell surface receptors for particular complement components, and microbial cell surfaces can become coated with complement. The functions that are generated work together to generate an effective immune response. Thus the release of inflammatory mediators from mast cells (a) occurring in response to complement components C3a and C5a (and to a lesser extent C4a) leads to an increase in vascular permeability. This allows neutrophils (b) to exit the circulation in response to an additional activity of C5a as a neutrophil chemoattractant. Microorganisms (c) opsonized with, for example, C3b and C3d, are effectively phagocytosed by these neutrophils due to the phagocytes expressing complement receptors. Once C5 convertase is deposited on the microbial surface, the terminal components (C5b–C9) of the complement system can assemble to form the membrane attack complex (MAC) with subsequent destruction of microorganisms (d). Because erythrocytes (e) bear complement receptors they are able to bind antigens that are coated in complement, and these are rapidly transported to the spleen and liver for destruction. Complement component C3d acts to facilitate B‐cell (f) activation by providing co‐stimulation via complement receptors on the B‐cell and/or by mediating the retention of immune complexes on follicular dendritic cells, and thereby is involved in the generation of specific antibody against the microbe.

Figure 2.6 Antibody‐mediated activation of phagocytosis. Binding of a bacterium to a phagocyte by multiple antibodies gives strong association forces and triggers phagocytosis by cross‐linking the surface Fc receptors (FcR).

Figure 2.7 The antibody molecule links the pathogen to other components of the immune response. Antibody provides a link between the infectious agent and the complement system (via the classical pathway), phagocytic cells such as neutrophils and macrophages, with killer cells (NK cells, eosinophils, etc.) via a mechanism referred to as antibody‐dependent cellular cytotoxicity (ADCC), and in the case of IgE antibodies to mast cells and basophils.

Figure 2.8 Cells involved in the acquired immune response. (a) Small lymphocyte. Typical resting lymphocyte with a thin rim of cytoplasm. Condensed chromatin gives rise to heavy staining of the nucleus. Giemsa stain. (b) Electron micrograph of a lymphocyte with an indented nucleus containing condensed chromatin, sparse cytoplasm: single mitochondrion shown (×13 000) (c) Immunofluorescence staining of B‐lymphocyte surface immunoglobulin using fluorescein‐conjugated (green) anti‐Ig. (d) Plasma cells. The nucleus is eccentric. The cytoplasm is strongly basophilic owing to high RNA content. The juxtanuclear lightly stained zone corresponds with the Golgi region. May–Grünwald–Giemsa. (e) Electron micrograph of a plasma cell. Prominent rough‐surfaced endoplasmic reticulum associated with the synthesis and secretion of Ig (×10 000). (f) Plasma cells fixed with acetic acid and ethanol and subsequently stained to show intracellular immunoglobulin using a fluorescein‐labeled anti‐IgG (green) and a rhodamine‐conjugated anti‐IgM (red).

Figure 2.9 The different types of lymphocyte are all derived from a common lymphoid progenitor. Hematopoietic stem cells (HSC) can develop down either the myeloid or lymphoid pathways of cellular differentiation, but all lymphocytes are derived via the latter route. Thus the common lymphoid progenitor (CLP) produces both T‐ and B‐lymphocytes. The T‐lymphocytes can possess either a γδ or an αβ T‐cell receptor (TCR). Those with an αβ T‐cell receptor are functionally divided into helpers (Th), regulatory suppressors (Treg), and cytotoxic (Tc) cells. The major division of B‐cells is into the B‐1 and B‐2 populations.

Figure 2.10 Helper T‐cells assist other cells in the immune response. The helper T‐cell population are involved in activating cytotoxic T‐cells, can activate macrophages (particularly via the secretion of the cytokine γ‐interferon) and are obligatory for most B‐cell responses.

Figure 2.11 Antigen activates those lymphocytes with a complementary antigen receptor. This process is referred to as clonal selection and ensures that only the relevant, antigen‐specific, lymphocytes are triggered to produce the appropriate effector cells and memory cells. (a) In the case of the antibody‐producing B‐lymphocytes they use a cell surface version of the antibody, which directly binds native antigen, as the B‐cell receptor (BCR). (b) T‐lymphocytes do not make antibody but also possess a cell surface antigen receptor, the T‐cell receptor (TCR) which recognizes processed protein antigen fragments presented to it by MHC molecules (see Figure 2.14 and Figure 2.15). Following their activation by antigen, lymphocytes undergo repeated cell division (clonal proliferation) and the progeny give rise to an expanded population of antigen‐specific cells. A fraction of the progeny of the original antigen‐reactive lymphocytes become memory cells whereas others differentiate into effector cells. In the case of B‐lymphocytes the effector cells are the antibody‐secreting plasma cells (PC), whereas for T‐lymphocytes the effector cells may be T‐helper cells (Th), cytotoxic T‐cells (Tc) or regulatory T‐cells (Treg).

Figure M2.1.1 Ehrlich’s side‐chain theory of antibody production.

Figure 2.12 Primary and secondary response. The first encounter with an antigen, for example associated with a pathogenic organism, elicits a primary immune response that is rather slow to get going because it takes a while for the naive lymphocytes to expand up to sufficient numbers. The response is not of great magnitude and fades relatively quickly. The response on the second contact with the same antigen is much more rapid and more intense. Memory cells generated during the primary response are both quantitatively and qualitatively superior to the naive lymphocytes, requiring fewer cycles of cell division before they develop into effectors. The generation of memory cells provides the basis for vaccination, where the immune response is primed by a relatively harmless form of the microbial antigen so that the immune system goes straight into making a secondary immune response upon the first encounter with the actual pathogen.

Figure 2.13 Memory for a primary response can be transferred by small lymphocytes. Recipients are treated with a dose of X‐rays that directly kill lymphocytes (highly sensitive to radiation) but only affect other body cells when they divide; the recipient thus permits the function of the donor cells to be followed. The reasons for the design of the experiment are given in the text.

Figure 2.14 Intracellular killing of microorganisms by macrophages. (a) An antigen peptide () derived from the intracellular microbes is complexed with cell surface class II MHC molecules (). (b) The primed T‐helper cell binds to this MHC–peptide complex using its T‐cell receptor (TCR) and is triggered to release the cytokine γ‐interferon (IFN

γ

). This process activates microbicidal mechanisms in the macrophage. (c) The infectious agent meets a timely death.

Figure 2.15 Killing virally infected cells. (a) Destruction of infected cells by the natural killer (NK) cells of the innate response can follow their recognition by the killer activating receptors. (b) In addition to the direct recognition by these receptors, NK cells possess Fc receptors and can therefore recognize any virus‐specific antibodies that are bound to any intact viral antigens present on the surface of infected cells. This is therefore an example of the innate and acquired responses working together to defeat the enemy and, in this case, is referred to as antibody‐dependent cellular cytotoxicity (ADCC). (c) The cytotoxic T‐cells of the acquired response recognize the infected target cell specifically through TCR recognition of virally derived peptides presented by MHC class I molecules.

Figure 2.16 T‐cells link with the innate immune system to combat intracellular infection. Class I () and class II () major histocompatibility molecules are important for T‐cell recognition of antigen. Dendritic cells (DC) utilize MHC class II plus peptide, together with a range of co‐stimulatory molecules, in order to activate T‐helper cells (Th). These then help activate cytotoxic T‐cells (Tc) and further activate the DCs. Interferon from both the Th and Tc cells inhibits viral replication and stimulates natural killer (NK) cells that themselves produce more interferon and, together with Tc, kill virus‐infected cells. The interferon also sets up a state of viral resistance in the surrounding uninfected cells.

Figure 2.17 Production of a protective acute inflammatory reaction by microbes either: (i) through tissue injury (e.g., bacterial toxin) or direct activation of the alternative or lectin complement pathways, or (ii) by antibody‐dependent triggering of the classical complement pathway or mast cell degranulation (a special class of antibody, IgE, does this).

Figure 2.18 Inappropriate immune responses can produce damaging reactions, such as the allergic response to inhaled otherwise innocuous antigens (allergens), the destruction of self tissue by autoimmune attack, and the rejection of tissue transplants.

Figure 2.19 The two pathways linking innate and acquired immunity that provide the basis for humoral and cell‐mediated immunity, respectively.

Chapter 03

Figure M3.1.1 The antibody basic unit (IgG is represented), consisting of two identical heavy and two identical light chains held together by interchain disulfide bonds (a), can be broken down into its constituent polypeptide chains and to proteolytic fragments, the pepsin F(ab′)

2

retaining two binding sites for antigen (c) and the papain Fab with one (b). After pepsin digestion the pFc′ fragment representing the C‐terminal half of the Fc region is formed and is held together by noncovalent bonds. The portion of the heavy chain in the Fab fragment is given the symbol Fd. The N‐terminal residue is on the left for each chain.

Figure 3.1 Simplified overall layout of the antibody molecule. The structure consists of four polypeptide chains, two identical heavy (H) chains and two identical light (L) chains, arranged to span three structural units as shown. The two identical Fab units bind antigen and the third unit (Fc) binds effector molecules to trigger antigen elimination and to mediate functions such as maternal–fetal transport.

Figure 3.2 The four‐chain structure of IgG (human IgG1). (a) Linear representation. Disulfide bridges link the two heavy chains and the light and heavy chains. A regular arrangement of intrachain disulfide bonds is also found. Fragments generated by proteolytic cleavage at the indicated sites are represented. (b) Domain representation. Each heavy chain (shaded dark) is folded into two domains in the Fab arms, forms a region of extended polypeptide chain in the hinge and is then folded into two domains in the Fc region. The light chain forms two domains associated only with a Fab arm. Domain pairing leads to close interaction of heavy and light chains in the Fab arms supplemented by a disulfide bridge. The two heavy chains are disulfide bridged in the hinge (the number of bridges depending on IgG subclass) and are in close domain‐paired interaction at their C‐termini. (c) Domain nomenclature. The heavy chain is composed of V

H

, C

H

1, C

H

2, and C

H

3 domains. The light chain is composed of V

L

and C

L

domains. All the domains are paired except for the C

H

2 domains, which have two branched

N

‐linked carbohydrate chains interposed between them. Each domain has a molecular weight of approximately 12 000, leading to a molecular weight of ˜ 50 000 for Fc and Fab and 150 000 for the whole IgG molecule. Antigen recognition involves residues from the V

H

and V

L

domains, complement triggering the C

H

2 domain, leukocyte Fc receptor binding the C

H

2 domain, and the neonatal Fc receptor the C

H

2 and C

H

3 domains (see text).

Figure 3.3 Modes of flexibility in the IgG (human IgG1) molecule. These modes have been described from electron microscopic studies (see Figure 3.10) and biophysical techniques in solution. Flexibility in structure probably facilitates flexibility in antigen recognition and effector function triggering.

Figure 3.4 The structure of a human IgG molecule. The heavy chains are shown in purple and the light chains in brown. Relative to the classical cartoon of an IgG molecule as a Y shape, this “snapshot” of the molecule finds the Fc (bottom) “side on” to the viewer and much closer to one Fab arm than the other.

Figure 3.5 The immunoglobulin fold (constant domain). An anti‐parallel three‐stranded β‐sheet (red) interacts with a four‐stranded sheet (blue). The arrangement is stabilized by a disulfide bond linking the two sheets. The β‐strands are connected by helices, turns, and other structures. A similar overall core structure is seen in all Ig‐like domains but with some modifications such as extra β‐strands or changes in how the edge strands pair with the β‐sheets.

Figure 3.6 The structure of Fab. The heavy chain is shown in green and the light chain in yellow. The V

H

and V

L

domains (top) are paired by contact between their five‐strand faces and the C

H

1 and C

L

domains between the four‐strand faces.

Figure 3.7 Amino acid variability in the V domains of human Ig heavy and light chains. Variability, for a given position, is defined as the ratio of the number of different residues found at that position compared to the frequency of the most common amino acid. The complementarity determining regions (CDRs) are apparent as peaks in the plot and the frameworks as intervening regions of low variability.

Figure 3.8 The proximity of complementarity determining regions (CDRs or variable loops) at the tip of the Fab arms creates the antibody combining site. The V

H

and V

L

domains are shown from the side (a) and from above (b). The six CDRs (see Figure 3.7) are numbered 1–3 as belonging to the heavy (H) or light (L) chain.

Figure 3.9 Structure of Fc of human IgG. The C

H

3 domains (bottom) are paired. The C

H

2 domains are not and have two carbohydrate chains filling some of the space between them. Binding sites for the leukocyte FcγRIII receptor (red), complement C1q (green), and neonatal Fc receptor FcRn (yellow) are shown. The FcγRIII and FcRn sites were determined in crystallographic studies (Sondermann P.

et al.

(2000)

Nature

406, 267; Martin W.L.

et al.

(2001)

Molecular Cell

7, 867) and the C1q site by mutation analysis (Idusogie E.E.

et al.

(2000)

Journal of Immunology

164, 4178).

Figure 3.10 (a,b) Electron micrograph (×1 000 000) of complexes formed on mixing the divalent dinitrophenyl (DNP) hapten with rabbit anti‐DNP antibodies. The “negative stain” phosphotungstic acid is an electron‐dense solution that penetrates into the spaces between the protein molecules. Thus the protein stands out as a “light” structure in the electron beam. The hapten links together the Y‐shaped antibody molecules to form trimers (a) and pentamers (b). The flexibility of the molecule at the hinge region is evident from the variation in angle of the arms of the “Y.” (c) As in (a), but the trimers were formed using the F(ab′)2 antibody fragment from which the Fc structures have been digested by pepsin (×500 000). The trimers can be seen to lack the Fc projections at each corner evident in (a).

Figure 3.11 Three dinitrophenyl (DNP) antibody molecules held together as a trimer by the divalent antigen (green bar). Compare Figure 3.10a. When the Fc fragments are first removed by pepsin, the corner pieces are no longer visible (Figure 3.10c).

Figure 3.12 Schematic structures of the antibody classes. The two heavy chains are shown in dark and pale blue (two colors to highlight chain pairing; the chains are identical) and the light chains in gray. The

N

‐linked carbohydrate chains (branched structures) are shown in blue and

O

‐linked carbohydrates (linear structures) in green. The heavy chain domains are designated according to the class of the heavy chain (e.g., Cγ2 for the C

H

2 domain of IgG, etc.). For IgG, IgA, and IgD, the Fc is connected to the Fab arms via a hinge region; for IgM and IgE an extra pair of domains replaces the hinge. IgA, IgM, and IgD have tailpieces at the C‐termini of the heavy chains. IgA occurs in monomer and dimer forms. IgM occurs as a pentamer. (a) IgG1. The other human IgG subclasses (and IgGs of most other species) have this same basic structure but differ particularly in the nature and length of the hinge. (b) IgA1. The structure resembles IgG1 but with a relatively long hinge bearing

O

‐linked sugar chains. The Fc also shows some differences from IgG1 (see Figure 3.13). In IgA2, the hinge is very short and, in the predominant allotype, the light chains are disulfide linked not to the heavy chain but to one another. (c) IgM monomeric unit. This representation relies greatly on comparison of the amino acid sequences of μ and γ heavy chains. (d) IgE. The molecule is similar to the monomeric unit of IgM. (e) IgD. The hinge can be divided into a region rich in charge (possibly helical) and one rich in

O

‐linked sugars. The structure of the hinge may be much less extended in solution than represented schematically here. It is, however, very sensitive to proteolytic attack so that serum IgD is unstable. Mouse IgD has a structure very different to that of human IgD, in contrast to the general similarity in structures for human and mouse Igs. (f) Secretory IgA (see also Figure 3.19). (g) Pentameric IgM. The molecule is represented as a planar star shape. One monomer unit is shown shaded as in (c). A minority of IgM units can also form a hexamer. For clarity the carbohydrate structures have been omitted in (f) and (g). The Fab arms can likely rotate out of the plane about their two‐fold axis (see also Figure 3.14).

Figure 3.13 The structures of the Fc regions of human IgG1, IgE, and IgA1. The structures shown were determined by crystallographic analysis of Fcs in complex with Fc receptors. One heavy chain is shown in red, the other in yellow and the N‐linked carbohydrate chains that are interposed between the penultimate domains are shown in blue. For IgE, the Fc structure is shown for the C ε4 –C ε3 domain fragment for comparison;. a structure is now available including the C ε2 domains. For IgA1, the N‐linked sugars are attached at a position quite distinct from that for IgG1 and IgE. Also the tips of the Cα2 domain are joined by a disulfide bridge.

Figure 3.14 Structural changes in IgM associated with complement activation. (a) The “star” conformation. Electron micrograph of an uncomplexed IgM protein shows a “star‐shaped” conformation (see Figure 3.12 g). (b) The “staple” conformation. Electron micrograph of a specific sheep IgM bound to a

Salmonella paratyphi

flagellum as antigen suggests that the five F(ab′)

2

units and Cμ2 domains have been dislocated relative to the plane of the Fcs to produce a “staple” or “crab‐like” conformation. Complement C1 is activated on binding to antigen‐complexed IgM (staple), but interacts only very weakly, yielding no significant activation, with free IgM (star), implying that the dislocation process plays an important role in complement activation. It is suggested that movement of the Fabs exposes a C1q‐binding site on the Cμ3 domains of IgM. This is supported by observations that an Fc5 molecule, obtained by papain digestion of IgM, can activate complement directly in the absence of antigen. Electron micrographs are negatively stained preparations of magnification × 2 × 10

6

, i.e., 1 mm represents 0.5 nm.

Figure 3.15 Structures of human leukocyte Fc receptors. In each case, a similar view of the receptor is shown. D1, membrane distal; D2, membrane‐proximal domain, except for FcγRI for which D3 is the proximal domain and FcαRI for which D2 is membrane proximal. For the FcγRs and Fc εRI, the Fc‐binding site is present at the “top” of the D2 domain, whereas for FcαRI the Fc‐interaction site is present at the top of the D1 domain.