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Tables of Contents for Molecular Biology of B Cells
Chapter/Section Title
Page #
Page Count
Preface
xiii
1. Human Immunoglobulin Heavy Chain Locus
FUMIHIKO MATSUDA
Organization of the Human VH Locus
2
5
Analysis of Human VH Segments
7
3
Evolution of the Human VH Locus
10
2
Human CH Locus
12
7
2. Immunoglobulin Heavy Chain Genes of Mouse
ROY RIBLET
Igh-V or VH Genes of the Ighb Haplotype
19
1
Polymorphism in VH Genes
20
4
Evolution
24
1
Genomic Considerations
24
3
3. Immunoglobulin K Genes of Human and Mouse
HANS G. ZACHAU
General Features of Human and Mouse K Genes
27
1
Human Immunoglobulin K Genes
27
3
Mouse Immunoglobulin K Genes
30
3
Aspects of Evolution of the K Genes
33
4
4. Immunoglobulin Lambda (IGL) Genes of Human and Mouse
MARIE-PAULE LEFRANC AND GÉRARD LEFRANC
IGL Genes and IMGT ONCOLOGY
37
3
The Human IGL Genes
40
10
The Mouse IGL Genes
50
12
5. The Mechanisms of V(D)J Recombination
JOANN SEKIGUCHI, FREDERICK W. ALT, AND MARJORIE OETTINGER
Antigen Receptor Gene Assembly
62
2
Mutational Analyses of Recombination Signal Sequences
64
1
"Beyond 12/23" Restriction of V(D)J
Rearrangements
64
1
Influence of Coding Flanks
65
1
The Biochemistry of V(D)J Cleavage
65
1
RAGT/2-RSS Binding
66
1
RAAG1/2 Post-Cleavage Complex
67
1
A Role for HMG1 (or HMG2) in V(D)J Recombination
67
1
A Closer Look at RAAG1 and RAG2
68
3
Golding and Signal Joint Formation Requires the NHEJ Pathway
71
12
6. Transcription of Immunoglobulin Genes
KATHRYN CALAME AND RANJAN SEN
Transcriptional Regulatory Elements in Immunoglobulin Heavy and Light Chain Genes
83
3
Proteins Binding in Ig Transcriptional Regulatory Elements
86
3
Areas of Current Research
89
4
Discoveries Resulting from the Study of Ig Gene Transcription
93
8
7. Early B Cell Development to a Mature, Antigen-Sensitive Cell
FRITZ MELCHERS AND PAUL KINCADE
Three Waves of Hematopoiesis During Embryonic Development
101
2
Pluripotent Hematopoietic Stem Cells
103
3
Pathways of Hematopoietic Progenitor Cells Toward B Lymphocyte Lineage Commitment and Differentiation
106
1
Control of Lymphoid Cell Development by Transcription Factors
107
2
Plasticity if PAX-5-Deficient Pre-B Cells
109
1
The Surrogate Light Chain
110
2
Pre-B Cells and Their Differentiation to More Mature B Lineage Cells
112
2
Rearrangements at the L Chain Loci at the Transition from Large to Small Pre-B-II Cells
114
2
Immature B Cells
116
1
Selections of Immature B Cells
117
10
8. Allelic Exclusion, Isotypic Exclusion, and the Developmental Regulation of V(D)J Recombination
MICHAEL S. KRANGEL AND MARK S. SCHLISSEL
Rag Expression
127
1
The 12/23 Rule
128
1
Accessibility Hypothesis
128
1
Enhancer and Promoter Control of V(D)J Recombination
128
2
Trans-Acting Factors
130
1
Chromatin Dynamics and V(D)J Recombination
130
2
Ordered Rearrangement Within Ig and TCR Loci
132
1
Allelic Exclusion at Ig and TCR Loci
133
3
Ig Light Chain Isotypic Exclusion
136
1
Future Directions
136
5
9. The Development of Human B Lymphocytes
PETER D. BURROWS, TUCKER LEBIEN, ZHIXIN ZHANG, RANDALL S. DAVIS, AND MAX D. COOPER
Stages of Human B Cell Differentiation
141
2
Sites of Human B Cell Development
143
1
Human Immunoglobulin Genes
143
1
The Role of Surrogate Light Chains in Human B Cell Development
144
1
Repertoire Diversification via Receptor Editing and VH Replacement
145
2
Regulation of Antibody Production by B Cell Receptors
147
1
Immunodeficiency Diseases
148
1
B Lineage Leukemia
149
7
10. Development and Function of B Cell Subsets
JOHN T. KEARNEY
Selection and Differential Survival Mechanisms-B Cell Receptor Signaling
156
1
Compartmentalization of B Cell Subsets
157
1
Other Factors Involved in Formation of B Cell Subsets
157
4
11. Structure and Function of B Cell Antigen Receptor Complexes
MICHAEL RETH AND JURGEN WIENANDS
Structure of the BCR Complex
161
1
Coupling Between the BCR and SYK
162
1
Redox Regulation of BCR Signaling
162
1
ITAM- and Non-ITAM-Controlled Signaling Pathways to SLP-65
163
2
ITAM-Independent Signaling and Fine-Tuning
165
6
12. Regulation of Antigen Receptor Signaling by the Co-Receptors, CD 19 and CD22
LARS NITSCHKE AND DOUGLAS T. FEARON
CD19
171
6
Inhibitory Co-Receptors on B Cells
177
10
13. The Dynamic Structure of Antibody Responses
IAN C. MACLENNAN AND DEBORAH L. HARDIE
Three Routes to Antibody Production
187
1
Stages of Adaptive Antibody Responses
187
1
How and Where B Cells Encounter Antigen
188
1
Primary Cognate Interaction of B Cells with Primed T Cells
189
1
Exponential Growth of Activated B Cells
190
2
Proliferation, Hypermutation, and Selection in GC
192
5
Sustained Survival of Memory B Cell Clones and Plasma Cells
197
6
14. Dynamics of B Cell Migration to and within Secondary Lymphoid Organs
JASON G. CYSTER AND ULRICH H. VON ANDRIAN
Lymphoid Organ Entry
203
6
Compartmentalization of Mature B Cells
209
4
B Cells at Sites of Inflammation
213
1
Homing of Antibody Secreting Cells (ACSs)
213
10
15. Characteristics of Mucosal B Cells with Emphasis on the Human Secretory Immune System
PER BRANDTZAEG, H. CRAIG MORTON, AND MICHAEL E. LAMM
Immune-Inductive Tissue Compartments
223
3
Characteristics of B Cells in Secretory Effector Tissues
226
3
B-Cell Stimulation in MALT Structures
229
3
Class Switch and Ig A Isotype Promotion
232
2
Mechanisms Directing Homing and Retention of Mucosal B Cells
234
4
What Is Actually Known About Human Mucosal B Cells?
238
9
16. The Cellular Basis of B Cell Memory
KLAUS RAJEWSKY AND ANDREAS RADBRUCH
Generation of B Cell memory and Memory B Cells in T Cell-Dependent Antibody Responses
247
5
Memory Plasma Cells
252
2
Adaptive B Cell Memory
254
7
17. Immunoglobulin Assembly and Secretion
LINDA M. HENDERSHOT AND ROBERTO SA
Mechanisms of IG Synthesis and Assembly
261
3
Multiple Layers of Quality Control Exist to Aid and Monitor the Assembly of Functional IGs
264
3
Transport of Assembled IG Molecules to the Golgi
267
1
Degradation of Misfolded and Unassembled IG Subunits
267
1
Differentiation to Plasma Cell
268
7
18. Fc and Complement Responses
JEFFREY V. RAVETCH AND MICHAEL C. CARROLL
Consequences of FCyRIIB Deficiency
275
1
Consequences of Complement and Complement Receptor Deficiencies
276
2000
Fc Receptors
2276
Complement Receptors
280
1
Co-Receptor Signaling Versus Antigen Localization to FDC
281
4
Frontiers: Complement Versus Fc Receptors
285
4
19. Regulation of Class Switch Recombination
MICHEL COGNÉ AND BARBARA K. BIRSHTEIN
CSR Requires Specific Stimuli Occurring in a Defined Germinal Center (GC) Microenvironment
289
2
Proximal CIS Regulatory Elements for GT
291
2
Distant Regulatory Region for GT and CSR: The 3' IGH Enhancers
293
2
Mechanisms for 3' IGH Regulatory Region-Mediated Regulation of GT
295
5
Coordinated Regulation of Transcription, Recombination, and Replication
300
7
20. Molecular Mechanisms of Class Switch Recombination
JANET STAVNEZER KAZUO KINOSHITA, MASAMICHI MURAMATSU, AND TASUKU HONJO
Outline of Mechanisms for CSR
307
5
Isotype Specificity of CSR
312
1
AID, The Sole B Cell-Specific Factor Required for CSR
313
1
Cleavage of the S Region
314
1
Processing and Joining of DNA Ends After Cleavage
315
4
Comparison of CSR with SHM
319
10
21. Molecular Mechanisms of Hypermutation
NANCY MAIZELS AND MATTHEW D. SCHARFF
Characteristics of Somatic Hypermutation of Immunoglobulin Variable Regions 327
Activation and Targeting of Hypermutation by Transcription and CIS-Elements
329
1
Hypermutation Occurs Within a Limited Window of B Cell development
330
1
The AID Gene Is Critical for Hypermutation
331
1
Phase One of Hypermutation: C -* U Deamination and Base Excision Repair
332
1
Mismatch Repair Factors in Phase Two of Hypermutation
332
2
DNA Breaks in Hypermutation
334
1
Competing Pathways of Repair: Error-Prone DNA Synthesis or Strand Transfer
335
1
Evolution and Hypermutation
335
4
22. Selection During Antigen-Driven B Cell Immune Responses: The Basis for High Affinity Antibody
MARK J. SHLOMCHIK
Overview of the B-Cell Immune Response
339
2
Affinity Maturation in the Early Stages of the B-Cell Immune Response
341
1
The CG Is a Second Major Site for Affinity Maturation
342
2
Affinity-Based Selection Continues After the GC Reaction Has Ended
344
1
An Integrated View of the Strategic Design of the B-Cell Immune Response: Future Directions
344
5
23. Chromosomal Translocations in B Cell Leulcemias and Lymphomas
A. THOMAS LOOK AND ADOLFO FERRANDO
Translocations Associated with a Block in Lymphoid Differentiation
349
3
Translocations Associated with Suppression of Apoptosis During Lymphoid Development
352
2
Translocations Associated with Increased Proliferation in Lymphoid Precursors
354
1
Activation Cell Cycle Regulation in Mantle Cell Lymphoma and Myeloma
355
11
24. Classification and Characteristics of Mouse B Cell-Lineage Lymphomas
HERBERT C. MORSE III
Comparative Classification of Mouse and Human B Cell-Lineage Neoplasms
366
2
Characteristics of Mouse B Cell-Lineage Lymphomas
368
5
Pathogenesis
373
9
25. B Cells Producing Pathogenic Autoantibodies
CONSTANTIN A. BONA AND FREDA K. STEVENSON
Subsets of Autoantibodies
382
1
Criteria to Define Pathogenic Autoantibodies
383
1
Genetics of Autoantibodies
384
4
Molecular and Immunochemical Characteristics of Human Pathogenic Autoantibodies
388
4
Human Pathogenic Autoantibodies with Murine Counterparts
392
11
26. Immunodeficiencies Caused by B Cell Defects
FRANCISCO A. BONILLA AND RAIF S. GENA
Clinical Features of the Agammaglobulinemias
403
7
Autosomal Recessive Hyper-IGM Syndrome
410
1
Murine Models of Human B-Cell Deficiency
411
6
27. Diverse Forms of Immunoglobulin Genes in Lower Vertebrates
GARY W. LITMAN, MARTIN F. FLADNIK, AND GREGORY W. WARR
Cartilaginous Fish: An Unusual Example of Gene Multiplicity
417
2
Bony Fish: IG Heavy Chain Genes Resemble IgM and IgD
419
3
Lobe-Finned Fish: A "Transitional" Arrangement of Recombining Elements
422
1
Fleshy-Finned Fish: An Ancient Origin for Isotype Diversity
422
1
Amphibians and Reptiles: The Possible Origins of Class Switching
422
1
Light Chain Genes: Diverse Structures and Organization in Lower Vertebrates
423
2
Transcriptional Control of IG Genes in Lower Vertebrates
425
2
A Unifying Hypothesis to Explain the Origins of the Adaptive Immune Receptor
427
1
Immune Molecules in Jawless Vertebrates
427
1
Protochordates: Different Contexts for Diversified B Regions
428
5
28. Immunoglobulin Genes and Generation of Antibody Repertoires in Higher Vertebrates: A Key Role for GALT
DENNIS LANNING, BARBARA A. OSBORNE, AND KATHERINE L. KNIGHT
Avians
433
3
Lagomorphs
436
4
Artiodactyla
440
4
Other Mammals
444
6
29. The Zebrafisk Immune System
LISA A. STEINER, CATHERINE E. WILLETr, AND NADIA DAMLOVA
Hematopoiesis
450
2
Adaptive Immunity in Zebrafisk: Organs and Molecules
452
5
Genetic Approaches
457
3
Major Histocompatibility Complex (MHC)
460
1
Innate Immunity
460
4
Infection
464
9
30. The Origin of V(D)J Diversification
SUSANNA M. LEWIS, GILLIAN E. WU, AND ELLEN HSU
The Alien Seed
473
8
The Evolution of BCR and TCR Loci
481
2
Considerations on the UR-V Gene
483
8
31. Antibody Structure and Recognition of Antigen
ERIC J. SUNDBERG AND ROY A. MARIUZZA
A Structural Framework for Molecular Recognition
491
22
32. Monoclonal Antibodies from Display Libraries
JIM MARKS
Overview of Antibody Phage Display
513
1
Prokaryotic Expression of Antibody Fragments
514
1
Generation of Antibody Gene Repertoires Using the
Polymerase Chain Reaction
515
1
Antibody Phage Display
516
3
Use of Phage Display to Bypass Hybridoma Technology
519
1
Use of Phage Display to Bypass Immunization
520
1
A Comparison of Different Phage Antibody Library Types and Applications
521
1
Strategies for Selection of Phage Antibodies
522
1
Increasing Antibody Affinity Using Phage Display
522
2
Alternative Antibody Display Technologies
524
9
33. Humanization of Monoclonal Antibodies
NAOYA TSURUSHITA AND MAXIMILIANO VASQUEZ
Murine, Chimeric, and Humanized Antibodies
533
1
Computer-Guided Design of Humanized V Regions
534
3
Other Humanization Methods
537
3
Immunogenicity of Humanized Antibodies
540
1
Humanized Antibodies Approved for Clinical Use
540
7
34. Human Monoclonal Antibodies from Translocus Mice
MARIANNE BRÜGGEMANN
Human IG Transloci
547
5
The Mouse Strains
552
11
Index
563