Advances in Immunology Volume 85: Cumulative Subject Index, Volumes 66-82

CONTENTS OF VOLUMES 66–82

Volume 66 The Role of CD45 in Signal Transduction Louis B. Justement HLA Class II Peptide Binding Specificity and Autoimmunity Juergen Hammer, Tiziana Sturniolo, and Francesco Sinigaglia Role of Cytokines in Sepsis

1

67

101

C. Erik Hack, Lucien A. Aarden, and Lambertus G. Thijs Role of Macrophage Migration Inhibitory Factor in the Regulation of the Immune Response Christine N. Metz and Richard Bucala The Intrinsic Coagulation/Kinin-Forming Cascade: Assembly in Plasma and Cell Surfaces in Inflammation Allen P. Kaplan, Kusumam Joseph, Yoji Shibayama, Sesha Reddigari, Berhane Ghebrehiwet, and Michael Silverberg

vii

197

225

viii

CONTENTS OF VOLUMES 66–82

CD8þ Cells in Human Immunodeficiency Virus Type I Pathogenesis: Cytolytic and Noncytolytic Inhibition of Viral Replication Otto o. Yang and Bruce D. Walker

273

Volume 67 Index of Volumes 37–65

Volume 68 Posttranscriptional Regulation of mRNAs Important in T Cell Function

1

James S. Malter Molecular and Cellular Mechanisms of T Lymphocyte Apoptosis Josef M. Penninger and Guido Kroemer

51

Prenylation of Ras GTPase Superfamily Proteins and Their Function in Immunobiology Robert B. Lobell

145

Generation and TAP-Mediated Transport of Peptides for Major Histocompatibility Complex Class I Molecules Frank Momburg and Gu¨nter J. Ha¨mmerling

191

Adoptive Tumor Immunity Mediated by Lymphocytes Bearing Modified Antigen-Specific Receptors Thomas Brocker and Klaus Karjalainen

257

Membrane Molecules as Differentiation Antigens of Murine Macrophages Andrew J. McKnight and Siamon Gordon

271

CONTENTS OF VOLUMES 66–82

Major Histocompatibility Complex-Directed Susceptibility to Rheumatoid Arthritis Gerald T. Nepom Immunological Treatment of Autoimmune Diseases J. R. Kalden, F. C. Breedveld, H. Burkhardt, and G. R. Burmester

ix

315

333

Volume 69 Molecular and Cellular Events in Early Thymocyte Development Hans-Reimer Rodewald and Hans Jo¨ rg Fehling Regulation of Immunoglobulin Light Chain Isotype Expression James R. Gorman and Frederick W. Alt Role of Immunoreceptor Tyrosine-Based Activation Motif in Signal Transduction from Antigen and Fc Receptors

1

113

183

Noah Isakov The Atypical Serine Proteases of the Complement System Ge´ rard J. Arlaud, John E. Volanakis, Nicole M. Thielens, Sthanam V. L. Narayana, Ve´ ronique Rossi, and Yuanyuan Xu Accessibility Control of V(D)J Recombination: Lessons from Gene Targeting William M. Hempel, Isabelle Leduc, Noelle Mathieu, Raj Kamal Tripathi, and Pierre Ferrier

249

309

x

CONTENTS OF VOLUMES 66–82

Interactions between the Immune System and Gene Therapy Vectors: Bidirectional Regulation of Response and Expression Jonathan S. Bromberg, Lisa Debruyne, and Lihui Qin How Do Major Histocompatibility Complex Genes Influence Individual Odor and Mating Preferences?

353

411

Dustin Penn and Wayne Potts Olfactory Receptor Gene Regulation Andrew Chess

437

Volume 70 Biology of the Interleukin-2 Receptor Brad H. Nelson and Dennis M. Willerford Interleukin-12: A Cytokine at the Interface of Inflammation and Immunity

1

83

Giorgio Trinchieri Recent Progress on the Regulation of Apoptosis by Bcl-2 Family Members Andy J. Minn, Rachel E. Swain, Averil Ma, and Craig B. Thompson Interleukin-18: A Novel Cytokine That Augments Both Innate and Acquired Immunity Haruki Okamura, Hiroko Tsutsui, Shin-ichiro Kashiwamura, Tomohiro Yoshimoto, and Kenji Nakanishi

245

281

CONTENTS OF VOLUMES 66–82

CD4þ T-Cell Induction and Effector Functions: A Comparison of Immunity against Soluble Antigens and Viral Infections Annette Oxenius, Rolf M. Zinkernagel, and Hans Hengartner Current Views in Intracellular Transport: Insights from Studies in Immunology

xi

313

369

Victor W. Hsu and Peter J. Peters Phylogenetic Emergence and Molecular Evolution of the Immunoglobulin Family John J. Marchalonis, Samuel F. Schluter, Ralph M. Bernstein, Shanxiang Shen, and Allen B. Edmundson Current Insights into the ‘‘Antiphospholipid’’ Syndrome: Clinical, Immunological, and Molecular Aspects David A. Kandiah, Andrej Sali, Yonghua Sheng, Edward J. Victoria, David M. Marquis, Stephen M. Coutts, and Steven A. Krilis

417

507

Volume 71 ab/gd Lineage Commitment in the Thymus of Normal and Genetically Manipulated Mice Hans Jo¨ rg Fehling, Susan Gilfillan, and Rhodri Ceredig Immunoregulatory Functions of gd T Cells Willi Born, Carol Cady, Jessica Jones-Carson, Akiko Mukasa, Michael Lahn, and Rebecca O’Brien

1

77

xii

CONTENTS OF VOLUMES 66–82

STATs as Mediators of Cytokine-Induced Responses Timothy Hoey and Michael J. Grusby

145

CD95(APO-1/Fas)-Mediated Apoptosis: Live and Let Die Peter H. Krammer

163

A CXC Chemokine SDF-1/PBSF: A Ligand for a HIV Coreceptor, CXCR4 Takashi Nagasawa, Kazunobu Tachibana, and Kenji Kawabata T Lymphocyte Tolerance: From Thymic Deletion to Peripheral Control Mechanisms Brigitta Stockinger Confrontation between Intracellular Bacteria and the Immune System

211

229

267

Ulrich E. Schaible, Helen L. Collins, and Stefan H. E. Kaufmann

Volume 72 The Function of Small GTPases in Signaling by Immune Recognition and Other Leukocyte Receptors Amnon Altman and Marcel Deckert Function of the CD3 Subunits of the Pre-TCR and TCR Complexes during T Cell Development Bernard Malissen, Laurence Ardouin, Shih-Yao Lin, Anne Gillet, and Marie Malissen

1

103

CONTENTS OF VOLUMES 66–82

Inhibitory Pathways Triggered by ITIM-Containing Receptors Silvia Bolland and Jeffrey V. Ravetch ATM in Lymphoid Development and Tumorigenesis Yang Xu Comparison of Intact Antibody Structures and the Implications for Effector Function Lisa J. Harris, Steven B. Larson, and Alexander McPherson

xiii

149

179

191

Lymphocyte Trafficking and Regional Immunity Eugene C. Butcher, Marna Williams, Kenneth Youngman, Lusijah Rott, and Michael Briskin

209

Dendritic Cells

255

Diana Bell, James W. Young, and Jacques Banchereau Integrins in the Immune System Yoji Shimizu, David M. Rose, and Mark H. Ginsberg

325

Volume 73 Mechanisms of Exogenous Antigen Presentation by MHC Class I Molecules in Vitro and in Vivo: Implications for Generating CD8þ T Cell Responses to Infectious Agents, Tumors, Transplants, and Vaccines Jonathan W. Yewdell, Christopher C. Norbury, and Jack R. Bennink

1

xiv

CONTENTS OF VOLUMES 66–82

Signal Transduction Pathways That Regulate the Fate of B Lymphocytes Andrew Craxton, Kevin Otipoby, Aimin Jiang, and Edward A. Clark

79

Oral Tolerance: Mechanisms and Therapeutic Applications Ana Faria and Howard L. Weiner

153

Caspases and Cytokines: Roles in Inflammation and Autoimmunity John C. Reed

265

T Cell Dynamics in HIV-1 Infection 301 Dawn R. Clark, Rob J. de Boer, Katja C. Wolthers, and Frank Miedema Bacterial CpG DNA Activates Immune Cells to Signal Infectious Danger

329

Hermann Wagner Neutrophil-Derived Proteins: Selling Cytokines by the Pound Marco Antonio Cassatella

369

Murine Models of Thymic Lymphomas: Premalignant Scenarios Amenable to Prophylactic Therapy Eitan Yefenof

511

CONTENTS OF VOLUMES 66–82

xv

Volume 74 Biochemical Basis of Antigen-Specific Suppressor T Cell Factors: Controversies and Possible Answers

1

Kimishige Ishizaka, Yasuyuki Ishii, Tatsumi Nakano, and Katsuji Sugie The Role of Complement in B Cell Activation and Tolerance Michael C. Carroll Receptor Editing in B Cells David Nemazee Chemokines and Their Receptors in Lymphocyte Traffic and HIV Infection Pius Loetscher, Bernhard Moser, and Marco Baggiolini Escape of Human Solid Tumors from T-Cell Recognition: Molecular Mechanisms and Functional Significance Francesco M. Marincola, Elizabeth M. Jaffee, Daniel J. Hicklin, and Soldano Ferrone The Host Response to Leishmania Infection Werner Solbach and Tama´ s Laskay

61

89

127

181

275

Volume 75 Exploiting the Immune System: Toward New Vaccines against Intracellular Bacteria Ju¨ rgen Hess, Ulrich Schaible, Ba¨ rbel Raupach, and Stefan H. E. Kaufmann

1

xvi

CONTENTS OF VOLUMES 66–82

The Cytoskeleton in Lymphocyte Signaling A. Bauch, F. W. Alt, G. R. Crabtree, and S. B. Snapper

89

TGF-b Signaling by Smad Proteins Kohei Miyazono, Peter ten Dijke, and Carl-Henrik Heldin

115

MHC Class II-Restricted Antigen Processing and Presentation Jean Pieters

159

T-Cell Receptor Crossreactivity and Autoimmune Disease Harvey Cantor

209

Strategies for Immunotherapy of Cancer Cornelis J. M. Melief, Rene´ E. M. Toes, Jan Paul Medema, Sjoerd H. van der Burg, Ferry Ossendorp, and Rienk Offringa Tyrosine Kinase Activation in the Decision between Growth, Differentiation, and Death Responses Initiated from the B Cell Antigen Receptor Robert C. Hsueh and Richard H. Scheuermann The 30 IgH Regulatory Region: A Complex Structure in a Search for a Function Ahmed Amine Khamlichi, Eric Pinaud, Catherine Decourt, Christine Chauveau, and Michel Cogne´

235

283

317

CONTENTS OF VOLUMES 66–82

xvii

Volume 76 MIC Genes: From Genetics to Biology

1

Seiamak Bahram CD40-Mediated Regulation of Immune Responses by TRAF-Dependent and TRAF-Independent Signaling Mechanisms Amrie C. Grammer and Peter E. Lipsky Cell Death Control in Lymphocytes Kim Newton and Andreas Strasser Systemic Lupus Erythematosus, Complement Deficiency, and Apoptosis M. C. Pickering, M. Botto, P. R. Taylor, P. J. Lachmann, and M. J. Walport Signal Transduction by the High-Affinity Immunoglobulin E Receptor FceRI: Coupling Form to Function Monica J. S. Nadler, Sharon A. Matthews, Helen Turner, and Jean-Pierre Kinet

61

179

227

325

Volume 77 The Actin Cytoskeleton, Membrane Lipid Microdomains, and T Cell Signal Transduction S. Celeste Posey Morley and Barbara E. Bierer Raft Membrane Domains and Immunoreceptor Functions Thomas Harder

1

45

xviii

CONTENTS OF VOLUMES 66–82

Human Basophils: Mediator Release and Cytokine Production John T. Schroeder, Donald W. MacGlashan, Jr., and Lawrence M. Lichtenstein Btk and BLNK in B Cell Development Satoshi Tsukada, Yoshihiro Baba, and Dai Watanabe Diversity and Regulatory Functions of Mammalian Secretory Phospholipase A2s Makoto Murakami and Ichiro Kudo

93

123

163

The Antiviral Activity of Antibodies in Vitro and in Vivo Paul W. H. I. Parren and Dennis R. Burton

195

Mouse Models of Allergic Airway Disease

263

Clare M. Lloyd, Jose-Angel Gonzalo, Anthony J. Coyle, and Jose-Carlos Gutierrez-Ramos Selected Comparison of Immune and Nervous System Development Jerold Chun

297

Volume 78 Toll-like Receptors and Innate Immunity

1

Shizuo Akira Chemokines in Immunity Osamu Yoshie, Toshio Imai, and Hisayuki Nomiyama

57

CONTENTS OF VOLUMES 66–82

Attractions and Migrations of Lymphoid Cells in the Organization of Humoral Immune Responses Christoph Schaniel, Antonius G. Rolink, and Fritz Melchers Factors and Forces Controlling V(D)J Recombination David G. T. Hesslein and David G. Schatz T Cell Effector Subsets: Extending the Th1/Th2 Paradigm Tatyana Chtanova and Charles R. Mackay MHC-Restricted T Cell Responses against Posttranslationally Modified Peptide Antigens Ingelise Bjerring Kastrup, Mads Hald Andersen, Tim Elliot, and John S. Haurum Gastrointestinal Eosinophils in Health and Disease

xix

111

169

233

267

291

Marc E. Rothenberg, Anil Mishra, Eric B. Brandt, and Simon P. Hogan

Volume 79 Neutralizing Antiviral Antibody Responses Rolf M. Zinkernagel, Alain Lamarre, Adrian Ciurea, Lukas Hunziker, Adrian F. Ochsenbein, Kathy D. McCoy, Thomas Fehr, Martin F. Bachmann, Ulrich Kalinke, and Hans Hengartner Regulation of Interleukin-12 Production in Antigen-Presenting Cells Xiaojing Ma and Giorgio Trinchieri

1

55

xx

CONTENTS OF VOLUMES 66–82

Mechanisms of Signaling by the Hematopoietic-Specific Adaptor Proteins, SLP-76 and LAT and Their B Cell Counterpart, BLNK/SLP-65 93 Deborah Yablonski and Arthur Weiss Xenotransplantation David H. Sachs, Megan Sykes, Simon C. Robson, and David K. C. Cooper Regulation of Antibacterial and Antifungal Innate Immunity in Fruitflies and Humans Michael J. Williams

129

225

Functional Heavy-Chain Antibodies in Camelidae Viet Khong Nguyen, Aline Desmyter, and Serge Muyldermans

261

Uterine Natural Killer Cells in the Pregnant Uterus

297

Chau-Ching Liu and John Ding-E Young

Volume 80 Protein Degradation and the Generation of MHC Class I-Presented Peptides Kenneth L. Rock, Ian A. York, Tomo Saric, and Alfred L. Goldberg Proteolysis and Antigen Presentation by MHC Class II Molecules Paula Wolf Bryant, Ana-Maria Lennon-Dume´ nil, Edda Fiebiger, Ce´ cile Lagaudrie`re-gesbert, and Hidde L. Ploegh

1

71

CONTENTS OF VOLUMES 66–82

xxi

Cytokine Memore of T Helper Lymphocytes 115 Max Lo¨ hning, Anne Richter, and Andreas Radbruch Ig Gene Hypermutation: A Mechanism Is Due Jean-Claude Weill, Barbara Bertocci, Ahmad Faili, Said Aoufouchi, Ste´ phane Frey, Annie de Smet, Se´ bastien Storck, Auriel Dahan, Fre´ de´ ric Delbos, Sandra Weller, Eric Flatter, and Claude-Agne`s Reynaud Generalization of Single Immunological Experiences by Idiotypically Mediated Clonal Connections Hilmar Lemke and Hans Lange The Aging of the Immune System B. Grubeck-Loebenstein and G. Wick

183

203

243

Volume 81 Regulation of the Immune Response by the Interaction of Chemokines and Proteases Sofie Struyf, Paul Proost, and Jo Van Damme

1

Molecular Mechanisms of Host–Pathogen Interaction: Entry and Survival of Mycobacteria in Macrophages John Gatfield and Jean Pieters

45

B Lymphoid Neoplasms of Mice: Characteristics of Naturally Occurring and Engineered Diseases and Relationships to Human Disorders Herbert C. Morse III, Tom McCarty, Chen-Feng Qi, Ted A. Torrey, Zohreh Naghashfar, Sisir K. Chattopadhyay, Torgny N. Fredrickson, and Janet W. Hartley

97

xxii

CONTENTS OF VOLUMES 66–82

Prions and the Immune System: A Journey Through Gut, Spleen, and Nerves Adriano Aguzzi

123

Roles of the Semaphorin Family in Immune Regulation Atsushi Kumanogoh and Hitoshi Kikutani

173

HLA-G Molecules: from Maternal–Fetal Tolerance to Tissue Acceptance Edgardo D. Carosella, Philippe Moreau, Joe¨ l Le Maoult, Magali Le Discorde, Jean Dausset, and Nathalie Rouas-Freiss The Zebrafish as a Model Organism to Study Development of the Immune System David Traver, Philippe Herbomel, E. Elizabeth Patton, Ryan D. Murphey, Jeffrey A. Yoder, Gary W. Litman, Andre´ Catic, Chris T. Amemiya, Leonard I. Zon, and Nikolaus S. Trede Control of Autoimmunity by Naturally Arising Regulatory CD4þ T Cells

199

253

331

Shohei Hori, Takeshi Takahashi, and Shimon Sakaguchi

Volume 82 Transcriptional Regulation in Neutrophils: Teaching Old Cells New Tricks Patrick P. McDonald

1

CONTENTS OF VOLUMES 66–82

Tumor Vaccines Freda K. Stevenson, Jason Rice, and Delin Zhu Immunotherapy of Allergic Disease R. Valenta, T. Ball, M. Focke, B. Linhart, N. Mothes, V. Niederberger, S. Spitzauer, I. Swoboda, S. Vrtala, K. Westritschnig, and D. Kraft

xxiii

49

105

Interactions of Immunoglobulins Outside the Antigen-Combining Site Roald Nezlin and Victor Ghetie

155

The Role of Antibodies in Mouse Models of Rheumatoid Arthritis, and Relevance to Human Disease Paul A. Monach, Christophe Benoist, and Diane Mathis

217

MUC1 Immunobiology: From Discovery to Clinical Applications

249

Anda M. Vlad, Jessica C. Kettel, Nehad M. Alajez, Casey A. Carlos, and Olivera J. Finn Human Models of Inherited Immunoglobulin Class Switch Recombination and Somatic Hypermutation Defects (Hyper-IgM Syndromes) Anne Durandy, Patrick Revy, and Alain Fischer The Biological Role of the C1 Inhibitor in Regulation of Vascular Permeability and Modulation of Inflammation Alvin E. Davis, III, Shenghe Cai, and Dongxu Liu

295

331

SUBJECT INDEX

Boldface numerals indicate volume number

A

polymerization regulation, 77:24–25 rapid remodeling, 77:30 structure, 77:23–24 and T cell signaling, 77:2 in T cell signal transduction, 77:33–34 Actin-binding proteins, regulation of actin cytoskeleton, 77:25–28 Actin-depolymerizing factor, see Cofilin Actin-related protein 2/3 complex, 77:12–13, 27 Actin, changes in, linked to ion channel control, 77:31–32 Actin, lymphocyte signaling actin cap effective molarity regulation, 75:110 function, 75:91–94 proximity regulator role, 75:110 structure, 75:90–91 cytoskeleton regulation, 75:105–107 polymerization regulation current view, 75:94–95

A39R, 81:191–192 AAV, see Adeno-associated virus Abortion, spontaneous, 69:429 Abs, see Antibodies Ac–Leu–Leu–nLeu–al, effect on proteasomes, 80:14 ACE, see Enzymes, angiotensin-converting Acetylhydroxylases, PAF, 77:163 ACF, see Auxiliary factor Acquired Immune Deficiency Syndrome, 69:367 Acquired immune response, intracellular bacteria infection, 75:15–20 Actin cytoskeleton actin-binding proteins, 77:25–28 in cross-talk with raft membrane domains, 77:75–76 exogenous agents modifying actin, 77:28–30 lipid rafts and, 77:21–23 microfilament reorientation, 77:14–15 1

2

SUBJECT INDEX

Actin, lymphocyte signaling (continued) nucleus signal propagation, 75:108–110 RAC role, 75:94–100 Rho family GTPases role, 75:99–100, 104 WASP role, 75:92–94, 104–107 Actinomycin D, 73:447 and AU-binding factor, 68:31 and c-fos ARE, GM–CSF discrepancies, 68:21 and c-fos mRNA, 68:28 effect on mRNA decay, 68:2–3, 7 IL-2 mRNA and, 68:11, 12 Activation basophils IgE dependent, 77:101–104 IgE independent, 77:104–106 Btk, 77:129–137 PLCg, 77:145–148 PTK, 77:7 serum response factor, 77:32 T cells, architecture of, 77:77–79 Activation markers, basophil, 77:96–98 Activation-induced cell death, 77:11 characterization, 70:15–19 T cell deletion, 70:62 Activation-induced cytidine deaminase (AID), 81:286–289; 82:306–311 Activation-induced cytidine deaminase, role in hypermutation, 80:195–196 Active immunization models current protocols, 77:273 immunization protocol, 77:267–273

introduction of allergen to lungs, 77:264–265 modulation of, 77:276 selection of antigen, 77:265–267 Active site-directed probe, targeting of cysteine protease, 80:82–86 Activin signal transducer, transforming growth factor- b signaling, 75:130–131 Acute distress respiratory syndrome, 73:426 Acute humoral xenograft rejection antibody role, 79:136, 141–142 endothelial cell activation, 79:151–152 macrophages, 79:146 monocytes, 79:146 natural killer cells, 79:143, 145 neutrophils, 79:148 Acute respiratory distress syndrome (ARDS) interleukin-8, 66:140 macrophage migration inhibitory factor, 66:214–215 Acylations, multiple, Src kinases membrane anchored by, 77:55–56 Adapter molecules, 69:200 Gads, interaction with SLP-76, 77:147–148 recruitment, 77:4–8 Adapter proteins, see specific proteins Adaptor proteins Grb2-related, 79:98–99, 118–120 in ITAM-coupled receptor signaling key events, 79:93–95 T cell linker, 79:95–97

SUBJECT INDEX

lipopolysaccharide-binding, 79:231 in PLC-g1 activation, 79:118–120 SLP-76, ITAM-coupled signaling, 79:98 Adaptive immune response, leishmaniasis, 74:285–299 antigen presentation, 74:285–286 antileishmanial effector mechanisms, 74:297–299 CD4þ T helper lymphocyte induction, 74:288–290, 302 co-stimulatory molecules, 74:287–288 cytokine determinants, 74:290–291 interleukin-4 role, 74:291–297 interleukin-12 role, 74:291–297 T helper cell development, 74:290–291 Adaptive immunity, 70:83–84; 81:46–51, 149 ontogeny from fishes to mammals, 81:272–289 and pre-exposure prophylaxis against prions, 81:150 ADCC, see Antibody-dependent cellular cytotoxicity; see Cytoxicity, antibody-dependent cellular Adeno-associated virus, 69:361 Adenocarcinomas, 82:259 Adenosine deaminase deficiency, 69:364 Adenosine triphosphate binding cassette, 68:191, 213–214, 239–240 dependent aminophospholipid translocase, 68:64

3

and necrosis, 68:73, 86 and permeability transition pore, 68:80–83, 86, 87 Adenosine–uridine-rich elements, 68:19–22 Adenovirus, 69:354–359, 364, 366–367, 381, 383 Adenovirus, neutralization, 77:210–211 Adenoviruses vectors, advantages, 73:62 Adhesion blocking, in autoimmune diseases, 68:365–371 integrin-dependent, 68:168 intracellular adhesion molecule-1, 68:26–27, 336, 367–371, 375 receptors, and CD45, 68:100 Adhesion molecules, 69:84–88 Adhesion molecules, basophil, 77:94–95 Adhesion, of lymphocytes, 66:15–17 Adipsin, 69:261 Adjuvant arthritis, 73:213–214 Adjuvant, in active immunization models, 77:270 Adjuvants cancer immunotherapy, 75:258–261 intracellular bacteria vaccination, 75:31–35 dendritic cells, 75:34–35 heat shock proteins, 75:29, 33–34 subunit vaccines, 75:31–33 ADPases, in xenotransplantation, 79:170–171

4

SUBJECT INDEX

ADP-ribosylation factor, see GTPases Adrenal gland, hypofunction, 70:516–517 Adriamycin, 68:105, 224 Adult diarrhea rotavirus, 69:213 Adult respiratory distress syndrome, 73:384 Agammaglobulinemia, X-linked, 72:159–160 Age, oral tolerance, 73:178–181 Aging activation and signal transduction in immune cells, 80:262–263 areas of scientific research, 80:243 B cells, and antibody production, 80:257–259 bone marrow progenitor cells, 80:248–249 cellular changes in, 80:246–247 deterministic theories, 80:245–246 excess immunoreactivity in, disorders due to, 80:266–268 macrophages and dendritic cells in, 80:260–261 memory/effector T cells, 80:251–257 naive T cells, 80:249–251 natural killer cells in, 80:261 stochastic theories, 80:244–245 thymic function in, 80:249 and thymic reconstitution, 80:268–271 Agonists, 82:27–28 AHVsema, 81:191–192

AHXR, see Acute humoral xenograft rejection AIA, see Arthritis AICD, see Activation-induced cell death AID, see Activation-induced cytidine deaminase AIDS, 71:188–190; 81:11, 13, 51; see Acquired Immune Deficiency Syndrome; see also Human immunodeficiency virus AIDS, FasL role, 73:282–283 Airway hyperresponsiveness in vivo, 77:266–267 mouse models of RSV, 77:285–286 and mouse strains, 77:271–273 passive transfer models and, 77:277–282 to spasmogenic stimuli, 77:263 Airway hyperresponsiveness, 70:154–155 AKV-1 gene, 73:517 Alanines, 82:252 Alcelaphine herpesvirus (AHV), 81:191–192 Alcohol-induced hepatitis, 73:286 Algorithms, 82:265–266 Algorithms, T cell epitope prediction, 66:78–84 All–elic exclusion anomalies, 69:317 in B cells, 69:115–116, 205–206 definition, 69:317 in heavy chains, 69:130–135 at immunoglobulin Ll locus, 69:333 and immunoglobulin M, 69:205–206

SUBJECT INDEX

in light chains, 69:136 mechanisms, 69:136–137 models, 69:129–130 pre-TCR role in, 69:38–44 Alleles, paternal versus maternal, 69:137; see also Allelic exclusion; Allelic inactivation Allelic exclusion, B cell receptor editing, 74:96–100 immunoglobulin-L chain, 74:99–100 inclusion problem, 74:113 mechanisms, 74:97–98 feedback suppression of recombination, 74:98 selective factors, 74:97–98 stochastic factors, 74:97 Allelic exclusion, V(D)J recombination, 78:199–201 Allelic inactivation, 69:441–445 Allelic probabilities, cytokine memory, 80:142–143 Allergen challenge late-phase response to, 77:112–113 transient gene transfer models, 77:284–285 Allergen(s), see also Sensitization, allergic classes/forms of, 82:108, 113–114 cross-reactive, 82:133 encoding DNA, 82:131 extract-based immunotherapy, 82:127–132, 128–129 factors, 82:109 food, 82:109 grass pollen, 82:135, 139 modified, 82:135–142 natural, 82:134–135 recombinant, 82:132–135

5

respiratory, 82:108–110 specific immunotherapy, 82:115–120 T cells and, 82:113–114 Allergic disease, basophils and, 77:112–114 Allergic diseases, contact activation in, 66:258–259 Allergic encephalomyelitis, see Encephalomyelitis, experimental allergic Allergic reactions, 68:172–173 Allergies, 72:293 animal models, 73:218, 221, 223 human models, 73:227–228, 231 Allergy(ies), see also Sensitization, allergic in children, 82:107 definition of, 82:105 mechanisms of, 82:164–165 Type I, 82:105–114 types of, 82:105–106 Allogeneic chimerism, in xenotransplantation, 79:172–173 Allograft rejection, 68:179; 70:155–157 Allografts, maternal donor, 73:229 Alloimmune response, 69:383 a/b T cell receptor interactions, major histocompatiblity complex class I, 76:1–5 aEb7, 72:346–348 a4b7, 72:220–223 inflammation blocking, 72:242–243 lymph node development, 72:343

6

SUBJECT INDEX

a4b7 (continued) lymphocyte homing, 72:220–222, 233–234 aLb2, 72:349–350 Alphaviruses, antibody protection against, 77:232–233 Alzheimer’s disease, 68:23; 69:295; 80:267; 81:123 Alzheimer’s disease, causes, 66:260–261 AMA1, see Antigens, apical membrane Amino acid sequences, 82:251 substitutions, 82:346 Amino acid residues, 82:157–161 between Fcc/RF, 82:179–180 of FcRn, 82:165–167 of IgG, 82:166–169 in SpA binding, 82:187, 188 in SpG binding, 82:190–192 Amino terminal nonserpin domains, 82:333–335 Aminopeptidases in catabolic pathway, 80:17–18 interferon-inducible, 80:41–43 puromycin-sensitive, 80:45 trimming of N-extended peptides, 80:51 AML, transforming growth factor-b signaling, 75:131–132 AML, see Leukemia, acute myeloid Amphyphysin II, 81:60 Ampicillin, 69:374 Amyloid protein precursor, 68:22–23, 35 b-amyloid protein, 69:295 Anaphylatoxins, 82:177 and pre-T-cell-receptor complex, 69:45–47

Anergy, 71:243–248 Anergy, oral tolerance, 73:172–174 Angioedema, 82:345–347 Angiogenesis, role of CD26/DPP IV in, 81:30–31 Animal models B cell differentiation via IgH 30 regulatory region, humanized mice, 75:337 transforming growth factor-b signaling C. elegans, 75:124 Drosophila, 75:124 human cancer, 75:140–143 Xenopus, 75:123–124 vaccine efficacy studies, 75:5–6 Animal models, see Disease models Animals, 82:222, 264–269 Animals, in xenotransplantation, 79:189 Antagonistic pleiotropism, 80:246 Antagonists, 82:349 Anti-IL1, 66:140 Anti-IL6, 66:132 Anti-inflammatory hormones, 79:80–81 Anti-MBP TCR transgenic mouse model, 81:358 Anti-myelin basic protein (MBP) TCR-transgenic mice, 81:334 Anti-TNF, treatment with, 66:124, 132, 150 Antibodies anti-b2-glycoprotein I, 70:510–512 anti-Gal, 79:136–137, 139–141, 157–161 anti-SIINFEKL, 80:44

SUBJECT INDEX

anticardiolipin, 70:543–544 antidiotypic, in xenotransplantation immunosuppression, 79:159 antigen-induced, idiotypic specificities of, 80:207–211 antiphospholipid, 70:508–509, 536–537 antiprothrombin, 70:534–535 antiviral responses, see Antiviral antibody responses auto-antibody responses, B cell induction, 79:19–21 in AXHR, 79:136, 141–142 B cell differentiation via IgH 30 regulatory region, 75:317–338 B cell development activity, 75:319–320 control region function possibilities, 75:330–337 chromatin structure, 75:335–337 germline transcription, 75:331–334 hypermutation, 75:330–331, 337 immunoglobulin class switching, 75:331–334, 337 immunoglobulin-H expression, 75:334–335 replication, 75:330–337 control region structure, 75:317–319 DNA-binding proteins, 75:323–330 30 enhancer synergies, 75:320–322 humanized mice, 75:337

7

overview, 75:317, 337–338 B cell receptor signaling, 75:292–295 cancer immunotherapy, 75:263–264 combined VH/VL regions, 80:205–206 heavy-chain, see Heavy-chain antibodies infection enhancement, 79:22 intracellular bacteria protection role, 75:6–7 lupus anticoagulant effects, 70:535–536 laboratory studies, 70:544–545 location, 70:509–510 memory maintenance, 79:29–30 monoclonal, neutralizing, 80:226 natural in antiviral responses, 79:9–10 xenotransplantation tolerance, 79:175–176 neutralization attenuated vaccines, 79:33 infective vaccines, 79:32–33 linear epitopes, 79:33–34 mechanisms, 79:6–8 structural studies, 79:8–9 vaccines, 79:32 viral sensitivity, 79:23–24 non-Gal determinants, 79:141–142 presence in elderly, 80:265–266 production, and B cell aging, 80:257–259 response neutralization hepatitis B virus, 79:26 hepatitis C virus, 79:26 HIV, 79:26–27

8

SUBJECT INDEX

Antibodies (continued) influenza viruses, 79:25–26 lymphocytic choriomeningitis virus, 79:27 tumor T-cell response induction, 75:245–246 virus-neutralizing, 79:3–4 in xenotransplantation immunosuppression, 79:162–163 Antibodies (Abs), see also Arthritis, Rheumatoid allergen-specific, 82:115–120 anti-CD20, 82:50, 53–54 auto, 82:179, 218–219 blocking, 82:121, 127 CamPath1, 82:53 cell-surface carbohydrate, 82:62 glycoprotein, 82:58 Herceptin, 82:62 IgG, 82:262 levels of, 82:52 monoclonal, 82:50–51, 62 MUC1 and, 82:252 responses of, 82:54 tumor, 82:58–61 Antibodies against prion protein, 81:151 Antibodies, see Immunoglobulins; see also Monoclonal antibodies against IL-1, 68:13 anti-CD3, 68:5, 12, 13, 15 anti-CD28, 68:13 antireceptor, infection inhibition by, 77:223–225 antiviral activity, 77:196 in established infection, 77:241–244 coating of virion particles, 77:214–219

cytotoxicity mediated by, 77:226 in vivo protection by, 77:227–240 neutralizing, 77:196 nonneutralizing, 77:199 in passive transfer models, 77:277 phagocytosis mediated by, 77:226 Antibodies, see specific types Antibodies, CEA monoclonal (MAbs), 82:61 Antibodies, immunoglobulin E (IGE), 82:105–106 epitopes, 82:109 mediated allergies, 82:109–110, 115–120 T cells and, 82:113–114 Antibody neutralization adenovirus, 77:210–211 based on coating of virion particles, 77:214–219 and binding to virus, 77:198–200 early studies, 77:200–202 HIV-1, 77:211–213 host cell-derived proteins incorporated into virions, 77:222 influenza virus, 77:220–222 picornaviruses, 77:202–205 rabies virus, 77:211 single-hit vs. multi-hit kinetics, 77:205–210 and vaccine design, 77:247–248 Antibody responses, 71:95–98 Antibody-dependent cellular cytotoxicity, HSV and, 77:236–237 Anticardiolipin antibodies, 70:543–544

SUBJECT INDEX

Anticoagulants, in xenotransplantation, 79:153–154 Anticoagulation, sPLA2-IIA and, 77:176 Anticytokine therapy, 66:151 Antigen presentation class II-restricted, 80:102 by dendritic cells, 80:81–82, 131 IFN-g-induced changes, 80:28–30 MHC class I molecules, 80:21–22 IFN-g role, 80:47–48 MHC class II molecules, 80:71–73 nonproteasomal pathways, 80:32–33 PA28 role, 80:30–31 process, 80:96–102 proteasome role, 80:26–28 proteolytic step in, 80:44–47 ubiquitination in, 80:25–26 virus effects, 80:50 Antigen presentation, CD40-mediated regulation, 76:76–78, 130–131 Antigen presenting cells (APCs), 81:7, 178, 286, 330, 341, 356, 357 mutual activation/differentiation, 81:235–236 Antigen presenting cells, 69:375–378, 382–387 anergy, 73:173–174 CpG effects, 73:336–338 development, 73:1–2 mucosal immune response, 73:192–193

9

oral tolerance induction, 73:161 pAPCS ablating in vivo, 73:23–24 generation, 73:14–15 types DCs, 73:15–16 Møs, 73:15 virosome presentation, 73:43 Antigen receptor homology 1 motif, 69:188–189 Antigen receptors analogy with olfactory genes, 69:446 and ITAMs, 69:183–247 Antigen receptors, signaling BLNK-associating proteins, 79:116–117 GEMs role, 79:110–113 SLP-76 coupling to downstream events, 79:113–116 Antigen specificity required for suppressor effector functions of Treg cells, 81:356–359 Antigen-combining sites, 82:198–201 anaphylatoxin binding and, 82:177 C3b/C4b and, 82:176–177 Cc2-Cc3 interface and, 82:197–198 Clg binding as, 82:160, 174–176 complement, 82:160, 173–177 Fc receptor-binding sites as, 82:155–173 lectins and, 82:184–186 peptides and, 82:178–181 polymeric immunoglobulin receptors and, 82:172–173

10

SUBJECT INDEX

Antigen-combining sites (continued) proteins and, 82:178–183, 186–197 RF and, 82:179–181 transcytosis/catabolism and, 82:165–172 Antigen-driven clonal expansion, 69:120 Antigen-presenting cells bacterial invasions, 71:292–295 cancer immunotherapy role, 75:237 dendritic cell system model, 75:187–189 DNA vaccine delivery, 75:37 location, 70:315 major histocompatibility complex class II subversion by pathogens, 75:189–191 MCH II loading, 70:320–321 negative selection, 71:232–234 protease activity in, 80:73–87 proteolytic activity, regulatory role of Ii, 80:94–96 role in induction of cytokine memory, 80:130–133 targeting soluble antigens, 70:321–323 Antigen-presenting cells, conjugate with T cells, 77:77–79 Antigen-presenting cells, tumors, T-cell recognition escape helper T cell interactions, 74:241 microenvironment association, 74:239–241 Antigen-specific tolerance, 68:389–397 Antigen, selection for active immunization models, 77:265–267

Antigenic spreading, 70:546 Antigens, see also Cells; Immune response; Major histocompatibility complex; Superantigen; specific antigens acquisition step, 80:97–100 allergies and, 82:108–111 in auto-antibody responses, 79:20–21 in B cell responses dose, 79:12–13 organization, 79:13–15 structure, 79:15–16 B cell response differentiation, see B cells binding, and idiotype expression: dichotomy, 80:204–206 capture, 72:262 CD1, 72:257–258 CLA, 72:265 cleavage of: proteolytic steps in, 80:39–40 clonal selection by, transformed by idiotypic network, 80:220–223 degradation, by endocytic proteases, 80:100–102 delivery of, 82:73 differentiation expressed by macrophages and monocytes, 68:227–298 and macrophage characterization, 68:298–303 endoplasmic reticulum processing of, 68:197–199 exogenous, class I-presented peptides generated from, 80:48–49 expression in cancer

SUBJECT INDEX

hepatitis B virus, 75:235, 240 human herpesvirus type, 75:8, 239–240 human papilloma virus, 75:237, 240 non-virus-induced tumors, 75:241–246 CEA, 75:243–244 HER-2/neu, 75:244 immunoglobulin, 75:245–246 MUC1, 75:244–245 p53, 75:242–243 virus-associated tumors, 75:240 Gal, in xenotransplantation, 79:137 generation of peptides by, 68:199–205 human leukocyte antigen complex disease susceptibility, 76:34–38 diversity, 76:25–26, 32–34, 41 induced antibodies, idiotypic specificities of, 80:207–211 in interleukin-12 production, 79:79 intestinal, 72:237–240 intracellular bacteria infection antigen transition mechanisms, 75:59–61 DNA microarrays, 75:59–60 genome microarrays, 75:59–60 proteomics, 75:60–61 vaccinomics, 75:61 bacteria as antigen carriers, 75:49–56

11

compartmentalized expression, 75:55–56 heterologous antigens, 75:51–53 Listeria monocytogenes, 75:50–51 r-carriers, 75:55–56 Salmonella, 75:53–55 conserved versus specific proteins, 75:28–30 processing pathways, 75:14–15 recombinant carrier expression, 75:30–31 vaccine physicochemical properties, 75:27–28 MAM-6 DF3, 82:250 manipulation of, 82:76–78 marking for degradation, 80:100 and peptide transporter, 68:193–197 phosphate-containing, 71:88–89 presentation of, and proteasome activators, 68:204–205 presenting cells, 72:264 processing by major histocompatibility complexes antigen internalization, 75:181–186 B cell receptor-mediated uptake, 75:183 Fc receptor-mediated uptake, 75:183–184 fluid-phase uptake, 75:181–182 mannose receptor-mediated uptake, 75:184–185 phagocytosis, 75:185

12

SUBJECT INDEX

Antigens (continued) receptor-mediated uptake, 75:182–185 tumor antigens, 75:246–247 biosynthesis and assembly, 75:171–173 endoplasmic reticulum–Golgi transport, 75:172–173 folding mechanisms, 75:172 transcriptional control, 75:171–172 cell surface transport, 75:180–181 complex structures class II-associated peptides, 75:165–166 HLA-DM molecules, 75:169–171, 177–180 HLA-DO molecules, 75:169–171 MHC class II complex, 75:162–164 polygenicity, 75:164–165 polymorphism, 75:164–165 dendritic cell system model, 75:187–189 endocytic pathway entry, 75:173–176 overview, 75:159–160, 191–192 pathogen subversion, 75:189–191 pathway mechanisms, 75:14–15, 160–162 peptide loading, 75:176–180 processing mechanisms, 75:186–187 subcellular organelles role, 75:176–180

trans-Golgi-mediated sorting, 75:174–176 tumor antigens, 75:246–247 vaccinology, 75:14–15, 62 processing, 72:264–265 protective, 71:328–329 recognition of, and triggering of interleukin-2, 68:92 specific tolerance to, 68:389–395 stabilizing cytokine mRNA in lymphoid cells, 68:31 systemic lupus erythematosus autoantigen source, 76:285–287 T cell response, see T cells T cell tolerance, 71:112–115 Tn, 82:266 transplantation, 82:55 tumor-associated, 68:257, 284 tumor, 82:58–61 VHH binding loop structures, 79:286–289 immune libraries, 79:281–284 specific binders from libraries, 79:280 viral, 82:52, 55 xenotransplantation genetic engineering, 79:167–168 pharmacotherapy, 79:181–182 Antigens, see also specific antigens CTB, 73:182–183 endogenous MHC generation, 73:4–9 presentation in vivo, 73:56–63 exogenous internalization modes, 73:12–14 presentation

SUBJECT INDEX

ablating pAPCs in vivo, 73:23–24 aggregated proteins, 73:49–50 artificial particles, 73:32–34 bacteria, 73:26–32 cell debris, 73:34–36 cellular sonicates, 73:50–51 complex quantitating, 73:17–19 denatured proteins, 73:49–50 endogenous antigens in vivo, 73:56–63 immunogenicity, 73:24–26 inactivated viruses, 73:23–24 ISCOM, 73:42–44 liposome, 73:42–44 mechanism, 73:19–23 native proteins, 73:44–45 pathways, 73:26–32 processing, 73:19–20 quantum theory, 73:51–52 receptor-mediated uptake, 73:46–49 srivastava saga, 73:52–56 viral, 73:32–38 virosome, 73:42–44 virus-like particles, 73:38–39 Ki67, expression dividing T cell humans, healthy, 73:316–319 humans, HIV-infected, 73:319–320 oral biologic filtration, 73:188–189 dosage, 73:196–197

13

enzymatic digestion, 73:188–189 feeding regimes, 73:196–197 immunological effects, 73:153–155 induction factors, 73:183–187 inflammatory processes, 73:194–195 intestinal absorption, 73:189–194 Peyer’s patches, 73:197–200 structure, 73:187–188 proteinaceous, Th1 response, 73:348 Antigens, apical membrane (AMA1), 82:73 Antigens, carcinoembryonic (CEA), 82:61 Antigens, epithelial membrane (EMA), 82:250 Antigens, major histocompatibility complex I, 69:281 Antigens, prostate-specific (PSA), 82:83 Antigens, suppressor T cell factor relationship, see Suppressor-T cells, antigen-specific factors Antigens, Thomsen-Friedenreich, 82:255 Antimicrobial activity, sPLA2-IIA, 77:175–176 Antimicrobial genes, in immune response differential expression, 79:248–249 GATA factors, 79:247–248 immune deficiency pathway, 79:245–247 induction and regulation, 79:238–240

14

SUBJECT INDEX

Antimicrobial genes, in immune response (continued) Relish pathway, 79:244–247 Toll pathway, 79:240–244 Antineutrophil cytoplasmic antibodies, 73:403 Antiphospholipid antibodies characterization, 70:508–509 endothelial cells, 70:536–537 Antiphospholipid syndrome, 73:221 adrenal manifestations, 70:516–517 animal models, 70:531–533 anticardiolipin antibodies, 70:543–544 antiphospholipid antibodies, 70:536–537 APS-associated, 70:515 AVN-associated, 70:518–519 cardiovascular manifestations, 70:512–513 characterization, 70:507–508 dermal manifestations, 70:518 endothelial cells, 70:536–537 future therapies, 70:545–547 b2-glycoprotein I antibody binding sites, 70:523 characterization, 70:520–523 gene encoding characterization, 70:530–531 cloning, 70:530–531 molecular modeling alignment, 70:524–525 cardiolipin-binding region, 70:529–530 comparisons, 70:524–525 electrostatic properties, 70:528–529

fifth domain, 70:525, 527–528 structure, 70:523–524 phospholipid sites, 70:523 thrombosis link, 70:539–540 hepatic manifestations, 70:517 laboratory studies, 70:543–548 lupus anticoagulant antibodies, 70:535–536 laboratory studies, 70:544–545 neurological manifestations, 70:513–514 obstetric manifestations, 70:519–520 pathogenesis, 70:537–543 phosphatidylethanolamine, 70:536 protein C activation, 70:535–536 pulmonary manifestations, 70:515–516 renal manifestations, 70:516 summary, 70:547–548 Antiprion defense and innate immunity, 81:148–150 Antisense oligonucleotides, 69:375 Antisilencers, see Silencers Antithrombin III, 66:238 Antiviral antibodies, V(D)J rearrangements, 79:3 Antiviral antibody responses complement role, 79:10–12 Fc-receptors role, 79:12 mechanisms, 79:5 natural antibody role, 79:9–10 overview, 79:2–3 protection, 79:5–6 Aortagonad-mesonephros (AGM), 81:278–280 AP, see Apyrimidinic-endonuclease AP-1, 72:23

SUBJECT INDEX

AP-1 transcription factor complex, transforming growth factor-b signaling, 75:131 AP-1, B cell immune response regulation by CD40-CD154-signaling, 76:79, 87–92 AP-1, lipopolysaccharide signaling in macrophages, 78:19–20 Apaf-1 adapter molecule, lymphocyte apoptosis-signaling, 76:184–186 APC, see Antigen-presenting cells; see Antigen presenting cells APCs, 82:72–75 antibodies and, 82:114 transfection of, 82:78 APECED (autoimmunepolyendocrinopathycandidiasis-ectodermal dystrophy), 81:358 Apical surface, 70:399–400 APO-1/Fas proteins, 71:164 Apoptosis, 69:379, 380–381; see Cell death; see also Programmed cell death AICD, 70:15–19 in anucleate cells, 68:70 as autoimmune disease therapy, 68:337 Bcl-2 proteins, 71:172–174 calcium ions and, 68:52, 56, 64, 65, 71 capase-induced, 71:176–180 caspases role in, 68:57–61 CD45 role in, 68:98–101 CD95/CD95L system

15

AIDS, 71:188–190 characterization, 71:166–167 chemotherapy, 71:184–188 death domain, 71:170 death receptor signaling, 71:175–180 discovery, 71:165 flips, 71:182 gene defects, 71:167–168 hepatic homeostasis, 71:169 peripheral T cell deletion, 71:168–169 signaling molecules, 71:170–172 signal transduction, 71:169–170 T cell sensitivity, 71:182–184 type I and type II cells, 71:180–182 cell structure changes, 68:54–55, 64 characterization, 71:163–164 clinical applications, 71:190–191 common pathway, 68:54–88 degradation phase, 68:54–65 dendritic cells, 72:263–264 DISC, 71:174–175 effector phase, 68:65–88 executioner, 68:66–88, 120–124 genetic susceptibility to, 68:68–69 GTPases role, 72:47–49 IL-2, 70:14–19 induced by tripeptidyl peptidase II inhibitors, 80:20 inducers of, 68:53–54, 74 inhibition, 70:251–253 initiating factor, 70:258–259 initiation phase, 68:89–122 ligands, 71:164–166

16

SUBJECT INDEX

Apoptosis (continued) lymphocyte death, 76:179–205 B cell development immature cell selection, 76:202–203 peripheral lymphoid organs, 76:203–205 pre-BCR checkpoint, 76:200–202 caspase role, 76:179–180, 184–186 immune system function, 76:189–190, 288–290 overview, 76:179, 205 regulation Apaf-1 signals, 76:184–186 Bcl-2 family, 76:184–189 caspase 9 signals, 76:184–186 death receptor signals, 76:180–184 transcriptional control, 76:188–189 T cell development peripheral lymphoid organs, 76:195–199 positive and negative selection, 76:192–195 pre-TCR checkpoint, 76:190–192 tumor necrosis factor-R family role, 76:199–200 magnesium ions and, 68:56 mechanism, 70:269–270; 71:163–164 mitochondrial control, 70:257–259 necrosis and, 68:55, 62, 72–73, 85–86 potassium ions and, 68:65

private pathways, 68:53, 63, 83, 89–122 promotion, 70:253–255 proteasome inhibitors and, 80:15 protein inhibition, 70:251–253 Ras role in, 68:168 receptors, 71:164–166 recognition of cells in, 68:56 regulatory processes of, 68:51, 54 rescue from, 68:111–113 signal transduction pathways and, 68:122 systemic lupus erythematosus, 76:283–292 anti-C1q autoantibody development, 76:292 apoptotic cell clearance, 76:287–288, 290–291 autoantigen source, 76:285–287 complement role, 76:290–291 immune response, 76:288–290 TNF-induced, 71:178–179 TRAF-mediated regulation, 76:134–136 types, 71:163 zinc ions and, 68:55, 56. Apoptosis, in JNK pathway, 77:139–140 Apoptosis, T cells, tumor recognition escape, microenvironmental inhibitory signals, 74:234–236 Apoptosis, TNF and, 66:114 APS, see Antiphospholipid syndrome Apyrimidinic (AP)-endonuclease, 82:310 Arachidonic acid, metabolism, 77:170–175

SUBJECT INDEX

Architecture poliovirus and HRV, 77:204–205 T cell activation, 77:77–79 Arenaviruses antibody protection against, 77:233 passive protection, 77:248 Arginyl bonds, 69:250 Aronica, M. G., 82:7–9 Arterial thrombosis, 70:513 Arthritis, see also Rheumatoid arthritis adjuvant, 82:228 antigen-induced (AIA), 82:224–225, 234–235 collagen-induced, 68:369–371, 375–377, 393–394; 73:272 collagen-induced (CIA), 82:223–224, 234–235 in HTLV mouse, 82:230–231 in IL-lra mouse, 82:232 immunizations and, 82:232–233, 234–235 in Ipr mouse, 82:230 K/BxN, 82:228–230, 235 mutant IL-6 mouse, 82:232 non-rheumatoid juvenile, 68:352 other models for, 82:232–233 pristane-induced, 82:226–227 proteoglycan-induced (PGIA), 82:226, 234–235 psoriatic, 82:233 rheumatoid, see Rheumatoid arthritis septic, 73:460–461 streptococcal cell wall (SCW), 82:226–227 zymosan-induced, 82:227–228

17

Arthritis, collagen-induced, 70:162–164 Arthritis, rheumatoid (RA), 82:235–238, see also Rheumatoid factors adjuvant arthritis and, 82:228 AIA and, 82:224–225 animal models of, 82:222 CIA and, 82:223–224 cytokines/macrophages and, 82:219 effector mechanisms and, 82:220–222 features of, 82:217 fibroblasts and, 82:219, 308 K/BxN arthritis and, 82:228–230 MHC and, 82:217–218 mouse models of, 82:217–237 PGIA and, 82:226 pristane-induced arthritis and, 82:227 SCW and, 82:226 T cells and, 82:217–218 theories of, 82:217–219 zymosan-induced arthritis and, 82:227–228 Arthritis, rheumatoid, 69:364 ASC-MUC1, see MUC1purified from ascites fluid of cancer patients Asparaginyl endopeptidase antigen degradation by, 80:100 present in APCs, 80:76 Assays, early thymocyte development in vitro, 69:3–4 in vivo, 69:5–6

18

SUBJECT INDEX

Asthma, 72:293–294; 82:21–22, 113–114 ABCD chemokine role, 78:148–149 CpG DNA role, 73:350–351 gastrointestinal eosinophils, 78:319–320 IL-8 production, 73:427 industrial model of, chemical compounds in, 77:267 RSV association with, 77:285–286 Ataxia telangiectasia (AT), 82:315–316 Ataxia telangiectasia, 69:311 Ataxia-telangiectasia gene, 72:180–181 lymphoid defects characterization, 72:179 dissecting, 72:181–185 tumorigenesis characterization, 72:179 dissecting, 72:181–185 ATF-2, transforming growth factor-b signaling, 75:131 Atherosclerosis, 69:367 autoimmune hypothesis, 80:263–265 HSP 60 and, 80:273 Atherosclerosis, sPLA2-IIA role, 77:177 ATM, 72:180–181 Atopic dermatitis, ABCD chemokine role, 78:149–150 Atopic disorders, 68:115–116 Atopy, 82:114 ATP, see Adenosine triphosphate ATP, protein degradation dependent on, 80:3

ATPase, in 26S proteasome base, 80:10–11 ATPases, in xenotransplantation, 79:170–171 Atrophy organ, 80:246–247 thymus, cytokines and, 80:269–270 Auto-Abs, 82:236 Auto-antibody responses, B cell induction, 79:19–21 Autoimmune disease, 69:363–364, 367–368; 81:331 abnormality in Treg cells, 81:335–336 HLA and, 66:67, 76, 84–85, 93 insulin-dependent diabetes mellitus, 66:91 methimazole-induced insulin autoimmune syndrome, 66:87–88 multiple sclerosis, 66:88–91 pemphigus vulgaris, 66:87 rheumatoid arthritis, 66:85, 87 immunointervention, 66:91–93 organ-specific, 70:157–158 pregnancy effects, 70:519 spontaneous, 70:165–166 Autoimmune disease, T-cell receptor crossreactivity role, 75:209–226 cytokine checkpoints, 75:223–226 low affinity ligands, 75:211–214 overview, 75:209 peripheral purging of useless T cells, 75:218–220 peripheral T-cell tolerance, 75:214–217

19

SUBJECT INDEX

T-cell antagonism, 75:211–217 viral-derived peptide agonists, 75:220–223 Autoimmune diseases, see also specific diseases animal model studies, 68:365–397 anti-CD7 monoclonal antibodies and, 68:358–359 apoptosis and, 68:51, 100 CD30 and, 68:115–116 cytokine treatment, 68:337–347 DR3 production, 73:286–287 interleukin-2 targeted approach to, 68:359–361 major histocompatibility complex and, 68:385–386 monoclonal antibodies and anti-CD4, 68:347–353 anti-CD5, 68:353–358 anti-CD7, 68:358–359 oral tolerance animal models, 73:218–223 humans, 73:227–228 worsening, 73:223–224 peptide transporters and, 68:226–228, 238–239 preventive therapy, 68:395 T cell receptor costimulation and, 68:381–385 TNF-a implications, 73:275–277 TRAIL production, 73:286–287 Autoimmune lymphoproliferative syndrome, 71:167 Autoimmune response, 69:363, 383, 387 Autoimmune vascular disease, 70:531–532

Autoimmunity control by naturally arising regulatory CD4þ T cells, 81:329–369 Treg cells in spontaneous models of, 81:335 Autoimmunity, B cell induction, 79:19–21 Autonomic nervous system, 81:143 Autoreactivity, 69:150–152, 155–156 AUUUA motifs AU-B and AU-C binding requirement, 68:34 in AU-binding factor, 68:30–31 in c-fos and c-myc mRNAs, 68:27–28 in ICAM-1, 68:27 long term repeats and, 68:22 in mRNA regulation, 68:5–8, 11–15, 19 Auxiliary factor (ACF), 82:306 Avascular necrosis of bone, 70:518–519 Avery, O. T., 82:50 AVN, see Avascular necrosis of bone AXB cells, 73:59 Axons, guidance to appropriate targets, 81:173 Azathioprin, 68:356

B B-cell attracting chemokine-1 (BCA-1), 81:6 B-cell development CD100 in, 81:183–184 in teleosts, 81:282–285 in zebrafish pancreas, 81:284–285

20

SUBJECT INDEX

B-cell differentiation, 81:103 B-cell lineage lymphomas, 81:99, 103 B-cell lineage lymphomas/ leukemias, human and mouse, 81:105 B-cell lineage neoplasms, 81:100, 113–115 B-cell lymphomas, 81:238–239 B-cell receptor (BCR), 81:286 B-cell receptors and ITAMs, 69:186, 205–206, 208, 211–212 and SHP-1, 69:222–223 structure of, 69:186–189 B-cells, 81:5, 47, 130, 134–136 self-reactive, 81:329 zebrafish, 81:255 b-globin, 68:19, 20, 25, 26 B-lineage cells, transformation, 81:111 B-lymphocytes, 81:47, 130 B-natural killer cell lymphoma, 81:105 B7 molecules, 68:280, 382–385 B1 receptors, 66:239, 240 B2 receptors, 66:240 Bacille Calmette Gue´ rin antigen carrier role, 75:49–53 tuberculosis vaccination, 75:29, 46–47 Bacillus Calmettte-Gue´ rin (BCG), 82:270 Bacteria, 69:295; 72:294 major histocompatibility complex class II antigen presentation subversion, 75:189–191 vaccinology, see Vaccines Bacteria, see also specific bacterium artificial particles, 73:32–34

DNA, CpG motifs as antitumor adjuvant, 73:349–350 cellular uptake, 73:333 CTL response, 73:353–354 evolution, 73:346–348 extramedullary hematopoiesis-induced, 73:351 immune cell activation, 73:352 immune response, 73:331–332 mediative effects in vivo, 73:349 as mucosal adjuvant, 73:351 sequence effects APCs, 73:336–338 B cells, 73:334–335 immunosuppressive, 73:342 independent, 73:333–334 macrophage receptors, 73:341 NK cells, 73:339 T cells, 73:338–339 TNF-a production, 73:342 signal mediation cell response, 73:352–353 cellular uptake, 73:343–344 chloroquine effects, 73:346 lysosomotropic compounds, 73:344–345 stress kinase pathway, 73:345–346 T cell effects as Th1 adjuvant, 73:348–349 Th2 pathology, 73:350–351 infections in vivo, 73:467–468 protein presentation, 73:26–32 Bacteria, see also specific species Bcl-2 homology, 70:263–264 IL-12 inhibition, 70:177–181

SUBJECT INDEX

Bacteria, interleukin-12 induction, 79:62–63 Bacterial DNA, 69:372–373 Bacterial pathogens, intracellular survival of, 81:65–70 Bacteriophage, DNA delivery, 75:58–59 Baculovirus, 68:60, 120, 216–217 BAF chromatin-remodeling complex, lymphocyte signaling role, 75:109–110 Bafilomycin A, 73:346 Bagnara, G. P., 82:7–9 BALB/c mice, 81:101 BALT, see Bronchial-associated lymphoid tissue Basic fibroblast growth factor (bFGF), 81:20 Basolateral surface, 70:399 Basophils activation IgE dependent, 77:101–104 IgE independent, 77:104–106 allergic disease and, 77:112–114 cell surface markers, 77:94–98 comparison with mast cells, 77:93 growth and maturation, 77:94 inflammatory mediators, 77:98–101 signal transduction and control of secretion, 77:106–112 Basophils, 68:173 Bax, 71:172–173 B cell activation and follicle formation, 78:126 compartmental homing within secondary lymphoid organs

21

B cell-rich areas, 78:130 microarchitecture formation role lymphotoxins and receptors, 78:131–133 tumor necrosis factor and receptor, 78:131–133 memory/effector cell migration features of cells, 78:143–144 plasma cells and chemokines, 78:144–145 T cell encounters and chemokines, 78:141–143 V(D)J rearrangements, see V(D)J recombination B cell linker protein–Grb2 complex, 73:96, 98 B cell linker protein associating proteins, 79:116–117 deficient B cells, 79:108–110 ITAM-coupled signaling, 79:99–100 B cell receptor antigen uptake role, 75:183 B cell activation, 74:68, 73, 82 editing, see B cells, receptor editing pre-BCR checkpoint, 77:126–127 signal pathway, 77:123 translocation into DRMs, 77:69 tyrosine kinase activation mechanisms, 75:288–292 response differences, 75:291–292 stage-specific differences, 75:289–291

22

SUBJECT INDEX

B cell receptors immunoreceptor tyrosine-based activation motifs, 76:326–328 pre-BCR apoptosis checkpoint, 76:200–202 signal transduction CD95, 73:132–134 CD19 regulation, 73:118–119 CD22 regulation CD22-deficient mice in vivo, 73:108–109 description, 73:107–108 MAP kinases, 73:115–119 SHP-1-deficient mice in vivo, 73:110–112 CD40 regulation apoptosis, 73:124–127 MAP kinase role, 73:128–129 overview, 73:122–124 P13K pathway, 73:129 PTK role, 73:127–128 TRNR factors, 73:129–132 CDw150 regulation, 73:121–122 B cells, see also pre-B cells activation and tolerance, complement role, 74:61–83 C3, 74:61–65 activation mechanisms, 74:63–64 C3d, 74:61–63 humoral immunity, 74:64–65 innate recognition, 74:63–64 source, 74:64–65 complement deficiency, 74:78–82

humoral immunity enhancement, 74:65–72 antigen retention on follicular dendritic cells, 74:69–72 B cell co-receptor signaling, 74:69–72 CD21/CD35 role, 74:64, 67–69, 82 classical pathway, 74:65–67 overview, 74:61, 82–83 self-reactive B cells, negative selection B cell energy alterations, 74:74–78 C4 deficiency effects, 74:74–78 Cr2/mouse impairment, 74:73–74 natural antibody role, 74:82 systemic lupus erythematosus induction, 74:78–82 aging, and antibody production, 80:257–259 allelic exclusion, 69:115–116, 137 and a4 integrins, 69:86 anti-C5 therapy and, 68:353, 356 antibody-producing, 71:96 antigen receptor complex, 73:89–91 antigen-receptor signaling in, 68:111 antigen-specific, 80:214 antigen-specific receptor BCR, 80:99 antigenic spreading, 70:546 apoptosis in, 68:96 apoptosis, 76:179–205

SUBJECT INDEX

caspase role, 76:179–180, 184–186 cell development immature cell selection, 76:202–203 peripheral lymphoid organs, 76:203–205 pre-BCR checkpoint, 76:200–202 immune system function, 76:189–190, 288–290 overview, 76:179, 205 regulation Apaf-1 signals, 76:184–186 Bcl-2 family, 76:184–189 caspase 9 signals, 76:184–186 death receptor signals, 76:180–184 transcriptional control, 76:188–189 autoimmune induction, 79:19–21 autoreactive, 69:150–152 B-2, antigen-inducible, 80:223 and bacterial DNA, 69:372 Bcl-2, and mitochondrial function of, 68:75 BLNK-deficient, 79:108–110 CD45 and, 66:22–31, 36–37 monoclonal antibody studies and, 66:12–15 CD4þ expression, 70:327–328 CD4þ priming, 70:325–326 and CD45, 68:98–99 CD45-deficient, 66:22–26 CD69 and, 68:14 cell death pathways mIgM model, 73:105–106

23

WEHI-231 model, 73:104–106 chemokine relationship, 74:139–144 CpG effects, 73:334–335 and CpG motifs, 69:372–373 death regulation, 73:84–87 –dendritic cell interaction B cell differentiation, 72:289–291 B cell proliferation, 72:289 dialogues, 72:288–291 follicular DC, 72:286–287 general, 72:285 germinal center DC, 72:287–288 development, 70:42–47; 72:339–340 BLNK and, 77:148–149 Btk and, 77:124–129 development, apoptosis role immature cell selection, 76:202–203 peripheral lymphoid organs, 76:203–205 pre-BCR checkpoint, 76:200–202 differentiation, 69:117, 119 differentiation via IgH 30 regulatory region, 75:317–338 B cell development activity, 75:319–320 control region function possibilities, 75:330–337 chromatin structure, 75:335–337 germline transcription, 75:331–334

24

SUBJECT INDEX

B cells (continued) hypermutation, 75:330–331, 337 immunoglobulin class switching, 75:331–334, 337 immunoglobulin-H expression, 75:334–335 replication, 75:330–337 control region structure, 75:317–319 DNA-binding proteins, 75:323–330 30 enhancer synergies, 75:320–322 humanized mice, 75:337 overview, 75:317, 337–338 differentiation via tyrosine kinase activation, 75:283–308 activation–cellular response connection, 75:304–307 development regulation, 75:284–288 heavy chain selection of preB cells, 75:284–286 mature B cell activation, 75:287–288 mature B cell maintenance, 75:288 tolerance induction of immature B cells, 75:286–287 immunoglobulin-a and -b coreceptors, 75:292–295 overview, 75:283–284, 307–308 receptor response mechanisms, 75:288–292 response differences, 75:291–292

stage-specific differences, 75:289–291 tyrosine kinase families, 75:295–304 Btk of the Tec family, 75:302–304 Src family, 75:296–300 Syk of the Syk/Zap70 family, 75:300–302 DNA activation, 73:347 FcgRII in, 68:278 glycosylation inhibiting factor effects, 74:50–51 GM-CSF production, 68:8 ICOS ligand expression, 80:154 idiotypic activation or suppression, 80:211–219 IL-10 production, 68:13 IL-12 effects, 70:148–151 IL-12 production, 70:102–104 IL-18 effect, 70:289 IL-18R expression, 70:296–297 immune response regulation by CD40-CD154-signaling, 76:86–145 activators, 76:80 AP-1 activation, 76:79, 87–92 CRE activation, 76:87, 92 functional outcomes, 76:126–136 adhesion, 76:129–130 antigen-presenting cell function, 76:130–131 apoptosis regulation, 76:134–136 cell survival and proliferation, 76:127–128 cytokine secretion, 76:131

SUBJECT INDEX

IgH class switching, 76:133–134 immunoglobulin production regulation, 76:131–134 inhibitors, 76:80 NF-AT activation, 76:79, 88–92 NF-kb activation, 76:87, 92–93, 100–103, 116–121 signaling cascades, 76:116–126 cAMP-mediated-signaling pathways, 76:144–145 ERK activation, 76:89–90, 120, 125–126 JAK–STAT pathways, 76:138–140 JNK activation, 76:90–91, 98–100, 120–124 NF-kb activation, 76:87, 92–93, 100–103, 116–121 p38 activation, 76:92, 98, 100, 124–125 reverse-signaling through CD154, 76:145 src activation, 76:140–143 tec family kinase activation, 76:140–143 ZAP-70 activation, 76:140–143 T cell collaboration, 76:69 TRAF adapter molecule discovery, 76:93–115 transcription factor activation, 76:87–93 immune response regulation by CD40/CD154-signaling, overview, 76:61, 69

25

immunoglobulin mRNA levels in, 68:17 inhibition, 69:218–219 interleukin-12 production EBV-transformed cells, 79:59–60 normal cells, 79:60 and ITAMs, 69:205–206 k and l LC genes, 69:116, 142, 145, 150–152 lineage, 69:18 lymphoma, and peptide transporter, 68:236 memory, 69:214; 72:237–240; 75:23–25 memory, diminished survival, 80:184 negative selection, 71:238–239 peptide transport and human, 68:239 PLCg2 activation in, 77:138 protooncogene levels in, 68:5 and protein tyrosine kinases, 69:194–195, 199 receptor editing, 74:89–114 allelic exclusions, 74:96–100 feedback suppression of recombination, 74:98 immunoglobulin-L chain, 74:99–100 mechanisms, 74:97–98 selective factors, 74:97–98 stochastic factors, 74:97 antigen-reactive B cells, 74:108–110 antigen receptor gene assembly, 74:89–90 clonal versus receptor selection, 74:89

26

SUBJECT INDEX

B cells (continued) developmental stage specificity, 74:107–108 editing analysis, 74:102–104 gene-targeted antibody gene mouse, 74:102–104 immunoglobulin genes, 74:91–92 in vivo monitoring, 74:100–102 locus specificity, 74:106–107, 110–111 mature B cells, 74:108–110 overview, 74:89, 114 rearrangement possibilities, 74:112 quasi-ordered rearrangements, 74:95–96 secondary rearrangements, 74:92–94 receptor diversification, 74:108 receptor revision, 74:108–111 receptor selection concept problems, 74:112–114 allelic inclusion, 74:113 disease applications, 74:113–114 need, 74:113 rearrangement possibilities, 74:112 receptor versus clonal selection, 74:89 recombinational accessibility, 74:94–95 recombination signals, 74:90–91 RS/kde element role, 74:93–94 12/23 rule, 74:90–91

tolerance developmental block association, 74:104–106 transgenic models, 74:100–102 V(D)J recombination role, 74:89–90 receptors, ITIM inhibition, 72:155–156 responses, antigen role dose, 79:12–13 organization, 79:13–15 structure, 79:15–16 and SHP-1, 69:222–223 signal transduction Grb2-related molecules, 73:97–100 MAP kinases, 73:101–104 overview, 73:79–80 P13K, 73:92–93 PLC-g, 73:92–93 pleckstrin homology domains, 73:101–102 PTKs, 73:91–92 Ras pathway, 73:95–97 Vav guanine-nucleotide exchange factor, 73:100 size, 73:85–86 subpopulations, 73:88–89 switch recombination, 80:186 T cell anergy, 71:245–246 gd T cell response, 71:93–95 thymus population, 71:9–10 tolerizing, 70:547 and transcription factor mutations, 69:79, 80, 81, 84 unresponsiveness, viral studies, 79:18–19 in viral infections, 79:16–17

SUBJECT INDEX

and V(D)J gene arrangement, 69:316, 318–319, 326, 329 in xenotransplantation pharmacotherapy, 79:181–182 B-effector 1 cells, generation, 80:132–133 BCG vaccine, 71:327–332 BCG, see Bacillus Calmette-Gue´ rin Bcl-2 and antagonist, Bax, 68:83 and apoptosis, 68:69–70, 73, 76, 80, 91–92 apoptosis inhibition, 70:251–253 promotion, 70:253–255 associated proteins, 68:83–84 Bad, 73:95 CD40 regulation, 73:125 cell physiology, 70:261 cell survival, 70:266–269 channel-like function, 68:74 characterization, 70:250–251 function, 70:256–257 genes for, 68:74, 91 ion channels, 70:265–266 localization, 70:255–256 mitochondrial permeability transition and, 68:74, 76, 80, 123 and necrosis, 68:73 and PC12 cells, 68:75 related proteins, 68:54, 83–84 and signal transduction modules, 68:107–111 structure, 70:263–264 Bcl-2 family proteins, lymphocyte apoptosis regulation, 76:184–189 Bcl-2 proteins, 71:172–174

27

BCL-6, competition with Stat6, 80:121 Bcl-xL CED, 70:268–269 ion channels, 70:265–266 structure, 70:261–263 BCR, see B cell receptor BCR/ABL tyrosine kinase, 81:102 BCRs, see Receptors, B cell Bellani, P., 82:22 Bennett, W. C., 69:116–117 b2m, 73:40–41 b7, 72:225–227 Bethesda proposals, 81:104 BFA, see Brefeldin A Biliary cirrhosis, T cell responses against modified peptides, 78:283 Biologic filtration, 73:188–189 Biotechnology, VHH role, 79:289–290 Biragyn, A., 82:72 Birth control pills, 69:422 Bleomycin, aminopeptidase hydrolyzing, 80:42 BLNK B cell development and, 77:148–149 Btk inducibly associated with, 77:134 and Btk, in early B cell development, 77:149–150 integration of Btk and Syk activities, 77:142–148 BLNK, see B cell linker protein Blood clotting, contact activation, see Contact activation Blood coagulation, 69:251–252 Blood mononuclear cells, 72:277 Bloodstream, 82:25–26

28

SUBJECT INDEX

Bombyx mori, immune response, 79:229 Bone marrow chemokine and receptor expression, 78:74–75 hematopoietic stem cell migration during embryogenesis integrins, 78:119 overview, 78:117–118 stem cell rolling, 78:118–119 Bone marrow cells CD34 progenitor, 68:6 deletion of derived, 68:89 primate stromal, 68:14 sialoadhesin in, 68:275 as source of F4/80 antigen, 68:272, 273 Bone marrow derived macrophages (BMM), 81:79 Bone marrow function, 73:306–307 Bone marrow progenitor cells, aging and, 80:248–249 Bone marrow transfer experiments, 81:135 Bone marrow, B cell selection, 76:202–203 Bone marrow, XLA, pre-B cells in, 77:125–127 Bone morphogenetic proteins, transforming growth factor-b signaling role, 75:115–116, 125–126 Bone, avascular necrosis of, 70:518–519 Bony fish complement system, 81:258–259 inflammatory processes, 81:259–260 innate immunity in, 81:257–260

Bordetella pertussis, 70:180 Borrelia burgdorferi, 70:180 Bovine leukemia virus, 69:121, 190 Bovine papillomavirus, antibody neutralization, 77:214 Bovine spongiform encephalopathy (BSE), 81:124 pathogenesis, 81:137 in sheep, 81:137 12/23-bp rule, 69:312 BRA, see Brefeldin A Bradykinin formation, 66:225, 226, 233–239 function, 66:239 receptors, 66:239–240 Bradykinins, 82:344–345, 346 Brain damage in prion diseases, 81:126–127 Brain microglia, macrophages in, 68:272 BrdU, see Bromodeoxyuridine Breast cancer IL-6 production, 73:440 TNF-a production, 73:440 Brefeldin A function, 73:21 Brefeldin A, 68:174, 196 Brizzi, M. F., 82:7–9 Bromodeoxyuridine, 73:315–316 Bronchial-associated lymphoid tissue, 73:203 Bruce effect, 69:421, 423 Brucella abortus, 70:180; 81:68 Brugia malayi, 70:187 Bruton’s tyrosine kinase activation, 77:129–137 B cell development and, 77:124–129

SUBJECT INDEX

and BLNK, in early B cell development, 77:149–150 calcium signaling downstream of, 77:137–138 SH3 domain, 77:135–136 and Syk, integration via BLNK, 77:142–148 tyrosine phosphorylation, 77:129–132 WASP and TFII-I pathways downstream of, 77:141–142 Bruton’s tyrosine kinase, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:331–332 BSAP, V(D)J recombination regulation, 78:206–207 Btk tyrosine kinase, cellular response differentiation in B lymphocytes, 75:302–304 Btk, 72:160; see Bruton’s tyrosine kinase Burkitt lymphoma (BL), 81:98, 108 Burkitt’s lymphoma, 69:213 Burkitt-like lymphoma, 81:108 Burn patients, 68:167 Burnet, Sir MacFarlane, 69:113

C C chemokines, 81:1–3 c-fos actinomycin-D and, 68:2–3 antigen receptor signal transduction and, 68:94 AUUUA motifs in mRNA, 68:19, 27 cis elements and, 68:18, 21 in fibroblasts, 68:27

29

instability determinants in, 68:27–28 mRNA decay, 68:2, 21 protein binding to, 68:35 truncation of, 68:31 c-jun, 68:94, 105 c-myc and apoptosis, 68:69–70 coding region instability element, 68:35 and mRNA regulation, 68:5, 18, 21–22, 27–29 30 untranslated region of, and AU-A, 68:34 c-fos, 70:26–27, 41 c-jun, 70:41 c-Jun N-terminal kinase (JNK), 82:32 c-jun N-terminal kinase pathway apoptosis and, 77:139–140 in Vav/Rac pathway, 77:10–11 c-jun amino-terminal kinases, 73:101–104 C-kit, 69:67–73 c-Maf, T helper cell differentiation role, 78:241 c-Maf, Th2 transcription factor, 80:127 c-myc, 70:26–27, 41 C-terminal peptides anchored at, 68:220–225 processing events at, 68:151–164, 171–172 C-type lectin (CTL) receptors, 81:269 C-type lectin receptor, 72:263 C/EBPb, see NF-IL6 C/EBP, see CCAAT/ enhancer-binding proteins

30

SUBJECT INDEX

C1 INH deficiency, in hereditary angioedema, 66:257–258, 259 C1, 69:249–250, 257 inhibitor of, 69:286, 289–291 C1q, 69:284–285 C1q complement protein, deficiency, systemic lupus erythematosus anti-C1q autoantibody development, 76:292 autoantibody production to C1q, 76:281–283 C1q-deficient mouse, 76:277–278 genetic deficiencies, 76:227–237 C1r and C1s, 69:278–290 catalytic activity, 69:285–291 and chymotrypsin, 69:282 esterolytic activity, 69:281–282 gene for, 69:278–279 protein modular structure, 69:279–282 protein-protein interactions, 69:282–285 substrates, 69:281–282 C1r complement protein, deficiency, systemic lupus erythematosus relationship, 76:238 C1s complement protein, deficiency, systemic lupus erythematosus relationship, 76:238 C2, 69:250, 257, 270–278, 294 C2, deficiency, systemic lupus erythematosus relationship deficient mouse model, 76:278 genetic deficiency, 76:243–251 null alleles, 76:269–272 C3, 69:249–250

C3 convertase complex, 81:52 C3 exotoxin, 72:33–34 C3-convertase, 69:273, 293–294 C3, deficiency, systemic lupus erythematosus relationship deficient mouse model, 76:278–279 genetic deficiencies, 76:251–252 C4, 69:286 C4, deficiency, systemic lupus erythematosus relationship deficient mouse model, 76:278–279 genetic deficiency, 76:238–243 null alleles, 76:265–269 C5, 69:249 C5-convertase, 69:293, 294 CA074, cathepsin B-specific inhibitor, 80:85 CaaX substrates CaaX prenyltransferases, 68:152–157, 175 farnesyltransferase, 68:152–157, 164–165, 175–178 geranylgeranyltransferase type-I, 68:152–157, 177–178 type-II, 68:152, 158–162 Cachectin, 66:105 Cactus, in Drosophila immune response, 79:243–244 CAD, see Chronic airway disease E-Cadherin, 72:333–334 Caenorhabditis elegans, transforming growth factor-b signaling by Smad proteins, 75:124 CAF, HIV-1 replication, 66:281, 282–283, 287 Calcineurin, 69:56; 82:23 Calcineurin, NF-AT and, 77:110

SUBJECT INDEX

Calcium and activation signals, 69:224 BCR-triggered, 72:156–157 Btk effects, 72:160 Ca2þ, dendritic cell, 72:273–274 and C1r and C1s, 69:283–284, 286 cytosolic, role in basophil pro-secretory events, 77:109–110 and epidermal growth factor-like module, 69:283 ITAM effects, 72:150 SHIP effects, 72:159 signaling BCR-induced, 77:144 downstream of Btk, 77:137–138 in T-cell development, 69:56 Calcium channels, L-type, actin-regulated, 77:32 Calcium flux, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:338–339 Calcium ionophore, 68:5, 13, 15, 16, 31 Calcium ions in antigen-receptor-induced activation, 68:93, 95–97 in apoptosis, 68:64, 65, 71 and AU-binding factor regulation, 68:32 and endonuclease activation, 68:56, 65, 71 and macrophage adhesion, 68:274–275 and mitochondrial membrane, 68:80, 83, 87, 96–97, 122–123

31

in thymocyte selection, 68:100–101 Calcium pyrophosphate dihydrate IL-1 association, 73:403 IL-8 association, 73:378 Calmodulin, transforming growth factor-b signaling, 75:128 Calpains, 68:61, 62–63 Calponin homology domains, 77:10 Calreticulin (CRT), 82:76–77 Camelidae, heavy-chain antibodies antigen-specific, isolation dromedary immunization, 79:275–276 monoclonal VHH, 79:277–281 proteolyzed HCAbs, 79:276–277 H chain CH1 domain removal, 79:265–266 variable domain, 79:266–269 L chain, 79:269–270 natural occurrence, 79:261–264 ontogeny, 79:272–275 VHH antigen-binding loop structures, 79:286–289 antigen-specific, immune libraries, 79:281–284 biotechnological role, 79:289–290 gene phylogeny, 79:270–272 structure, 79:285 VL-side conformation, 79:285–286 cAMP, and pre-T-cell-receptor, 69:55–56 cAMP, B cell immune response regulation, 76:144–145

32

SUBJECT INDEX

Camptothecin, 68:105 Cancer, 69:215–216, 367; see Tumors; see also Carcinogenesis breast, 82:270 cervical, 82:255 heptocellular, 82:49 immune responses to, 82:261–264 immunity evasion/tolerance and, 82:55–58 immunotherapy strategies, 75:235–264 adjuvants, 75:258–261 antigens eliciting T-cell responses CEA, 75:243–244 future research directions, 75:246–247 HER-2/neu, 75:244 immunoglobulin, 75:245–246 MUC1, 75:244–245 non-virus-associated tumors, 75:241–246 p53, 75:242–243 virus-associated tumors, 75:240 CD4þ cells role, 75:237, 247–249 CD28 costimulation pathway, 75:261–262 cytokines, T cell response enhancement, 75:262–263 dendritic cells role, 75:247–249 monitoring methods, 75:263 monoclonal antibodies, 75:263–264

natural protection, 75:238–240 overview, 75:235–238, 264 T cell adoptive transfers, 75:256–258 tumor antigen processing, 75:246–247 tumor escape mechanisms, 75:253–256 tumor necrosis factor family, 75:249–253 4-1BB, 75:252–253, 256 CD30, 75:252 CD40, 75:238, 248–252, 256 CD95, 75:250–251 minor family members, 75:253 Ox-40, 75:253 incidence of, 82:53–54 in mice, 82:53 renal cell, 82:281 transforming growth factor-b signaling Smad proteins, 75:140–143 treatment of, 82:49–52, 50 tumor antigens and, 82:58–61 vaccinations for, 82:53–54, 79–80 Cancer, sPLA2-IIA role, 77:177–178 Cancer biology, 81:98 Candida albicans, 68:282; 70:184–185; 73:469–471; 81:54 CAP proteins, 71:174–176 CAPD, see Continuous ambulatory peritoneal dialysis Captoprils, 82:348, 349 CAR, see Carrageenan Carbohydrate recognition domain, sPLA2 receptor, 77:182

SUBJECT INDEX

Carbohydrate recognition domains, innate immune system role, 74:63–64 Carbohydrates, 82:58, 64, 255 Carboxymethylation, 68:162, 172 Carcinogenesis, 82:258–259 Carcinoma MCA-38 colon, 69:215 nasopharyngeal, 69:213 Carcinomas, see Cancer breast, 68:237–238 cervical, 68:237 colon adenocarcinoma, 68:236 colorectal, 68:237 hepatocellular, 68:236 KB epidermal cells, 68:105 lung, non-small cell, 68:237 murine CMT64.5, 68:237 pancreas, lung and colon, 68:149 peptide transporters and, 68:224, 236–238 prostate, and peptide transport, 68:237 small cell lung, 68:236 CARDIAK, 73:271 Cardiogenesis, 71:216–217 Cardiolipin, 70:529–530 Cardiovascular disease, 70:512–513; 73:284 Cardiovascular system, xenotransplantation barrier, 79:185 Carrageenan, 73:458 Caspase 3, deletion, 77:312–313 Caspase-1, 70:286–287 Caspases, 71:176–180 and anucleate cells, 68:70 in apoptosis, 68:57–61, 70–72, 85, 88, 123–124 autoamplification in, 68:72

and Bcl-2, 68:111 caspase-1 IL-18 and, 73:274 IL-1b and, 73:271–273 INF-b and, 73:275 caspase-3 IL-16 and, 73:274 caspase-4 IL-1b processing, 73:273 caspase-8 CrmA, 73:278 DR3 ligand and, 73:286 FasL, 73:277–280 inflammatory process, 73:276–277 caspase-10 CrmA, 73:278 caspase-11, 73:273 classification, 73:266 –cytokine interaction DR3 ligand, 73:286 FasL, 73:277–280 IL-1, 73:270–273 IL-6, 73:273 IL-16, 73:274 IL-18, 73:274–275 INF-b, 73:274–275 overview, 73:267–270 TNF-a, 73:275–277 function, 73:265–266 inhibitors of, 68:60 and interferon-g processing, 68:72 and interleukin-b processing, 68:72 and mitochondrial membrane, 68:76 and necrotic cell death, 68:73 and permeability transition, 68:83

33

34

SUBJECT INDEX

Caspases (continued) and phosphatidylserine, 68:64 recruitment domains, 73:266 sepsis and, 73:285 subcellular localization of, 68:60 Caspases, lymphocyte apoptosis, 76:179–180, 184–186 Catabolism FcRn and, 82:165–166, 169–171 IgG and, 82:166–169, 170–171 Rc receptors in, 82:165, 166 therapeutic implications of, 82:171–172 Cathepsin D, 72:272 Cathepsins Cat L, p41 and, 80:95–96 identified in APC types, 80:76–77 regulation of each other, 80:82 role in antigen degradation, 80:101–102 Ii proteolysis, 80:87–88 tissue-specific expression, 80:79 Cationic Ags, 82:224 Caveolin lipid rafts associated with, 77:18–19 major constituent of DRMs, 77:50–51 CBFA, transforming growth factor-b signaling, 75:131–132 Cbl, 72:12–14 CBP transcriptional coactivator, transforming growth factor-b signaling, 75:134 CC chemokine receptor see CCR CC chemokines, 81:1–3, 12 basophils primed by, 77:105

CCR5, in HIV-1, 77:224–225 as protease substrates, 81:20–23 CCAAT/enhancer-binding proteins (C/EBP), 82:30–31 CCR, 81:10, 349 CCR1, 81:9, 10, 22, 23, 28 CCR2, 81:9, 10, 13 CCR3, 81:10, 22, 23 CCR4, 81:6 CCR5, 81:9, 11–13, 22, 23, 28; see Chemokine receptor 5 CCR6, 81:9 CCR7, 81:6 CCR8, 81:2 CD1 antigens, 72:257–258 CD1, acquired immune response role, 75:18–19 CD2, 68:16 CD2, CD45 and, 66:7–8, 33, 35–36 CD3, 68:16, 34, 93–97, 100–101, 266; 69:45–47, 188, 249 CD3, CD45 and, 66:9–12, 34 CD3d, and pre-TCR complex, 69:25–27, 47 CD3e, 69:190 CD3z, 69:25–27, 47 CD3 z, p21 form, 77:34 CD4, 69:190, 195, 197–198, 214, 358 and antigen recognition, 68:93 and apoptosis, 68:97 in autoimmune diseases, 68:333–334, 347–352 and CD8: coreceptors for MHC, 77:74–75 and encephalomyelitis, 68:379–380 and Fv receptors, 68:259–261 in HIV-1 infection, 77:223–224

SUBJECT INDEX

and rheumatoid arthritis, 68:347–353 and T cell differentiation, 68:17 CD4þ acquired immune response role, 75:15–20 antigen-processing pathways, 75:14–15 CD45 and, 66:18, 26, 35–36 CD8þ antiviral effect, 66:274–275, 282–283, 292–294 chemokine relationship, 74:137–139 leishmaniasis adaptive immune response antigen presentation, 74:285–286 elimination, 74:300 induction, 74:288–290, 302 development cytokine role, 74:290–291 interleukin-4 role, 74:291–294 lumors, T-cell recognition escape, antigen-presenting cell interactions, 74:241 tumor immunity role, 75:237, 247–249 CD4þ, inhibition, 81:235–236 CD4þ, major histocompatibility complex interactions, 76:1 CD4þ cells, 81:47–49, 51 CD4þ T cells, 81:341 autoimmunity by naturally arising regularity, 81:329–369 CD4þ T-cells, 81:49, 51 differentiation of naive, 81:355

35

organ-specific autoimmunity induced by elimination of subpopulations, 81:332–334 CD4þ Treg cells development, specificity and homeostasis, 81:350–362 key roles of naturally arising, 81:331 phenotype of naturally arising, 81:336–340 CD5, 68:111, 353–357; 69:57 CD7, 68:358–359 CD7, CD45 and, 66:34–35 CD8, 68:93, 191, 193–194, 334, 380–381; 69:195, 197–198, 367 CD8þ, see also Cytotoxic T lymphocytes acquired immune response role, 75:15–20 antigen-processing pathways, 75:14–15 HIV suppression, 74:146–147, 151 tumor immunity role, 75:237–240 tumor-associated antigen identification, 74:181, 186 CD8þ, major histocompatibility complex interactions, 76:1 CD8þ inhibition, 81:235–236 CD8þ lymphocytes CD45 and, 66:18, 26, 35–36 in HIV-1 infection, 66:283–291, 297–298 antiviral activity, 66:274–275 antiviral therapy, 66:295–297 lytic activity, HIV-1-specific, 66:275–277 viral inhibition, mechanism, 66:280–291

36

SUBJECT INDEX

CD8þ T-cells, 81:47–49, 341 CD11, 68:365–367 CD11b/CD18, lipopolysaccharide binding, 78:11–12 CD14, 68:295 lipopolysaccharide binding, 78:10 signaling, see Lipopolysaccharide CD16, 68:278–279; 69:190, 215 CD18, 68:369–371 CD18, Taxol binding, 78:26 CD19, 73:118–119 CD19, complement enhancement, 74:67–68, 70, 82 CD21 B cell anergy alterations, 74:74–78 complement enhancement, 74:64, 67–69, 82 self-reactive B cells, negative selection, 74:73–74 systemic lupus erythematosus induction role, 74:78–82 CD21, in enhancement of HIV-1 infection, 77:209 CD22, 69:217, 221, 225 B cell transduction CD22-deficient mice in vivo, 73:108–109 description, 73:107–108 Lyn-deficient mice in vivo, 73:109–110 MAP kinases regulation, 73:115–119 PTK pathway, 73:112–113, 115 PTPase pathway, 73:112–113, 115 SHP-1-deficient mice in vivo, 73:110–112 CD22, CD45 and, 66:50–51

CD25, 69:56–57, 190 CD25 marker for Treg cells, 81:337–338 CD25þ CD4þ T-cell population, 81:334 CD25þ CD4þ T-cells, 81:359, 360, 361–362 anergic/supressive, 81:342 CD25þ CD4þ Treg cells, 81:335–337 CTLA-4 as co-stimulatory molecule for, 81:346–347 functional characteristics, ex vivo and in vitro, 81:340–343 repertoire selection, 81:353–354 CD25þ CD4þ, 81:334 CD26-chemokine connection, 81:23–31 CD26/DPP IV, 81:21 in angiogenesis, 81:30–31 anti-HIV-activity of chemokines modified by, 81:28–30 biology of, 81:24–26 in hematopoiesis, 81:30–31 inflammation modulated by, 81:26–28 microenvironment influence, 81:27 CD27, T-cell response in cancer, 75:253 CD28, 68:14, 111, 122, 261, 280 CD28/B7 interaction, 69:358–359 CD28, leishmaniasis, adaptive immune response role, 74:287–288 CD28, tumor immunotherapy via costimulation, 75:261–262 CD30, 68:114–116 CD30 ligand, 73:398–399

SUBJECT INDEX

CD30, T-cell response in cancer, 75:252 CD31, 68:280–281 CD32, 68:278–280 CD35 B cell anergy alterations, 74:74–78 complement enhancement, 74:64, 67–69, 82 self-reactive B cells, negative selection, 74:73–74 systemic lupus erythematosus induction role, 74:78–82 CD38, 68:10, 91–92 CD40 BCR regulation apoptosis, 73:124–127 overview, 73:122–124 discovery, 76:61–69 immune response regulation, 76:61–146 antigen presentation, 76:76–78 B cell responses, 76:86–145 AP-1 activation, 76:79, 87–92 CRE activation, 76:87, 92 NF-AT activation, 76:79, 88–92 NF-kb activation, 76:87, 92–93, 100–103, 116–121 T cell collaboration, 76:69 TRAF adapter molecule discovery, 76:93–115 transcription factor activation, 76:87–93 event delineation, 76:115–136 functional outcomes, 76:126–136

37

signaling cascades, 76:116–126 expression regulation, 76:78–86 functional outcomes, 76:126–136 adhesion, 76:129–130 antigen-presenting cell function, 76:130–131 apoptosis regulation, 76:134–136 cell survival and proliferation, 76:127–128 cytokine secretion, 76:131 humoral immune responses, 76:70–76 T cell-dependent responses, 76:70–75 T cell-independent responses, 76:75–76 inflammatory responses, 76:76–78 mechanisms, 76:78–86 overview, 76:61, 145–146 signaling cascades, 76:116–126 cAMP-mediated-signaling pathways, 76:144–145 ERK activation, 76:89–90, 120, 125–126 JAK–STAT pathways, 76:138–140 JNK activation, 76:90–91, 98–100, 120–124 NF-kb activation, 76:116–121 p38 activation, 76:92, 98, 100, 124–125

38

SUBJECT INDEX

CD40 (continued) reverse-signaling through CD154, 76:145 src activation, 76:140–143 tec family kinase activation, 76:140–143 ZAP-70 activation, 76:140–143 thrombosis, 76:76–78 TRAF adapter molecule apoptosis regulation, 76:134–136 CD40 event mediation, 76:115–145 discovery, 76:93–115 expression regulation, 76:114–115 I-TRAF/TANK, 76:109–114 MAPK activation, 76:97–100 NK-kb activation, 76:100–103 structure–function relationship, 76:95–104 TRAF-CD40 association, 76:65, 104–109 transcriptional regulation, 76:82–83 properties, 76:64, 69, 94 CD40/CD40L, 69:359; 72:269–270 CD40, basophils expressing, 77:98 CD40, T-cell response in cancer, 75:238, 248–252, 256 CD43, 72:226–227 CD44, 68:295–296; 69:87; 72:226–227 CD45, 68:15, 93, 98–101, 296–297; 69:49–50 B lymphocyte studies, 66:12–14, 22–37

CD2 and, 66:7–8, 33, 35–36 CD3 and, 66:9–12, 34 CD4þ and, 66:18, 26, 35–36 CD7 and, 66:34–35 CD8þ lymphocytes and, 66:18, 26, 35–36 CD22 and, 66:50–51 CD100 and, 66:16–17 characterization, 66:1–5, 55–56 functions, 66:55 CD45-deficient cell line studies, 66:18–26 gene-targeted mouse studies, 66:26–31 lymphocyte development and activation, 66:4, 5–17 molecular mechanisms, 66:31 regulation, 66:45–49, 56 Src family kinases, regulation, 66:4, 23, 39–45 structure–function analysis, 66:46–49 Lck activity and, 77:58 lymphocyte adhesion, 66:15–17 p53/56lyn and, 66:24, 37, 39, 44 p56lck and, 66:11, 12, 19–21, 26, 37–39, 39–44, 53 p59fyn and, 66:19–21, 37, 38, 39–43 p70zap and, 66:21–22, 26 p72syk and, 66:21, 23–24, 26, 45 phosphorylation, 66:53–54 posttranslational modification, 66:4, 53–55 proteolysis, 66:46–47 regulation, 66:49–53, 56 segregated from IRR patches, 77:73

SUBJECT INDEX

structure domain structure, 66:2 isoforms, 66:2–3, 5 structure–function analysis, 66:46–49 substrates, 66:31–39, 49–53, 55 T lymphocyte studies, 66:6–12, 18–22, 32–36 CD45-deficient cell lines B cells, 66:22–26 T cells, 66:18–22 CD45, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:333–334 CD45RA, 66:7, 15, 16, 36 CD45RB, 66:35 CD45RC marker, 81:332–334 CD45RO, 66:7, 15, 16, 35 CD47, in interleukin-12 production, 79:79 CD51C, 68:356–358 CD52, 68:362–365 CD59 delayed partitioning into DRMs, 77:51 GPI-linked, 77:22 CD64, 68:276–278 CD69, 69:190 CD70, T-cell response in cancer, 75:253 CD71, 68:297 CD72, 81:181, 181–183 regulation by CD100, 81:183 CD80, 68:280; 69:225 CD80, leishmaniasis, adaptive immune response role, 74:287–288

39

CD80, tumor immunotherapy via costimulation, 75:249, 261–262 CD81, 69:88 CD86, 68:280; 69:225 CD86, leishmaniasis, adaptive immune response role, 74:287–288 CD86, tumor immunotherapy via costimulation, 75:249, 261–262 CD95, induced death, 73:132–134 CD95, T-cell response in cancer, 75:250–251 CD100, 81:177–187 biological activities as ligand, 81:179–180 biological activities as receptor, 81:180 biologically active soluble form, 81:180–181 discovery, 81:177–178 expression, 81:178 in B-cell development, 81:183–184 in cellular immunity, 81:185–187 in humoral immunity, 81:184–185 involvement in activation and maturation of DCs, 81:185–186 involvement in in vivo generation of antigen-specific T-cells, 81:187 receptors, 81:181–183 regulation of, by CD72, 81:183 structure, 81:178 T-cell derived, in T-cell differentiation, 81:186–187

40

SUBJECT INDEX

CD100, CD45 and, 66:16–17 CD108, 81:192 CD154 discovery, 76:61–69 disease role, 76:63 immune response regulation antigen presentation, 76:76–78 B cell responses, 76:86–87 B cell–T cell collaboration, 76:69 endothelial cell function modulation, 76:77–79 expression regulation, 76:78–86 humoral immune responses, 76:70–76 T cell-dependent responses, 76:70–75 T cell-independent responses, 76:75–76 inflammatory responses, 76:76–78 mechanisms, 76:78–86 thrombosis, 76:76–78 transcriptional regulation, 76:82–83 properties, 76:64, 69, 94 Cdc-42, 72:33–34 Cdc42sp, 72:36–37 CDR loops, 71:84–85 CEA, see Antigens, carcinoembryonic CEA, tumor T-cell response induction, 75:243–244 CED Bcl-xL, 70:268–269 characterization, 70:248–250 mammalian homologs, 70:260–261

Celiac disease, T cell responses against modified peptides, 78:282–283 Cell communication, see Signal transduction Cell culture studies, 71:52–53 Cell cycle and apoptosis, 68:70 control, aging and, 80:245 cytokine memory dependent on, 80:141–142 GGTase-I inhibitors and, 68:178 Rac1 and, 68:150 and Ras mutation, 68:151 Cell cycle regulation, 70:11–12 Cell death anti-Ig-induced, 73:124–127 B cells, regulation, 73:84–87 BCR pathways mIGD model, 73:105–106 mIgM model, 73:105–106 WEHI-231 model, 73:104–105 CD95-induced, 73:132–134 FasL-induced, 73:394–397 induction, 73:79–80 inhibition, 73:83–84 Cell death, see Apoptosis Cell debris, 73:34–36 Cell differentiation granulated metrial gland cells, 79:306–307 human uNK cells, 79:310 Cell migration dendritic, 72:265–268 diapedesis, 72:338 Cell morphology, 68:149–50, 174 Cell proliferation, human uNK cells, 79:310

SUBJECT INDEX

Cell surface markers application, 71:13–14 description, 71:5–8 Cell surface markers, basophil, 77:94–98 Cell surface receptors, 71:234–236 Cell surface receptors, mRNA regulation of, 68:14–16, 36 Cell survival, 70:266–269 Cell viability pathways, 70:41–42 Cell-mediated immunity, see also Humoral immunity, Inmale immune system leishmaniasis, 74:285–299 antigen presentation, 74:285–286 antileishmanial effector mechanisms, 74:297–299 CD4þ T helper lymphocyte induction, 74:288–290, 302 co-stimulatory molecules, 74:287–288 cytokine determinants, 74:290–291 interleukin-4 role, 74:291–297 interleukin-12 role, 74:291–297 T helper cell development, 74:290–291 Cells antigen-presenting, 82:72–75 endothelial, 82:341–344 of immune system, 82:221–222 Kuppfer, 82:222 malignant, 82:59, 60 mast, 82:221–222, 225 mononuclear, 82:230 moraxella catarrhalis, 82:194

41

specialized, 82:59 Staphylococcus aureus, 82:186–190 suppressor, 82:57 tumor, 82:65–66, 255, 258–260, 275 Wrzburg T, 82:21 Cells, B, 82:53, 233–234 activation of, 82:300 DCs and, 82:65–66 deficiencies, 82:305–313, 307, 310, 312 immature/mature, 82:296 malignancies, 82:59–60 of patients, 82:301–302 Cells, dendritic (DCs), 82:221, 271–276, 281, 303 Cells, follicular dendritic (FDCs), 82:72 Cells, germinal (GC) founder, 82:307 Cells, natural killer (NK), 82:53 Cells, polymorphonuclear (PMN), 82:5 Cells, see also specific types cytosolic trimming of N-extended epitopes, 80:41 immune, in old age, 80:262–263 MBP-reactive, 80:217 proteasome inhibitor effect, 80:27 senescent, impaired function, 80:247 sentinel, 80:48 Cells, T, 82:50, 233–234, see also Cytoxic T lymphocytes allergies and, 82:113–114, 120 CD4þ, 82:54, 63–64, 70, 77, 230 CD8þ, 82:54, 63–64, 71 expansion of, 82:54

42

SUBJECT INDEX

Cells, T (continued) HIGM and, 82:315 IGE and, 82:113–114 leukemia virus type I, human (HTLV-1), 82:230–231 MUC1 and, 82:257 of newborns, 82:299 priming, 82:68 proliferation of, 82:63–64 protein, 82:182–183 provision of, 82:69–71 RA and, 82:217–218 receptors, 82:51–52 responses, 82:52, 54, 56 tumor-infiltrating, 82:56–57 Cellular autoimmunity, increase with age, 80:266–267 Cellular interactions idiotypic, 80:212–213 role of idiotype-specific T cells, 80:216–218 Cellular responses, 82:1 Cellular responses, in xenotransplantation acquired response, 79:148–150 immunosuppression, 79:163–164 innate, see Innate cellular responses Cellular therapy, 82:51 CEMF, see Corneal endothelium modulation factor Central nervous system (CNS), 81:124, 134 prion spread within, 81:145–148 prion transfer to, 81:143–144 Central nervous system, embryonic derivation, 77:300–303 Ceramide, 68:101–102, 105, 120–122, 168

Ceramide, lipopolysaccharide signaling in macrophages, 78:16–17 Cerebral cortex embryonic development, 77:303–309 initial process outgrowth, 77:308–309 neurogenesis, 77:306–307 CF, see Cystic fibrosis CFA, see Complete Freund’s adjuvant CFSE, 81:294 CFU-S, 69:18–19, 59 CH1 domain, in heavy-chain antibody H chain, 79:265–266 Chakraborty, A., 82:24 Challenge, allergen late-phase response to, 77:112–113 transient gene transfer models, 77:284–285 Challenge dose, effect on antibody activity, 77:240 Chaperones function, 73:6, 8 immunization, 73:52–56 Chaperones, protein assembly, 70:385–387 Chase–Sulzberger phenomenon, 73:156–157 Chelation, 68:32, 64, 71 Chemical compounds, in model of industrial asthma, 77:267 Chemoattractants, in xenotransplantation, 79:147 Chemokine induction, 71:276–278 Chemokine ligand 2, see MCP-1

SUBJECT INDEX

Chemokine receptor 5, in interleukin-12 production, 79:77 Chemokine receptor expression, 81:7, 9 Chemokine receptors, 81:8–11 activation, 81:8 CCR7, in T cell migration, 80:155 T cell recruitment and, 80:150–152 Chemokines, 66:281–282; 74:127–158 ABCD chemokines and disease asthma, 78:148–149 atopic dermatitis, 78:149–150 endotoxemia, 78:147–148 human immunodeficiency virus, 78:151 knockout mouse studies, 78:153 lymphoma, 78:150 prospects for study, 78:151–153 sepsis, 78:148 B cell/T cell interactions, 78:141–143 CCR6 interaction with b-defensin, 78:138–139 characterization, 73:373, 375 chromosomal localization chemokines, 78:68–70, 72 receptors, 78:68, 71 dendritic cell antigen uptake and migration MIP-3a/CCR6 interaction, 78:137–138 overview, 78:136–137 receptor expression, 78:137

43

discovery, 78:58, 63 dose–response of cell migration, 78:115, 117 ELR motifs, 78:63 expression and function in immune system bone marrow, 78:74–75 dendritic cells CCR6, 78:88–89 CCR7, 78:88–89 chemokine production, 78:89–90 receptor expression in maturation, 78:88–89 lymph nodes, 78:77–80 mucosal immune system CCR6 expression by dendritic cells, 78:86 fractalkine, 78:87 LARC, 78:86 MEC/CCL28, 78:87 overview, 78:85 TECK/CCL25, 78:86 Peyer’s patches, 78:77–80 skin CCR4, 78:88 CCR6, 78:87–88 dendritic cells, 78:87 ILC/CTACK/CCL27, 78:88 MEC/CCL28, 78:88 spleen, 78:77–80 T helper cells CCR3, 78:82, 245–246 CCR4, 78:82–83, 246 CCR5, 78:81–82, 244–245 CCR7, 78:83–84, 244 CCR8, 78:83 CXCR3, 78:81–82, 244 CXCR5, 78:84–85, 239, 247–248

44

SUBJECT INDEX

Chemokines (continued) follicular T helper cell migration, 78:247–248 inhibitors of receptors, 78:246–247 intervention therapy, 78:92 overview, 78:242–244 receptor expression by cell type, 78:80–81 Th1 responses, 78:244–245 Th1/Th2 polarization role, 78:90, 140–141, 246 Th2 responses, 78:245–246 thymus, 78:75–77 functional classification, 78:64 functional implications, 74:127–129 gene clusters, 78:58 gene duplications, 78:68 HIV infection, 74:146–158 coreceptors description, 74:146–149 signaling mechanisms, 74:150–151 therapy, 74:155–158 variation, 74:149–150 pathogenesis, 74:151–155 HIV suppression, 74:151–154 infection enhancement, 74:155 viral entry mechanisms, 74:146–149 HIV-1 antiviral effect, 66:281–282 immune chemokines and receptors, 78:66–67 in immune response, 81:1–44 inflammatory, 82:2, 13, 16

as inhibitors of HIV infection, 81:11–13 in migration/recruitment of Treg, 81:348–349 knockout mouse studies of immunity, 78:90–91 letter codes, 78:116–117 lymphocyte compartmental homing within secondary lymphoid organs BLC, 78:135–136 CXCR5, 78:134–136 ELC, 78:133–134 SLC, 78:133–134 lymphoid cell movements into secondary lymphoid organs during T cell-dependent, antigen-specific immune response B cell activation and follicle formation, 78:126 CCR7 role, 78:129–130 circulation, 78:123–124, 128 dendritic cell activation and maturation, 78:125, 139 ELC role, 78:128–129 SLC role, 78:128–130 T cell activation, 78:127 as mediators, 82:1–2 nomenclature, 81:2 overview, 74:127; 81:1–13 phylogenetic relationships, 78:59–60, 63, 68, 72–73, 112 plasma cells migration, 78:144–145 receptors desensitization, 78:115 ligand specificity, 78:113–115

SUBJECT INDEX

phylogenetic relationships, 78:65–66, 113 signal transduction, 78:67–68, 115, 151–152 structural homology, 78:65–66 receptors in lymphocytes, 74:129–144 B lymphocytes, 74:139–141 lymphocyte progenitors, 74:142–144 memory T lymphocytes, 74:132–137 naive T lymphocytes, 74:132–137 natural killer cells, 74:141–142 T helper cells, 74:137–139 sepsis and interleukin-8, 66:135–141 MCP-1, 66:141–142 signal transduction mediation, 74:144–146 structural homology, 78:64, 114 subfamilies, 78:58, 62–64 T cell memory/effector cell migration CCR4 role, 78:146–147 CCR6 role, 78:146–147 CCR7 role, 78:145–147 features of cells, 78:143–145 secondary lymphoid organs, 78:145 tables of types and receptors, 78:61–62, 65, 116–117 therapeutic applications and targeting, 78:91–92 types GROs, 73:382–385 IL-8, 73:375–382

45

MCPs, 73:389–390 MIPs, 73:387–389 Chemokines, lymphocyte trafficking, 72:227–228 Chemotaxis, 82:344 Chemotaxis, impaired, 68:167 Chemotherapy, 71:184–188; 82:53–54 Chicken, 69:333–334 Chimerism, mixed, xenotransplantation hematopoietic cell, 79:171–177 pig-to-primate model, 79:171–177 Chimpanzees, 82:264–265 Chinese hamster ovary (CHO) cells, 70:91 Chlamydia, 81:69 Chlamydia trachomatis, 72:214; 81:65, 69 Chlamydia trachomatis, neutralization, 77:217–218, 244 Chlamydial infection, characteristics, 75:11–12 Chloroquine, 73:346 Cholera toxin coupled-antigens, 73:182–183 tolerance induction, 73:186–187 Cholesterol, 68:151, 175, 179; 69:365–366 depletion on entry of different species of bacteria, 81:80 distribution during mycobacterial uptake, 81:79 extraction by MbCD, 77:71–72

46

SUBJECT INDEX

Cholesterol (continued) interaction with sphingomyelin, 77:47 involvement in complement receptor type 3-mediated mycobacterial entry, 81:81 lateral assembly, 77:45 Cholesterol-dependent mycobacterial entry into macrophages, 81:83 Cholesterol, in elderly, 80:247 Chordata, inter-relationships, 81:274 Chromatin condensation, in apoptosis, 68:54, 56, 63–64 Chromatin immunoprecipitation experiments (ChIP), 81:209–211 Chromatin, 69:316–317, 319 Chromatin structure DNA methylation of CpG motifs hypomethylation and transcription, 78:184–186 Igk locus methylation, 78:185 methyl cytosine binding protein function, 78:183–184 methyltransferases, 78:184 b-globin locus transcription cis-acting elements as assembly platforms, 78:182–183 histone acetylation, 78:187–188 linking model, 78:193 looping model, 78:192 model for V(D)J recombination, 78:179 organization and expression, 78:182

heterochromatin versus euchromatin, 78:181 interchromatin granules and splicing factors, 78:181 nucleosome structure, 78:179 transcription site visualization, 78:182 V(D)J recombination DNase sensitivity and recombination, 78:186–188 high-mobility group protein effects on RAG cleavage, 78:188–189 histone acetylation, 78:188 nucleosome remodeling complexes, 78:189–190 promoter exposure, 78:189 recombination signal sequence accessibility modeling, 78:213–215 sterile transcripts, 78:190–191 Chromosomal damage, T cells, 73:312–313 Chronic airway disease PMN role, 73:427 treatment, 73:380 Chronic myelogenous leukemia, immunotherapy, 75:236 CIA, see Arthritis; see Collagen-induced arthritis CIITA transcription factor, Th1, 80:129–130 Ciliary neurotrophic factor, 70:92–94 CIS, 81:110–111; see Protein, cytokine-inducible SH2 cis-regulatory factors, see also Enhancers; Promoters; Silencers

SUBJECT INDEX

and recombinational accessibility, 69:318–319, 321–337 and T-cell-receptora/d locus, 69:336–337 and Vg gene segments, 69:337–338 Cisplatinum, 68:105 Class Switch Recombination (CSR), 82:316 primary antibody repertoire in, 82:295–296 secondary repertoire in, 82:296–298 Clathrin, 81:62–63 endocytosis, 73:12–13 nocytosis, 73:12–13 Clathrin-coated vesicle pathway, 77:18 CLICK148, cathepsin L-specific inhibitor, 80:86 Clinical trials, in xenotransplantation, 79:190 ab–CLIP complexes, 80:89–90 CLL, see Leukemia, chronic lymphocytic CLNK, see Cytokine-dependent hematopoietic cell linker Clonal expansion, CD8þ T cells, 80:252–253, 272 Clonal selection theory, 69:113; 81:329 Clonal selection, transformed by idiotypic network, 80:220–223 Cloning, VHH immunized Camelidae, 79:277–279 naive and synthetic banks, 79:279

Clostridium botulinum, 69:53 Clostridium difficile, 81:58 Clotting, in xenotransplantation, 79:155 CML, see Leukemia, chronic myeloid CMV, see Cytomegalovirus CNTF, see Ciliary neurotrophic factor Co-stimulatory molecules, 81:361–362 Coagulation systems, xenotransplantation clotting, 79:155 disordered thromboregulation, 79:152–153 disseminated intravascular coagulation, 79:153 fibrinolytic abnormalities, 79:154–155 natural anticoagulants, 79:153–154 platelet agonists, 79:152 platelets, 79:155 prevention, 79:169–171 regulators, 79:153–154 thrombotic diathesis, 79:152 xenogeneric molecular incompatibilites, 79:153 Coat protein complex (COP), 81:216 Coat proteins families, 70:374–375 functions, 70:376–377 GTPases regulating, 70:377–381 Coccidioides immitis, 70:186 Coding end, 69:310–311 Coding joint, 69:315, 342

47

48

SUBJECT INDEX

Cofilin inactivation by LIM kinase, 77:32 nuclear translocation, 77:26–27 Colchicine, 73:403–404 Colitis, 73:221 Colitis, eosinophils, 78:301 Colitis, experimental, 70:164–165 Colitis, ulcerative, 72:213 Collagen Ab, anti, 82:224 induced arthritis, 82:223–224, 234–235 caspase-1 effect, 73:272 oral tolerance model animal, 73:211–213 human, 73:230 nasal administration, 73:205 oral, systemic sclerosis, 73:231 xenogenic type II, 82:223 Collagen II, 68:393–394 Collagen-induced arthritis, 70:162–164 Collagenase, 73:424–425 Collagenous receptors, 68:286–289 Collapsin, 81:173 Collectins, in insect immune response, 79:232 Colloral, 73:230 Colony stimulating factor-1, 79:311–312 Competitive rearrangement model description, 71:17 revised, 71:57 Complement in antiviral response, 79:10–12 coating with, and virion neutralization, 77:210 in interleukin-12 production, 79:78

neutralization of sensitized virus with, 77:207 virolysis mediated by, 77:225–226 xenotransplantation humoral responses, 79:135 xenotransplantation immunosuppression, 79:161–162 Complement activation mechanism, 81:52–53 Complement receptor type, 81:3, 54–55 Complement receptor type 3-mediated phagocytosis, 81:60–61 Complement receptor type 3-mediated uptake of non-opsonized mycobacteria, 81:81 Complement regulatory proteins, 79:166–167 Complement system, 81:149; see also Enzymes, proteolytic activation pathways, 69:249–251, 267, 270, 282–283, 291–293 bony fish, 81:258–259 deficiencies, 69:295 and pathogenesis of disease, 69:295 viral interference, 69:380 Complement(s) activation regulation, 82:337–339 C3 component, 82:218–219 cascades, 82:220–221 Complement, B cell activation and tolerance, 74:61–83 C3, 74:61–65 activation mechanisms, 74:63–64

SUBJECT INDEX

C3d, 74:61–63 humoral immunity, 74:64–65 innate recognition, 74:63–64 source, 74:64–65 complement deficiency, 74:78–82 humoral immunity enhancement, 74:65–72 antigen retention on follicular dendritic cells, 74:69–72 B cell co-receptor signaling, 74:69–72 CD21/CD35 role, 74:64, 67–69, 82 classical pathway, 74:65–67 overview, 74:61, 82–83 self-reactive B cells, negative selection B cell anergy alterations, 74:74–78 C4 deficiency effects, 74:74–78 Cr2/ mouse impairment, 74:73–74 natural antibody role, 74:82 systemic lupus erythematosus induction, 74:78–82 Complement, deficiency, systemic lupus erythematosus relationship, 76:227–299 animal models autoimmunity, 76:297–298 B-deficient mouse, 76:278 C2-deficient mouse, 76:278 C3-deficient mouse, 76:278–279 C4-deficient mouse, 76:278–279 C1q-deficient mouse, 76:277–278

49

CR1-deficient mouse, 76:227, 278–279 CR2-deficient mouse, 76:278–279 other nonhuman species, 76:279 apoptosis, 76:283–292 anti-C1q autoantibody development, 76:292 apoptotic cell clearance, 76:287–288, 290–291 autoantigen source, 76:285–287 complement role, 76:290–291 immune response, 76:288–290 association hypotheses, 76:283–297 apoptosis, 76:283–292 humoral immune response, 76:294–297 immune complex clearance, 76:292–294 autoantibody production to C1q, 76:281–283 complement null alleles, 76:259–272 C2 null alleles, 76:269–272 C4 null alleles, 76:265–269 complement receptor type 1, 76:273–276 acquired numbers reduction, 76:274–276 inherited numerical polymorphisms, 76:273–274 inherited structural polymorphisms, 76:276 genetic deficiencies, 76:228–259 acquired complement deficiency, 76:259

50

SUBJECT INDEX

Complement, deficiency, systemic lupus erythematosus relationship (continued) ascertainment artifacts, 76:257–259 C2 deficiency, 76:243–251 C3 deficiency, 76:251–252 C4 deficiency, 76:238–243 C1q deficiency, 76:227–237 C1r deficiency, 76:238 C1s deficiency, 76:238 homozygous classical pathway deficiency, 76:228–229 mannose-binding lectin deficiency, 76:252–257 terminal pathway component deficiency, 76:252 inflammation, 76:279–281 overview, 76:227–228, 298–299 Complements C5, 71:325–326 CD3, 71:91–92 receptors, 71:271–272 Complete Freund’s adjuvant (CFA), 82:62, 223 Complete hydatidform mole (CHM), 81:229 Component-resolved diagnosis (CRD), 82:132 Con A, 68:11, 13, 15 Conserved noncoding sequence-1, GATA-3 binding site, 80:124 Contact activation, 66:225, 233–239 allergic diseases and, 66:258–259 bradykinin, 66:225, 226, 233–240 defined, 66:225 disease states and

allergic diseases, 66:258–259 Alzheimer’s disease, 66:260–261 endotoxic shock, 66:260 hereditary angioedema, 66:257–258 pancreatitis, 66:260 rheumatoid arthritis, 66:260 factor XI, 66:225, 226, 230, 237, 244 factor XII, 66:225, 226–229, 234–236, 244, 246, 249–257 high-molecular-weight kininogen (HK), 66:225, 226, 230–233, 245, 247–257 interaction with cells and, 66:258–259 kallikrein, 66:225, 238, 243–244 low-molecular-weight kininogen, 66:233 mechanism, 66:225–226 prekallikrein, 66:225, 226, 229–230, 236 regulation, 66:235–239 Continuous ambulatory peritoneal dialysis IL-8 production, 73:427–428 Contraceptives, oral, 69:422 Coombs, R. R. A., 82:105, 111 COP9 signalosome, 80:11 COPI, 81:62–63 COPII, 81:62–63 Corneal endothelium modulation factor, 73:424 Coronaviruses, antibody protection against, 77:233–234 Cortical plate, cerebral cortex, 77:304–305 Corticotropin-releasing hormone, 73:399–400

SUBJECT INDEX

Costimulation, 71:317–318 Co-stimulatory molecules, 81:361–362 Cowpox virus, 69:378, 379 Cowpox virus protein FAS ligand and, 73:278 T cell selection, 73:280 TNF-a and, 73:276 COX2, 81:259 Coxiella burnetti, 81:69 Coxiella, 81:70 CpG dinucleotides as antitumor adjuvant, 73:349–350 CTL response, 73:353–354 description, 73:329–330 evolution, 73:346–348 extramedullary hematopoiesis-induced, 73:351 immune cell activation, 73:352 mediative effects in vivo, 73:349 as mucosal adjuvant, 73:351 sequence effects DNA vaccines, 73:340–341 immunosuppressive, 73:342 macrophage receptors, 73:341 TNF-a production, 73:342 sequence-specific effects APCs, 73:336–338 B cells, 73:334–335 NK cells, 73:339 T cells, 73:338–339 signal mediation cell response, 73:352–353 cellular uptake, 73:343–344 chloroquine effects, 73:346

51

lysosomotropic compounds, 73:344–345 stress kinase pathway, 73:345–346 T cell effects as Th1 adjuvant, 73:348–349 Th2 pathology, 73:350–351 CpG motifs, 69:373–375 methylation hypomethylation and transcription, 78:184–186 Igk locus methylation, 78:185 methyl cytosine binding protein function, 78:183–184 methyltransferases, 78:184 Toll-like receptor recognition, 78:33–34 CPPD, see Calcium pyrophosphate dihydrate CR1, complement deficiency, systemic lupus erythematosus relationship acquired numbers reduction, 76:274–276 animal models, 76:227, 278–279 inherited numerical polymorphisms, 76:273–274 inherited structural polymorphisms, 76:276 CR2, complement deficiency, systemic lupus erythematosus relationship, animal models, 76:278–279 CRD, see Component-resolved diagnosis CRE-BP-1, transforming growth factor-b signaling, 75:131

52

SUBJECT INDEX

CRE, B cell immune response regulation by CD40-CD154signaling, 76:87, 92 CREB, see Cyclic AMP response element-binding protein Creutzfeldt-Jakob disease (CJD), 81:123–124 epidemiology, 81:124 risk factors, 81:124 CRH, see Corticotropin-releasing hormone CrmA, see Cowpox virus protein Crohn’s disease, 68:338, 342; 70:164–165; 72:213; 73:231 Cross-linking GPI-anchored proteins, 77:64–65 lateral, plasma membrane proteins, 77:53–54 Cross-priming, development, 73:2–3 Cross-talk actin cytoskeleton with raft membrane domains, 77:75–76 sPLA2-IB to other enzymes, 77:183 Crossreactive idiotype A, 80:209–210 Crossreactivity T-cell receptor role in autoimmune disease, 75:209–226 cytokine checkpoints, 75:223–226 low affinity ligands, 75:211–214 overview, 75:209 peripheral purging of useless T cells, 75:218–220

peripheral T-cell tolerance, 75:214–217 T-cell antagonism, 75:211–217 viral-derived peptide agonists, 75:220–223 transforming growth factor-b signaling, Smad proteins, 75:137–140 MAP kinase pathways, 75:138–139 nuclear steroid receptor, 75:140 Smad pathways, 75:137 STAT pathways, 75:139–140 CRT, see Calreticulin Cryptococcus neoformans, 70:185 Crystal cells, phenoloxidase, 79:236 CSA, see Cyclosporin CSF-1, see Colony stimulating factor-1 Csk-binding protein, association with PAG, 77:58, 60 CSR, see Class Switch Recombination CTAP-III, 81:17 CTL, see Cytoxic T lymphocytes CTLA-4 as co-stimulatory molecule for CD25þ CD4þ Treg cells, 81:346–347 CTLA-4, 69:217, 225; 71:244–245 CTLs (cytotoxic T lymphocytes) antiviral therapy, 66:295–298 CD8þ and HIV-1 immunopathology, 66:273–274, 276, z277, 281 epitopes, 66:276–280

SUBJECT INDEX

HIV-1 persistence, 66:287, 292–294 Cullin-1, 80:4 Cutaneous hypersensitivity, 71:111–112 Cutaneous lymphocyte antigen, 72:265 Cutaneous necrosis, superficial, 70:518 CXC chemokine SDF-1/PBSF cardiogenesis, 71:216–217 CXCR4 receptor expression, 71:219 HIV-1 and, 71:219–222 identification, 71:217–218 signal transduction, 71:217–218 structure, 71:217–218 development, 71:215 discovery, 71:211–212 expression, 71:213–214 gene, 71:212–213 hematopoiesis, 71:215–216 identification, 71:212 structure, 71:214–215 CXC chemokines, 81:1–3 posttranslational modification, 81:13–20 variants, 81:14–16 CXCL7, 81:17 CXCR-4, 66:282 CXCR2, 81:31 CXCR3, 81:9, 19 CXCR4, 81:5, 11–13, 19, 28, 31 Cyclic AMP response element-binding protein (CREB), lipopolysaccharide signaling in macrophages, 78:19 Cyclic AMP, 69:55–56

53

Cycloheximide, 73:21 and apoptosis induction, 68:69 and AU-binding factor, 68:31 and CD45 isoforms, 68:15 and c-jun mRNA, 68:5–6 and GM-CSF, 68:15, 19 interleukins and, 68:11, 12, 13, 15 and lymphotoxin, 68:14 perforin mRNA and, 68:26 Cyclooxygenase isozymes, sPLA2-IIA and, 77:171–172 Cyclophilin, 73:336–337 Cyclophilins, 68:55, 80 Cyclophosphamides, 82:277 Cyclosporin, 73:528 Cyclosporin A, 68:11–15, 80, 333; 71:4–5; 73:336–337 Cystatins, 80:80–81 Cysteine protease inhibitors present in APCs, 80:80–82 targeting of, 80:82–86 Cysteine residues, 81:1–3 Cystic fibrosis, 69:364; 73:380, 426–427 Cytidine deaminase, activation-induced, role in hypermutation, 80:195–196 Cytochalasin D and FceRI signaling, 77:76 modification of actin, 77:28–29 Cytochalasin, 73:23 Cytochrome c, 68:74–78, 85–88 Cytokine memory allelic probabilities, 80:142–143 APC role in induction of, 80:130–133

54

SUBJECT INDEX

Cytokine memory (continued) induction and maintenance, 80:122–130 scenario for, 80:143–145 of memory T cells, 80:154–158 part of T cell differentiation programs, 80:149–154 persistence, 80:156–158 stability and plasticity, 80:145–149 TCR signals in induction of, 80:133–138 Cytokine receptor g chain, 69:70–76 Cytokine receptors, 68:14–16, 293–294 Cytokine receptors, basophil, 77:95–96 Cytokine receptors, regulation of T cell effector functions, 80:152–154 Cytokine-dependent hematopoietic cell linker, 79:100 Cytokine–endotoxin score, 66:123 Cytokine-modulating therapy, 66:151 Cytokines, 81:49, 242; 82:263 action of, 82:25 basophil-releasing, 77:99–101, 113–114 blockade of, 82:236 CIA and, 82:223–224 and CpG motifs, 69:372–373 and DNA vaccination, 69:363–364 function, 66:103–104 genes, epigenetic modifications, 80:138–145

induction of sPLA2-IIA expression, 77:170 and inflammation, 81:224–225 inflammatory, 80:267; 82:2–3, 13, 16 inhibition of viral replication, 66:288, 290 instructive, for Th1 and Th2 differentiation, 80:117–122 interleukin-12 production, 79:73–77 leishmaniasis, adaptive immune response, T helper cell development role, 74:290–291 measurement of circulating levels, 66:104–105 as mediators, 82:1–2 production in old age, 80:253–256, 271 proinflammatory function, 69:378–379 RA and, 82:219 regulation of protease activity, 80:78–79 role in Treg-mediated suppression, 81:343–345 secretion by T cells, 80:116 sepsis and, 66:101–102, 104 granulocyte colony-stimulating factor, 66:149–150 granulocyte–macrophage colony-stimulating factor, 66:150 interferon-g and, 66:145–146 interleukin-1, 66:104, 117–127, 150 interleukin-4, 66:144–145 interleukin-6, 66:130–135 interleukin-8, 66:135–141

SUBJECT INDEX

interleukin-10, 66:142–145 interleukin-12, 66:146–147 leukemia inhibitory factor, 66:147–148 macrophage migration inhibition factor, 66:147–148 MCP-1, 66:104, 135, 141–142 TNF, 66:104, 117–127, 150 signals, in memory persistence, 80:156–158 Th1, 82:120 Th2, 82:113, 120, 122 and thymic atrophy, 80:269–270 and thymocyte development, 69:57–58, 76–77 tumors, T-cell recognition escape immunoregulation, 74:229–234 microenvironmental inhibitory signals, 74:229–236 uNK cell production, 79:311–314 and vectors, 69:366–371, 386 Cytokines, see also specific cytokine and autoimmune disease therapy, 68:337–347 AUUUA motifs in, 68:22 AUUUUA motifs in, 68:13 CD4þ secretion, 70:332–334 deprivation of, 68:105 in experimental autoimmune diseases, 68:371–379 genes coding for, 68:93 IL-12-induced, 70:122–126 irradiation effect on, 68:9 mRNA regulation and, 68:8–14, 17, 31, 36

55

network modulation experiments, 68:371–378 nucleotide sequence in 30 UTR of, 68:19 production, 70:146–148 rescuing lymphocytes from apoptosis, 68:91 tumor necrosis factor effect on, 68:12 Cytokines, see also specific cytokines –caspase interaction DR3 ligand, 73:286 FAS ligand, 73:270–273 overview, 73:267–270 TRAIL, 73:286–287 CpG DNA, 73:352 neutrophil-derived acute inflammation in vivo, 73:462–467 antitumor response in vivo, 73:472–473 associated infections, 73:437 bone formation in vivo, 73:476 general features, 73:369–373, 375 HIV-associated, 73:439–440 immune response in vivo, 73:472–473 infections in vivo, 73:467–471 LPS effects in vivo, 73:454, 457–462 molecular regulation evidence, 73:447–448 mRNA stability, 73:449–450 postranslational, 73:452–453 transcriptional, 73:448–449 translational, 73:450–452 pancreatitis in vivo, 73:474

56

SUBJECT INDEX

Cytokines (continued) periodontitis in vivo, 73:473–474 pulpitis in vivo, 73:473–474 shigellosis-associated, 73:437 specific substance, 73:373 wound healing in vivo, 73:474–475 neutrophils expression, see also specific cytokines nonexpression, 73:425–426 NK cells-produced, 73:415 production CpG effects, 73:335 neutrophil role, 73:369–373 T cell production, 73:338–339 Cytokines, see also specific types autoimmune disease generation role, 75:223–226 innate immune response role, 75:13–14 tumor-specific T cell response enhancement, 75:262–263 Cytokines, CD40-mediated immune response regulation, 76:131 Cytokines, interleukin (IL), 82:2, 182 blockage of, 82:219, 225 STATs and, 82:13–14 Cytokines, pleiotropic (IFN-c), 82:11–14, 76–78 Cytolysis, HIV-1-specific, 66:283–284, 287–298 Cytolytic mediators, human uNK cells, 79:309–310 Cytolytic T lymphocytes, 79:303, 305

Cytomegalovirus, 68:205, 235, 240; 69:381; 70:168–171; 72:296–297 Cytomegalovirus (CMV), 82:50–51 Cytoplasm, 68:34, 54 peptide generation in, 80:24–25 proteolytic pathways in, 80:19–20 trimming of peptides in, 80:40–43 Cytoplasmic adaptor protein, SLP76, 79:98 Cytoplasts, 68:70, 75 Cytoskeleton reorganization, 72:27–34 Cytoskeleton, lymphocyte signaling, 75:89–110 actin cap effective molarity regulation, 75:110 function, 75:91–94 proximity regulator role, 75:110 structure, 75:90–91 actin cytoskeleton regulation, 75:105–107 actin polymerization regulation current view, 75:94–95 nucleus signal propagation, 75:108–110 RAC role, 75:94–100 Rho family GTPases role, 75:99–100, 104 WASP role, 75:92–94, 104–107 BAF chromatin-remodeling complex, 75:109–110 guanine nucleotide exchange factors, Vav family, 75:95–98

SUBJECT INDEX

ligand-induced actin-dependent assemblies, functions, 75:91–94 overview, 75:89–94 Rho family GTPases, 75:98–100 actin polymerization, 75:99–100, 104 description, 75:98–99 supramolecular activation complexes functions, 75:91–94 structure, 75:90–91 WASP actin regulation, 75:92–94, 104–107 cytoskeleton regulation, 75:105–107 structure, 75:102–104 Vav-deficient mouse phenotype compared, 75:107–108 Wiskott-Aldrich syndrome, 75:100–104 Cytoskeletons, 69:207–209 Cytosol, 68:32, 71, 76, 86, 191 Cytosolically-derived peptides, 81:47–49 Cytotoxic lymphocytes (CTLs), 81:199, 330 Cytotoxic T lymphocytes; see also CD8þ cancer immunity, 75:236–240, 247–248, 256 HIV suppression, 74:146–147, 151 host adjuvant use, 75:33–34 human leukocyte antigen class I polymorphism, 74:226–228

57

immunoregulatory cytokines, 74:229–234 protection correlates, 75:25–26 target cell recognition studies, 74:181, 186–190 tumor cells as targets, 74:195–226 activity reduction, tumor-associated antigen epitope mimics, 74:202–203 down regulation, 74:195–204 masking, 74:203–204 processing machinery abnormalities, 74:217–221 tumor microenvironment, immunogenicity inadequacy, 74:236–241 tumor-associated antigen identification, 74:181, 186 tumor-escape mechanisms, 74:190–195 Cytotoxic T lymphocytes, histamine effect on, 77:98–99 Cytotoxicity antigen-specific MHC class I restricted, 80:272 memory/effector T cells, 80:256 Cytoxic T lymphocytes (CTL), 82:52–53 activities of, 82:76–77 in vitro, 82:64–66 MUC1 and, 82:262–263, 277 responses of, 82:57, 61–62, 71 Cytoxicity, antibody-dependent cellular (ADCC), 82:5, 176 Cytoxicity, cellular, 82:156

58

SUBJECT INDEX

D D6, 81:10 Danio rerio see Zebrafish DARC, 81:10, 11 Daunorubicin, 68:107, 119 Davidson, D., 82:22 DAXX proteins, 71:171 DC, see Dendritic cell DCs, see Cells, dendritic; see Dendritic cells Deadenylation, 68:21, 28 Death effector domains, 73:266 Death receptors, lymphocyte apoptosis-signaling, 76:180–184 Death-inducing signaling complex, 68:116–119; 71:174–176, 182–184 Decidua, uterine natural killer cell role, 79:319–320 DED, see Death effector domains Defective ribosomal products, 80:22–23 Defensins, 82:72 CCR6 interaction with b-defension, 78:138–139 types, 78:138 Degranulation, 68:172–174 Degranulation, sPLA2-IIA and, 77:176–177 Delayed-type hypersensitivity, 70:152–153; 72:349–350 inhibition, 73:177 measurement, 73:155 OVA reaction, 73:185–186 suppression, 73:174 Demethylation, 69:319, 320–321, 329–330

Demethylation, DNA, connection to DNase I hypersensitivity, 80:140–141 Dendritic cell (DC) activation and maturation, 78:125, 137 chemokine and receptor expression antigen uptake and migration of immature cells MIP-3a/CCR6 interaction, 78:137–138 overview, 78:136–137 receptor expression, 78:137 CCR6, 78:88–89 CCR7, 78:88–89 chemokine production, 78:89–90 receptor expression in maturation, 78:88–89 T cell interactions and chemokines, 78:139–140 Dendritic cells (DCs), 69:19–20, 72–73, 81–82; 70:113–114; 71:11; 81:178, 199 activation and maturation, 80:130–131; 81:179 CD100 involvement in, 81:185–186 adhesion molecules, 72:265 allogeneic, 81:194 antigen capture, 72:262 antigen presentation, 72:264 antigen-presenting properties, 75:187–189 apoptosis, 72:263–264 atrophic follicular, 80:258–259 –B cell interaction B cell differentiation, 72:289–291

SUBJECT INDEX

B cell proliferation, 72:289 dialogues, 72:288 follicular DC, 72:286–287 general, 72:285 germinal center DC, 72:287–288 C-type lectin receptors, 72:263 Ca2þ, 72:273–274 cancer immunotherapy role, 75:247–249 Cat S/, 80:94 characterization, 73:15–16 clinical studies allergies, 72:293 asthma, 72:293–294 bacteria, 72:294 parasites, 72:294–295 psoriasis, 72:291 retroviruses, 72:298–300 rheumatoid arthritis, 72:291 transplantation, 72:291–293 tumors general, 72:300–302 human, 72:303–305 mouse, 72:302–303 viruses, 72:295–298 cytomegalovirus, 72:296–297 herpesvirus, 72:296 influenza, 72:297 measles, 72:297–298 control mechanism, 73:337 costimulatory molecules, 72:268–269 CpG effects, 73:340 development into APCs, 80:79 development, 72:262 lymphoid pathway, 72:277–278 stages, 72:259–260 theories, current, 72:278–279

59

enzymes, 72:272–273 Fce receptors, 72:262 Fcg receptors, 72:262 FLT-3 ligand, 72:278 generation blood mononuclear cells, 72:277 hematopoietic progenitor cells, 72:274–277 murine cell lines, 72:274 generation of class I-presented peptides, 80:48–49 humoral responses in vitro, 72:289 in vivo, 72:288–289 identification, 72:255 immature, 80:81–82 immune response, 72:255 in vivo role, 73:16–17 increased production in elderly, 80:260–261 influenza virus, 73:34 intracellular bacteria vaccination, 75:34–35 macropinocytosis, 72:262 mannose receptor, 72:263 maturation IL-10 inhibition, 72:280–281 stimulators, 72:279–280 MHC class I loading, 72:264–265 migration control, 72:266–268 patterns, 72:265–266 morphology, 72:257 NK phenotype, 72:273 OVA presentation, 73:44–45 physiology, 72:255–257 signaling CD40/CD40L, 72:269–271 Fas/FasL, 72:272

60

SUBJECT INDEX

Dendritic cells (DCs) (continued) OX40/OX401, 72:271 RANK-L/TRANCE/ODF, 72:271–272 RANK/TRANCE-R/ osteoprotein, 72:271–272 TNF/TNF-R, 72:269 T cell interaction cytokine role, 72:282 in vivo association, 72:281–282 T cell priming, 72:282–283 tolerance central, 72:283–284 peripheral, 72:284 treated with LHVS, 80:90 Dendritic cells, CD40-mediated maturation, 76:72 Dendritic cells, interleukin-12 production, 79:61–62, 77 Dental infections, 73:434–437 Dephosphorylation, 69:225 Dermatitis IL-8 production, 73:427 nickel sulfite, 73:229 Dermatitis, atopic, 82:113–114 Destruction antigenic peptides by peptidase, 80:44–47 Cat L, preventive role of p41, 80:96 Detergent insolubility cell membranes, 77:48–49 lipid rafts, 77:17 Detergent lysis, 82:12 Detergent-resistant membrane association with FceRI, 77:67–69 PIP2, 77:65–66 BCR translocated into, 77:69

LAT targeting into, 77:61 lipidated proteins associated with, 77:49–51 Lo-like membrane phase, 77:48–49 TCR recruited into, 77:70–71 Deterministic theories, aging, 80:245–246 Diabetes mellitus, 70:303–304 caspase-1 role, 73:281 FAS ligand role, 73:280–281 OVA-induced, 73:224 tolerance models, 73:215–216 Diabetes mellitus, insulin-dependent and albumin-induced CD8þ T cells, 68:334 animal studies in, 68:367–369, 380–381, 383–386, 394 anti-TNF-a experiment on, 68:374–375 and ICAM-1, 68:367–369, 375 interleukin-2 targeting, 68:359–361 peptide transporter and, 68:238–239 Diabetes, juvenile, 69:364 Diabetes, see Insulin-dependent diabetes mellitus Diarrhea, of infant rats, 69:213 DIC, see Disseminated intravascular coagulation Dicentrarchus labrax, 81:287 Dictyostelium discoideum, 81:82 Di, Toll signaling, 78:3 Differentiation B cell, 69:117, 119 thymocyte, 69:57–77

SUBJECT INDEX

Differentiation, in thymus, 68:17–18, 89–91 Diffuse large B-cell lymphoma (DLBCL), 81:104, 106–108, 112, 115 DiGeorge syndrome, 81:275 Digestion, 69:251–252 Digestion, enzymatic, 73:188–189 Digestive system, xenotransplantation barrier, 79:184 Diisopropyl fluorophosphonate (DGP), 82:6 Dilysine motif, 70:391–392 Dimyristoyl phosphatidylcholine, in raft domains, 77:53 Dinitrofluorobenzene, 72:282–283 DIP, see Distal interphalangeal Diptheria, 82:50, 276 Diphtheria toxin, 70:264 Diptericin A, in immune response, 79:248–249 Direct cell to cell interactions, 81:345–346 DISC, see Death-inducing signaling complex Disease models, complement deficiency–systemic lupus erythematosus relationship autoimmunity, 76:297–298 B-deficient mouse, 76:278 C1q-deficient mouse, 76:277–278 C2-deficient mouse, 76:278 C3-deficient mouse, 76:278–279 C4-deficient mouse, 76:278–279

61

CR1-deficient mouse, 76:227, 278–279 CR2-deficient mouse, 76:278–279 other nonhuman species, 76:279 Disease, see Autoimmune disease; Infectious disease; specific diseases Disease, age-related, 80:263–265 Disease, graft-versus-host (GvH), 82:51 Disease, graft-versus-leukemia (GvL), 82:51 Diseases antibody-mediated, 82:220–222, 238 infectious, 82:49, 83 Diseases, see specific diseases Diseases, allergic, see also Allergen(s); Allergy(ies); Sensitization, allergic immunotherapy of, 82:105–106 Type I, 82:105–114 Disseminated intravascular coagulation, 79:153 Disseminated intravascular coagulation (DIC), endotoxic shock, 66:260 Distal interphalangeal (DIP), 82:217 Divalent metal transporter-1 (DMT-1), 81:311 DLI, see Donor lymphocyte infusion DM, see H-2M/HLA-DM DNA adjuvant effect, 69:374–375 aging of, 80:245

62

SUBJECT INDEX

DNA (continued) bacterial versus mammalian, 69:372–373 CpG motifs as antitumor adjuvant, 73:349–350 cellular uptake, 73:333 CTL response, 73:353–354 description, 73:329–330 evolution, 73:346–348 extramedullary hematopoiesis-induced, 73:351 immune cell activation, 73:352 mediative effects in vivo, 73:349 as mucosal adjuvant, 73:351 sequence-independent effects, 73:333–334 sequence-specific effects APCs, 73:336–338 B cells, 73:334–335 immunosuppressive, 73:342 macrophage receptors, 73:341 NK cells, 73:339 T cells, 73:338–339 TNF-a production, 73:342 signal mediation cell response, 73:352–353 cellular uptake, 73:343–344 chloroquine effects, 73:346 lysosomotropic compounds, 73:344–345 stress kinase pathway, 73:345–346 T cell effects as Th1 adjuvant, 73:348–349 Th2 pathology, 73:350–351

demethylation, connection to DNase I hypersensitivity, 80:140–141 fragmentation of, 68:52, 54, 55–56 mitochondrial, 68:55 nuclear, 68:76 oligonucleosomal, 68:55, 56, 63–64 plasmid, 69:374–375 plasmids, 73:56–60 transforming growth factor-b signaling, direct binding, 75:128–129 and vaccination, 69:362–364 vaccines bacterial vector delivery mechanisms, 75:35–41 intracellular bacteria vaccination, 75:35–41 administration routes, 75:35–37 APC delivery methods, 75:37 DNA microarrays, 75:59–60 immunogenicity advances, 75:37–38 listeriosis vaccination, 75:38–39 tuberculosis vaccination, 75:39–41 vaccines, 73:340–341 DNA (deoxyribonucleic acid), 82:82 allergen-encoding, 82:131 breaks, 82:297 naked vaccines, 82:66–68 sequences, 82:62, 232 single-stranded, 82:310

SUBJECT INDEX

technology, 82:115 tumor vaccines, 82:68–71, 74–75, 78–79, 271 DNA-binding proteins, B cell differentiation via IgH 30 regulatory region, 75:323–330 DNA-dependent protein kinase (DNA-PK), 82:295–296 DNA, bacterial, interleukin-12 induction, 79:63–64 DNA, double-strand break (DSBs), 82:295, 308–309 DNA microarray, differentially-expressed genes in T cell subsets humans, 78:252 mice, 78:252–253 overview, 78:250–251 table of genes, 78:251 DNA, naked, 71:333–335 DNA polymerase error-prone, 80:191–192 generation of Ig hypermutation, 80:188–191 pol, 80:194 sloppy, 80:196 DNA rearrangement, nonhomologous end-joining and, 77:313–316 DNase I, hypersensitivity, connection to DNA demethylation, 80:140–141 DNFB, see Dinitrofluorobenzene Donor lymphocyte infusion (DLI), 82:51 Doppel deficiency, 81:155–158 Doppel gene, 81:157 Dorsal, Toll activation, 78:2–3

63

Dose antigen, in active immunization models, 77:271 neutralizing antibody, 77:204 virus challenge, 77:240 Dose, antigens in B cell responses, 79:12–13 Double-strand breaks, repair, 80:187 Double-stranded break, 69:310 Doxorubicin, 68:105, 224 Dpl mRNA, 81:153–154 DR3 ligand, 73:286 Dreyer, W. J., 69:116–117 DRM, see Detergent-resistant membrane Dromedaries epitope recognition, 79:284 immunization, 79:275–276 Drosomycin, in immune response, 79:248–249 Drosophila, 81:55, 56, 263, 309 Drosophila melanogaster immune response antimicrobial genes, 79:238, 248–249 C-type lectins, 79:233 GATA factors, 79:247–248 gram-negative binding protein, 79:231–232 humoral response, 79:226–227 immune deficiency pathway, 79:245–247 model, 79:227–228 overview, 79:226 peptidoglycan recognition proteins, 79:229–230 phenoloxidase, 79:236 Relish pathway, 79:244–247

64

SUBJECT INDEX

Drosophila melanogaster (continued) scavenger receptors, 79:233–234 thioester proteins, 79:237 Toll pathway, 79:240–244 pathogen exposure, 79:227 Drosophila, transforming growth factor-b signaling by Smad proteins, 75:124 DSBs, see DNA, double-strand break DTH, see Delayed-type hypersensitivity DTV, see Dual tropic virus Dual tropic virus characterization, 73:514–515 lymphomagenic, 73:516 thymic function, 73:515, 526 Duchenne’s muscular dystrophy, 69:364 Dyax Corporation, 82:349 Dynamin, 81:2, 60 Dyslipidaemia, 69:365–366 Dysplasia, extodermal, 82:305

E E2A, V(D)J recombination regulation, 78:201–203 E3 enzymes, 80:4 mE3-binding proteins, V(D)J recombination regulation, 78:204–205 EAE, see Encephalomyelitis, experimental autoimmune; see Experimental-allergic encephalomyelitis; see

Experimental autoimmune encephalomyelitis EAMG, see Experimental autoimmune myasthenia gravis EAN, see Experimental allergic neuritis Early B cell factor (EBF), V(D)J recombination regulation, 78:206 Early studies, antibody neutralization, 77:200–202 EAU, see Experimental uveoretinitis EBF, see Early B cell factor EBV-induced protein, 70:3, 94 EBV, see Epstein-Barr virus; see Virus, Epstein-Barr E-Cadherin, 72:333–334 E-cadherin, 69:86–87 ECM proteins, see Extracellular matrix proteins ECSIT, interleukin-1 receptor signaling, 78:5–6 18W, Toll homology, 78:3 Ectoderm, 81:275 Ectromelia, 70:344–346 Ectromelia virus, 69:379 EDTA, 81:180 Effector cells, neurons, 77:297–299 EGF, see Epidermal growth factor EGTA, 81:180 Ehrlich, Paul, 82:50 Eicosanoid biosynthesis, sPLA2-IIA, 77:170–175 COX-2 role, 77:171–172 heparan sulfate proteoglycan, 77:172–173 membrane asymmetry, 77:173–174

SUBJECT INDEX

oxidation of cPLA2-derived products, 77:174–175 EL4 cells, 73:51 Electrophoretic Mobility Shift Assay (EMSA), 81:209 Electrophoretic mobility shift assay (EMSA), 82:6, 8 analyses, 82:9, 24 mobility, 82:21 Electroporation, 82:78 ELISA testing, 82:280 ELISPOT assays, 82:284 ELISPOT assays, xenotransplantation tolerance, 79:175 ELRþ CXC chemokines, 81:17–19, 30 ELR CXC chemokines, 81:19–20, 30 Em intronic enhancer, B cell differentiation via IgH 30 regulatory region, 75:317–318, 321, 330 EMA, see Antigens, epithelial membrane Embryogenesis, transforming growth factor-b signaling by Smad proteins, 75:142 Embryonic development, cerebral cortex, 77:303–309 Embryonic divisions, nervous system, 77:299–303 Embryonic stem (ES) cells, 81:98, 154 EMSA, see Electrophoretic mobility shift assay Encephalomyelitis, 71:111 Encephalomyelitis (EAE), 81:334

65

Encephalomyelitis, experimental allergic adhesion blocking in, 68:365–367 anti-CD4 monoclonal antibody and, 68:379–380 antigen-specific tolerance in, 68:389–391 cytokines and, 68:371–374 spreading peptide administration, 68:396 T cell receptor costimulation and, 68:381–385 Encephalomyelitis, experimental autoimmune, 72:348–353 Encephalomyelitis, experimental autoimmune (EAE), 69:363 Encephalomyelitis, experimental-allergic, 70:160–162 Endocrine system, xenotransplantation barrier, 79:185–186 Endocytic compartment class I-presented peptides generated in, 80:48–49 targeting class II molecules to, 80:92–93 Endocytic pathway, major histocompatibility complex class II role antigen processing mechanisms, 75:173–176 peptide loading, 75:176–180 trans-Golgi-mediated sorting, 75:174–176 Endocytic proteases activity in APCs, 80:73, 76–77 antigen degradation by, 80:100–102 regulation by

66

SUBJECT INDEX

Endocytic proteases (continued) cytokines, 80:78–79 endogenous inhibitors, 80:80–82 intracellular pH, 80:77–78 Endocytosis, 68:172–173, 278; 70:393–394 clathrin-mediated, 73:12–13 inhibition, 73:23 non-clathrin mediated, 73:13–14 Endoderm, 81:275 Endogenous antigens MHC generation, 73:4–9 presentation in vivo, 73:56–63 Endonucleases, in apoptosis, 68:52–57, 124 Endoplasmic reticulum, 69:381; 82:76 antigen processing in, 68:191, 197–199 BFA inhibition, 73:21 bidirectional transport, 70:389–390 degradation studies, 70:387–389 description, 70:369–372 export of peptides from, 68:233–234 extra, MHC loading, 73:9–12 MHC class I molecules in, 80:23–24 MHC II, 70:391 peptide loading of class I molecules in, 68:205–209 peptide transport in, 68:192, 196, 214–215 peptide trimming in, 80:43–44 protein degradation in, 80:20–21 retention studies, 70:387–389 transport, 73:6–9

Endoplasmic reticulum (ER), 81:48, 61, 63, 69, 221 Endoplasmic reticulum, major histocompatibility complex class II transport mechanisms, 75:172–173 Endosomal proteases, 73:23 Endosomal system, 70:372 Endosomal–lysosomal pathway, degradation, 81:61–65 Endosomal/lysosomal system, peptides derived from, 81:49 Endosomes, regulation of, 68:174 Endothelial cells, 70:536–537, 542; 81:10 HEV, levels, 72:213–214 –lymphocyte interaction b7 role, 72:225–227 characterization, 72:211 IEL role, 72:225–227 LFA-1 role, 72:225 E-selection role, 72:225–227 L-selection role, 72:224–225 P-selection role, 72:225–227 sialomucin role, 72:226–227 Endothelial cells, activation, CD40/ CD154-mediated regulation, 76:77–79 Endothelial cells, in xenotransplantation AHXR, 79:151–152 HAR, 79:150 Endothelin Converting Enzyme-1 (ECE-1), 81:278 Endothelin-1, 71:217 Endothelin-A Receptor (ETAR), 81:278

SUBJECT INDEX

Endotoxemia, see also Human experimental endotoxemia; Sepsis interleukin-1, 66:116–117 sepsis and, 66:130–131 TNF and, 66:114–116 Endotoxemia, ABCD chemokine role, 78:147–148 Endotoxic shock, contact activation proteins, 66:260 Endotoxin shock, 82:351–355 Endotoxin tolerance, 79:80 Endotoxin-induced liver injury, 70:301–303 Energy transfer, GPI-linked proteins, 77:51–52 Enhancers, see also cis regulatory factors analysis by gene targeting, 69:323–339 for IgH, 69:328–331 at IgLk locus, 69:331–333 and k expression, 69:138–141, 144–145, 146–150 mechanisms, 69:124–128, 136–137, 320–321, 334 and RS/kde, 69:155–156 for TCRa, 69:326–328 for TCRb, 69:323–326 ENU mutagenesis, 81:299 Envelope spikes antibody binding, 77:198–199 heterogeneous, 77:246 HIV-1, 77:213 neutralization-irrelevant, 77:215 Enzymatic digestion, 73:188–189 Enzymatic properties, sPLA2s, 77:167–168 Enzymes, 82:343

67

Enzymes, angiotensin-converting (ACE), 82:343 Enzymes, proteolytic, see also C1; C1q; C1r and C1s; C2 factor B and C3-convertase, 69:294 catalytic activity, 69:276–278 and factor D, 69:251, 267–268 gene for, 69:271 ligand binding site, 69:272, 273–276 protein structure and function, 69:271–276 factor D blood level, 69:267 catabolic rate, 69:267 catalytic activity, 69:261, 266–268 in complement activation, 69:267, 293–294 esterolytic activity, 69:267 and factor B, 69:267–268, 251 gene for, 69:261 and isocoumarin, 69:266 structure, 69:255, 257, 262–266, 294 substrate, 69:261, 265–267 and trypsin, 69:265 factor H, 69:258–259 factor I and C3- and C5-convertase, 69:294 and isocoumarin, 69:270 mechanism, 69:251 structure and function, 69:257, 260–261, 268–270, 294 substrate, 69:270 and trypsin, 69:270

68

SUBJECT INDEX

Enzymes, proteolytic (continued) and MASPs, 69:251–259, 291–293, 294 modular structure, 69:257–261, 269–270 serine proteases catalysis, 69:252 substrate recognition, 69:252–253 Eosinophil cytokine production, 78:291–292 functional overview, 78:291–292 gastrointestinal eosinophils developmental biology, 78:316–317 disease roles asthma, 78:319–320 colitis, 78:301 colonic cell migration, 78:310 eotaxin regulation of lamina propria cells in allergy, 78:303–304, 317 esophageal cell migration, 78:310–311 experimental eosinophilic gastroenteritis, 78:302–303 food allergy, 78:300 gastroenteritis, 78:300–301 gastroesophageal reflux, 78:301 helminth infection and cell recruitment, 78:311–315 inflammation role, 78:302, 314–315

inflammatory bowel disease, 78:301 interleukin-5 regulation role in allergy, 78:304–307, 317 levels of cells, 78:292–293, 299 Peyer’s patch migration in allergy, 78:307–310 T cell overexpression effects on lamina propria eosinophils, 78:305–309 eotaxin role in homing, 78:296–297 hematopoietins and accumulation granulocyte-macrophage colony-stimulating factor, 78:298 interleukin-3, 78:298 interleukin-5, 78:298 immunoglobulin E-mediated reactions, 78:299–300 inflammatory mediators and accumulation, 78:296 interepithelial cells, 78:294 lamina propria, 78:294 mouse versus humans, 78:293–294 perinatal mice and endogenous flora, 78:294–296 Peyer’s patch, 78:294 T cell interactions, 78:298–299, 315–316 secondary granule contents, 78:291 Eosinophils, 82:114, 221

SUBJECT INDEX

Eotaxin eosinophil homing role, 78:296–297 regulation of lamina propria eosinophils in allergy, 78:303–304, 317 Epidermal growth factor, 69:259; 79:312 Epidermal growth factor (EGF), 82:3 Epidermal growth factor receptor, 70:396 Epigenetic modifications, cytokine genes, 80:138–145 Epilepsy, APS-associated, 70:514 Epithelial cells intestinal, 69:386 olfactory, 69:441 respiratory, 69:383–386 Epithelial cells, 81:275 Epithelial homeostasis, 71:122–123 Epitope mapping, 70:523 Epitopes antibody neutralization, 79:33–34 dromedaries, 79:284 Gal, 79:136–139 HIV CTL epitopes, 66:276–280 T cell, autoimmune diseases and, 66:88–91 Epitopes, neutralizing, 77:197–198 Epoxyketones, proteasome inhibitors, 80:14 Epstein-Barr virus 68:115, 324; 69:190, 212–214, 380 FasL production, 73:398 GM-CSF effects, 73:451 IL-8 production, 73:381–382

69

IL-1RI/IL-1RII production, 73:408 SAP link, 73:122 Epstein-Barr virus (EBV), 81:100 Epstein–Barr virus, antigen expression in human cancer, 75:235–236, 240, 256 Epstein–Barr virus, latency, 80:50 ER, see Endoplasmic reticulum ERK, see Extracellular signal-regulated kinases ERK, CD40-induced activation, 76:89–90, 120, 125–126 ERK, Ras/ERK MAPK pathway, 80:133–134 ERKs, Extracellular–regulated kinases ERM transcription factor, Th1, 80:129 Erythroid cells, 69:78 precursors, 69:59 Erythroid precursors, 68:26 Erythropoietic porphyria syndromes, 81:301 Erythropoietic porphyria, congenital, 69:364 ES-62, dendritic cells stimulated by, 80:132 Escherichia coli, 82:309 Escherichia coli, 68:30, 324; 81:76, 79 E-Selection, 72:225–227 Ethics, in xenotransplantation, 79:188–190 N-Ethylmaleimide, 70:381–382 Ethylnitrosourea (ENU), 81:255 Etoposide, 68:105, 224 ETS proteins, V(D)J recombination regulation, 78:203–204

70

SUBJECT INDEX

Evi-1, transforming growth factor-b signaling, 75:133 Evolution combinatorial system, 70:418 foundations gene specificity, 70:421–424 mechanism, 70:418–420 superfamilies, 70:420–421 immunoglobulins amphibians, 70:437 birds, 70:437–438 bony fishes, 70:436–438 chondrichthytes, 70:433–436 emergence, 70:425–430 gene organization arrangement, 70:479–480 basic elements, 70:475–476 intron removal, 70:476–477 promoters, 70:478–479 species comparisons, 70:480–485 transcription, 70:477–478 heavy chains isotypes, 70:470–475 universal m, 70:465, 467–470 variable domains, 70:460, 463–465 jawed vertebrates, 70:430–433 light chains, 70:451–460 mammals, 70:438–439 molecular events, 70:485, 488–491 reptiles, 70:437–438 overview, 70:417 T-cell receptors, 70:425–430 jawed vertebrates, 70:430–433 species comparisons, 70:441–451

variable domain, 70:439, 441 Exocytosis, 68:172–174 Exogenous antigens internalization modes, 73:12–14 presentation ablating pAPCs in vivo, 73:23–24 aggregated proteins, 73:49–50 bacteria artificial particles, 73:32–34 pathways, 73:26–32 cell debris, 73:34–36 cellular sonicates, 73:50–51 complex quantitating, 73:17–19 denatured proteins, 73:49–50 endogenous antigens in vivo, 73:56–63 immunogenicity, 73:23–24 inactivated viruses, 73:23–24 ISCOM, 73:42–44 liposome, 73:42–44 mechanism, 73:19–23 native proteins, 73:44–45 processing, 73:19–20 quantum theory, 73:51–52 receptor-mediated uptake, 73:46–49 srivastava saga, 73:52–56 viral, 73:32–38 virosome, 73:42–44 virus-like particles, 73:38–39 Exosomes, characterization, 73:11 Exotoxin, C3, 72:33–34 Experimental allergic neuritis, 73:221 Experimental autoimmune encephalitis, MBP and PLP and, 66:88, 90

71

SUBJECT INDEX

Experimental autoimmune encephalomyelitis, 72:348–353 MBP administration active suppression, 73:164–165, 206–208 glatiramer acetate, 73:211 Lewis rat, 73:208, 210 murine, 73:210–211 nasal aerosol, 73:211 neonatal, 73:223–224 oral tolerance models, 73:164–169 Experimental autoimmune encephalomyelitis (EAE), 81:187 Experimental autoimmune myasthenia gravis, 73:305 Experimental colitis, 70:164–165 Experimental models, see Animal models Experimental uveoretinitis, 70:162 Experimental viral infections, 70:168–171 Experimental-allergic encephalomyelitis, 70:160–162 Expressed sequence tags (ESTs), 81:5, 255, 312 Extracellular matrix proteins, 72:27–28 Extracellular matrix, uterus, 79:319 Extracellular signal-regulated kinase, see ERK; see also Mitogen-activated protein kinase cPLA2 and, 77:108 Extracellular signal-regulated kinases activation, BCR-induced, 73:96

B cell transduction CD22 regulation, 73:115–119 description, 73:101–104 Extracellular-regulated kinases IRR activation, 72:3 NFAT activation, 72:34–35 T cell activation, 72:16–17 Ezrin/radixin/moesin proteins, 77:27–28

F F2 genetic screens, 81:299–301 F4/80 monoclonal antibody, 68:272–275 FV fragment, immunogenic epitopes, 80:205 Fab fragments neutralization of viral particles, 77:218–219 in RSV, 77:242 Fab regions, 82:155 proteins and, 82:181–183 RF-Fc IgG interactions of, 82:180–181 SpA and, 82:188–190 SpG and, 82:192 FACS, see Fluorescence-activated cell sorter Factor B, see Enzymes, proteolytic Factor D, see Enzymes, proteolytic Factor H, see Enzymes, proteolytic Factor H, 70:524–525 Factor I, see Enzymes, proteolytic Factor XI, 66:225 activation, 66:230, 237 platelet receptors, 66:244 properties, 66:226 structure, 66:230

72

SUBJECT INDEX

Factor XIa inhibition, 66:239 platelet receptors, 66:244 Factor XII, 66:225 activation, 66:225, 227, 234, 235–236 autoactivation, 66:234–235, 236, 245, 248 endothelial cell receptor, 66:249–257 function, 66:241 interaction with cells, 66:244, 246 properties, 66:226 structure, 66:226–229 Factor XIIf, 66:227–228, 229 function, 66:241 inactivation, 66:238 Factor XIIa, 66:225, 228, 229 inactivation, 66:238 FADD proteins CD95 signaling, 71:170–172 DISC signaling, 71:174–176 Farnesyltransferase, 68:152–157, 164–165, 175–178 Fas, 72:47–49 as apoptosis inducer, 68:53, 61, 92 caspases and, 68:57, 61, 72 role in apoptosis, 68:114–116 surface receptor, 68:100 TCR/CD3, 68:94 FAS gene, 71:101 Fas ligand AIDS, 73:282–283 B cell regulation, 73:121–122, 132–134 cardiovascular disease, 73:284 caspase-8 and, 73:277–280 characterization, 73:277–278

GVHD, 73:283–294 Hashimoto’s thyroiditis, 73:281–282 hepatic diseases, 73:284–286 IBD, 73:286 IDDM and, 73:280–281 multiple sclerosis, 73:281 PMN expression, 73:397–398 TRAIL and, 73:287 Fas receptors, 70:63 Fas/FasL, 72:272 Fasciclin IV, 81:173 Fc receptor-binding sites Fcc receptors as, 82:155–161 transcytosis/catabolism and, 82:165–173 Fc receptor, antigen uptake role, 75:183–184 Fc receptors inhibitory signals, 69:206–207, 217, 218–220 and ITAMs, 69:186, 189, 190, 208 structure, 69:189 Fc receptors, expressed by APCs, 80:98–99 Fc-receptors in antiviral antibody responses, 79:12 Fcg, in interleukin-12 production, 79:78–79 FcaR signaling, raft role, 77:68 FceRI cross-linked, 77:23 signaling and control of secretion, 77:106–112 cytochalasin D and, 77:76 raft role, 77:66–69 FceRIa, and IgE levels, 77:97

SUBJECT INDEX

FcgRIIA, 77:63, 68 Fce receptors, 72:262 FceRI, see Immunoglobulin E Fcg receptors characterization, 72:154–158 dendritic cells, 72:262 FcgR monoclonal antibodies, 68:276–279 FDC, see Follicular dendritic cells FDCs, see Cells, follicular dendritic Felodipine, 73:231–232 Ferroportin 1 mutations, 81:301 Fertilization, 69:251–252 Fetal liver kinase, 72:2, 278–279 Fetal thymus organ culture, 73:307 a-Fetoprotein, in pregnancy, 79:298 Fibrinogen, in xenotransplantation, 79:170 Fibrinolysis, 69:251–252 Fibrinolytic pathways, 79:154–155 Fibroblast-like stromal cells, CD40 engagement effects, 76:76 Fibroblasts, 82:219–308 and apoptosis, 68:91 Bcl-2 and mitochondrial function, 68:75 c-fos mRNA, 68:5, 27 cycloheximide and, 68:6, 11 cytomegalovirus, peptide transport and, 68:235 FTase inhibitors in, 68:176 GM-CSF production, 68:8, 9 phorbol ester and, 68:11 prenylated proteins in, 68:174 protein production, 68:9 R2 mRNA in 3T3, 68:27 Rho proteins and, 68:150 TNF-a and, 68:11

73

transition from G0 to S, 68:27 ultraviolet light on, 68:27 Fibroma virus, 69:379 Fibronolytic cascade, 66:240–254 Fibrosarcoid cells, 68:87 Fibrosarcoma, murine, 68:237; 69:369 Fibrosis, 73:420 Filament assembly/disassembly, 77:25–28 nucleation by cytochalasin D, 77:29 Filaviviruses, antibody protection against, 77:235–236 Filoviruses, antibody protection against, 77:234–235 Filtration, biologic, 73:188–189 Fish, 69:441 FLAP, see 5-Lipoxygenase-activating protein Flavivirus, 69:386 FLICE inhibitory proteins, 71:182 FLT-3, 72:278 Fluid mosaic model, plasma membrane structure, 77:45 Fluorescence-activated cell sorter (FACS), 82:14, 23 Fluorochromes, 68:77–78 F-Met-Leu-Phe, histamine induced by, 77:104 fMLP, see Peptides, N-formulated Fn, see Protein(s) Focal adhesion kinase, 72:66–68 Follicular B-cell lymphoma (FBL), 81:104, 107 Follicular dendritic cells, 73:123

74

SUBJECT INDEX

Follicular dendritic cells (FDCs), 81:137–145, 149, 150 Food allergies, 73:223 Food allergy, gastrointestinal eosinophils, 78:300 Forkhead activin signal transducer, transforming growth factor-b signaling, 75:130–131 Formyl-methionyl-leucylphenylalanine (fMLP), 81:7, 9 4-1BB, T-cell response in cancer, 75:252–253, 256 Fragments FV, immunogenic epitopes, 80:205 generated by proteasomes, 80:16–17 France, 82:279 Free radicals, aging and, 80:244 Freeze-thaw cycles, 82:5–6, 12 Friend-MuLV, antibody protection against, 77:230–231 FTase, see Farnesyltransferase FTOC, see Fetal thymus organ culture Fucosyltransferases, in selectin ligand generation, 80:150 Functional domains, SLP-76 coupling, 79:113–116 Fungi, for active immunization models, 77:265 FV receptors, single chain, 68:258–266 FV-1 gene, 73:516 Fyn kinase enrichment, 77:78

N-terminal region mutations, 77:57 raft-associated, 77:55–56 Fyn, 72:117–119

G G protein-coupled receptors, 81:2, 12 G proteins activation, 81:8 binding to, 81:9 G proteins, heterotrimeric, bg dimer, 77:133 G proteins, lipopolysaccharide signaling in macrophages, 78:15–16 G8 clone, 71:90 G-actin ATP-bound form, 77:24 pool, buffering by thymosins, 77:27 Gads, see Grb2-related adaptor protein Gads, interaction with SLP-76, 77:147–148 Gal anti-Gal antibodies, 79:136–137, 139–141, 157–161 antigens in xenotransplantation, 79:137 epitopes, 79:136–139 gene transfer, 79:165 knockout technology, 79:168 non-Gal determinants, 79:141–142 Galactosyltransferases (GT), 82:186 Galectin-1, 68:99–100 Galectins, 82:185

SUBJECT INDEX

GALT, see Gut-associated lymphoid tissue g/d T cell receptor, major histocompatibility complex class I interactions, 76:19–22, 42 GAPs, see GTPase-activation proteins GAS, see Interferon-activated sequences, c Gastroenteritis, eosinophils, 78:300–301 Gastroesophageal reflux, eosinophils, 78:301 Gastrointestinal tract inflammation a4b7 blocking, 72:234–237 lymphocyte recruitment role, 72:242–243 GATA-3 expression and activity, regulation, 80:125–127 induction of IL-4 memory, 80:148 recruitment of chromatin-remodeling factors, 80:141 for Th2 cytokine memory, 80:123–125 GATA-3, T helper cell differentiation role, 78:241 GATA, 69:78–79 GATA factors, in immune response, 79:247–248 Gated opening, 20S proteasome a-rings, 80:8–9, 12, 37–38 GC, see Cells, germinal founder GCs, see Germinal centers G-CSF, see Granulocyte-colony stimulating factor G-CSF, 82:4–7

75

GEF, see Guanine nucleotide exchange factors Gelatinase B, 81:18 Gell, P. G. H., 82:105, 111 Gelonin, 73:22 Gelsolin, actin filament-binding, 77:27 GEMs, signaling protein recruitment, 79:110–113 Genbank database, 81:255 Gene expression profiles, 81:111–113, 343 Gene expression screens, 81:310–311 Gene expression, see Major histocompatibility complex; Transcription Gene rearrangements BID, 71:86 gene-targeted mice, 71:44–47 general considerations, 71:19 models, 71:34–35 molecular analysis, 71:20–22 TCRa locus, 71:32–34 TCRb locus, 71:28–32 TCRd locus, 71:24–27 TCRg locus, 71:22–24 Gene targeting description, 69:321–322 and LC, 69:128–129, 145–146 and recombinational accessibility, 69:332–339 Gene therapy, see also Vectors administration and delivery, 69:362, 364–365, 386–387 autoimmune response, 69:383 hypercholesterolemia, 69:365 inflammatory disease, 69:382–383, 386

76

SUBJECT INDEX

Gene therapy, see also Vectors (continued) metabolic disorders, 69:382–383, 386 microbial immunity, 69:382, 386 persistence, 69:364–365 for tumor immunity, 69:382, 386 unexpected effects, 69:375–387 Gene transcripts distinguishing plasmacytoma, 81:113 Gene transfer systems tissue-specific expression systems, 77:283–285 transgenic models, 77:282–283 Gene-targeted mice lineage commitment, 71:47–50 rearrangements, 71:44–47 TCR chain disruptions, 71:43–44 Gene-targeting strategies in zebrafish, 81:308–309 Gene(s) -based tumor vaccines, 82:66 CD40, 82:303–304 expression, 82:2–3, 78 human TNF (huTNF), 82:231 immediate-early, 82:17 kB (NEMO), 82:304–305 PU.1, 82:28–30 transcription, 82:2, 17–28 uracil-N glycosylase (UNG), 82:311–314 Genes antimicrobial, see Antimicrobial genes apoptosis-inhibitory, 68:74 Diptericin A, 79:248–249 Drosomycin, 79:248–249 Gal, 79:165 involved in T cell activation, 68:93

killer, 68:68–69 LMP2 and LMP7, 68:203, 210 Metchnikowin, 79:249 and MHC class I-bound peptides, 68:193 NHEJ, 77:314–315 p35, 79:56–58, 71–72 p40, 79:56–58, 67–71 posttranscriptional regulation of, 68:1–49 pro-cell death, 77:311–312 regulation of peptide transporter, 68:209–211 and rheumatoid arthritis, 68:315–332 rheumatoid arthritis susceptibility, 68:315–317 Saccharomyces cerevisiae, 68:157 sialodhesin, 68:276 sPLA2-X, 77:166 US6, 68:235 VHH, see VHH genes VHH-D-J, 79:272–274 Genes, see also specific genes antigen transition mechanisms in intracellular bacteria, 75:59–61 DNA microarrays, 75:59–60 genome microarrays, 75:59–60 proteomics, 75:60–61 vaccinomics, 75:61 Genes, see also Gene targeting; Gene therapy; V(D)J gene rearrangement ampicillin resistance, 69:374 assembly, theories, 69:116–120 for C1R and C1S, 69:278–291 for C2, 69:271 evolutionary adaptation, 69:446

SUBJECT INDEX

factor B, 69:271 factor D, 69:261 factor I, 69:268 GATA, 69:78–81 Ikaros, 69:7, 81–82 immunoglobulin loci, 69:121–129 kanamycin resistance, 69:374 MASP, 69:291 olfactory receptor, 69:437–447 and pre-TCR complex, 69:56–57 PU.1, 69:80 RAG and GATA, 69:78–79 and HC allelic exclusion, 69:134–135 and LC gene rearrangement, 69:133, 152 and lymphocyte development, 69:133 and recombinational accessibility, 69:313–315, 316, 317 segments heavy chain loci, 69:121 IgL, 69:124–129 k locus, 69:121–123, 126–129, 141–142 l locus, 69:123–124, 141–152 light chain loci, 69:135–136, 141–152 V(D)J gene arrangement, 69:116–120, 133 XRCC4, 69:315 Genetic disease, 69:363, 364 Genetic engineering, xenotransplantation donor modification, 79:166–169 pig, 79:133

77

recipient modification, 79:164–165 Genetic mutations, zebrafish, 81:298–299 Genetic screens, 81:295–298 combinations and variations, 81:304–305 large-scale, 81:299–330 Genetically engineered mice (GEM), 81:99, 100, 102 Genetics, mouse strains used in active immunization models, 77:271–273 Genomics, zebrafish, 81:312–314 Genotypes, 82:303 Geranylgeranyltransferase type-I, 68:152–157, 177–178 type-II, 68:152, 158–162 Germinal center reaction CD154-expressing B cells role, 76:74 T cell-dependent activation, 76:70, 132 Germinal center response, in aging, 80:258–259 Germinal centers, 73:87–88 Germline diversity theory, 69:116–120 Germline transcription, 69:138, 326–327, 329–330, 334–335, 340–341 Gerontogenes, 80:245–246 Gestational trophoblastic disease, 81:229–230 GFP, 81:295 GFP transgenes, use to define zebrafish blood lineages, 81:291–294 Gingival crevicular fluid, 73:434–437

78

SUBJECT INDEX

GITR, 81:347–348 GlaR, as endothelial cell receptor, 66:249–257 gld gene, 71:167–168 Glia, as noneffector cells of nervous system, 77:299 b-Globin locus transcription, see Chromatin structure Glomerulonephritis, 68:377–378 b-1,3-Glucan-binding protein, 79:230–232 Glucocorticoids, 68:7, 12, 56, 71, 75 receptors, 71:152 sensitivity, 71:4–5 Glucocorticoids, immune system and, 66:197, 218 l-Glutamic acid50-l-alanine30-l-tyrosine10 suppressor-T cell interactions, 74:2–3, 6, 8, 11 Glutamines, 82:252 Glutathione, 68:25, 64–65, 70 Glycerophospholipids, esterification, 77:46 Glycloproteins, 82:264, 273–274 as tumor vaccines, 82:61–64 Glycolipid presentation, 71:303–306 Glycolipids, 82:58 Glycolipids, signaling via, 77:63–65 Glycopeptides, 82:274 b2-Glycoprotein I antibody binding sites, 70:523 characterization, 70:520–523 gene encoding characterization, 70:530–531 cloning, 70:530–531 molecular modeling alignment, 70:524–525

cardiolipin-binding region, 70:529–530 comparisons, 70:524–525 electrostatic properties, 70:528–529 fifth domain, 70:525, 527–528 structure, 70:523–524 phospholipid sites, 70:523 thrombosis link, 70:539–540 Anti-b2-Glycoprotein I antibodies, 70:510–512 Glycoproteins, 82:58 Glycoproteins, histidine-rich (HRG), 82:183 Glycosaminoglycans, 79:64–65 Glycosaminoglycans (GAG), 81:3 Glycosphingolipid-enriched membrane microdomains, see Lipid rafts Glycosphingolipids, ceramide-based, 77:46–47 Glycosylation inhibiting factor, suppressor-T cell subunit, 74:33–54 antigen-primed B cells, 74:50–51 antigen-primed T cells, 74:48–50 cellular mechanisms, 74:5, 40–45 1-J determinant association, 74:39–40 immunoregulation mechanisms, 74:48–51 overview, 74:51–54 structural basis of bioactivity, 74:34–39 T cell receptor derivative formation, 74:40–45 target cells, 74:45–48 Glycosylation, see Major histocompatibility complex molecules

SUBJECT INDEX

Glycosylation, aging and, 80:244 Glycosylation, xenotransplantation genetic engineering, 79:167–168 Glycosylphosphatidylinositol (GPI), 81:137, 174 GM-CSF, see Granulocyte-macrophage colony-stimulating factor GM–CF, see Granulocyte–macrophage colony-stimulating factor GM–CSF, tumor-specific T-cell response enhancement, 75:262–263 GMG cells, see Granulated metrial gland cells GMP, see Guanosine monophosphate GNBP, see Gram-negative binding protein Goldfish macrophages, 81:264 Golgi complex, major histocompatibility complex class II transport mechanisms biosynthesis and assembly, 75:172–173 sorting, 75:174–176 Golgi network cis-, 70:391 trans-, 70:371 Gout, inflammation in, 66:260 gp130, 66:127–128 Gp33, 69:23 gp96, 73:53–54 GPI-anchored proteins energy transfer measurements, 77:51–52 enriched in DRMs, 77:49 signaling via, 77:63–65

79

GPI-linked folate receptor, 77:18 Graft versus host disease, 71:119–120 Graft protection by HLA-G, 81:234 Graft-versus-host disease, 70:153–154 Graft-versus-host disease, 73:283–294 Gram-negative binding protein, 79:230–232 Gram-positive bacterium, 81:67 Granulated metrial gland cells, rodents cell differentiation, 79:306–307 morphology and phenotypes, 79:302–305 origin, 79:300–302 overview, 79:299–300 Granulocyte chemotactic protein-2 (GCP-2), 81:18–19 Granulocyte colony-stimulating factor (G-CSF), 66:149 sepsis and, 66:104, 149–150 Granulocyte-colony stimulating factor, 73:422 Granulocyte-derived factor, 73:423–424 Granulocyte–macrophage colony-stimulating factor Act-D and, 68:2, 19 anti-CD28 plus anti-CD3 and, 68:11 antigen and, 68:8 AU-binding factor and, 68:33, 34 AUUUA repeats in mRNA, 68:19–20 calcium flux and, 68:10 and c-kit, 68:6 irradiation and, 68:9

80

SUBJECT INDEX

Granulocyte–macrophage colony-stimulating factor (continued) mitogenic anti-cell surface antibodies, 68:8 protein secretion levels, 68:13 0 3 untranslated region of, 68:34 TNF-a, TPA or cycloheximide and, 68:14 Granulocyte-macrophage colony-stimulating factor (GM-CSF), 82:2 effects of, 82:63–64 encoding plasmids, 82:70 STATs and, 82:7–11 Granulocyte-macrophage colony-stimulating factor (GM-CSF), gastrointestinal eosinophil accumulation role, 78:298 Granulocyte-macrophagecolony-stimulating factor (GM-CSF), 81:73, 241 Granulocyte–macrophage colony-stimulating factor, sepsis and, 66:150 Granulocyte/macrophage colony-stimulating factor, CD40 expression regulation, 76:80 Granulocytes, 69:18–19 FcgRII and FcgRIII in, 68:278 Ras activation in, 68:167 Granulocytes macrophage-stimulating factor neutrophil-derived EBV effects, 73:446–447 modulation, 73:446–447

Granulocytes, zebrafish, 81:267–268 Granuloma formation, 71:319–321 Granulomatous disease, chronic, 68:169 Granulopoiesis, 82:5, 30 Granzyme B, 68:70, 72; 73:271 Grapefruit juice, 73:231–232 Grb2 B cell pathway, 73:97–100 –BLNK complex, 73:96 Grb2/Sos Ras activation, 72:8–11 T cell activation, 72:11–12 Grb2, 72:37–38 Grb2-related adaptor protein ITAM-coupled signaling, 79:98–99 PLC-g1 activation, 79:118–120 GRO, see Growth-related gene products GROb, 81:18, 31 Growth factor(s), 82:2 epidermal, 82:62 HER2, 82:62 receptors, 82:3–4 Growth factor, 68:70, 71, 84, 108–110, 111 Growth factors activation, model, 70:19–20 IL-2, 70:10–11 Growth-related gene products neutrophil-derived associated diseases, 73:428 characterization, 73:382–385 GT, see Galactosyltransferases GTP-binding protein, 70:393–394 GTPase p21ras, 69:52 GTPase Rho, 69:52–53 GTPase-activating protein, 77:9

SUBJECT INDEX

GTPase-activation proteins function, 72:2 Ras activation, 72:14–15 GTPases Fas apoptosis, 72:47–49 HIV infection, 72:59–63 Rab family, 72:52–53 Ras family CD28 signaling, 72:49–51 cytokine receptor signaling, 72:25 function, 72:1–2 IRR activation, 72:3–5 Cb1 role, 72:12–14 Grb2/Sos role, 72:8–11 PTK role, 72:5–8 SLP-76 role, 72:12–14 Vav role, 72:12–14 IRR signaling effectors, 72:15–18 negative factors, 72:23–25 transcription factors, 72:18–23 lymphocyte development, 72:64–66 regulation, 72:1–2 T cell anergy, 72:53–59 regulation, 72:68–69 Rho family CD28 signaling, 72:51–52 cell adhesion, 72:41–43 chemoattractant responses, 72:44–46 hematopoietic cells regulation, 72:38–39 Vav integration, 72:34–35 integrin adhesion, 72:41–43 IRR signaling activation, 72:39–41 characterization, 72:25–26

81

leukocytes cytoskeleton, 72:27–34 lymphocyte development, 72:66–68 p38 pathway, 72:68 SEK1 pathway, 72:68 selections, 72:43–44 signal control, 72:34–35 Wiskott-Aldrich syndrome, 72:63–64 GTPases subfamilies, 70:377–381 Guanine nucleotide exchange factor, 68:147, 164, 166; 77:7–11 Guanine nucleotide exchange factors Grb2 interaction, 73:97–98 Ras activation, 73:95–96 Guanine nucleotide exchange factors, lymphocyte signaling, Vav family, 75:95–98 Guanine nucleotides, 68:93, 147, 148, 164, 166, 169–170 Guanosine monophosphate (GMP), 82:64 Guanosine triphosphatase, 68:147–148, 164–165, 173–174 Guanosine triphosphatases, Rho family role in lymphocyte signaling actin polymerization, 75:99–100, 104 description, 75:98–99 Guinea pig, xenotransplantation, 79:156 Gut mucosa, 73:153 Gut-associated lymphoid tissues age factors, 73:179 antigen production, 73:159

82

SUBJECT INDEX

Gut-associated lymphoid tissues (continued) Th2 generation, 73:160 GvH, see Disease, graft-versus-host GVHD, see Graft-versus-host disease ; see Graft versus host disease GvL, see Disease, graft-versus-leukemia Gylcosylation, 82:254–255 Gynogenetic diploid screens, 81:302–304

H H-2M/HLA-DM nonclassical class II dimer, 80:73 peptide loading mediated by, 80:91–92 HA, see Hemagglutinin HAART, see Highly active antiretroviral therapy Hageman factor, see Factor XII Haines, B. A., 82:72 Hamster, xenotransplantation, 79:156 Hamsters, Syrian, and TAP, 68:211–213, 225–228 Haploid screens, 81:302–304 Haptens, immune responses to, 80:209–210 HAR, see Humorally mediated rejection Hashimoto’s thyroiditis, 73:281–282 Hayflick phenomenon, 80:245 HBV, see Hepatitis B virus

HC, see Heavy chains HCAb, see Heavy-chain antibodies H chain, see Heavy chain HCC-1, 81:23 HCV, see Hepatitis C virus Heart, 68:86, 87, 284 Heart transplantations, 71:118 Heart, xenotransplantation, 79:130–131 Heat shock, 68:105, 122, 197, 205; see also Burn patients Heat shock proteins, 71:333 HSP 60, atherosclerosis and, 80:264–265, 273 HSP70, immunization, 73:52–53 HSP90, immunization, 73:52–53 peptides bound to, 80:49 Heat shock proteins, intracellular bacteria vaccination, 75:29, 33–34 Heavy chain, in H chain antibodies CH1 domain removal, 79:265–266 variable domain, 79:266–269 Heavy chains allelic exclusion, 69:130–135 locus gene segments, 69:121 transcriptional enhancers, 69:125–126, 136–137 Heavy-chain antibodies, Camelidae antigen-specific dromedary immunization, 79:275–276 monoclonal VHH, 79:277–281 polyclonal VHH, 79:276–277 VHH immune libraries, 79:281–284

SUBJECT INDEX

H chain CH1 domain removal, 79:265–266 variable domain, 79:266–269 L chain, 79:269–270 natural occurrence, 79:261–264 ontogeny, 79:272–275 VHH antigen-binding loop structures, 79:286–289 biotechnological role, 79:289–290 gene phylogeny, 79:270–272 structure, 79:285 VL-side conformation, 79:285–286 HEL cells, 73:119 HeLa cells, 73:12 Helicobacter hepaticus, 81:358 Helminth infection, eosinophil recruitment, 78:311–315 Helper cells, see T helper cells Hemagglutinin (HA), 82:71, 73 Hemagglutinin, associated with raft-like lipid assembly, 77:52 Hematolymphoid cells, 81:289 Hematopoetic progenitor cells, murine, 68:6 Hematopoiesis, 71:215–216 in zebrafish, 81:290 role of CD26/DPP IV in, 81:30–31 Hematopoiesis, extramedullary, 73:351 Hematopoiesis, mutants affecting, 69:83–84 Hematopoietic cell transplantation (HCT), zebrafish, 81:291

83

Hematopoietic cells and protein tyrosine kinases, 69:193–194, 198–199 and pro-thymocyte development, 69:6–8 Ras signals, 72:34–35 Rho signals regulation, 72:38–39 Vav integration, 72:34–35 Hematopoietic cells, xenotransplantation allogeneic engraftment, 79:177–180 mixed chimerism, 79:171–177 xenogeneic engraftment, 79:177–180 Hematopoietic progenitor cells, 72:274–277 Hematopoietic stem cell chemokine and receptor expression within primary lymphoid organs, 78:121–123 differentiation, 78:119–120 migration during embryogenesis integrins, 78:119 overview, 78:117–118 stem cell rolling, 78:118–119 thymus homing, 78:119–121 Hematopoietic stem cells, 69:6–8; 70:119–121; 72:338–339 Hematopoietic stem cells (HSCs), 81:289 Hemocyanin, see Keyhole limpet hemocyanin Hemocytes, insects, 79:227 Hemofiltrate CC chemokine-1 (HCC-1), 81:6

84

SUBJECT INDEX

Hemophilia, 69:364 Hemorrhages, intraalveolar pulmonary, 70:515 Heparan sulfate proteoglycan, sPLA2-IIA and, 77:172–173 Heparanoids, sPLA2-binding, 77:168 Heparin, 81:3; 82:335–336 Hepatitis 68:165–166, 352 alcohol-induced, 73:286 B/C, 73:285 HGF production, 73:438–439 Hepatitis B, 82:49 Hepatitis B virus, 69:367; 70:340–341; 73:38–41; 79:26 Hepatitis B virus, antigen expression in human cancer, 75:235, 240 Hepatitis C virus, 73:438–439; 79:26 Hepatocyte growth factor, 73:421–422 Hepatocyte-stimulating activity, 73:425 Hepatocytes, 68:87 HER-2/neu, tumor T-cell response induction, 75:244 Hereditary angioedema contact activation and, 66:239 kinin formation in, 66:257–258, 259 Herpes immunodeficiency virus, 69:361, 387 Herpes simplex virus, 68:234–235, 240; 69:361, 380; 70:348–349; 72:295–296; 73:415 antibody protection against, 77:236–237

ligand recognition, 71:90–91 neutralization, 77:219 gd response, 71:105–106 Herpetic stromal keratitis, 73:468 HGF, see Hepatocyte growth factor High mobility group proteins, 69:314 High-molecular-weight kininogen (HK), 82:340–343 contact activation and, 66:236, 237 endothelial cell receptor, 66:249–257 inactivation, 66:245 properties, 66:226, 256 structure, 66:230–233 Highly active antiretroviral therapy description, 73:311–312 T cell depletion, 73:320–322 HIGM, see Hyper-IgM syndromes Histamine-releasing factor, 77:104–106 Histamine, synthesized by basophils, 77:98–99 Histiocyte-associated DLBCL, 81:105 Histocompatibility antigens, pig, 79:133 Histoplasma capsulatum, 70:185–186 HIV, see Human immunodeficiency virus HIV infection, 81:28–30, 224 chemokines as inhibitors of, 81:11–13 inhibitors of, 81:22

SUBJECT INDEX

HIV infection, chemokine role, 74:146–158 coreceptors description, 74:146–149 signaling mechanisms, 74:150–151 therapy, 74:155–158 variation, 74:149–150 pathogenesis, 74:151–155 HIV suppression, 74:151–154 infection enhancement, 74:155 viral entry mechanisms, 74:146–149 HIV-1, 81:54, 206 antibody neutralization and binding to, 77:198–199 CD4 in, 77:223–224 CD8þ cells and, 66:285–291, 297–298 antiviral activity, 66:274–275 antiviral therapy, 66:295–299 lytic activity, HIV-1-specific, 66:275–277 enhancement of infection, 77:208–209 importance of binding site occupancy, 77:211–213 inhibition, 66:280–291 CD8þ cell-derived antiviral factor, 66:282–283 chemokines and, 66:281–282 interleukin-16, 66:283 and LDV: comparing antibody activities, 77:239–240 pathogenesis, progression, 66:283 perinatal transmission, 81:206 persistence, 66:291–295 targets for therapy, 66:295–297

85

CTLs, 66:283, 286, 292–293 cytolysis, 66:284–286 epitopes, 66:276–280 HK, see High-molecular-weight kininogen HL-60 cells, 68:62, 75 HLA class I gene promoters downstream SZY module, 81:207–209 regulatory sequences in, 81:207–209 upstream module, 81:207 HLA class II genes, 81:209 HLA-E, expression and function, 81:223–224 HLA-G alleles and protein polymorphism, 81:203 HLA-G expression, 81:201 by tumor cell-lines, 81:240–241 in tumors, 81:242–243 HLA-G protein expression, 81:206–207 HLA-G protein polymorphism, 81:204–205 HLA-G transactivation, 81:210 HLA-G transcription, 81:209–211 HLA-G transcripts, 81:211 HLA-G, 81:199–252 alternative splicing of transcripts and protein isoforms, 81:200 binding of intracellular peptides with TAP-dependent mechanism, 81:214–216 cytokines and inflammation, 81:224–225 ex vivo expression, 81:238 expression and function, 81:223–224

86

SUBJECT INDEX

HLA-G (continued) expression in tumors, 81:238–243 failures of pregnancy, 81:227–232 gene structure, 81:200 graft protection by, 81:234 immunosuppressive properties, 81:201 in gestational trophoblastic disease, 81:229–230 in vivo relevance, 81:233–234 inhibition of adhesion and transendothelial migration, 81:234–235 inhibition of CD4þ, CD8þ, APC mutual activation/ differentiation and effector functions, 81:235–236 in malignancies, 81:236–243 membrane-bound isoforms, 81:200, 217 in normal and ectopic implantation, 81:228–229 in organ transplantation, 81:232–236 polymorphism, 81:206 potential inhibitory effect on allogeneic response, 81:237 in pre-eclampsia, 81:230–232 in pregnancy, 81:225–232 fetal–maternal interface, 81:225–226 protective effect toward maternal cytotoxic cells, 81:226–227 primary transcript, 81:200, 217 processing and transport of molecules, 81:213–217 in recurrent miscarriage, 81:229

secretion, 81:217, 239 soluble, 81:200, 221–223, 239 in serum obtained from cancer patients, 81:240 structural and functional properties, 81:217–225 transport to cell surface, 81:216–217 upregulated by soluble mediators of placental or tumor microenvironments, 81:212–213 HLA-G1 full-length protein, 81:218–220 interactions with immune cells, 81:219 HLA-G2, -G3 and -G4 truncated proteins, 81:220–221 HLA-G5, 81:221, 222 HLA-G6, 81:221, 222 HLA-G7, 81:222 HLA-G gene, 81:201–206 homologs in nonhuman primates, 81:202 polymorphism in non-coding region, 81:205 polymorphism, 81:202–204 silencing, 81:211 specific regulatory sequences, 81:209–211 HLA-G gene expression epigenetic mechanism, 81:211–212 modulation, 81:210 regulation, 81:206–213 HLA-G gene promoter regulatory sequences, 81:207–209 schematic representation, 81:208 HMG box family, 69:82–84

SUBJECT INDEX

Hodgkin’s lymphoma, CD30 and, 68:115, 119 Homeostasis epithelial, 71:122–123 hepatic, 71:169 Hormones, and thymic involution, 80:269 Hormones, in interleukin-12 production, 79:80–81 Horseradish peroxidase (HRP), 81:71 Host defense mechanisms, 66:101 Host mechanisms controlling intracellular mycobacteria, 81:73–75 Host–pathogen interaction, molecular mechanisms, 81:45–96 HPV, see Virus, human papilloma H-ras detection in DRMs, 77:50 membrane-anchored, 77:72 HRG, see Glycoproteins, histidine-rich hsc70, interaction with Ii, 80:93 HSPs, see Proteins, heat shock HSV, see Herpes simplex virus HSV-1, see Virus, herpes simplex hTERT, see Telomerase reverse transcriptase HTLV-1, 81:100; see Cells, T Human BLNK-deficient, 79:108–110 uterine natural killer cells, 79:307–310, 316–318 Human cytomegalovirus (HCMV), 81:206–213 Human cytomegalovirus, neutralization, 77:218

87

Human experimental endotoxemia, see also Endotoxemia; Sepsis interleukin-1, 66:116–117 interleukin-8, 66:137–138 model, 66:102 TNF, 66:114–116 Human hepatitis A virus cellular receptor (hHAVcr-1), 81:190–191 Human herpesvirus type 8, antigen expression in human cancer, 75:239–240 Human immunodeficiency virus (HIV), 69:214, 361, 380; 79:26–27; 82:49, 182–183 -1, 82:196–197 treatment of, 82:50, 71 Human immunodeficiency virus (HIV), ABCD chemokine role in infection, 78:151 Human immunodeficiency virus, 68:97, 115, 258; 71:219–222; 79:26–27; see also AIDs dendritic cells, 72:298–300 CD30 production, 73:399 cytokine production, 73:439–440 G protein role, 72:59–63 IL-12 production, 70:172–176 pathological changes, 70:339–340 type 1 T cell depletion causes, 73:320–322 mechanism, 73:301–303 T cell renewal bone marrow function, 73:306–307 development, 73:307 impact, 73:305–306

88

SUBJECT INDEX

Human immunodeficiency virus (continued) thymic function, 73:307–308 T cells Ki67 expression, 73:319–320 turnover, 73:309–310 Human immunodeficiency virus type 1, see HIV-1 Human leukocyte antigen class I, tumors, T-cell recognition escape polymorphism role, 74:226–228 tumor cells as targets loss or down regulation, 74:204–214 processing defects, 74:214–226 Human leukocyte antigen Class II autoimmune disease associations, 66:67, 76, 84–85, 93 immune intervention, 66:91–93 insulin-dependent diabetes mellitus, 66:91 methimazole-induced insulin autoimmune syndrome, 66:87–88 multiple sclerosis, 66:88–91 pemphigus vulgaris, 66:87 rheumatoid arthritis, 66:85, 87 genes, 66:67 ligands Class II-binding groove, 66:68–69 Class II-binding motifs, 66:69–77 computational identification, 66:77–84

HLA-DP and -DQ, 66:76–77 HLA-DR, 66:70, 72–76 pocket specificity profiles, 66:74–76 quantitative matrices, 66:72–76 peptide binding motifs, 66:69–77 structure, 66:68–69 Human leukocyte antigen class II, tumors, T-cell recognition escape, immunogenicity inadequacy, 74:238–239 Human leukocyte antigen complex, see also Major histocompatibility complex antigen processing role, 75:169–171, 177–180 disease susceptibility, 76:34–38 diversity, 76:25–26, 32–34, 41 Human papilloma virus, antigen expression in human cancer, 75:237, 240 Human rhinovirus antibody neutralization, 77:214 neutralization, 77:203–205 Humans k loci:l loci ratio, 69:159–160 and MHC-based odors, 69:416–417, 421–422 Humoral immunity, see also Cell-mediated immunity, Innate immune system complement source, 74:64–65 enhancement, 74:65–72 antigen retention on follicular dendritic cells, 74:69–72

SUBJECT INDEX

B cell co-receptor signaling, 74:69–72 CD21/CD35 role, 74:64, 67–69, 82 classical pathway, 74:65–67 Humoral immunity, and viral vectors, 69:380 Humoral mediators, in xenotransplantation, 79:152 Humoral response acquired xenotransplantation anti-Gal antibodies, 79:136–137, 139–141 Gal antigen, 79:137 Gal epitopes, 79:136–139 non-Gal determinants, 79:141–142 overview, 79:135–136 Drosophila, 79:226–227 innate xenotransplantation, 79:133–135 Humorally mediated rejection endothelial cell activation, 79:150 innate responses, 79:134–135 huTNF, see Gene(s) Hyaluronan, interleukin-12 induction, 79:64–65 Hybrid proteasomes, 80:12–13 Hybridizations, 82:306 Hybridomas, 68:17, 97, 261, 266 Hydrolysis bleomycin, by aminopeptidase, 80:42 protein and ATP, 80:9–10 6-Hydroxydopamine (6-OHDA), 81:144 Hygiene hypothesis, 82:108

89

Hypermutation, in virusneutralizing antibodies, 79:3–4 Hyper-IgM syndromes (HIGM) AT and, 82:315–316 -1 and, 82:301–303 -2, 82:306–311 -3 and, 82:303–304 -4 and, 82:313–314 B cell deficiencies and, 82:305–313 CD40/CD40-L defects and, 82:298–301 other, 82:315–316 T cell deficiencies and, 82:315 UNG deficiencies and, 82:311–315 Hypercholesterolemia, 69:365–366 Hypercholesterolemia, APS-associated, 70:513 Hypermutation activation-induced cytidine deaminase role, 80:195–196 Ig genes DNA polymerase-generated, 80:188–191 mismatch repair role, 80:183–186 nickase role, 80:186–187 transcription role, 80:187–188 IgG, in germinal center cells, 80:259 Hyperoxia, 68:25 Hyperplasia, organ, 80:247 Hyperplasia, synovial, 82:230 Hyperresponsiveness, airway, 70:154–155

90

SUBJECT INDEX

Hypersensitivity DTH, see Delayed-type hypersensitivity Hypersensitivity, cutaneous, 71:111–112 Hypersensitivity, delayed-type, 70:152–153; 72:349–350 Hypoprothrombinemia, APS-associated, 70:516 Hypoxemia, 82:351–352 Hypoxia, 68:14, 53, 71

I IAP, see Inhibitors of apoptosis proteins IBD, 81:359–360; see Inflammatory bowel disease IC, see Immune complexes ICAM-1, see Intracellular adhesion molecule-1, 69:383, 386; 81:193 ICAM-2, 81:193 ICAM-3, 81:193 ICAM, 69:354, 383, 386 ICAMs, see Intercellular adhesion molecules ICOS, expression on Th2 cells, 80:153–154 ICOS, T helper cell function, 78:248–249 Ictalurus punctatus, 81:254 IDDM, see Insulin-dependent diabetes mellitus Idiotype activation or suppression of B and T cells, 80:211–219 expression, and antigen binding: dichotomy, 80:204–206

Idiotypic interactions between B and T cells, 80:213–219 and D region variability, 80:207–211 in individual immune system, 80:206–207 within peripheral immune system, 80:221 Idiotypic network theory, 80:203–204, 211–212 transformation of clonal selection, 80:220–223 IFD, Inflammatory bowel disease IFN-a, 81:238 IFN-g, 81:4, 241, 242, 358; see Interferon-g IFN-c, see Cytokines, pleiotropic IFN, 81:242; see Interferon Igb, V(D)J recombination regulation, 78:208 Ig, see Immunoglobulins IgD, see Immunoglobulin D IgE receptors interreceptor spacing, 77:73 numbers on basophils, 77:96–97 patches, 77:67 IgE, basophil activation and, 77:101–106 IGE, see Antibodies, immunoglobulin E IGF-1, 81:113 IgH translocations, 81:115 IgH, see Immunoglobulin H IgL, see Immunoglobulin L IgM, see Immunoglobulin M Ii, see Invariant chain I-J determinants, antigen-specific suppressor-T cells

SUBJECT INDEX

glycosylation inhibiting factor bioactivity association, 74:39–40 historical perspectives biochemical characteristics, 74:11–12 cell properties, 74:4–7 factor properties, 74:7–8 I-J paradox, 74:14–17 suppressor T cell cascade, 74:8–11, 54 IKB kinase complex (IKK), 82:17 Ikaros gene, 69:7, 81–82 Ikaros, V(D)J recombination regulation, 78:208 IKK, see IKB kinase complex IKKc, see Gene(s) IL, see Cytokines, interleukin IL-1a, see Interleukin-1 a IL-1 b, 81:4 IL-1, 81:4, 73, 259; see Interleukin-1 IL-2, 81:241; see Interleukin-2 IL-3, see Interleukin-3 IL-4, 81:343–345; see Interleukin-4 IL-6, 81:109, 113; see Interleukin-6 IL-7, see Interleukin-7 IL-8, 81:4, 13, 18, 30, 259; see Interleukin-8 IL-10, 81:242, 343–345, 355; see Interleukin-10 IL-10, viral, see Interleukin-10, viral IL-11, see Interleukin-11 IL-12, 81:51; see Interleukin-12 IL-13, see Interleukin-13 IL-15, see Interleukin-15 Imaging techniques, 81:294–295 Immature dendritic cells, 70:316 Immuglobulins IgA, 72:290

91

IgM, 72:289–290 Immune complex disease, 69:295; 73:221 Immune complexes (IC), 82:155, 218–219 Immune deficiencies, 82:298; see also Hyper-IgM syndromes Immune deficiency pathway, in immune response, 79:245–247 Immune effector cells, 79:315–318 Immune interferon, 66:145 Immune receptor tyrosine-based inhibitory motifs characterization, 72:149–150 families, 72:150, 152, 154 inhibitory signal, FcgRII-mediated, 72:154–158 KIR receptor inhibition, 72:161–163 mouse models, 72:161–165 Immune receptor-tyrosine-based activation motif, 77:3, 5, 34, 66–70 Immune recognition receptor signaling, 77:54 raft perturbation effects, 77:71–73 Immune recognition receptors Ras activation, 72:3–5 Cb1 role, 72:12–14 Grb2/Sos role, 72:8–11 PTK role, 72:5–8 Shc role, 72:8–11 SLP-76 role, 72:12–14 Vav role, 72:12–14 signal transduction, 72:2–3 signaling Ras effectors, 72:15–18

92

SUBJECT INDEX

Immune recognition receptors (continued) negative factors, 72:23–25 transcription factors, 72:18–23 Rho characterization, 72:25–26 effectors, 72:39–41 Immune response, see also B cells; T cells anti-phOx, 80:227 antigen-induced, 80:220–222 apoptosis role, 76:189–190, 288–290 B cell response differentiation via tyrosine kinase activation, 75:283–308 activation–cellular response connection, 75:304–307 development regulation, 75:284–288 heavy chain selection of pre-B cells, 75:284–286 mature B cell activation, 75:287–288 mature B cell maintenance, 75:288 tolerance induction of immature B cells, 75:286–287 immunoglobulin-a and -b coreceptors, 75:292–295 overview, 75:283–284, 307–308 receptor response mechanisms, 75:288–292 response differences, 75:291–292 stage-specific differences, 75:289–291

tyrosine kinase families, 75:295–304 Btk of the Tec family, 75:302–304 Src family, 75:296–300 Syk of the Syk/Zap70 family, 75:300–302 cancer immunotherapy strategies antigens eliciting T-cell responses CEA, 75:243–244 future research directions, 75:246–247 HER-2/neu, 75:244 immunoglobulin, 75:245–246 MUC1, 75:244–245 non-virus-associated tumors, 75:241–246 p53, 75:242–243 virus-associated tumors, 75:240 cytokines, T-cell response enhancement, 75:262–263 CD40-mediated regulation, 76:61–146 antigen presentation, 76:76–78 B cell responses, 76:86–145 AP-1 activation, 76:79, 87–92 CRE activation, 76:87, 92 NF-AT activation, 76:79, 88–92 NF-kb activation, 76:87, 92–93, 100–103, 116–121 T cell collaboration, 76:69

SUBJECT INDEX

TRAF adapter molecule discovery, 76:93–115 transcription factor activation, 76:87–93 event delineation, 76:115–136 functional outcomes, 76:126–136 signaling cascades, 76:116–126 functional outcomes, 76:126–136 adhesion, 76:129–130 antigen-presenting cell function, 76:130–131 apoptosis regulation, 76:134–136 cell survival and proliferation, 76:127–128 cytokine secretion, 76:131 IgH class switching, 76:133–134 immunoglobulin production regulation, 76:131–134 humoral immune responses, 76:70–76 T cell-dependent responses, 76:70–75 T cell-independent responses, 76:75–76 inflammatory responses, 76:76–78 mechanisms, 76:78–86 overview, 76:61, 145–146 signaling cascades, 76:116–126 cAMP-mediated-signaling pathways, 76:144–145 ERK activation, 76:89–90, 120, 125–126

93

JAK–STAT pathways, 76:138–140 JNK activation, 76:90–91, 98–100, 120–124 NF-kb activation, 76:116–121 p38 activation, 76:92, 98, 100, 124–125 reverse-signaling through CD154, 76:145 src activation, 76:140–143 tec family kinase activation, 76:140–143 ZAP-70 activation, 76:140–143 thrombosis, 76:76–78 TRAF adapter molecule apoptosis regulation, 76:134–136 CD40 event mediation, 76:115–145 discovery, 76:93–115 expression regulation, 76:114–115 I-TRAF/TANK, 76:109–114 MAPK activation, 76:97–100 NF-kb activation, 76:100–103 structure–function relationship, 76:95–104 TRAF–CD40 association, 76:65, 104–109 transcriptional regulation, 76:82–83 intracellular bacteria infection acquired response, 75:15–20 innate response, 75:13–14

94

SUBJECT INDEX

Immune response (continued) systemic lupus erythematosus, complement deficiency role, 76:288–290, 294–297 thymus-dependent, 80:225 tumor T-cell response induction, 75:245–246 Immune response regulation by interaction of chemokines and proteases, 81:1–44 connection of innate and adaptive, 81:260 zebrafish in development of, 81:253–328 Immune responses antimicrobial genes differential expression, 79:248–249 GATA factors, 79:247–248 immune deficiency pathway, 79:245–247 induction and regulation, 79:238–240 Relish pathway, 79:244–247 Toll pathway, 79:240–244 to cancer, 82:261–264, 268 Drosophila model, 79:227–228 of humans/MUC1, 82:260–261 humoral, 82:263 insects C-type lectins, 79:232–233 function, 79:225–226 b-1,3-glucan recognition, 79:230–232 gram-negative binding proteins, 79:230–232 hemocytes, 79:227 peptidoglycan recognition proteins, 79:229–230

scavenger receptors, 79:233–234 toll-like receptors, 79:234–235 mammals scavenger receptors, 79:233 toll-like receptors, 79:234–235 phenoloxidase role, 79:236 thioester protein role, 79:236–237 vertebrates, 79:226 Immune surveillance, antigen presentation levels and, 80:46–47 Immune system, see Adaptive immune response; Humoral immunity; Innale immune system adaptive responses, 70:83–84 aged innate: overactivity of, 80:261 aging of, 80:248–263 cell interactions antibody response, 71:95–98 B cell/T cell, 71:93–95 evolution combinatorial system, 70:418 foundations gene specificity, 70:421–424 mechanism, 70:418–420 superfamilies, 70:420–421 immunoglobulins, 70:425–430, 463–475 amphibians, 70:437 birds, 70:437–438 bony fishes, 70:436–438 chondrichthytes, 70:433–436 gene organization, 70:475–491

SUBJECT INDEX

heavy chains, 70:460 jawed vertebrates, 70:430–439 light chains, 70:451–460 mammals, 70:438–439 molecular events, 70:485, 488–491 reptiles, 70:437–438 overview, 70:417, 491–492 T-cell receptors, 70:425–430 jawed vertebrates, 70:430–439 species comparisons, 70:441–451 variable domain, 70:439, 441 function, 70:313–314 IL-2R role, 70:58–60 individual, idiotypic interactions in, 80:206–207 infectious agents and, 70:85, 351–352 integrin ligands function, 72:330–331, 337–343 localization, 72:333–334 signaling, 72:335–337 structure, 72:331–333 intracellular bacteria conflict, 71:267–268 memory, 71:2 senescence consequences of, 80:263–268, 272–273 controversies about, 80:271 T cell deviation, 71:248 Immune system, glucocorticoids and, 66:197, 218 Immune system, virus outside, 79:21–22 Immune tolerance, see Tolerance

95

Immunity, 82:54 adaptive/innate, 82:53, 219 evasion/tolerance of, 82:55–58 induced, 82:78 Immunity, sterile, 77:246–247 Immunization, llamas and dromedaries, 79:275–276 Immunization protocol, for active immunization models, 77:267–273 Immunizations, see also Vaccination(s) arthritis and, 82:232–233, 234–235 DC-tumor cell, 82:275 intramuscular, 82:75 intrasplenic (i.spl), 82:75 of mice, 82:276 somatic transgene, 82:75–76 Immunobiology, MUC1 in animal models, 82:264–269 biosynthesis/structure of, 82:251–256 history of, 82:250–251 in human milk, 82:253 immune responses to, 82:260–264 o-linked glycosylation of, 82:254–255 physiology of, 82:256–260 studies of, 82:249 tumor cells and, 82:258–260, 281–282, 283 vaccines, 82:269–275, 276–281, 282–284 VNTR region and, 82:252–253, 255, 266 Immunobiology, pregnancy, 79:297–299

96

SUBJECT INDEX

Immunodeficiencies, 82:301 Immunodeficiency, 68:51 Immunogenicity, 70:531–533; 82:81 Immunoglobulin, 81:174, 272, 273 gene hypermutation generated by DNA polymerase, 80:188–191 mismatch repair role, 80:183–186 nickase role, 80:186–187 transcription role, 80:187–188 IgG, hypermutation in germinal center cells, 80:259 syngeneic IgE, immune response to, 80:225–226 Immunoglobulin chain rearrangement, see V(D)J recombination Immunoglobulin D, 69:119 Immunoglobulin E receptors, 68:172–173 Immunoglobulin E, high-affinity receptor FceRI signal transduction, 76:325–344 calcium flux integration, 76:338–339 ITAM role, 76:327–328 lipid rafts, 76:343–344 lipid–protein interactions, 76:338–339 overview, 76:325–327, 344 phosphate transfer Bruton’s tyrosine kinase, 76:331–332 CD45, 76:333–334 LYN transfer kinase, 76:328–331 phosphate transfer kinases, 76:328–332

protein tyrosine phosphatases, 76:332–335 SHP-1, 76:334–335 SHP-2, 76:335 SYK role, 76:328–331 serine–threonine protein kinases, 76:339–342 protein kinase C, 76:339–341 protein kinase D, 76:341–342 signaling molecules LAT adapter protein, 76:335–336 SLP-76 adapter family, 76:336–337 VAV, 76:337–338 Immunoglobulin G, 68:278–279 Immunoglobulin G, CD40-mediated secretion regulation, 76:131–134 Immunoglobulin genes in teleosts, 81:282–284 Immunoglobulin genes, B cell receptor editing L-chain allelic exclusion, 74:99–100 locus specificity, 74:106–107, 110–111 organization, 74:91–92, 95 quasi-ordered rearrangement, 74:95–96 rearrangement possibilities, 74:112 RS/kde element, 74:93–94 secondary rearrangement, 74:92–94 Immunoglobulin H, 69:121, 316, 328–331, 338, 340

SUBJECT INDEX

Immunoglobulin H, CD40-mediated regulation, class switching, 76:133–134 Immunoglobulin L, 69:137–138, 316, 317 allelic exclusion at l locus, 69:333 k locus, regulation, 69:331–334, 339, 340 transcriptional regulation, 69:124–129 Immunoglobulin M, 69:119, 373 a and b, 69:205–206, 218–219 monoclonal anti-suppressor T cell factor antibodies, 74:12–14 self-antigen identification, 74:64, 83 Immunoglobulin M, CD40-mediated secretion regulation, 76:131–134 Immunoglobulin, in xenotransplantation immunosuppression, 79:159 Immunoglobulin-binding protein, 70:385–387 Immunoglobulin-L chain, B cell receptor editing, allelic exclusion, 74:99–100 Immunoglobulins, 71:97–98 assembly theories, 69:116–120 asynchronous rearrangement, 69:136–137 B cell differentiation via IgH 30 regulatory region, 75:317–338 B cell development activity, 75:319–320

97

control region function possibilities, 75:330–337 chromatin structure, 75:335–337 germline transcription, 75:331–334 hypermutation, 75:330–331, 337 immunoglobulin class switching, 75:331–334, 337 immunoglobulin-H expression, 75:334–335 replication, 75:330–337 control region structure, 75:317–319 DNA-binding proteins, 75:323–330 30 enhancer synergies, 75:320–322 humanized mice, 75:337 overview, 75:317, 337–338 B cell receptor signaling, 75:292–295 diversity, 69:116, 119–120 evolution amphibians, 70:437 birds, 70:437–438 bony fishes, 70:436–438 chondrichthytes, 70:433–436 emergence, 70:425–430 gene organization arrangement, 70:479–480 basic elements, 70:475–476 intron removal, 70:476–477 promoters, 70:478–479 species comparisons, 70:480–485 transcription, 70:477–478 heavy chains

98

SUBJECT INDEX

Immunoglobulins (continued) isotypes, 70:470–475 universal m, 70:465, 467–470 variable domains, 70:460, 463–465 jawed vertebrates, 70:430–439 light chains, 70:451–460 molecular events, 70:488–491 reptiles, 70:437–438 Fc receptors, 69:189 and HC allelic exclusion, 69:130–135 IgA, 73:153–155, 175–176 IgE, IL-18 effect, 70:292–294 IgM, 73:115 intracellular transport, 70:400–402 LC activation, 69:135–136 allelic exclusion, 69:136 k expression, 69:137–141 rearrangement, regulation, 69:141–157 molecular structure, 69:113–115 and olfactory system, 69:440 T cell tolerance to peptide antagonists, 75:215–216 theories Burnet’s clonal selection theory, 69:113 germline diversity theory, 69:116–120 Jerne’s theory, 69:113 transcriptional regulation of, 69:124–129 tumor T-cell response induction, 75:245–246

V(D)J rearrangement, 69:119–129 Immunoglobulins (Ig), 82:198–201, see also Class Switch Recombination anaphylatoxin binding and, 82:177 C3b/C4b and, 82:176–177 Cc2-Cc3 interface and, 82:197–198 Clg binding as, 82:160, 174–176 classes of, 82:157–165 complement-binding sites and, 82:160, 173–177 constant domains of, 82:155 Fc receptor-binding sites of, 82:155–173 human, 82:178, 181–182, 189 interactions of, 82:155–201 lectins and, 82:184–186 mouse, 82:189 peptides and, 82:178–181 polymeric receptors, 82:172–173 proteins and, 82:178–183, 186–197 RF and, 82:179–181 structural unit of, 82:155, 156 transcytosis/catabolism and, 82:165–172 Immunoglobulins, intravenous (IVIG), 82:171–172 Immunoglobulins, polymeric (pIgs), 82:172 Immunointervention in autoimmune diseases, 66:91–93 in sepsis, 66:150–151

SUBJECT INDEX

Immunological experiences maternal, transfer to offspring, 80:223–228 single, idiotypic transformation, 80:204–223 Immunological memory antibody memory maintenance, 79:29–30 biological relevance, 79:29 overview, 79:28 T cell memory, 79:30–31 Immunological memory, intracellular bacteria infection, 75:23–25 Immunological unresponsiveness to self-constituents, 81:329 Immunology, 82:2, 57, 249 Immunomodulation, context of, 68:396–397 Immunoprecipitation, 82:18 Immunoproteasomes cleavages by, 80:33–36 degradation of substrate ovalbumin, 80:37 peptides produced by, 80:29–30 viral inhibition, 80:50 Immunoreactivity, excess, disorders due to, 80:266–268 Immunoreceptor tyrosine-based activation motifs and B-cell unresponsiveness, 69:211–212 and cancer, 69:215–216 and cytoskeletons, 69:207–209 inhibited by Fc receptors, 69:220 and inhibitory signals, 69:216–226 and multiple effector molecules, 69:199–209

99

phosphorylation of tyrosine residues, 69:183–247 and protein tyrosine kinases, 69:192–199 roles in mast cells, 69:206–207 in T cells, 69:202–205 as signaling modules, 69:189–191 and T-cell anergy, 69:209–211 and viral mimicry, 69:212–215 Immunoreceptor tyrosine-based activation motifs, high- affinity immunoglobulin E receptor FceRI signal transduction, 76:326–328 Immunoreceptor tyrosine-based activatory motifs (ITAMs), 81:59 Immunoreceptor tyrosine-based inhibition motifs (ITIMs), 81:269–271 Immunoreceptor tyrosine-based inhibitory motifs, 69:189, 217–218, 220–221; 73:107 Immunoreceptor tyrosine-based activation motif-coupled receptor signaling BLNK-deficient B cells, 79:108–110 BLNK protein, 79:99–100 CLNK protein, 79:100 Gads, 79:98–99 key events, 79:93–95 LAT-deficient T cells, 79:101–103 LAT- and SLP-76-deficient mice, 79:105–108

100

SUBJECT INDEX

Immunoreceptor tyrosine-based activation motif-coupled receptor signaling (continued) linker for activation of T cells, 79:95–97 SH2-domain-containing leukocyte protein, 79:98 SLP-76-deficient T cells, 79:103–104 Immunostimulating complex, 73:123–124 Immunostimulatory sequences (ISSs), 82:67 Immunosuppression, 69:365–366; 82:53, 82 virus neutralization, 79:22–23 xenotransplantation accomodation, 79:160 antidiotypic antibodies, 79:159 anti-Gal antibodies, 79:157–161 cellular response, 79:163–164 complement, 79:161–162 human immunoglobulin, 79:159 induced antibody response, 79:162–163 Immunosuppressive factors, 79:298 Immunotherapy, see also Vaccines allergen extract-based, 82:127–132 allergen-specific, 82:121–127 of allergic diseases, 82:105–142 cancer treatment, 75:235–264 adjuvants, 75:258–261 antigens eliciting T-cell responses CEA, 75:243–244 future research directions, 75:246–247

HER-2/neu, 75:244 immunoglobulin, 75:245–246 MUC1, 75:244–245 non-virus-associated tumors, 75:241–246 p53, 75:242–243 virus-associated tumors, 75:240 CD4þ cells role, 75:237, 247–249 CD28 costimulation pathway, 75:261–262 cytokines, T-cell response enhancement, 75:262–263 dendritic cells role, 75:247–249 monitoring methods, 75:263 monoclonal antibodies, 75:263–264 natural protection, 75:238–240 overview, 75:235–238, 264 T-cell adoptive transfers, 75:256–258 tumor antigen processing, 75:246–247 tumor escape mechanisms, 75:253–256 tumor necrosis factor family, 75:249–253 4-1BB, 75:252–253, 256 CD30, 75:252 CD40, 75:238, 248–252, 256 CD95, 75:250–251 minor family members, 75:253 Ox-40, 75:253 models, 82:122–127

SUBJECT INDEX

modified allergens for, 82:135–142 passive, 82:49–52 recombinant allergens and, 82:132–135 targets, 82:115–120 Type I allergy and, 82:105–114 In situ end-labeling plus (ISELþ), 77:310–312 Inducible nitric oxide synthase, 79:320–321 INF, see Interferon INFa, see Interferon a INFg, see Interferon g Infection antibody role, 77:196 antibody-mediated enhancement, 77:199–200, 208–209 established, antiviral antibody activity in, 77:241–244 inhibition by antireceptor antibodies, 77:223–225 retardation by antibody, 77:208 viral, mouse models, 77:285–286 Infection, antibody-dependent enhancement, 79:22 Infection, pyogenic, 69:295 Infections in children, 82:54 cytokine role in vivo, 73:467–471 dental, 73:434–437 treatment of, 82:49–52 Infections, experimental viral infections, 70:168–171 Infectious agents, in xenotransplantation, 79:187–188

101

Infectious disease, see also Vaccines; specific diseases infection compared, 75:3 intracellular bacteria vaccination, 75:7–12 chlamydial infections, 75:11–12 listeriosis, 75:10–11, 38–39 salmonellosis, 75:8–10 tuberculosis, 75:3, 7–8, 39–41, 46–47 vaccination goals, 75:4 Infectious disease, consequence of immune senescence, 80:263–265 Infectious virus, persistent fraction, 77:206–207 Infiltration, synovial, 82:230 Inflammation, 70:166–168; 71:108–111; 82:223 allergic, 77:263 a4b7 blocking, 72:242–243 C11NH treatments and, 82:349–350 chemokines and, 66:135 cytokine effects in vivo, 73:454, 457–467 cytokine production, 73:378–379 and cytokines, 81:224–225 endotoxin shock and, 82:351–355 ICAM-1 and, 68:27 and IgE receptors on mast cells, 68:172–173 IL-1RI/IL-1RII production, 73:408–409 integrin-mediated, 72:350–353 interleukin-6 and, 66:129 intrinsin coagulation/ kinin-forming cascade and, 66:225–261

102

SUBJECT INDEX

Inflammation (continued) lesions, VEGF production, 73:420–421 lymphocyte-mediated clinical study, 72:350–351 recruitment role, 72:234–237 macrophage migration inhibitory factor (MIF), 66:206–207 mediators of, 68:19, 121, 172–173, 282 modulation of, 82:331–332 MOS role, 73:15 oral antigens, 73:194–195 phagocytic theory of, 81:261 pulmonary CpG DNA role Th1, 73:349 Th2, 73:350–351 IL-8 production, 73:380–381 and Ras, in granulocytes, 68:167, 169–170 reperfusion injury and, 82:350–351 selectins and, 68:285 sepsis contact cascade and, 66:235 cytokines and, 66:103–150 MIF and, 66:210–212 sPLA2-IIA role, 77:177 stimuli of, 68:284 TGF-b production, 73:420 TGR-a production, 73:418–419 transplant rejection and, 82:351 tumor necrosis factor and, 68:12 Inflammation, leishmaniasis, lost innate response, 74:281–282 Inflammatory bowel disease animal models, 73:194–195 cytokine production, 73:428–430

FasL production, 73:286 IL-1 implications, 73:272–273 Inflammatory chemokines, 81:3–5 Inflammatory cytokines, 81:192 Inflammatory disease, 69:382 Inflammatory diseases, see also specific disease DR3 ligand role, 73:286 IL-1b implications, 73:270–271 INF-b production, 73:274–275 TNF-a implications, 73:275–277 TRAIL production, 73:286–287 Inflammatory diseases, macrophage migration inhibitory factor (MIF), 66:210 acute respiratory distress syndrome, 66:214–215 arthritis, 66:213–214 delayed-type hypersensitivity, 66:212 glomerulonephritis, 66:212–213 malaria, 66:215–216 septic shock, 66:210–212 Inflammatory mediators, 66:101 Inflammatory processes, bony fish, 81:259–260 Inflammatory response, 69:354, 378–379 Inflammatory responses CD40/CD154-mediated regulation, 76:76–78 systemic lupus erythematosus complement deficiency, 76:279–281 Inflammatory skin diseases, 68:179 Influenza hemagglutinin, 71:238 Influenza virus, 68:194, 197, 199; 72:297

SUBJECT INDEX

antibody neutralization, 77:220–222 antibody protection against, 77:237 CpG motifs DNA role, 73:351 DC processing, 73:34 processing pathway, 73:36 Influenza virus, neutralizing antibody response, 79:25–26 Influenza, 70:341–344; 82:71, 73 Informed consent, in xenotransplantation, 79:189–190 Ingested antigens, 71:112–115 Inhibitions of alternative pathway activation, 82:339 of complement pathway activation, 82:337, 338 of lectin pathway activation, 82:337–339 serpine mechanisms of, 82:333, 334 Inhibitor-user responsibility code, 73:19 Inhibitor, C1 (C11NH), 82:356 contact system activation and, 82:340–345 factors, 82:331–332 function/structure of, 82:333–336 heparin and, 82:335–336 inflammation and, 82:349–355 mouse analysis, 82:347–349 role of, 82:332 serpin/nonserpin mechanisms and, 82:333–335 vascular permeability and, 82:345–349

103

Inhibitors of apoptosis proteins, 73:83 Inhibitory signals, 69:216–226 Injury, reperfusion, 82:350–351 Innate cellular responses, xenotransplantation gamma–delta T cells, 79:142–143 macrophages, 79:146–148 moncytes, 79:146–148 natural killer cells, 79:143–146 neutrophils, 79:148 NK/T cells, 79:142 Innate immune response, intracellular bacteria infection, 75:13–14 Innate immune system, 81:50–51; see also Cell-mediated immunity; Humoral immunity B cell activation and tolerance, complement role, 74:61–83 C3, 74:61–65 activation mechanisms, 74:63–64 C3d, 74:61–63 humoral immunity, 74:64–65 innale recognition, 74:63–64 source, 74:64–65 complement deficiency, 74:78–82 humoral immunity enhancement, 74:65–72 antigen retention on follicular dendritic cells, 74:69–72 B cell co-receptor signaling, 74:69–72 CD21/CD35 role, 74:64, 67–69, 82 classical pathway, 74:65–67

104

SUBJECT INDEX

Innate immune system (continued) overview, 74:61, 82–83 self-reactive B cells, negative selection B cell energy alterations, 74:74–78 C4 deficiency effects, 74:74–78 Cr2/ mouse impairment, 74:73–74 natural antibody role, 74:82 systemic lupus erythematosus induction, 74:78–82 leishmaniasis inflammation, 74:281–282 lymph node invasion, 74:284–285 natural killer cell role, 74:282–284 parasite dissemination versus containment, 74:282–284 zebrafish, 81:260–268 Innate immunity, 81:45–46, 149 and antiprion defense, 81:148–150 bony fish, 81:257–260 specificity, 78:1 Toll receptor role in Drosophila, 78:2–4 zebrafish, 81:268 Innate recognition of pathogens, 81:51–57 iNOS, see Inducible nitric oxide synthase Inositol 5-polyphosphate phosphatase SH2-containing FcgRII inhibition, 72:156 mechanism, 72:158–161

mouse models, 72:163–165 phosphoinositol hydrolyzation, 72:150 properties, 72:24–25 Inositol polyphosphate 50 -phosphatase, 69:206, 223–224 Insects, immune response antimicrobial genes differential expression, 79:248–249 GATA factors, 79:247–248 immune deficiency pathway, 79:245–247 induction and regulation, 79:238–240 Relish pathway, 79:244–247 Toll pathway, 79:240–244 C-type lectins, 79:232–233 function, 79:225–226 b-1,3-glucan recognition, 79:230–232 gram-negative binding proteins, 79:230–232 hemocytes, 79:227 peptidoglycan recognition proteins, 79:229–230 phenoloxidase role, 79:236 scavenger receptors, 79:233–234 thioester protein role, 79:236–237 toll-like receptors, 79:234–235 Insulin, 68:111 Insulin autoimmune syndrome, 66:88 Insulin receptor substrate-1, 70:33 Insulin-dependent diabetes mellitus (IDDM), HLA Class II peptide binding and, 66:91

SUBJECT INDEX

Insulin-dependent diabetes mellitus, 70:303–304 Insulin-like growth factor II, 68:21, 25 Integrin adhesion receptors a4b7, 72:220–223 autoimmune blocking, 72:242–243 gastrointestinal tract inflammation, 72:242–243 inflammation blocking, 72:242–243 lymph node development, 72:343 lymphocyte homing, 72:220–222, 233–234 lymphoid malignancies, 72:241 vaccine development, 72:241–242 b7, 72:225–227 LFA-1 cascading, 72:232–233 characterization, 72:225 signaling, 72:335–337 Integrins, 68:100, 168, 291–293 a4, 69:85–86 aEb7, 72:346–348 aLb2, 72:349–350 b1, 69:84–85, 88 B cell development, 72:339–340 characterization, 72:325–326 E-cadherin, 69:86–87 hematopoietic organ seeding, 72:338–339 inflammatory disease, 72:350–351 in interleukin-12 production, 79:77–78 ligand binding sites, 72:326–330

105

function, 72:330–331 inflammatory response, 72:351–353 localization, 72:333–334 mucosal immunity, 72:334–335 structure, 72:331–333 lymphocyte recirculation, 72:344–348 signaling, 72:335–337 trafficking control, 72:337–338 Vanin-1, 69:87–88 in xenotransplantation, 79:170 Integrins, on basophils, 77:95 Intercellular adhesion molecules dendritic cells, 72:265 inflammatory response, 72:351–353 integrin ligand domains, 72:333–334 Rho function, 72:33–34 Interferon, 69:379 Interferon g receptor, 77:281 Interferon (IFN), 82:53, 261 Interferon a, 69:379–380 Interferon b (IFNb), 81:4 Interferon g, 69:364, 367–371, 373 Interferon consensus sequence-binding protein (ICSBP), 81:207 Interferon regulatory factor-1 (IRF-1), 81:207 Interferon-a, for Th1 differentiation, 80:119 Interferon-a/b, 73:339 Interferon-a, autoimmune effects of, 68:346 Interferon-b, 68:10, 342–343

106

SUBJECT INDEX

Interferon-g, 68:346, 375–377; 81:51, 71 AUUUA repeats in, 68:19 CD23, IL-4 and, 68:16 caspase-1 and, 73:275 characterization, 73:274 and c-fos mRNA, 68:5 and c-myc mRNA, 68:5 and encephalomyelitis, 68:373–376 function, 66:145 and GM-CSF mRNA, 68:8 granuloma formation, 71:320 and ICAM-1 mRNA, 68:27 IL-7 and, 68:10 IL-12 expression, LPS-induced, 73:414–415 inappropriate responses, 71:321 induced changes in proteasomes, 80:28–30 induced oral tolerance, 73:175 inducing factor, 68:72 induction, 71:274–275 lymphopoeisis, 71:321–322 macrophage activation, 71:319 and macrophage B7 levels, 68:280 macrophage priming, 71:104–105 memory for, 80:146–149 and monocyte microbial activity, 68:300 neuterophil expression, 73:415–417 neutrophil modulation, 73:441–442 and peptide transporter, 68:210 production in old age, 80:254 production, CpG effects, 73:335 and proteasomes, 68:202–203

receptors for, 68:15 role in MHC class I antigen presentation, 80:47–48 sepsis and, 66:104, 145–146 STAT-deficient mice, 71:152–155 and TAP/LMP defects in lung carcinoma, 68:236 T cell regulation and, 68:8 and TNF-a message, 68:12–13 Interferon-g, innate immune response role, 75:13–14 Interferon-activated sequences, c (GAS), 82:4, 11 Interferon-induced transcription factors, 81:207 Interferon-regulated factors (IRF), 82:28–29 Interferon-stimulated gene factor-3 (ISGF-3), 81:207 Interferon-stimulated regulatory element (ISRE), 81:207 Interferon-stimulated response element (ISRE), 82:4 Interferons, 66:145 CD40 expression regulation, 76:80 IF-g, 79:68–69, 313–314 immune response effects, 76:72 platelet activation, 76:77 type I, 79:75 Interleukin CD40 expression regulation, 76:80 CD154 expression regulation, 76:80 immune response effects, 76:72 platelet activation, 76:77 Interleukin 3, basophils primed by, 77:105–106, 111

SUBJECT INDEX

Interleukin 4 basophils as major source, 77:99–101 tissue-specific expression systems, 77:283 Interleukin 11, effector functions, 77:284 Interleukin 13, generation, 77:111 Ig isotype switch induced by, 77:99–100 tissue-specific expression systems, 77:284 Interleukin-1, 79:312–313 anti-IL1, 66:140 biochemistry, 66:105–107 cardiomyocytes and, 66:114 circulating levels, 66:104–107 and collagen II arthritis, 68:377 in endotoxemia, 66:116–117 IL-1a, 66:106, 107, 117 IL-1b, 66:106–107, 116, 117, 122 in vitro effects, 66:110–112 in vivo effects, 66:112–114 ligation to IL-1 receptor, 68:15 neutrophils and, 66:111 PKC-dependent stabilization of, 68:11 production of, 68:10–11 regulation, 66:108–110 and rheumatoid arthritis, 68:339, 340, 341, 344 sepsis and, 66:104, 126–127, 150 animal models, 66:117–121 clinical, 66:121–124 treatment, 66:124–126, 134 in thymic epithelial cells, 68:17 Interleukin-1 converting enzyme, 73:80

107

Interleukin-1 receptor ECSIT in signaling, 78:5–6 IRAK deletion studies, 78:6–7 MyD88 deletion studies, 78:6, 23 p62 in signaling, 78:6 phosphorylative signaling, 78:4, 6 signal transducing complex, 78:4 TAK1 in signaling, 78:4–5 Toll signaling homology, 78:7 toll-like receptor signaling homology, 78:9 TRAF6 in signaling, 78:4–7 Interleukin-1 receptors, 66:108 Interleukin-1 receptor antagonist (IL1-ra), 66:104, 116–117, 120, 121 interleukin-6 and, 66:132 treatment with, 66:124–126 Interleukin-1 receptor-associated kinase, 79:241–242 Interleukin-1, T helper cell differentiation role, 78:240 Interleukin-2, 72:4–5, 289–290 Interleukin-2, 69:195–196, 364 Interleukin-2 antigen-recognition and triggering of, 68:92 and apoptosis in T-lymphocytes, 68:91–92 and autoimmune disease therapy, 68:359–362 and encephalomyelitis animal model, 68:371, 379 and LAK cells, 68:265 in MLA-144 and FL5.12, 68:22 in natural killer cells, 68:26 receptor, 68:166, 359–361, 379 recombinant, 68:13, 261–262 and regulation of mRNAs, 68:6, 8, 9, 11–12, 13

108

SUBJECT INDEX

Interleukin-2 (continued) and serine/threonine PKB, 68:111 and transferrin receptors, 68:16 30 untranslated region of, and AU-A, 68:34 viral insertions in 30 UTR region of, 68:31 Interleukin-2 receptors binding, 70:3–4 cell cycle regulation, 70:11–12 cell survival regulation, 70:14–19 expression, 70:7–10 function, 70:2 immune function, 70:58–60 lymphocytes characterization, 70:42–47 genetic studies, 70:47–49 structure, 70:53–58 mechanism, 70:19–21 PROX region, 70:24–26 PRRIII, 70:29–30 signaling cell viability, 70:41–42 characteristics, 70:21–22 downstream factors, 70:37–38 downstream pathways, 70:24–27 generation, 70:1–2 intracellular, 70:21–24 Stat proteins, 70:27–30 IRS-1, 70:33 JAK 3 defects, 70:52–53 lymphocyte effector function, 70:13–14 MAP kinase pathways, 70:30–32 mitogenic, 70:34–37 P13 kinase, 70:38–39 responses to, 70:10–19

SHP-2, 70:33–34 Src family kinases, 70:32–33 STAM role, 70:40–41 Stat5, 70:38 target genes, 70:41 TOR role, 70:39–40 subunit chains cloning, 70:4–5 sharing, 70:5–6 structure, 70:4–5 T cells deletion, 70:61–63 growth, 70:63–64 Interleukin-2, production in old age, 80:253 Interleukin-2, sepsis and, 66:104 Interleukin-2, tumor-specific T-cell response enhancement, 75:262–263 Interleukin-2Rb, 69:190 Interleukin-3, 68:6, 13, 22, 31, 108–109 Interleukin-3, gastrointestinal eosinophil accumulation role, 78:298 Interleukin-4, 69:364 GATA-3–dependent enhancer activity, 80:124 memory in Th2 cells, stabilization, 80:147 receptor, 68:15 and regulation of mRNAs, 68:6, 10, 12–13, 16 and rheumatoid arthritis, 68:345–346 selective enhancement of B7.2, 80:132 sustained gene transcription, 80:139

SUBJECT INDEX

for Th2 differentiation, 80:119–121 Interleukin-4 receptor, and TCR, concomitant signaling, 80:142 Interleukin-4, leishmaniasis, adaptive immune response role, 74:291–297 Interleukin-4, sepsis and, 66:144–145 Interleukin-4, T helper cell differentiation role, 78:239–240 Interleukin-5 eosinophil regulation role in allergy, 78:304–307, 317 gastrointestinal eosinophil accumulation role, 78:298 Interleukin-6, 66:127 anti-IL6, 66:132 biochemistry, 66:127–128 and CpG motifs, 69:372–373 in thymic epithelial cells, 68:17 in vitro effects, 66:128–129 in vivo effects, 66:129–130 receptor, 68:15–16 and regulation of mRNAs, 68:13–14, 15 and respiratory syncytial virus, 69:58–61, 383–386 and rheumatoid arthritis, 68:340, 344–345 sepsis and, 66:104, 127, 130–135 and T-cell receptors, 69:58–61 Interleukin-6 receptor, structure, 66:127 Interleukin-6, for Th2 differentiation, 80:121–122 Interleukin-7, 68:10, 13 and T-cell-receptors, 69:61–67

109

and V(D)J rearrangement, 69:338–339 Interleukin-7 receptor, V(D)J recombination regulation, 78:207 Interleukin-7, B cell receptor specificity role, 74:108 Interleukin-7, intrathymically available, 80:269–270 Interleukin-8, 69:383–386 biochemistry, 66:135–136 regulation, 66:136 sepsis and, 66:104, 137–141 Interleukin-8 receptors, 66:136 Interleukin-10, 68:338, 345, 373, 376 Interleukin-10, DC, 72:280–281 Interleukin-10, production in old age, 80:254–256 Interleukin-10, sepsis and, 66:104, 142–145 Interleukin-10, viral, 69:380 Interleukin-11, 68:14 Interleukin-12, 66:146–147; 69:372–373 allograft rejection, 70:155–157 antitumor effects, 70:187–193 autoimmune disease generation role, 75:223–226 B cell response, 70:148–151 bacteria, 70:177–181 biological functions, 79:58 blockade of, 68:10 CHO cells, 70:91 CIA, 70:162–164 cloning, 70:86 colitis, 70:164–165 and collagen II arthritis, 68:375–376 Crohn’s disease, 70:164–165

110

SUBJECT INDEX

Interleukin-12 (continued) discovery, 70:85–86; 79:55–56 EAE, 70:160–162 EB13, 70:94 and encephalomyelitis, 68:372 endotoxin tolerance inhibition, 79:80 expression, 70:114–119 fungal pathogens, 70:184–186 graft rejection, 70:153–154 helminthic parasites, 70:186–187 heterodimers, 70:90–92 homodimers, 70:90–92 hyperresponsiveness, 70:154–155 hypersensitivity, 70:152–153 IL-18-regulated, 70:294–295 induction activated T cells, 79:65–66 cytokine, 70:122–126 dendritic cells, 70:113–114 hyaluronan, 79:64–65 infectious pathogens, 70:106–107 inflammatory extracellular matrix, 70:107 modulation, 70:108–113 pathogens, 79:62–64 T-cell dependent, 70:107–108 inflammation, 70:166–168 mitogen-activated protein kinase role, 79:70–71 mitogenic activity, 70:127–129 molecular structure, 79:56–58 multiple sclerosis, 70:160–162 NK cell-induction, 70:129–131 NK1 T cell induction, 70:133–134 nonhuman sources, 70:89–90

organ-specific autoimmune disease, 70:157–158 p35 gene, 79:71–72 p35 subunit, 70:87–89 p40 gene interferon-g priming, 79:68–69 promoter elements, 79:67–68 promoter polymorphisms, 79:71 transcriptional factor PU.1, 79:69–70 p40 subunit, 70:86–87, 90–92, 94 and perforin in NK cells, 68:26 production anti-inflammatory hormones, 79:80–81 B cell, 70:102–104 CD47 role, 79:79 chemokine receptor 5 role, 79:77 complement role, 79:78 cytokine role, 79:73–77 dendritic cells, 79:61–62 EBV-transformed B cells, 79:59–60 Fcg receptor role, 79:78–79 integrins role, 79:77–78 mast cells, 79:61 measurement, 70:101–102 normal B cells, 79:60 phagocytic cells, 70:104–106; 79:60 small molecules, 79:80–81 protozoan parasites, 70:181–184 purification, 70:86 receptor, 70:95–101 recombinant, 68:10 sepsis and, 66:104, 147 signaling, 70:95–101

SUBJECT INDEX

spontaneous autoimmune disease, 70:165–166 stem cell effects, 70:119–121 structure, 70:92–94 T-cell induction, 70:131–133 Thl cells differentiation, 70:141–143 generation importance, 70:138–140 NK cells role, 70:139–140 process, 70:143–146 role, 70:134–136 polarization, 70:140–141 tumor-specific T-cell response enhancement, 75:262–263 vaccinations, 70:148–151 viruses experimental, 70:168–171 HIV, 70:172–176 MAIDS, 70:176–177 measles, 70:171–172 with natural killer cells, 68:10 Interleukin-12, for Th1 differentiation, 80:117–118 Interleukin-12, leishmaniasis, adaptive immune response role, 74:291–297 Interleukin-12 receptor signaling, 79:58–59 Interleukin-12, T helper cell differentiation role, 78:239–240 Interleukin-13, 68:345, 376 Interleukin-15, 69:76–77 interleukin-16, 66:283 Interleukin-16, HIV-1, 66:281, 283 Interleukin-18 B cell effect, 70:289 biology, 70:287–294 characterization, 70:304–305

111

history, 70:282–283 host defenses, 70:298–301 IgE effect, 70:292–294 IL-12 regulation, 70:294–295 NK cell effects, 70:291–292 osteoclast effects, 70:294 pathological roles, 70:301–303 processing, 70:286–287 producing cells, 70:285–286 receptors, 70:294–298 role, 70:281–282 structure, 70:283–285 T cell effect, 70:287–289 Interleukin-18 receptor, expression on Th1 cells, 80:152 Interleukin-18, T helper cell function, 78:240, 249–250 Interleukin-1a, 69:77 Interleukin-1b-converting enzyme, 73:266 Interleukin-23, for Th1 differentiation, 80:118 Interleukins, 81:224 genetic infection-linkage, 71:326 granuloma formation, 71:320 see also IL IL-1 characterization, 73:270–270 neutrophil-derived characterization, 73:399–405 GDF, 73:434–437 modulation, 73:447 IL-10, neutrophil-derived, 73:443–445 IL-12 CpG effects APCs, 73:336–338 B cells, 73:335

112

SUBJECT INDEX

Interleukins (continued) neutrophil-derived, 73:413–415 IL-13, neutrophil-derived, 73:446 IL-16, neutrophil-derived, 73:274 IL-18 caspase-1 and, 73:274 characterization, 73:274 IL-1b caspase-1 and, 73:271–273 caspase-4 and, 73:273 MS, 73:281 neutrophil-derived IFD, 73:428–430 RA, 73:430–432 sepsis, 73:432–434 SLE, 73:432 proteolytic processing, 73:271–273 IL-1RI/IL-1RII, 73:405–409 IL-2R, TNF-a release, 73:395–396 IL-4 arthritis, 73:214 neutralization, 73:529 neutrophil-derived, 73:446 RadLV role, 73:524–525 IL-6 cancer, 73:409 caspase processing, 73:273 characterization, 73:409 CpG effects APCs, 73:336–338 B cells, 73:335 neutrophil-derived, 73:409–412 IL-8 neutrophil-derived

associated diseases, 73:426–429 characterization, 73:375–382 sepsis, 73:432–434 inappropriate responses, 71:321 induction, 71:274–275, 275 lymphopoeisis, 71:321–322 macrophage activation, 71:104 STAT function, 71:155–156 thymopoiesis, 71:52–53 TNF-a neutrophil-derived, 73:434–437 Intermediate zone, cerebral cortex, 77:304–305 Intestinal antigens, 72:237–240 Intestinal flora, 73:183 Intracellular adhesion molecule-1, 68:26–27, 336, 367–371, 375 Intracellular bacteria, see also specific species description, 71:268–269 host invasion antigen processing, 71:292–300 unconventional, 71:302–307 costimulation, 71:317–318 cytoplasm escape, 71:290, 292 fusion inhibition, 71:285–286 granuloma formation, 71:319–321 host genetics, 71:322–326 immune failsafe measures, 71:321 lymphopoeisis, 71:321–322 macrophage activation, 71:318–319

SUBJECT INDEX

maturation, 71:269–273 mechanism, 71:269–273 MHC class II presentation, 71:300–302 phagolysosome survival, 71:288–290 survival, 71:284–292 T cell subsets conventional, 71:307, 310–312 unconventional, 71:313–317 vaccines naked DNA, 71:333–335 protective antigens, 71:328–329 strains, 71:329–331 strategies, 71:326–328 subunits, 71:331–333 Intracellular iron, 71:281–282 Intracellular mycobacteria, host mechanisms controlling, 81:73–75 Intracellular survival of bacterial pathogens, 81:65–70 Intracellular trafficking in macrophages, 81:57–65 Intracellular transport coat proteins, 70:374–377 endocytic pathways, 70:372 description, 70:392–393 mechanisms, 70:393–394 MHC II, 70:396–398 T-cell activation, 70:394–396 GTPases regulation description, 70:377–381 SNARE mediation, 70:381–384 subfamilies, 70:377–381 in vivo cytoskeleton role, 70:384–385

113

models, 70:383–384 organelle structure, 70:385 mechanism, 70:373–374 overview, 70:369, 402 polarized cells apical surface, 70:399–400 basolateral surface, 70:399 description, 70:398–399 polymeric immunoglobulin receptor, 70:400–402 secretory pathway bidirectional transport, 70:389–390 characterization, 70:385 immunoglobulin-binding protein, 70:385–387 MHC II, 70:390–392 T-cell antigen receptor, 70:387–389 secretory pathways characterization, 70:369–372 Intraepithelial lymphocytes, 71:113–114; 72:346–347 Intravital microscopy (IVM), 81:294, 297 Intrinsic coagulation/kinin-forming cascade, 66:240–243 bradykinin formation, 66:225, 226, 233–239 functions, 66:239 receptors, 66:239–240 contact activation, 66:225, 233–239 allergic diseases, 66:258–259 Alzheimer’s disease, 66:260 disease states and, hereditary angioedema, 66:257–258 endotoxic shock, 66:260

114

SUBJECT INDEX

Intrinsic coagulation/kinin-forming cascade (continued) interaction with cells, 66:243–248 pancreatitis, 66:260 rheumatoid arthritis, 66:260 endothelial cells and, 66:245 factor XI, 66:225, 226, 230, 237, 244 factor XII, 66:225, 226–229, 234–236, 244, 246, 249–257 high-molecular-weight kininogen (HK), 66:225, 226, 230–233, 245, 247–257 kallikrein, 66:225, 238, 243–244 low-molecular-weight kininogen, 66:233 mechanism, 66:225–226 platelets and, 66:244–245 prekallikrein, 66:225, 226, 229–230, 236 Intronic enhancers, B cell differentiation via IgH 30 regulatory region, 75:317–318, 321, 330 Invariant chain complex with class II, 80:72, 78 ab–Ii conversion to ab–Iip10, 80:88–89 interaction with hsc70, 80:93 processing, relation to endocytic pathway, 80:93–94 proteolysis, 80:73 cathepsin role, 80:87–88 regulatory role in APCs proteolytic activity, 80:94–96 Ion channels, 70:265–266

IRAK, see Interleukin-1 receptorassociated kinase interleukin-1 receptor signaling role, 78:6–7 lipopolysaccharide signaling role, 78:23 IRF, see Interferon-regulated factors Iron response element, 68:24, 32 Iron, 68:16, 21–22 Irradiation, 68:7, 9, 12, 102, 119, 122; see also Radiotherapy g-Irradiation, 72:181 Irradiation, induced thymic lymphoma, 73:518–520 IRRs, see Immune recognition receptors Ischemia, 68:122 focal cerebral, 70:513 ocular, 70:515 Ischemia-reperfusion, 69:367 Ischemia, sPLA2-IIA role, 77:177 ISCOM, see Immunostimulating complex Isoelectric point, changes after neutralizing antibody binding, 77:203 Isohemagglutinins, 82:305 Isotype exclusion, 69:116, 141 i.spl, see Immunizations ISRE, see Interferon-stimulated response element ISSs, see Immunostimulatory sequences ITAM, see Immune receptor-tyrosine-based activation motif; see Tyrosine-based activator

115

SUBJECT INDEX

ITAM-coupled receptors, see Immunoreceptor tyrosinebased activation motif-coupled receptor signaling ITAMs, see Immunoreceptor tyrosine-based activation motifs ITIM, see Tyrosine-based inhibitor ITIMs, see Immune receptor tyrosine-based inhibitory motifs; see Immunoreceptor tyrosine-based inhibitory motifs Ity gene, 71:107–108 IVIG, see Immunoglobulins, intravenous

J Jacalins, 82:184 JAK kinases CD40 association, 76:64–65 JAK–STAT-signaling pathways, 76:138–140 Jak kinases, 71:148 Jak-binding protein, see SOCS-1 Janus kinases (JAKs), 82:3 -1, 82:11 -2, 82:7–8, 11, 14 STAT cascades, 82:4, 10, 16 Janus tyrosine kinases mitogenic signaling, 70:34–35 signaling pathways, 70:24–27 Jarisch–Herxheimer reaction, release of IL6, 66:1134 Jasplakinolide, modification of action, 77:30 Jenner, Edward, 82:49 Jerne, Neils K., 69:113

JNK, see c-jun amino-terminal kinases; see c-Jun N-terminal kinase; see c-jun N-terminal kinase pathway; see Jun–N–terminal kinase cascade, 72:36–37 –c-Jun, 21 IRR signaling, 72:39–41 JNK, CD40-induced activation, 76:90–91, 98–100, 120–124 JNK, inhibitory role in Th2 differentiation, 80:134–135 Joints, 82:217 carpal/tarsal, 82:229 destruction of, 82:222, 223–224 JPM-565, inhibitor of cysteine proteases, 80:85 Jun-N-terminal kinase, 68:93, 150 JunB, Th2 transcription factor, 80:128 Jurkat cells, 68:11, 30, 56, 96, 105

K Kallikrein, 66:225 in allergic reactions, 66:259 inhibition, 66:238 interactions with cells, 66:243–244 Kallikreins, 82:340–343, 344, 345, 346, 349 Kanamycin, 69:374 Kaposi’s sarcoma-associated herpesvirus, 69:380 Kaposi’s sarcoma-associated human herpes virus-8, 68:60 Karyorrhexis, 68:54 KDEL proteins, 70:380, 390

116

SUBJECT INDEX

Keratinocyte growth factor, 71:122 Keratitis herpetic stromal, 73:468 Keyhole limpet hemocyanin, 73:228 antigen-specific suppressor-T cell generation, 74:1–5, 7 B cell immunity enhancement, 74:64 Keyhole limpet hemocyanin (KLH), 81:189; 82:56, 270 Ki67 antigen, 73:316–320 Kidney regeneration, 73:421 Kidney, xenotransplantation, 79:130, 185 Kidneys, 68:87, 377–378 Kidneys disease, 70:516 Killer cell inhibitory receptors, 69:221; 72:161–163 Killer cells, see Cytotoxic T lymphocytes; Natural killer cells Kin recognition, 69:428–429 P13 Kinase, 70:380, 390 Kinase inhibitory domain (KIR), 82:4 Kinases, 68:61, 101–107, 111–113, 122, 149; see also Protein kinase B; Protein kinase C Kinetics models neutralization, 77:197, 204 single-hit vs. multi-hit, 77:205–210 Kinin in hereditary angioedema, 66:257–258, 259 inactivation, 66:240 Kinin generation, 69:251–252 Kininogen genes, 66:233 KIR, see Kinase inhibitory domain

Klebsiella, 81:55 Klebsiella pneumoniae, 81:54 KLH, see Keyhole limpet hemocyanin Klyushnenkova, E., 82:72 KN6 clone, 71:90, 98–99 Knockout mice cathepsin, 80:86–87 PA28b, 80:31 pol m, 80:194 Kupfer cells, 69:357, 370 Kupffer cells, 68:272, 300 Kwak, L. W., 82:72

L L. major, 81:358, 359 Lactacystin, 68:61–62, 199; 73:20–21 Lactacystin, proteasome inhibitor, 80:14 Lactate dehydrogenase-elevating virus, neuropathogenic, 77:239–240 Lactation, 82:181 Lactobacillus casei, 81:79 Lactoferricin, 73:378–379 Lactoferrin, 73:378–379 lacZ gene, Btk gene replaced with, 77:128 Lag time, virus neutralization, 77:201, 205–206 LAK cells, see activated killer cells; Lymphokine Lamina propria cells, 73:193–194 Lamina propria, gastrointestinal eosinophils normal tissue, 78:294

SUBJECT INDEX

T cell overexpression effects, 78:305–309 Lamins, 68:61, 63 Langerhans cells, 68:272, 273, 300 Langerhans cells, decreased numbers in elderly, 80:260 LAT adapter protein, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:335–336 LAT, see Linker activation of T cells; see Linker for activation of T cells; see Linker of activated T cells Late endocytic compartments, proteolytic pathway in, 80:2–3 Late-phase response, to allergen challenge, 77:112–113 Latrunculin, modification of actin, 77:29–30 LBK5 clone, 71:89–90 LBP, see Lipopolysaccharidebinding protein lipopolysaccharide binding, 78:10–11 signaling, see Lipopolysaccharide L chain, see Light chain LC, see Light chains Lck enrichment, 77:78 HIV, 72:61–62 mutant: deregulated activity, 77:57–58, 60 pre-TCR sensor, 72:117–119 raft-associated, 77:55–56 LCMV, see Lymphocytic choriomeningitis virus LCR, see Locus control region LDGF, see Leukocyte-derived growth factor

117

LDL, see Low density lipoprotein LDV, see Lactate dehydrogenase-elevating virus Lectin pathway, 69:249–250, 291, 293 Lectin receptor, C-type, 72:263 Lectin, mannose-binding lectin deficiency, systemic lupus erythematosus relationship, 76:252–257 Lectins, 68:99–100, 281–285; 81:53–54, 54–55 animal, 82:185–186 antigen-combining sites and, 82:184–186 Galectin-1/-3, 82:185 GT, 82:186 Jacalin as, 82:184 mannan-binding (MBL), 82:337–339 mannose-binding proteins as, 82:185–186 pathway activation, 82:337–339 Lectins, C-type, in insect immune response, 79:232–233 Lef-1, 69:83 Legionella, 81:69 Legionella pneumophila, 81:65, 68 Leishmania, 81:55, 69 Leishmania donovani, 81:54, 69 Leishmania major, 70:299 Leishmania mexicana, 71:285, 288 Leishmania monocytogenes, 73:30–31 Leishmania pneumophila, 71:285, 288 Leishmania spp., 70:181–183; 72:294–295

118

SUBJECT INDEX

Leishmaniasis, 74:275–303 host response, 74:281–285 adaptive immune response, 74:285–299 antigen presentation, 74:285–286 antileishmanial effector mechanisms, 74:297–299 CD4þ T helper lymphocyte induction, 74:288–290, 302 co-stimulatory molecules, 74:287–288 cytokine determinants, 74:290–291 interleukin-4 role, 74:291–297 interleukin-12 role, 74:291–297 T helper cell development, 74:290–291 innate response inflammation, 74:281–282 lymph node invasion, 74:284–285 natural killer cell role, 74:282–284 parasite dissemination versus containment, 74:282–284 Leishmania life cycle, 74:277–281 mammalian host, 74:278–281 sand fly host, 74:277–278 overview, 74:275–276, 302–303 persistence, 74:299–300 resistance genetics, 74:300–302 susceptibility, 74:300–302 LESTR, 66:282

Leucine/isoleucine residues, 69:189, 191 Leukemia inhibitory factor, 69:59–60; 79:313 Leukemia inhibitory factor (LIF), 66:147–148 sepsis and, 66:104, 148 Leukemia Inhibitory Factor (LIF), 81:212 Leukemia virus Mø presentation, 73:34 radiation description, 73:518 induced lymphomagenesis, 73:520–525 Leukemia, 68:51, 149, 224, 236; 82:51 Leukemia, acute myeloid (AML), 82:279 Leukemia, chronic lymphocytic (CLL), 82:53 Leukemia, chronic myeloid (CML), 82:60 Leukemia, immunotherapy, 75:236 Leukemia virus, bovine, 69:121, 190 Leukemias in mice, 81:97 Leukocyte migration billiard theory of chemoattraction, 78:117–118 chemokine direction, see Chemokines compartmental homing within secondary lymphoid organs B cell-rich areas, 78:130 microarchitecture formation role lymphotoxins and receptors, 78:131–133

SUBJECT INDEX

tumor necrosis factor and receptor, 78:131–133 T cell-rich areas, 78:130 lymphocyte recirculation, 78:73, 111 lymphoid cell movements into secondary lymphoid organs during T cell-dependent, antigen-specific immune response B cell activation and follicle formation, 78:126 circulation, 78:123–124, 128 dendritic cell activation and maturation, 78:125 T cell activation, 78:127 lymphopoiesis, 78:73 steps, 78:57–58 T cell subtypes, 78:73–74 Leukocyte protein, SLP-76, 77:7–8 Leukocyte receptor complex (LRC), 81:269 Leukocyte-derived growth factor, 73:423 Leukocyte-derived growth factor (LDGF), 81:17 Leukocytes 82:1, 7, 352, 354–355 homeostasis mechanism of, 68:91–93 and methylation of prenylated proteins, 68:171–172 prenylation inhibitors affecting, 68:178–179 Rab proteins and, 68:172–174 Rho/Rac pathway and, 68:168–169 skeletal organization of, 68:168–169 tethering, 68:285 trafficking, 68:27

119

Leukocytes, see also specific leukocyte cytoskeletons, 72:27–34 Rab function, 72:52–53 trafficking, 72:337–338 Leukocytes in bony fish, 81:257–258 Leukotriene B4, 82:1 Leukotriene C4 basophil-generated, 77:99 generation and release, 77:102 LFA-1 cascading, 72:232–233 characterization, 72:225 dependent adhesion, 72:33–34 signaling, 72:335–337 LHVS, see Vinyl sulfones LIF, see Leukemia inhibitory factor Ligand recognition HSV-specific, 71:90–91 MHC-specific, 71:89–90 sTCR constructs, 71:92–93 Ligands, 82:198 CD40, 82:298–301 HIGM1, 82:301–303, 302 lymphocyte signaling, actin-dependent assembly induction, 75:91–94 T-cell activation in autoimmune disease, 75:211–214 Ligands, integrin function, 72:330–331 inflammatory response, 72:351–353 localization, 72:333–334 mucosal immunity, 72:334–335 structure, 72:331–333 Ligands, MIC ligands, 76:19–23 Light chain, heavy-chain antibodies, 79:269–270

120

SUBJECT INDEX

Light chains allelic exclusion, 69:129–130, 136 asynchronous gene rearrangement, 69:136–137 isotype exclusion, 69:116, 141 k loci, 69:121–123, 126–129, 137–141 autoreactivity, 69:150–152 enhancers, 69:126–129, 138–141, 144–145, 148–150 function, 69:161 gene targeting studies, 69:145–146 germline transcription, 69:137–138 and murine leukemia virus, 69:143–144 overview, 69:121–123 rearrangement models, 69:142–143, 146, 150, 156–157, 440 and recombination signals, 69:154, 155–157 silencers and antisilencers, 69:147–148 versus l, 69:141–142, 143–144, 150, 154–155, 156–161 versus recombination signal/ kde rearrangement, 69:156–157 l loci, 69:123–124 pre-BCR, HC and, 69:135–136 V(D)J rearrangement enhancers, 69:144–145 LIM kinase actin polymerization and, 77:26 inactivation of cofilin, 77:32

LIMP-II, see Lysosomal integral membrane protein-II Linker activation of T cells, 72:12 Linker for activation of T cells, 73:96–97 deficient mouse, 79:105–108 deficient T cells, 79:101–103 Gads association, 79:98–99 ITAM-coupled signaling, 79:95–97 in PLC-g1 activation, 79:118–120 signaling protein recruitment, 79:110–113 Linker of activated T cells complexes with signaling proteins, 77:60–61 mutants defective in DRM association, 77:61 palmitoyl acceptor sites, 77:49–50 in T cell signal transduction, 77:6–7 Lipid, 68:14–15, 65, 150, 171 mediators, 82:1 monophosphoryl A (MPL), 82:127 Lipid domains formation, 77:47–48 ordered-phase, stabilization, 77:53–54 Lipid metabolism, PI3K and, 77:9 Lipid rafts and actin cytoskeleton, 77:21–23 domains immunoreceptor signaling and, 77:54–79 structure in plasma membrane, 77:51–53 functions, 77:18–23

SUBJECT INDEX

microscopic analysis, 77:17–18 in signal transduction, 77:19–21 structure, 77:16–17 Lipids, high-affinity immunoglobulin E receptor FceRI signal transduction lipid rafts, 76:343–344 lipid–protein interactions, 76:338–339 Lipoarabinomannan (LAM), 81:75 Lipophosphoglycan (LPG), 81:55 Lipopolysaccharide bacteria, 73:183 cytokine effect in vivo, 73:454, 457–562 FasL expression, 73:285 IL-12 expression, 73:414 PRR, 73:329–330 TNF-a expression, 73:392–393 Lipopolysaccharide (LPS), 81:9, 51; 82:14 activation by, 82:21–22, 301 binding molecules CD11b/CD18, 78:11–12 CD14, 78:10 LBP, 78:10–11 scavenger receptor, 78:12 components, 78:9 inhibition of, 82:23 internalization in macrophages, 78:24–25 IRAK role in signaling, 78:23 macrophage stimulation, 78:9–10 MyD88 role in signaling, 78:22–24 signal transduction by LPS/LBP/ CD14 ternary complex AP-1, 78:19–20 ceramide, 78:16–17

121

cyclic AMP response element-binding protein, 78:19 G proteins, 78:15–16 mitogen-activated protein kinase, 78:14–15 NF-IL6, 78:19 nuclear factor-kB, 78:18–19 p70 S6 kinase, 78:17 peroxisome proliferator-activated receptor g antagonism, 78:20 phosphatidylinositol 3-kinase, 78:14 phospholipase A2, 78:15 phospholipase C, 78:13 phospholipase D, 78:15 protein kinase A, 78:16 protein kinase C, 78:13–14 protein tyrosine kinases, 78:13 Rho, 78:17 Spl, 78:20 species differences in response, 78:25 Taxol mimetic activity, 78:26 TLR2 signaling, 78:29–30 TLR4 signaling, 78:21–24 tolerance mechanisms cytokine roles, 78:27 nuclear factor-kB activation defects, 78:28 prostaglandin E2 role, 78:27–28 signaling pathway downregulation, 78:28 Lipopolysaccharide-binding protein, 79:231

122

SUBJECT INDEX

Lipopolysaccharides, 71:270; 79:230–232 and c-fos mRNA, 68:5 and chemokine mRNAs, 68:14 and macrophages, 68:10, 12–13, 172, 280 stabilizing cytokine mRNA, 68:31 Lipopolysaccharides, CD154 expression regulation, 76:80 Lipoproteins, low-density, 70:537–539 Liposomal delivery, 69:386–387 Liposomes, 82:127 5-Lipoxygenase-activating protein, 73:404 5-Lipoxygenase, 73:404 Listeria monocytogenes, 70:177–181; 81:67 cytolytic CD8þ T cells, 71:312 IL-6 induction, 71:276 mouse models, 71:106–111 gd T cells, 71:313–314 Listeria, 81:56, 68 Listeriosis antigen carriers, 75:50–51 characteristics, 75:10–11 DNA vaccines, 75:38–39 Livedo reticularis, 70:518 Liver, 68:87, 272, 273, 275; see also Hepatitis diseases, 70:517 injury, 70:301–303 Liver diseases FasL production, 73:284–286 oral tolerance, 73:200–201 Liver homeostasis, 71:169 Liver regeneration, 73:421 Liver, fetal, 72:338–339 Liver, xenotransplantation, 79:131

Livers, 82:222 Llamas, immunization, 79:275–276 LLO, 73:48–49 LMP2, proteasomes containing, 80:28–30 Local factor access, 69:319 l loci function, 69:161 gene targeting studies, 69:145–146 and k light chain genes, 69:141–142, 143–144, 150, 154–155, 156–161 and murine leukemia virus, 69:143–144 rearrangement models, 69:142–143, 146, 150, 156–157, 440 and recombination signals, 69:154–155 Locus control region, 69:124, 336–337, 339 Long-term nonprogressors, 73:307 Loveless, Mary, 82:121 Low density lipoprotein, 69:365–366 Low-density lipoprotein receptor deficiency, 69:364 Low-molecular-weight kininogen (LK), 66:233 12/15-LOX, 77:174–175 LPA, see Lysophosphatidic acid LPCs, see Lamina propria cells lpr gene, 71:167–168 LPS-cytokine score, 66:134 LPS, see Lipopolysaccharide; see Lipopolysaccharides L-Selection, 72:224–225, 232–233

SUBJECT INDEX

LTNPs, see Long-term nonprogressors Luizonnyia spp., Leishmania host role, 74:277–281 Lung diseases, 70:515–516 Lung inflammation CpG DNA role Th1, 73:349 Th2, 73:350–351 cytokine role in vivo acute effects, 73:464–465 LPS effects, 73:454, 457–458 IL-8 production, 73:380–381 Lungs, 68:105, 120, 284 Lungs, xenotransplantation barrier, 79:185 Lupus anticoagulant antibodies, 70:535–536 characterization, 70:509–510 laboratory studies, 70:544–545 phosphatidylethanolamine and, 70:536 LY294002, 70:39 Lymph node, prion infectivity in, 81:141–143 Lymph nodes, as source of F4/80 antigen, 68:273 Lymph nodes, chemokine and receptor expression, 78:77–80 Lymph nodes, leishmaniasis, host response, 74:284–285 Lymphadenopathy, 68:51, 100 Lymphoblastoid cells, 68:207, 225 Lymphocyte effector function, 70:13–14 Lymphocytes 82:232, 263; see B cells; Cytotoxic T lymphocytes; T cells; see Natural killer cells; see also Lymphoid cells

123

adhesion, 66:15–17 apoptosis in peripheral, 68:78 apoptosis versus necrosis in, 68:86 AU-binding factor in resting, 68:31 CD45 and, 66:4, 5–31 B cells, 66:12–15, 36–37 lymphocyte adhesion, 66:15–17 monoclonal antibody studies, 66:1, 3, 5–17 T cells, 66:6–12, 32–36 CDC42 and, 68:150 homing, 68:285 hyperplasia, 68:51 permeability transition pores in, 68:87 and prion pathogenesis, 81:134–137 Rac1 and, 68:150 RAG-1 and RAG-2 genes in, 68:17–18 straining, 81:136–137 tumor-infiltrating, 68:258 Lymphocytes, as effector cells of immune system, 77:298–299 Lymphocytes, cholesterol overload, 80:247 Lymphocytes, development of, 69:131–134, 311 Lymphocytes, see also specific lymphocyte blood-borne, recruitment chemotactic factors, 72:227–229 integrin-triggering, 72:227–229 required steps, 72:211–212 development

124

SUBJECT INDEX

Lymphocytes (continued) Ras role, 72:64–66 Rho role, 72:66–68 –endothelium interaction b7 role, 72:225–227 characterization, 72:211 IEL role, 72:225–227 LFA-1 role, 72:225 E-selection, 72:225–227 L-selection role, 72:224–225 P-selection, 72:225–227 sialomucin role, 72:226–227 growth signals, 72:34–35 homing a4a7 preactivation, 72:233–234 a4b7 characterization, 72:220–223 segregation, 72:237–241 adhesion cascade naive effectors, 72:232–233 nonintestinal tissue, 72:234 MAdCAM-1, 72:213–220 memory effectors, 72:231–232 naive effectors, 72:231–232 T cells in vivo, 72:229–230 inflammatory disease, 72:350–351 mixed reactions, 72:268 trafficking alterations, 72:234–237 characterization, 72:209 muscularis patterns, 72:237 serosa patterns, 72:237 studies, 72:210–211 theory, 72:210 Lymphocytes, see also specific lymphocytes

gc deficiency, 70:52–53 development characterization, 70:42–47 genetic studies, 70:47–49 gc role, 70:49–52 peripheral, structure, 70:53–58 Lymphocytic choriomeningitis virus, 68:392; 69:375–378; 70:168–171, 336, 338–339; 79:27 B. pertussis inactivation, 73:48 chaperore immunization, 73:53 diabetes induction, 73:216 Lymphocytopenia, 68:351 Lymphoid aggregates, 81:286 Lymphoid cells Burkitt, 68:236–237 cytokine mRNA stabilization in, 68:31 EL4, and Fv receptors, 68:259–266 mannose receptor macrophages and, 68:284 mRNA degradation in, 68:17 order of apoptosis events in, 68:78 Lymphoid chemokines, 81:5–7 Lymphoid malignancies, 69:311 Lymphoid mutants, zebrafish screens for, 81:305–306 Lymphoid neoplasms of mice, 81:97–121 Lymphoid organs, 82:295, 306–307 Lymphoid organs, prions in, 81:137–141 Lymphokine-activated killer cells, 68:257–258, 262–266; 79:303, 305 Lymphoma, ABCD chemokine role, 78:150

125

SUBJECT INDEX

Lymphoma, African Burkitt’s, 69:213 Lymphomas 68:28, 51, 236, 259; 82:52 follicular, 82:56 murine, 82:306 non-Hodgkin’s, 82:53 Raji Burkitt’s, 73:122 thymic carcinogen-induced, 73:516–518 generation AKR mice, 73:514–515 immunobiology, 73:513–514 PLCs, 73:515 preventive therapy, 73:525–529 RadLV-induced, 73:520–525 radiation-induced, 73:518–520 Lymphomas, modeling, 81:113–115 Lymphopoeisis, 69:72, 82; 71:321–322 Lymphopoietin, thymic stromal cell-derived, 69:77 Lymphotactin (XCL1), 81:3 Lymphotoxin-a, 81:130 Lymphotoxin, 68:14 Lymphotoxin, lymphocyte compartmental homing role within secondary lymphoid organs, 78:131–133 Lymphotropism of prions, 81:141–143 LYN transfer kinase, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:328–331 Lyn/FceRI ratio, 72:121 Lyn, B cell regulation

PTK pathway, 73:112–113, 115 PTPase pathway, 73:112–113, 115 role, 73:109–110 Lysis, 69:249–250 Lysophosphatidic acid, 72:33 Lysosomal associated membrane protein-1, 70:397 Lysosomal integral membrane protein-II (LIMP-II), 82:78 Lysosomal membrane glycoproteins (LAMPs), 81:64, 71 Lysosomal proteases antigen presentation dependent on, 80:102 propiece, 80:77 Lysosomal storage diseases, 69:364, 378 Lysosomal thiol reductase (GILT), 80:100

M M cells, 73:189–190 MbCD, extraction of cholesterol from membranes, 77:71–72 M-cells, 81:130–133 transepithelial transport of prions via, 81:132 M-CSF receptor in zebrafish, 81:265 mAbs, see Monoclonal antibodies MAbs, see Antibodies, CEA monoclonal MAC, see Membrane attack complex Macaques, 82:264–265 Macrophage avoidance, 81:65–68

126

SUBJECT INDEX

Macrophage inflammatory proteins, 73:387–389 Macrophage migration inhibitory factor (MIF), 66:197 background, 66:197–199 history, 66:198 immune system and, 66:218–219 localization, 66:202–206 MIF gene, 66:199–202, 206 properties, 66:199, 206–210 sepsis and, 66:104, 148–149 structure–function studies, 66:216–218 Macrophage monocytes bacterial exposure, 73:28–29 characterization, 73:15 in vivo role, 73:16–17 leukemia virus, 73:34 macropinocytosis, 73:44 Macrophage-derived chemokine (MDC), 81:6 Macrophage–Mycobacterium interaction, 81:81 Macrophages 69:18–19, 373, 383; 82:232 activation, 71:318–319 alveolar, 82:222 antimicrobial defense mechanisms intracellular iron, 71:281–282 peptides, 71:282–283 toxic effector molecules, 71:278–281 chemotactic proteins, 71:277 differentiation antigens and, 68:271–314 early lineage, 81:261–267 generation of class I-presented peptides, 80:48–49

interleukin-4 and murine, 68:12–13 interleukin-12 production, 79:60 lipopolysaccharide-activated serum and, 68:10, 172 mannose receptor, 71:270 mannosylated antigen uptake, 80:99 participation in clearance of prions, 81:148 prenylated proteins in murine, 68:174–175 production in elderly, 80:260–261 RA and, 82:219, 221–222 in skin, 68:284 surviving in, 81:68–70 gd T cells and, 71:102–105 in xenotransplantation, 79:146–148 Macropinocytosis, 72:262; 73:14, 44 Macrosialin, 68:273, 289–91 MAdCAm-1, see Mucosal vascular addressin Magnesium ions, 68:32–33, 56, 80 MAIDS, see Murine AIDS Major histocompatability complex, see MHC as abortion cause, 69:429 CD4 and CD8 coreceptors, 77:74–75 CD4 engaged by, 77:5 class I, 68:191–199, 205–209, 225, 239, 281 a/b T cell receptor interactions, 76:1–5 antigen generation, 73:4–9 and C1s, 69:281 characterization, 73:1

SUBJECT INDEX

CTL responses, 73:353–354 DC expression, 73:16 in direct gene transfer, 69:365 disease susceptibility, 76:37–38 endosomal trafficking, 73:11 evolution, 73:1 extra-ER loading, 73:9–12 g/d T cell receptor interactions, 76:19–22, 42 gene products, 73:6–9 and gene therapy, 69:353, 381–382, 386–387 histocompatibility mechanisms, 76:38–39 MIC genes, see MIC genes natural killer cell receptor interactions, 76:21–23, 42 phylogeny, 76:9–14 restriction, 73:2–3 seminal features, 76:2, 4, 41 SHP-1 regulation, 73:115 as vector, 69:368 class Ia restricted, 71:296–300 class Ib, 71:302–303, 316–317 class II, 68:191, 193, 300, 315–332, 385–386; 69:353, 386, 387, 419; 71:300–302 a/b T cell receptor interactions, 76:1–5 antigen presentation, 70:317–321 CTL responses, 73:353–354 DC expression, 73:16 endocytic compartments, 70:396–398 immune response effects, 76:72 secretory system, 70:390–392 SHP-1 regulation, 73:113

127

dendritic cell loading, 72:264–265 maturation, 72:279–280 genetic infection-linkage, 71:324–325 ligand recognition, 71:86–87 and odors and mating, 69:411–430 and chemosensory system, 69:427–428 individual odor variations, 69:414, 417–427, 430 mating preferences, 69:413–417 peptide antigens and, 68:191 peptide-pulsed, 77:15–16 recombinant, 69:418–419, 421 and rheumatoid arthritis susceptibility, 68:315–332 T cell expression, 71:86–87 and T cell selection, 68:89 gd T-cell restrictions, 71:103 Major histocompatibility complex (MHC), 82:228 Class I, 82:64, 76 Class II-associated, 82:59–61, 77, 182 Class II-restricted, 82:114 RA and, 82:217–218 role of, 82:227 Major histocompatibility complex (MHC) molecules length by class, 78:267 posttranslational modification effects on presentation and T cell recognition acetylation, 78:269–270, 275 binding studies glycopeptides, 78:272–273 phosphopeptides, 78:273

128

SUBJECT INDEX

Major histocompatibility complex (MHC) molecules (continued) deamidation, 78:269 glycosylation Apa-derived peptides, 78:271 linkages, 78:268–269 processing inhibition, 78:271 subcellular distribution, 78:269 terminal modifications of class I molecules, 78:275, 277 immunological relevance, 78:284–286 mass spectrometry characterization, 78:285–286 overview, 78:267–268 phosphorylation, 78:270–271 presentation effects vivo, 78:274–277 protease blocking effects, 78:270–271 T cell recognition studies cysteinyl residue recognition, 78:281 epitope analogs, 78:277 glycopeptide complexes with H-2Db, 78:279 glycopeptide complexes with H-2Kb, 78:279, 281 hybridoma studies, 78:277–278 phosphopeptide studies, 78:280–281 Tn-modified analogs, 78:278–279

in vitro, 78:274 in vivo, 78:276, 281–284 T cell responses against modified peptides bee venom phospholipase A2, 78:283 biliary cirrhosis and a-ketoglutarate dehydrogenase peptide modification, 78:283 celiac disease, 78:282–283 collagen-induced arthritis, 78:282 TAP transport effects, 78:271 types of modifications, 78:268 presentation pathways class I, 78:270 class II, 78:270 Major histocompatibility complex (MHC), structure, 66:68–69 Major histocompatibility complex class I acquired immune response role, 75:15–20 antigen-processing pathways overview, 75:160–162 tumor antigens, 75:237, 246–247, 256–259 vaccinology, 75:14–15, 62 Major histocompatibility complex class II acquired immune response role, 75:15–20 antigen processing antigen internalization, 75:181–186 B cell receptor-mediated uptake, 75:183

SUBJECT INDEX

Fc receptor-mediated uptake, 75:183–184 fluid-phase uptake, 75:181–182 mannose receptor-mediated uptake, 75:184–185 phagocytosis, 75:185 receptor-mediated uptake, 75:182–185 biosynthesis and assembly, 75:171–173 endoplasmic reticulum–Golgi transport, 75:172–173 folding mechanisms, 75:172 transcriptional control, 75:171–172 cell surface transport, 75:180–181 complex structures class II-associated peptides, 75:165–166 HLA-DM molecules, 75:169–171, 177–180 HLA-DO molecules, 75:169–171 MHC class II complex, 75:162–164 polygenicity, 75:164–165 polymorphism, 75:164–165 dendritic cell system model, 75:187–189 endocytic pathway entry, 75:173–176 overview, 75:159–160, 191–192 pathogen subversion, 75:189–191

129

pathway mechanisms, 75:14–15, 160–162 peptide loading, 75:176–180 processing mechanisms, 75:186–187 subcellular organelles role, 75:176–180 trans-Golgi-mediated sorting, 75:174–176 vaccinology, 75:14–15, 62 Major outer membrane protein (MOMP), 81:69 Malaria, 70:299–300; 82:73 Malignancies, HLA-G in, 81:236–243 Malignancies, of lymphoid origin, 69:311 Mammals, immune response antimicrobial genes differential expression, 79:248–249 GATA factors, 79:247–248 immune deficiency pathway, 79:245–247 induction and regulation, 79:238–240 Relish pathway, 79:244–247 Toll pathway, 79:240–244 scavenger receptors, 79:233 thioester protein role, 79:236–237 toll-like receptors, 79:234–235 uterine natural killer cells, 79:310 Mammary tumor viruses (MMTV), 81:98 Mannose-binding lectin, 69:249, 251

130

SUBJECT INDEX

Mannose-binding lectin deficiency, systemic lupus erythematosus relationship, 76:252–257 Mannose-binding lectin-associated serine protease, 69:251–259, 291–293 Mannose-binding-lectin (MBL) pathways, 82:220, 220 Mannose-binding proteins A (MBP-A), 82:185–186 Mannose receptor, 72:263; 81:53–54 Mannose receptor, antigen uptake role, 75:184–185 Mannose receptor-mediated phagocytosis of mycobacteria, 81:82 Mannose receptors, 68:281–284 MAP kinase pathways, 70:30–32 MAP kinase, signaling pathway cross-talk, 75:138–139 MAP kinases, BCR transduction CD22 regulation, 73:115–119 CD40 regulation, 73:128–129 description, 73:101–104 MAPK, see MAP kinases; see Mitogen-activated protein kinase MAPKAP kinase-2, 72:39–41 Marginal zone lymphoma (MZL), 81:104, 106–107 MARs, see Matrix attachment regions Mason-Pfizer monkey virus (MPMV), 69:213 MASP, see Mannose-binding lectin-associated serine protease

Mast cells 68:13–14, 172–173, 278–279 and ITAMs, 69:206–207 and ITIMs, 69:223–224 serotonin release, 69:220–221 Mast cells, comparison with basophils, 77:93 Mast cells, interleukin-12 production 79:61 Maternal donor allografts, 73:229 Mating preferences in humans, 69:416–417 in mice, 69:412, 415–416 Matrix attachment regions, 69:124, 137, 328 Matrix metalloprotease 9 (MMP-9), 81:18 Maturation amyloid plaques, 80:267 dendritic cells, 80:130–131 T cells, 80:249 Maturation, basophils, 77:94 MBL-associated proteases (MASPs), 82:337–339 MBL, see Lectins MBP, see Myelin basic protein MBP-A, see Mannose-binding proteins A mBSA, see Methylated bovine serum albumin MCMV, see Murine cytomegalovirus MCP, see Metacarpophalangeal; see Monocyte chemotactic proteins MCP-1, 81:4, 10, 22 MCP-1, for Th2 differentiation, 80:122 MCP-2, 81:22, 23 MCP-3, 81:23

SUBJECT INDEX

Measles virus 68:115–116; 72:297–298 CD4þ control, 70:344 immune deviation, 70:171–172 Mediators, 82:263 chemokine, 82:1–2 cytokine, 82:1–2 inflammatory, 82:32, 114, 156 Meiosis I and II, 81:303 MEK-1, 72:118 MEK1, 71:237 MEKK-1, 72:21–22, 39–41 Melanocytes, 82:59 Melanomas, 82:59, 60 Membrane attack complex (MAC), 81:52; 82:220, 220 Membrane attack complex, 69:249–250, 269 Membrane-anchored adaptor protein, 79:95–97 Membrane binding, 68:162–164, 170 Membrane complement receptors, 69:295 Membrane molecules, macrophages and, 68:257–314 Membranes, see also Plasma membrane cell asymmetry: sPLA2-IIA and, 77:173–174 detergent-insoluble, 77:48–49 phase behavior, lipid domain formation and, 77:47–48 targeting of Btk, 77:132–134 Membranous epithelial cells (M-cells), 81:130–133 Memory B cells, diminished survival, 80:184

131

cytokine, see Cytokine memory for IFN-g, 80:146–149 IL-4, GATA-3 induction of, 80:148 Memory B cells, 69:214 Memory cells, 72:237–241 Memory T cells central and effector, 80:154–156 persistence, 80:156–158 Memory/effector T cells cytokine production, 80:253–256 phenotypic changes, 80:251–252 proliferation, 80:256–257 repertoire, 80:252–253 Memory, intracellular bacteria infection, 75:23–25 Meningitis, 73:437–438 Mesenteric vessels, thrombosis, 70:517 Mesoderm, 81:275 Mesometrial triangle, granulated metrial gland cells, 79:299 Messenger RNA, IL-4, 77:102–103 MET, 82:267–268, 269 Metabolic disorders, 69:378, 382–383 Metabolites, 82:27 Metacarpophalangeal (MCP), 82:217 Metal ion-dependent adhesion site, 72:329 Metal ions, 69:272, 276 Metallopeptidases, in catabolic pathway, 80:17 Metatarsophalangeal (MTP), 82:217 Metchnikowin, in immune response, 79:249 Meth-A tumor, 70:192

132

SUBJECT INDEX

Methimazole-induced insulin autoimmune syndrome, HLA Class II peptide binding and, 66:87–88 Methotrexate, 68:340, 351, 356; 73:214 Methylated bovine serum albumin (mBSA), 82:224–225 Methylated-CpG binding protein 2, 80:139 Methylation, 68:162–163, 164–65, 171–172 MHC, 81:272, 273; see Major histocompatability complex MHC class I 81:46–50, 71, 255 antigen presentation, IFN-g role, 80:47–48 molecules, structure and assembly, 80:21–22 peptides presented by generation frequency, 80:38–39 generation from exogenous antigens, 80:48–49 nonproteasomal pathways, 80:32–33 origin of, 80:22–25 restricted cytotoxicity, antigen-specific, 80:272 MHC class II, 81:49, 50, 71, 255 MHC class II molecules antigen presentation by, 80:71–73 IFN-g-induced expression, 80:78–79 targeting to endocytic compartment, 80:92–93 MHC molecules, see Major histocompatibility complex molecules

MIC genes, 76:1–46 biochemistry, 76:18–19 characteristics, 76:5–6 diversity, 76:25–39 disease susceptibility, 76:34–38 histocompatibility, 76:38–39 repertoire, 76:25–34 genomics, 76:6–9 ligands, 76:19–23 MICAB/ individuals, 76:39–41 overview, 76:1–5, 41–42 phylogeny, 76:9–14 structure, 76:23–25 transcription, 76:15–18 mechanisms, 76:16–18 transcripts, 76:15–16 MICA, 81:46, 242 Mice cancer in, 82:53 CIA and, 82:223–224 gene-targeted lineage commitment, 71:47–51 rearrangements, 71:44–47 TCR chain disruptions, 71:43–44 HTLV, 82:230–231 Ig, 82:189 IL-1ra, 82:232 immunization of, 82:276 Ipr, 82:230 models of RA, 82:217–237, 220, 234, 235 mutant IL-6, 82:232 RA models in, 82:217–237 STAT-deficient, 71:152–155 transgenic DEC, 71:38–39, 42–43 G8, 71:40–43

SUBJECT INDEX

TCRab, 71:35–37 TCRgd, 71:37–43 wild-type, 82:349 Microangiopathy, 70:516 Microcrystals monosodium urate IL-1 association, 73:403 IL-8 association, 73:378 Microorganisms, 82:1 Microscopic analysis, lipid rafts, 77:17–18 Microtubule-organizing center, reorientation, 77:14 MIDAS motif, 69:272, 276 MIDAS, see Metal ion-dependent adhesion site MIF gene, 66:199–202 Migraines, 70:514 MIP-1a, 81:9, 10, 31 MIP-1b, 81:9 MIP3b, 72:228 Mismatch repair, role in Ig gene hypermutation, 80:183–186, 189 Mitochondria apoptotic membrane changes, 68:74, 76, 87, 123 BCL-2 in, 68:110 calcium and, 68:87, 96–97 ceramide effect on, 68:122 as executioner, in apoptosis, 68:73–88, 123–124 in thymocytes, 68:91 Mitogen-activated protein kinase (MAPK), lipopolysaccharide signaling in macrophages, 78:14–15 Mitogen-activated protein kinase, 68:148–149; 79:70–71 activation: correlation with apoptosis, 77:139

133

p38, Cdc42-regulated, 77:10 Ras/MAPK pathway, 77:8 Mitogen-activated protein kinases, CD40-induced activation ERK, 76:89–90, 120, 125–126 JNK, 76:90–91, 98–100, 120–124 p38 activation, 76:92, 98, 100, 124–125 CRE transcription, 76:92 Mitogen-activated-protein kinase cascade, 69:54–55 MKK7, 72:39–41 MMR, see Macrophage mannose receptor Models, see Disease models active immunization, 77:264–273 Drosophila immune response, 79:227–228 late-phase response to allergen challenge, 77:112–113 mixed chimerism, 79:171–177 molecular, picornavirus neutralization, 77:219–220 mouse, limitations, 77:286–287 passive transfer, 77:277–282 rafts serving as signaling platforms, 77:20–21 xenotransplantation, 79:155–157, 180–181 Modules, see Protein modules Molecules, 82:1, 256–257 alternative adjuvant, 82:63 CD40, 82:298–301 inflammatory, 82:219 J chain, 82:172–173 Monoallelic expression, 69:441–445 Monoclonal antibodies against tumor antigens, 68:258–266

134

SUBJECT INDEX

Monoclonal antibodies (continued) anti-B7-1 and anti-B7-2, 68:382–384 anti-CD2, 68:384–385 anti-CD4, 68:333, 347–353, 379–380 anti-CD5, 68:353–358 anti-CD52, 68:362–365 anti-CD7, 68:358–359 anti-nucleoprotein, 77:234 anti-TCR, 77:12 anti-tumor necrosis factor-a, 68:338–342 antiviral, 77:229 neutralizing, 77:243 nonneutralizing, 77:207 and rheumatoid arthritis, 68:336, 338–342, 344–345, 347–359 Monoclonal antibodies, anti-suppressor T cell factor antibodies, 74:12–14 Monoclonal antibodies, cancer immunotherapy, 75:263–264 Monoclonal antibodies, CD45 studies, 66:1, 3, 5–17 Monoclonal antibody, 69:358 Monoclonal gammopathy of undetermined significance (MGUS), 81:106 Monoclonal TCR transgenic mice, organ-specific autoimmunity in, 81:334–335 Monocyte chemoattractant protein-1 (MCP-1), 66:135 sepsis and, 66:104, 141–142 Monocyte chemoattractant protein-1, see MCP-1 Monocyte chemotactic proteins, 73:389–390; 77:96

Monocytes 69:383 amyloid protein precursor in, 68:23 CD2 mRNA levels in, 68:16 CFS-1 in phorbol-stimulated, 68:15 differentiation antigens expressed by, 68:271–298 F4/80 in peripheral blood, 68:272 GM-CSF production, 68:8 interleukin-12 production, 79:60 interleukins and, 68:13, 15 prenylated proteins in human, 68:174 protein kinase C and, 68:11 in xenotransplantation, 79:146–148 Monocytes, CD40-mediated maturation, 76:72 Mononuclear phagocytes, innate immune response role, 75:13–14 Mononucleosis, 69:213 Morphine, 82:24–25 Morpholinos, 81:256 transient gene knockdown using, 81:309–310 Morphology, rodent granulated metrial gland cells, 79:302–305 Mouse antigen differentiation in, 68:271–314 arthritis studies in, 68:339, 340, 369–371, 375–377, 393 B cell-lineage lymphomas background, 81:102–106 classification, 81:102–109 hierarchic clustering, 81:114

SUBJECT INDEX

BCL-2 studies in, 68:107 BLNK-deficient, 79:108–110 Bruce effect, 69:421, 423 c-kit-deficient, 69:72–76 CD30 experiments in, 68:116 diabetes studies in, 68:374–375, 380–381, 383–386, 392, 394 adhesion molecule blocking, 68:367–369 cytokine modulation and, 68:374–375 oral albumin and, 68:334 familial hypercholesterolemia, 69:365–366 FTase inhibitors in tumors in, 68:176 FV receptor studies in, 68:259–266 gene targeting, 69:321–339 granulated metrial gland cells morphology and phenotypes, 79:302–305 origin, 79:300–302 hematopoietic cells, 81:100 hematopoietic neoplasms, classification, 81:103–104 Ikaros gene, 69:81 LAT- and SLP-76-deficient, 79:105–108 LIF-deficient, 69:59–60 k loci:l loci ratio, 69:157–159, 160–161 lymphoid neoplasms, 81:97–121, 101 lymphomas and leukemia, 81:99 macrophage and myeloid dendritic cells in, 68:271–314 and man, fundamental differences between, 81:99

135

MHC studies familial imprinting, 69:428–429 mating preferences, 69:412, 415–416, 428–429 odor discrimination, 69:417–421 as model for human neoplasmic diseases, 81:97 peptide transport and, 68:192–195, 211–213, 225–228, 236, 237, 239 protein tyrosine kinase studies in, 68:97–98 protein tyrosine phosphatase studies in, 68:99–100 RAG gene-deficient, 69:86, 133, 313, 317, 327 SCID, 69:32–33, 37 sphingomyelinase studies in, 68:120 stress kinase studies on, 68:106 susceptibility to prions, 81:135 systemic lupus in, 68:337, 377–378, 384–385 Tcf-1-deficient, 69:82–83 TCRb-deficient, 69:33–35 uterine natural killer cells, 79:316–318 and V(D)J rearrangement, 69:311, 313, 315 xenotransplantation, 79:156–157 ZAP-70-deficient, 69:197–198 Mouse mammary tumor virus, 70:350–351 Mouse mammary tumor virus, nonneutralizing mAbs against, 77:207 Mouse strains, genetic background, 77:271–273

136

SUBJECT INDEX

MPL, see Lipid mRNA amyloid protein precursor, 68:22–23, 35 AU-containing, 68:19–20, 34, 35 chimeric, 68:20–21, 25 cis elements, 68:18–29 coding for CD isoforms, 68:15 cytokine, 68:8–14, 19, 31 in developing thymus, 68:17 decay rate, 68:1–3, 6, 21 differentiation of, 68:18, 29 posttranscriptional control, 68:4–5 in T cells, 68:1–50 trans factors, 68:29–36 translation measurement, 68:3–4 mRNA stability, 73:449–450 MSG1, transforming growth factor-b signaling, 75:135 MSH2/MSH6 complex, mismatch repair and, 80:185 MSU, see Microcrystals monosodium urate MTP, see Metatarsophalangeal m–g switch, Camelidae heavy-chain antibodies, 79:275 MUC1, tumor T-cell response induction, 75:244–245 MUC1purified from ascites fluid of cancer patients (ASC-MUC1), 82:273–274 Mucin, polymorphic epithelial (PEM), 82:250 Mucin, polymorphic urinary (PUM), 82:250 Mucins, 68:290–291; see also Immunobiology, MUC1 family of, 82:249, 250–251

MUC1 as, 82:61, 250–251 Mucosa-associated lymphoid tissue chemokine and receptor expression CCR6 expression by dendritic cells, 78:86 fractalkine, 78:87 LARC, 78:86 MEC/CCL28, 78:87 TECK/CCL25, 78:86 gastrointestinal eosinophils, see Eosinophil overview, 78:85 Mucosa, see Gut mucosa Mucosal immunity, intracellular bacteria infection, 75:20–23 Mucosal vascular addressin aEb7 integrins, 72:346–348 autoimmune blocking, 72:242–243 inflammation blocking, 72:242–243 integrin ligands, 72:334–335 lymph node development, 72:343 lymphocyte-endothelium interaction, 72:213–220, 233–234 Mucosal-associated lymphoid system (MALT), 81:131 Mucosal-associated lymphoid tissue, 73:181 Multiple autoimmune diseases, 73:221–222 Multiple organ failure, 70:303–304 Multiple sclerosis 69:364; 70:160–162 anti-CD52 therapy and, 68:364 CD4 monoclonal antibody and, 68:352

SUBJECT INDEX

FasL role, 73:281 interferon-b treatment of, 68:342–343 oral tolerance, 73:229 peptides and, 68:238, 387 Multiple sclerosis, HLA Class II peptide binding and, 66:88–91 Murine AIDS, 70:176–177 Murine cytomegalovirus, 70:168–171 Murine hepatitis viruses, antibody protection against, 77:233–234 Murine leukemia virus, antibody protection against, 77:230–231 Murine leukemia viruses (MuLV), 81:98, 101, 104, 109 Murine models, 82:265–269 Muscular dystrophy, 69:364 Mutagenesis, 68:23, 24, 26, 27, 31 Mutagenic frequency, 81:299 Mutation in E1 ubiquitin-activating enzyme, 80:5 Ig genes, mismatch repair role, 80:183–186 targeting to non-Ig genes, 80:195 Mutations, 82:297–298 adaptive responses, 72:138–140 in adhesion molecules, 69:84–88 CD44, 69:87 CD81, 69:88 e-cadherim, 69:86–87 redundancy, 72:138–140 in transcription factors, 69:77–84 Mutations, Fyn N-terminal region mutations, 77:57 Mycobacteria mannose receptor-mediated phagocytosis of, 81:82

137

phagocytic receptors for, 81:72–73 Mycobacterial infection, 81:70–84 plasma membrane cholesterol in, 81:77–84 Mycobacterial phagosome, 81:71–72 Mycobacterial virulence genes, 81:75–76 Mycobacterium avium, 70:179; 71:277; 81:70 Mycobacterium bovis, 71:330; 81:70, 71, 82 Mycobacterium intracellulare, 81:70 Mycobacterium kansasii, 81:81 Mycobacterium leprae, 70:179 Mycobacterium marinum, 81:75 Mycobacterium spp., 71:286–288 Mycobacterium tuberculosis 68:195, 282; 70:178–179; 81:45, 54, 65, 70–75 chemokine response, 71:277 cytolytic CD8þ T cells, 71:312 granuloma formation, 71:320 IL-6 response, 71:276 gd T cells, 71:306–307, 313–314 gd T-cell response, 71:103, 107 toxic effector molecules, 71:278 vaccines, 71:327–328 Mycobacterium, 81:68, 82 Mycoplasma penetrans, 68:56 MyD88 interleukin-1 receptor signaling, deletion studies, 78:6, 23 lipopolysaccharide signaling role, 78:22–24 Myelin basic protein (MBP), multiple sclerosis and, 66:88, 90 Myelin basic protein, 68:389–392

138

SUBJECT INDEX

Myelin basic protein (continued) bystander suppression, 73:168–169 EAE models active suppression, 73:164–168, 206–208 glatiramer acetate, 73:211 Lewis rat, 73:208, 210 murine, 73:210–211 nasal aerosol, 73:211 neonatal administration, 73:223–224 Myelin basic protein, reactive cells, 80:217 Myelin oligodendrocyte glycoprotein (MOG)–peptide administration, 81:187 Myelogenous leukemia, immunotherapy, 75:236 Myeloid cells, 68:278–279, 282; 69:18–19 precursors, 69:59 Myeloid mast cell progenitors, 68:6 Myeloma, 68:28 Myelomas, 82:53, 64 Myelopoiesis, 69:82; 71:216 Myocardial infarction, 70:533–534 Myocardiocytes, 68:86, 87 Myxoma virus, 69:379

N N-Ethylmaleimide, 70:381–382 NADPH oxidase chemoattractant responses response, 72:46–47 Rho signal regulation, 72:38–39 Naked DNA, 71:333–335 Nasal tolerance, 73:203–206

Natural antibodies, in antiviral responses, 79:9–10 Natural killer (NK) cells, 81:46, 199, 242 in zebrafish, 81:268–272 Natural killer (NK) receptors, 81:272 Natural killer cell stimulatory factor, see Interleukin-12 Natural killer cells as apoptosis inducers, 68:53 bacterial invasions, 71:315–316 CD4 role, 72:108 CD69 and, 68:14 CD95L expression, 71:166 chemokine relationship, 74:141–144 CpG effects, 73:339 and CpG motifs, 69:372–373 cytokine production, 73:415 DC phenotype, 72:273 development, 70:46–47 DNA activation, 73:347 FcgRIII in, 68:278–279 from human colorectal cancer, 69:215 IL-12-induced, 70:129–131 IL-18 effect, 70:291–292 inhibitory receptors, 69:221 and interleukin-2, 68:26 leishmaniasis, 74:282–284 lineage of, 69:14–18 as lymphoid DCs, 72:257 major histocompatibility complex class I interactions, 76:21–23, 42 peptide transporter and, 68:194, 236 perforin in, 68:26 progenitor, 69:6

SUBJECT INDEX

properties, 76:64 radiation function, 73:527 Rho signal regulation, 72:38–39 stimulators, 69:371, 373 gd T cells and, 71:101–102 Thl generation, 70:139–140 thymus population, 71:10–11 and ZAP-70, 69:197–198 Natural killer cells, in old age, 80:261 Natural killer cells, innate immune response role, 75:13–14 Natural killer cells, xenotransplantation NK cells, 79:143–146 NK/T cells, 79:142 pharmacotherapy, 79:181–182 tolerance, 79:176–177 Natural killer complex (NKC), 81:269 Natural selection theory, 69:113 Necrosis, 68:55, 62, 72–73, 85–86 Negative selection, self-reactive B cells B cell anergy alterations, 74:74–78 C4 deficiency effects, 74:74–78 Cr2/ mouse impairment, 74:73–74 natural antibody role, 74:82 NEM-sensitive factor, 70:381–382 NEMO, see Gene(s) Nerve growth factor 81:144 characterization, 73:80, 83–84 Nervous system effector cells: neurons, 77:297–299 embryonic divisions, 77:299–303 noneffector cells: glia, 77:299

139

Neural crest cell–endoderm interaction, 81:276 Neuroblasts, programmed cell death: ventricular zone, 77:309–313 Neurodegenerative process, 69:295 Neurogenesis, cerebral cortex, 77:306–307 Neurons, 68:72, 86, 87; 69:361, 438–439, 446 Neurons, as mature effector cells of nervous system, 77:297–299 Neuropilin-1 in initial T-cell/DC contacts, 81:193–194 Neuropilins, 81:176–177 Neutralization antibody, see Antibody neutralization attenuated vaccines, 79:33 hepatitis B virus, 79:26 hepatitis C virus, 79:26 HIV, 79:26–27 immunosuppression, 79:22–23 in vitro, mechanisms, 77:195 infection enhancement, 79:22 infective vaccines, 79:32–33 influenza viruses, 79:25–26 intracellular, 77:227 linear epitopes, 79:33–34 lymphocytic choriomeningitis virus, 79:27 mechanisms, 79:6–8 outside immune system, 79:21–22 picornavirus, molecular model, 77:219–220 single-hit vs. multi-hit kinetics, 77:205–210 stoichiometry, 77:214–219

140

SUBJECT INDEX

Neutralization (continued) structural studies, 79:8–9 vaccines, 79:32 viral sensitivity, 79:23–24 virions, by coating with complement, 77:210 virus, kinetic studies, 77:197, 204 Neutropenia, 82:303 Neutrophil chemotactic activity, 81:18 Neutrophil-activating peptide-1 (NAP-1), 66:135 Neutrophil(s), 82:221, 341 activation of, 82:1, 18–22, 28–34 aggregation/degranulation of, 82:344–345 apoptosis, 82:25–28, 27 differentiation, 82:30–31 extracts, 82:19–20 future direction for, 82:15–17, 16, 32–34 G-CSF and, 82:4–7 GM-CSF and, 82:7–11 IFN-c and, 82:11–14 IL-10 and, 82:13–14 morphine and, 82:24–25 NF-kB family and, 82:17–28 other agent in, 82:14–17 polymorphonuclear, 82:1 roles of, 82:1–3 STATS and, 82:4–17 Neutrophile, TNF and interleukin-1 and, 66:111 Neutrophils CD30 ligand expression, 73:398–399 CEMF expression, 73:424 CINC production, 73:384–385 cytokine expression

antitumor response in vivo, 73:472–473 bone formation in vivo, 73:476 general features, 73:369–373, 375 HIV-associated, 73:439–440 immune response in vivo, 73:472–473 infections in vivo, 73:467–471 LPS effects in vivo, 73:454, 457–462 meningitis-associated, 73:437–438 modulation, 73:440–447 molecular regulation evidence, 73:447–448 mRNA stability, 73:449–450 postranslational, 73:452–453 transcriptional, 73:448–449 translational, 73:450–452 pancreatitis in vivo, 73:474 shigellosis-associated, 73:437 specific substance, 73:373 wound healing in vivo, 73:474–475 FAS ligand production, 73:397–398 function, 73:369 G-CSF expression, 73:422 GDF expression, 73:423–424 GRO production, 73:382–385 HGF expression, 73:421–422 HSF expression, 73:425 IL-1 expression, 73:434–437 production, 73:399–405 IL-1 and TNF-a effect on, 68:11 IL-6 expression cancer, 73:440

SUBJECT INDEX

characterization, 73:409–412 IL-8 expression associated diseases, 73:426–429 production, 73:375–382 sepsis, 73:432–434 IL-12 expression, 73:413–415 IL-1b expression, 73:428–430, 432–434 RA, 73:430–432 SLE, 73:432 IL-1RI/IL-1RII production, 73:405–409 INF-a expression, 73:415–417 impaired chemotaxis in, 68:167, 169 impaired phagocytic function in, 68:167 LDGF expression, 73:423 MCP production, 73:387–389 MIP production, 73:387–389 noncytokine, 73:425–426 OSM expression, 73:412–413 Rab proteins and, 68:173–174 Ras activation in, 68:167 SCF expression, 73:422–425 TGR-a expression, 73:418–419 TGR-b expression, 73:419–420 TNF-a expression cancer expression, 73:440 characterization, 73:390–397 GDF-associated, 73:434–437 IFD-associated, 73:428–430 Neutrophils, in xenotransplantation, 79:148 Newcastle disease virus, mAbs against, 77:209–210 NFkKB, interleukin-12 production, 79:80–81

141

NF-kB, 81:259; see Nuclear factor-kB p50 deficiency, 80:126 regulatory role in Th cytokines, 80:135–136 NF-kb, CD40-mediated regulation B cell responses, 76:87, 92–93, 100–103, 116–121 positive and negative regulation, 76:80 signaling cascades, 76:116–121 TRAF adapter molecule, 76:100–103 NF-AT, see Nuclear factor of activated T cells NF-AT, B cell immune response regulation by CD40-CD154-signaling, 76:79, 88–92 NF-IL6, lipopolysaccharide signaling in macrophages, 78:19 NFAT, Nuclear factor of activated T cells NFATc, regulatory role in cytokine gene expression, 80:136–137 NFATp, T cells deficient for, 80:137–138 NFS.V þ mice, 81:101, 109 NG, see Nerve growth factor NHEJ, see Nonhomologous end-joining pathway Nickel sensitization animal model, 73:222 human model, 73:229 Nicks, presence during Ig hypermutation, 80:186–187 Nitric oxide, 71:104–105, 278–281; 81:73–74 Nitric oxide (NO), 82:24–25

142

SUBJECT INDEX

Nitric oxide synthase, 79:320–321 Nitric oxide-synthase (iNOS), 81:73, 259 Nitric oxide, Leishmania elimination mechanisms, 74:297–300 Nitric oxide, in apoptosis, 68:60, 80, 123 Nitrogen cavitation, 82:5–6, 19 NK cells, see Natural killer cells NK, see Cells, natural killer NKR-P1, 72:273 N-methyl-N-nitrosourea, 73:516–517 NMR, see Nuclear magnetic resonance NMU, see N-methyl-N-nitrosourea NO, see Nitric oxide Nocytosis, clathrin-mediated, 73:12–13 Non-Hodgkin lymphomas, 81:99 Non-lymphoid leukemia, 81:113–115 Non-specific cytotoxic cells (NCC), 81:260, 268–269 Nonhomologous end-joining (NHEJ) pathways, 82:295, 310 Nonhomologous end-joining, and DNA rearrangement, 77:313–316 Nonlymphoid cells, apoptosis in, 68:78 Nonneutralizing antibodies, 77:199 Nonreleaser phenotype, basophil, 77:107 Nonsteroidal antiinflammatory drugs, 73:230 Notch protein, 71:50–51

Novel immune-type receptors (NITRs), 81:270–272 NRAMP-1, 81:74 Nramp, 71:322–324 NSAIDs, see Nonsteroidal antiinflammatory drugs N-terminal extensions aminopeptidase-trimmed, 80:51 MHC-presented peptides with, 80:40–42 Nuclear factor of activated T cells, see NFAT calcineurin and, 77:110 characterization, 72:5 growth signals, 72:34–35 Ras signaling, 72:19–20, 23 transcriptional activation, 77:6–7 translocation, 77:11 Nuclear factor-kB (NF-kB) activation defects in lipopolysaccharide tolerance, 78:28 lipopolysaccharide signaling in macrophages, 78:18–19 Nuclear magnetic resonance (NMR), 82:161, 252 Nuclear steroid receptor, signaling pathway cross-talk, 75:140 Nuclear transfer, xenotransplantation genetic engineering, 79:169 Nuclear transport, transforming growth factor-b signaling, 75:127–128 Nucleation, actin filaments, by cytochalasin D, 77:29 Nucleolin, 68:35–36

SUBJECT INDEX

Nucleus apoptosis and, 68:54, 70, 76, 85, 122 endonucleases from, in vitro, 68:56 ribonuclear proteins of, 68:35 Nyppostrongylus brasiliensis, 70:187

O Occupancy antibody, at neutralization, 77:217–219 binding site, importance in HIV-1, 77:211–213 neutralization in relation to, 77:244 Oct1, V(D)J recombination regulation, 78:205–206 Oct2, V(D)J recombination regulation, 78:205–206 ODNs, see Oligonucleotides Odors, MHC-based and humans, 69:421–422 mechanisms, 69:422–427 and mice, 69:417–421 Offspring, transfer of maternal immunological experience to, 80:223–228 Olfactory system axon guidance, 69:446 gene regulation, 69:437–447 and major histocompatibility complex, 69:427–428 and monoallelic expression, 69:441–445 Oligonucleotides, synthetic CpG

143

as antitumor adjuvant, 73:349–350 cellular uptake, 73:333 CTL response, 73:353–354 evolution, 73:346–348 extramedullary hematopoiesis-induced, 73:351 immune cell activation, 73:352 immune responses, 73:331–332 mediative effects in vivo, 73:349 as mucosal adjuvant, 73:351 sequence effects APCs, 73:336–338 B cells, 73:334–335 immunosuppressive, 73:342 macrophage receptors, 73:341 NK cells, 73:339 T cells, 73:338–339 TNF-a production, 73:342 sequence-independent effects, 73:333–334 signal mediation cell response, 73:352–353 cellular uptake, 73:343–344 chloroquine effects, 73:346 lysosomotropic compounds, 73:344–345 stress kinase pathway, 73:345–346 T cell effects as Th1 adjuvant, 73:348–349 Th2 pathology, 73:350–351 Oligopeptides, produced by proteasomes, fate of, 80:17–19 Oligosaccharides, 82:176 Oncogenes, products of, 68:54 Oncorhynchus mykiss, 81:254 Oncostatin M, 69:60–61; 73:412–413

144

SUBJECT INDEX

Ontogenetic waves, 71:79–81 Ontogeny, Camelidae heavy-chain antibodies, 79:272–275 Open reading frame (ORF), 81:153, 191–192 Open reading frames (ORFs), 82:79, 306 Oppenheimer, J. J., 82:72 Oral antigens biologic filtration, 73:188–189 enzymatic digestion, 73:188–189, 196–197 feeding regimes, 73:196–197 immunological effects, 73:153–155 induction factors, 73:183–187 inflammatory processes, 73:194–195 intestinal absorption, 73:189–194 Peyer’s patches, 73:197–200 structure, 73:187–188 Oral cancer IL-6 production, 73:440 TNF-a production, 73:440 Oral contraceptives, 69:422 Oral tolerance allergy models animal, 73:218, 221 human, 73:227–228, 231 arthritis models adjuvant, 73:213–214 antigen-induced, 73:214 collagen-induced, 73:211–213 human, 73:230 pristane-induced, 73:214 autoimmune models animal, 73:164–165, 206–208 worsening, 73:223–224 cellular, 73:174–176 Crohn’s disease, 73:231

definition, 73:157–158 diabetes models, 73:215–216 EAE models, MBP glatiramer acetate, 73:211 Lewis rat, 73:208, 210 murine, 73:210–211 nasal aerosol, 73:211 effector phase active suppression anergy, 73:172–174 bystander, 73:167–170 characterization, 73:163–167 clonal deletion, 73:172 gd T cells, 73:170–171 idiotypic cells, 73:171–172 regulatory cells, 73:171–172 overview, 73:161–163 history, 73:155–157 humoral, 73:174–176 as immunologic event, 73:158–159 induction factors animal models age, 73:178 genetic background, 73:181 immunological status, 73:181–183 intestinal flora, 73:183 types, 73:178 antigens biologic filtration, 73:188–189 dosage, 73:196–197 enzymatic digestion, 73:188–189 feeding regimes, 73:196–197

SUBJECT INDEX

inflammatory processes, 73:194–195 intestinal absorption, 73:189–194 liver’s role, 73:200–201 Peyer’s patches, 73:197–200 spleen’s role, 73:200–201 structure, 73:187–188 types, 73:183–187 inductive phase, 73:159–161 kinetics, 73:176–178 maintenance factors maternal donor allografts, 73:229 modulation, 73:201–202 multiple sclerosis, 73:229 nasal, 73:203–206 nickel allergy, 73:229 senescence, 73:180 thyroid, 73:231 uveitis, 73:231 uveitis models, 73:216–217 ORFs, see Open reading frames Organ transplantation, 81:232–236 Organ-specific autoimmune disease, 70:157–158 Organ-specific autoimmunity induced by elimination of subpopulations of CD4þ T cells, 81:332–334 in monoclonal TCR transgenic mice, 81:334–335 Organ-specific autoimmunity induced by T-lymphopenia, 81:331–336 Organelle ultrastructure, apoptosis and, 68:55 Organization, cerebral cortex, 77:303–305 Organs, aging effects, 80:246–247

145

Orthomyxoviruses, antibody protection against, 77:237 Osteoarthritis, 73:431–432 Osteoclast, 70:294 Osteoclasts, 82:222 Osteoporosis, postmenopausal, 80:268 Osteoprotegerin ligand, 80:268 OT-1 cells, 73:56–57 Outgrowth, initial process of cerebral cortex, 77:308–309 Ovalbumin liposomal association, 73:42–43 oral tolerance anergy, 73:173 biologic filtration, 73:188–189 bystander suppression, 73:170 DTH, 73:185–186 enzymatic digestion, 73:188–189 feed regimens, 73:196–197 high doses, 73:163 humoral responses, 73:177 induced-diabetes, 73:224 presentation native proteins, 73:44–45 pathways, 73:28–30 Ovalbumin, class I-presented peptide generated from, 80:35–36 Ovalbumin, for active immunization models, 77:266–267 Overexpression Btk and Syk, 77:146 sPLA2-IID, 77:180 Ox-40, T-cell response in cancer, 75:253, 256 OX40/OX40L, 72:271 Oxidation, cPLA2-derived products, 77:174–175

146

SUBJECT INDEX

Oxidative stress, 73:285–286 Oxygen, reactive species and apoptosis, 68:64–65, 70–71, 76, 77 and permeability transition pore, 68:80, 123

P P1 position, preferred by proteasome active site, 80:36–37 P13K, see Phosphatidylinositol 3-kinase p35, 70:87–89 p35 gene encoding gene, 79:56–58 transcriptional control, 79:71–72 p38, 73:345 activation, 76:92, 98, 100, 124–125 CRE transcription, 76:92 –JNK, 72:39–41 –SEK1, 72:68 p38 MAPK pathway, 80:134 p40, 70:86–87, 90–92, 94 p40 gene encoding gene, 79:56–58 interferon-g priming, 79:68–69 promoter elements, 79:67–68 promoter polymorphisms, 79:71 transcriptional factor PU.1, 79:69–70 p40 subunit, 70:90–92, 94 p41, and Cat L, 80:95–96 p53/56lyn, CD45 and, 66:24, 37, 39, 44 p53, 68:7, 69–70, 91

p53, tumor T-cell response induction, 75:242–243 p56, 71:237 p56lck, 69:47–49 p56lck, CD45 and, 66:11, 12, 19–21, 26, 37–39, 39–44, 53 p59fyn, CD45 and, 66:19–21, 37, 38, 39–43; 68:93, 95, 96, 97–98; 69:47–49 p62, interleukin-1 receptor signaling, 78:6 p70 S6 kinase, lipopolysaccharide signaling in macrophages, 78:17 p70zap, CD45 and, 66:21–22, 26 p72syk, CD45 and, 66:21, 23–24, 26, 45 p300 transcriptional coactivator, transforming growth factor-b signaling, 75:134 PA28 complex with 20S proteasome, 80:12–13 role in antigen presentation, 80:30–31 PACAP, see Pituitary adenylate cyclase-activating polypeptide PAF, see Platelet-activating factor PAG, association with Csk, 77:58, 60 PAK2, 71:179 Palmitoylation protein, effect of PUFAs, 77:72–73 Src kinase, 77:56–57 Pancreatitis, 73:474 Pancreatitis, sPLA2-IB role, 77:169 Papillomavirus, 69:378 Papillomaviruses, outside immune system, 79:21

SUBJECT INDEX

Paraformaldehyde, 73:20 Paramyxoviruses, antibody protection again: 77:238 Paranasal sinus disease, 73:427 Parasites, 69:295; 72:294–295 Parasites, for active immunization models, 77:2 Parkinson’s disease, 81:123 Passive transfer models, lymphocyte CD4þ T cells, 77:277–278 effector Th cells, 77:279 modulatory effect of effectors, 77:279–282 T cell clones, 77:278–279 Pathogen associated molecular patterns (PAMPs), 81:51, 55 Pathogen resistance, 71:105–108 Pathogenic mycobacteria, trafficking in macrophages, 81:78 Pathogens, see also Antigens; Vaccines major histocompatibility complex class II antigen presentation subversion, 75:189–191 Drosophila exposure, 79:227 interleukin-12 induction, 79:62–64 pathogenicity—virulence compared, 75:3 in xenotransplantation, 79:187 Pathogens, interfering with generation of presented peptides, 80:49–50 Pathology, uterine natural killer cells, 79:318 Patient confidentiality, in xenotransplantation, 79:190 Pattern recognition, 81:46

147

Pattern recognition receptors (PRR), 81:45–46 Pattern recognition receptors description, 73:329 LPS, 73:329–330 Pattern-recognition receptor (PRR) Drosophila, see Toll receptor innate immunity concept, 78:1 PAX5, 81:115 PBMC, see Peripheral blood mononuclear cells PCR, 81:110; see Polymerase chain reaction PDb1 element, immunoglobulin heavy chain gene assembly role, 78:195–196 PDGF, see Platelet-derived growth factor PDQ52 element, immunoglobulin heavy chain gene assembly role, 78:194–195, 209 PDTC, see Pyrrolidine dithiocarbamate PEBP2a, transforming growth factor-b signaling, 75:131–132 PEG, see Polyethyleneglycol Pegoraro, L., 82:7–9 PEM, see Mucin, polymorphic epithelial Pemphigus vulgaris, HLA Class II peptide binding and, 66:87 Pentoxifylline, sepsis and, 66:130 Peptide transporter, 68:191–255; see also Peptides antigen presentation and, 68:193–197 biochemical characteristics of, 68:228–231

148

SUBJECT INDEX

Peptide transporter (continued) chemotherapy resistance and, 68:224 deficiency, 68:192, 194, 209, 235–236 diseases, 68:234–239 genes for, 68:209–211, 235 kinetic parameters, 68:228–229 molecular structure, 68:214–215 nucleotide usage, 68:229–231 peptide binding and transport assays, 68:216–219 as peptide supplier for MHC molecules, 68:192–199 proteins of human, 68:211–213, 225, 227 species differences, 68:211–213, 219, 225–228 structure and function, 68:231–233, 234 Peptide-binding motifs, HLA Class II molecules, 66:69–71 Peptide(s), 82:58 antigen-combining sites and, 82:178–181 Fc-binding, 82:179 identification of, 82:60–61 immunologenic, 82:278 MHC Class I, 82:64, 76 MHC Class II-associated, 82:59–61, 77, 182 MHC Class II-restricted, 82:114 poly, 82:179 synthetic, 82:264 tumor vaccines and, 82:64–66 vaccines, 82:269–271 Peptides 69:423–425, 427; 81; see also Peptide transporter

altered, in T cell receptors, 68:386–389 antigenic, 68:199–203 antigenic, destruction by peptidases, 80:44–47 arthritogenic shared epitope, 68:318–326 binding and transport assays, 68:216–219 class II-associated Ii derived (CLIP), 80:72, 89–90 cytosolically-derived, 81:47–49 derived from endosomal/ lysosomal system, 81:49 effect on T cell clones, 68:14 export from endoplasmic reticulum, 68:233–234 idiotypic, recognized by Id-specific T cells, 80:216, 219 loading, DM-mediated, 80:91–92 MHC class I-presented generation frequency, 80:38–39 generation from exogenous antigens, 80:48–49 nonproteasomal pathways, 80:32–33 origin of, 80:22–25 pathogen interference, 80:49–50 and permeability transition pore, 68:80 photolabile, 68:231–233 rubella-derived, 68:322 selectivity and specificity, 68:217, 218–228 targeting of, to transporter, 68:205 trimming

SUBJECT INDEX

in cytoplasm, 80:40–43 in endoplasmic reticulum, 80:43–44 Peptides, complex with TCR and MHC, 77:15–16 Peptides, N-formulated (fMLP), 82:15, 19–120 Peptidoglycan recognition proteins, 79:229–230 Peptostreptococcal magnus, 82:193–194 Peri-arteriolar lymphoid sheath (PALS), 81:5 Periarteriolar lymphoid sheath, 73:86–87 Peripheral blood mononuclear cells (PBMC), 81:11; 82:12, 15, 23–24, 139 Peripheral lymphoid organs, lymphocyte apoptosis B cell development, 76:203–205 T cell development, 76:195–199 Peripheral nerves, 81:143 Peripheral nervous system, placodes, 77:300 Permeability transition, 70:257–259 Permeability transition pore, 68:74, 80–88, 110, 123 Peroxisome proliferator-activated receptor g (PPARg), lipopolysaccharide signaling antagonism in macrophages, 78:20 Peroxynitrites, 82:25 Persistent fraction, infectious virus, 77:206–207 PERUN (software), T cell epitope prediction, 66:82

149

PERVs, see Porcine endogenous retroviruses Peyer’s patch chemokine and receptor expression, 78:77–80 eosinophil migration in allergy, 78:307–310 normal tissue gasrointestinal cells, 78:294 Peyer’s patches oral tolerance, 73:197–200 tolerance induction, 73:186 and prion susceptibility, 81:130 Peyer’s patches, macrophages in, 68:273 PF-4, 81:4 PG, see Proteoglycan PGIA, see Arthritis PGRP, see Peptidoglycan recognition proteins pHi, regulation of protease activity, 80:77–78 PHA, see Phytohemagglutinin Phagocytes 82:1, 5 origin of, 81:261 receptor usage during mycobacterial entry into, 81:80 Phagocytes, CD40-mediated maturation, 76:72 Phagocytes, phosphatidylserine receptors on, 68:64 Phagocytic cells, 70:298 IL-2 production, 70:84 Phagocytic cells, interleukin-12 production, 79:60 Phagocytic receptors for mycobacteria, 81:72–73

150

SUBJECT INDEX

Phagocytic theory of inflammation, 81:261 Phagocytosis 68:167, 282; 69:250; 71:270–272; 72:34; 81:46, 52, 57–65; 82:74, 156 antibody-mediated, 77:226 characterization, 73:14 complement receptor type 3-mediated, 81:60–61 inhibition, 73:23 mechanisms, 81:58–61 role of actin, 81:58–59 signaling in FcR-mediated, 81:59–60 sPLA2-IIA and, 77:175 Phagocytosis, antigen uptake role, 75:185 Phagolysosomes, 71:288–290 Phagosomal escape, bacterial carriers, 75:56–58 Phagosome maturation 81:64–65 blocking, 71:286–288 cytoplasm escape, 71:290, 292 mechanism, 71:283–286 Pharmacotherapy, in xenotransplantation, 79:181–182 Phenoloxidase, in immune responses, 79:236 Phenotypes, 82:303 Phenotypes, rodent granulated metrial gland cells, 79:302–305 Phenotypic changes, memory/ effector T cells, 80:251–252 Phenotypic characterization of zebrafish, 81:289–295 Phenylmethylsulfonyl fluoride (PMSF), 82:9

Phlebotoinus spp., Leishumania host role, 74:277–281 Phorbol myristate acetate, activator of basophils, 77:109 Phorbol myristic acetate, 73:44 Phosphatases, 82:4 Phosphate-containing antigens, 71:88–89 Phosphates, transfer, high-affinity immunoglobulin E receptor FceRI signal transduction Bruton’s tyrosine kinase, 76:331–332 CD45 role, 76:333–334 LYN transfer kinase, 76:328–331 phosphate transfer kinases, 76:328–332 protein tyrosine phosphatases, 76:332–335 SHP-1 role, 76:334–335 SHP-2 role, 76:335 SYK role, 76:328–331 Phosphatidyl-inositol-3-kinase (PI3K), 81:59, 60 Phosphatidylcholine hydrolyzed by sPLA2-X, 77:181 sPLA2-binding, 77:167–168 Phosphatidylethanolamine, 70:536 Phosphatidylinositol 3-kinase (PI3K), lipopolysaccharide signaling in macrophages, 78:14 Phosphatidylinositol 3-kinase 73:92–93, 129 coexpression with Btk, 77:133–134 lipid metabolism and, 77:9 p85 subunit, 77:132 pYxxM binding, 77:5

SUBJECT INDEX

Phosphatidylinositol 4,5-bisphosphate, in raft dynamics, 77:65–66 Phosphatidylserine, 68:64, 70, 76, 80 Phospholipase A2 (PLA2) lipopolysaccharide signaling in macrophages, 78:15 T cell responses against modified bee venom peptides, 78:283 Phospholipase A2 secretory enzymatic properties, 77:167–168 heparanoid binding, 77:168 sPLA2 receptors, 77:182–183 structures, 77:164–167 sPLA2-IB, 77:168–169 sPLA2-IIA anticoagulation, 77:176 antimicrobial activity, 77:175–176 degranulation, 77:176–177 eicosanoid biosynthesis, 77:170–175 expression, 77:169–170 pathology, 77:177–178 sPLA2-III, 77:181 sPLA2-V, expression and functions, 77:178–180 sPLA2-X, expression and functions, 77:181 Phospholipase C (PLC), lipopolysaccharide signaling in macrophages, 78:13 Phospholipase C-g1 pathway, T cell signaling, 77:8 Phospholipase C-g2 activation in B cells, 77:138

151

Syk connected with, 77:144–146 Phospholipase C-g, 73:92–93 Phospholipase C-g1, 68:93–95 Phospholipase D (PLD), lipopolysaccharide signaling in macrophages, 78:15 Phospholipase D, 72:47 Phospholipids, 70:523 Phosphoprotein associated with glycolipid-enriched membranes, see PAG Phosphorylation, 68:32, 35, 86, 93, 109–110; 69:191–192, 211, 215–216, 225 CD45, 66:53–54 Src family kinases, 66:40–41 Phosphorylcholine, immune response to, 80:210 Phosphotyrosine binding domain, 77:4–5 Phosphotyrosine phophatases, SH2-containing, 72:24 Phygocytic cells, 70:104–106 Phylogeny, Camelidae VHH genes, 79:270–272 Phytohemagglutinin, 73:425 Phytohemaglutinin, 68:7, 10, 17, 31, 35 PI3K, see Phosphatidylinositol 3-kinase PIAS, see Protein inhibitors of activated STATs Picornaviruses, 70:349–350 antibody protection against, 77:237–238 neutralization, 77:202–205 molecular model, 77:219–220 pIgR, see Receptors

152

SUBJECT INDEX

Pigs Gal-knockout technology, 79:168 non-Gal determinants, 79:141–142 uterine natural killer cells, 79:310 as xenograft donor, 79:131–133, 180–181 pIgs, see Immunoglobulins, polymeric PIP, see Proximal interphalangeal PIP2, see Phosphatidylinositol 4,5-bisphosphate Pituitary adenylate cyclaseactivating polypeptide, 79:81 Pituitary cells, 68:173 PKA, see Protein kinase A PKB, see Protein kinase B PKC, see Protein kinase C PLA2, see Phospholipase A2 PLA2, see Phospholipase A2 Placenta, uterine natural killer cell role, 79:319–320 Placental alkaline phosphatase, GPI-linked, 77:18, 48, 54 Placodes, akin to neural crest, 77:300 Plasma cell neoplasms, 81:109 Plasma cells, 68:17; see also Lymphoid cells Plasma membrane, 68:54–55, 64, 65, 164; 69:339 raft domain structure in, 77:51–53 structural models, 77:45 Plasma membrane cholesterol in mycobacterial infection, 81:77–84

Plasma membrane, fluidization, 80:247 Plasmacytoma (PCT), 81:98, 101, 109, 112, 113 gene transcripts distinguishing, 81:113 Plasmids encoding, 82:70 Fas/EGFP, 82:74 Plasmids, DNA delivery, 75:58–59 Plasminogen activator inhibition, 73:84 Plasminogen, activation, 66:241 Plasmodium yoelii, 71:108 Plasmodium spp., 70:184 Plasticity, cytokine memory, 80:145–149 Platelet basic protein (PBP), 81:4 Platelet factor-4 (PF-4), 81:4 Platelet-activating factor (PAF), 82:19 Platelet-activating factor, acetylhydroxylases, 77:163 Platelet-derived growth factor (PDGF), 82:3 Platelet-derived growth factor (PGDF), IL-6 production and, 66:128 Platelet-derived growth factor, 68:8 Platelets, 68:14, 169, 172; 82:341, 344 Platelets, activation, CD40/ CD154-mediated regulation, 76:77 Platelets, contact activation system, 66:244 Platelets, in xenotransplantation, 79:152, 155, 169–171

SUBJECT INDEX

Platforms, signaling, rafts serving as, 77:20–21 PLC, see Phospholipase C PLC-g, see Phospholipase C-g PLC-g1 adaptor protein role, 79:118–120 LAT coupling, 79:101–103 tyrosine kinase interaction, 79:103–104 PLD, see Phospholipase D Pleckstrin homology domain Btk, 77:127, 132–134 PTK, 77:124 Pleckstrin homology domains, 73:101–102 Plexin-B1, 81:181, 182 Plexins, 81:176–177 PLGA, see Poly-d,l-lactic-coglycolic acid PMA, see Phorbol myristic acetate PMN, see Cells, polymorphonuclear PMSF, see Phenylmethylsulfonyl fluoride Pneumocystis carinii, 68:282, 351; 81:54 Pneumonia, 82:50 Pocket specificity profiles, quantitative matrices and, 66:74–76 pol e, in hypermutation process, 80:192 pol m, homology with Tdt, 80:194 Polarized cells apical surface, 70:399–400 basolateral surface, 70:399 characterization, 70:398–399 polymeric immunoglobulin receptor, 70:400–402

153

Polio virus, 70:349–350 Poliovirus, neutralization, 77:202–205 Poly-d,l-lactic-coglycolic acid (PLGA), 82:267 Polychondritis, 68:352 Polyethyleneglycol (PEG), 82:130 Polymerase chain reaction (PCR), 82:139, 308 Polymeric immunoglobulin receptor, 70:400–402 Polymerization, actin cytoskeleton, regulation, 77:24–25 Polymorphisms, 82:255 Polymorphisms, in interleukin-12 gene promoter, 79:71 Polyomavirus enhancer-binding protein, 81:2 (PEBP2), 205 Polypeptides, 82:179 Polysomes, 68:4, 21, 33, 35 Polyunsaturated fatty acids, effect on protein palmitoylation, 77:72–73 Porcine endogenous retroviruses, in xenotransplantation, 79:187–188 Post-acidic site, 20S proteasome, 80:8 Potassium ions, in apoptosis, 68:65, 95, 175 Poxviruses, 70:344–346 PPARg, see Peroxisome proliferator-activated receptor g PpL, see Protein, peptostreptococcal L Pre-B-cell receptor, 69:131–134 Pre-B-cells k, and l, 69:146

154

SUBJECT INDEX

Pre-B-cells (continued) and murine leukemia virus, 69:143–144 receptors, and allelic exclusion, 69:131–134 transition from pro-B cell, 69:134 Pre-eclampsia, 81:230–232 Pre-T cell receptors allelic exclusion, 72:127–128 assembly, 72:116–117 CD3 components, 72:114–115 cell survival, 72:131–138 function, 72:131 abgd lineage role, 72:124–127 sensor characterization, 72:119, 121–122 downstream effectors, 72:117–119 TCR-b locus role, 72:127–128 Pre-T-cell receptor a, 69:23–25 Pre-T-cell receptor b, 69:33–38 Pre-T-cell receptor and allelic exclusion, 69:38–44 and gene expression, 69:56–57 identification, 69:20–23 signaling pathways, 69:32–35, 51–57 structural features, 69:23–27 and thymocyte development, 69:27–38, 56–57 Precursor cells, 72:337–338 Precursor-B-cell lymphoblastic leukemia/lymphoma, 81:102, 106 Pregnancy, 71:120–122 a-fetoprotein, 79:298 immunobiology, 79:297–298

immunosuppressive factors, 79:298 uterine changes, 79:298–299 uterine natural killer cells colony stimulating factor-1 production, 79:311–312 cytolytic activity, 79:315–318 epidermal growth factor production, 79:312 interferon-g production, 79:313–314 interleukin-1 production, 79:312–313 leukemia inhibitory factor production, 79:313 uteroplacental unit, 79:318–321 Pregnancy, failures, 70:519 Pregnancy, HLA-G in, 81:225–232 Prekallikrein, 66:225 activation, 66:249 function, 66:236 properties, 66:226, 229 structure, 66:229 Prekallikreins, 82:340–343, 342 Prelymphocytes, 69:131–134 Prelymphoma cells characterization, 73:515 emergence, 73:520 persistence, 73:524 TNF-a against, 73:527 Prenancies, 82:260–261 Prenylation, of Ras GTPase proteins, 68:145–189 Prenyltransferase, 68:152–157, 175–178 Primates, as xenograft recipients, 79:180–181 Prion bioassay by incubation time method, 81:128

SUBJECT INDEX

Prion biology basic facts, 81:123–127 open questions, 81:125 Prion disease diagnosis, 81:130–131 identification of infectious agent, 81:130–131 Prion diseases, 81:124 brain damage in, 81:126–127 Prion doppelganger, 81:153–158 Prion immunization and its reduction to practice, 81:152–153 Prion immunology, future directions, 81:158–159 Prion infectivity, 81:128 in lymph node, 81:141–143 in spleen, 81:141–143 Prion neuroinvasion, 81:143–148 Prion pathogenesis and lymphocytes, 81:134–137 Prion protein, antibodies against, 81:151 Prion replication, 81:125–126 in lymphoid organs, 81:140 Prion susceptibility and Peyer’s patches, 81:130 Prion transfer to CNS, 81:143–144 Prions adaptive immunity and pre-exposure prophylaxis against, 81:150 and immune system, 81:123–171 in lymphoid organs, 81:137–141 lymphotropism of, 81:141–143 macrophages participation in clearance of, 81:148 orally administered, 81:129 peripheral entry sites, 81:128–134

155

spread within central nervous system (CNS), 81:145–148 susceptibility of various strains of immuno-deficient mice, 81:135 terminology, 81:159–160 transepithelial enteric passage of, 81:131–133 transepithelial transport, 81:132 uptake through skin, 81:133–134 Pristane, 73:214 Prl, see Protein(s) Prnp deficient mice, 81:154–155 Prnp gene, 81:125 Procoagulant enzymes, 68:64 Producing cells, 70:285–286 Profilin, as ATP nucleotide exchange factor, 77:25–26 Progenitor cells extrathymic, 69:9–11 intrathymic, 69:11–14 thymus-colonizing, 69:6–8 Progenitor cells, bone marrow: aging and, 80:248–249 Programmed cell death, see Apoptosis; see also Apoptosis genetics, 70:247–250 neuroblast: ventricular zone, 77:309–313 nonhomologous end-joining and, 77:313–316 pathway, 70:251 significance, 70:245–247 Proinflammatory cytokines, 81:191 Proinflammatory status, Alzheimer’s disease and, 80:267 Proliferation, memory/effector T cells, 80:256–257 Prolines, 82:251, 252

156

SUBJECT INDEX

Promoters cis-acting sequences, 69:124, 319 cytokines and viral, 69:366–371 function, 69:124 TEA, 69:334–336, 339, 340 Promoters, interleukin-12 p40 gene, 79:67–68, 71 Prostaglandin D2, 82:27 Prostaglandin E2, lipopolysaccharide tolerance role, 78:27–28 Prostaglandin2, 73:424–425 Prostaglandins, 68:13, 345 Protease resistance, 81:131 Protease sensitive PrPSc, 81:130 Protease substrates, CC chemokines as, 81:20–23 Proteases in immune response, 81:1–44 Proteases, 68:54, 61–64, 199–200; see also Caspases; Proteasomes; see C1; C1q; C2; Enzymes, proteolytic Proteases, endosomal, 73:23 Proteasome function, 73:6 inhibition, 73:20–21 Proteasome activating nucleotidase complex, 80:11 Proteasomes, 68:61–62, 199–205; see also Immunoproteasomes cleavage of antigens, 80:39–40 degradation of proteins, products of, 80:15–17 generation of presented peptide: frequency, 80:38–39 hybrid, 80:12–13 IFN-g-induced changes, 80:28–30

oligopeptides produced by, fate of, 80:17–19 role in antigen presentation, 80:26–28 protein degradation in vivo, 80:13–15 substrate cleavage sites, 80:36–38 20S, see 20S proteasome 26S, see 26S proteasome Protection cancer immunotherapy strategies, natural protection, 75:238–240 intracellular bacteria infections antibodies role, 75:6–7 antigen characteristics conserved versus specific proteins, 75:28–30 processing pathways, 75:14–15 recombinant carrier expression, 75:30–31 vaccine physicochemical properties, 75:27–28 quantitative correlates, 75:25–26 Protection, antiviral antibody responses, 79:5–6 Protein antigens, for active immunization models, 77:266–267 Protein assembly, 70:385–387 Protein binding, 68:22–23 Protein C, 70:535–536 Protein, cytokine-inducible SH2 (CIS), 82:4 Protein degradation blocking, 80:50 in cytoplasm, 80:19–20

SUBJECT INDEX

in endoplasmic reticulum, 80:20–21 by proteasomes, products of, 80:15–17 proteolytic pathway, 80:2–3 role of proteasomes in vivo, 80:13–15 20S proteasome, 80:6–9 ubiquitin conjugation and, 80:3–6 Protein folding, major histocompatibility complex class II complex, 75:172 Protein inhibitors of activated STATs (PIAS), 82:4 Protein kinase A (PKA), lipopolysaccharide signaling in macrophages, 78:16 Protein kinase B, 68:111–113 Protein kinase C F-actin association, 77:31 isozymes in basophils, 77:108–109 PKCu, 77:8, 11, 13, 33, 35 Protein kinase C (PKC), lipopolysaccharide signaling in macrophages, 78:13–14 Protein kinase C, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:339–341 Protein kinase D, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:341–342 Protein modules complement control, 69:258, 272, 274–275, 280–281, 285–287

157

in complement enzymes, 69:255, 257–261 CUB, 69:259, 279–280, 283–284, 286 Cys-rich, 69:260–261 epidermal growth factor-like, 69:259, 280, 283, 286 factor I/membrane attack, 69:260 LDL receptor class A, 69:261 von Willebrand factor type A, 69:260, 272, 276 Protein, peptostreptococcal L (PpL), 82:193–194 Protein, staphylococcus A (SpA), 82:186–190 Protein, streptococcal G (SpG), 82:190–192 Protein, streptococcal H (SpH), 82:192 Protein synthesis inhibitors, 73:21–22 Protein synthesis, 68:15, 16, 19, 36 Protein turnover, balancing act, 80:1–2 Protein tyrosine kinase activation, 77:7 Btk/Tec family, 77:123–124 recruitment, 77:4–8 Src family, link with Btk, 77:129–130 Protein tyrosine kinases, 68:93, 97–98; 69:183; 71:172 BCR transduction biochemical pathways, 73:112–113, 115 CD40 regulation, 73:127–128 relation, 73:91–92 death capase cascade, 73:133 Src family, 69:192–196, 215

158

SUBJECT INDEX

Protein tyrosine kinases (continued) Syk family, 69:196–197, 198–199, 200, 201–202, 208–209 and ZAP-70, 69:197–198, 200–201, 202, 208–209 Protein tyrosine kinases, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:328–332 Protein tyrosine phosphatase (PTP), 81:180 Protein tyrosine phosphatase, 68:93, 98–101 Protein tyrosine phosphatases, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:332–335 Protein-only hypothesis, 81:124–125, 159 Protein(s), 82:58, see also Signal transducers and activators of transcription ATF/CREB, 82:31–32 bacterial immunoglobulin-binding, 82:186–190, 188 Cc2-Cc3, 82:197–198 clusterin, 82:178 corresponding, 82:2–3 cytokine signaling, 82:4 fibronectin (Fn), 82:178 Fos family of, 82:31–32 Fv, 82:181–182 inflammatory, 82:21–22 Jun family of, 82:31–32 prolactin (Prl), 82:181 rag, 82:295 synthesis, 82:2 T cell, 82:182–183

as tumor vaccines, 82:61–64 viral immunoglobulin-binding, 82:195–197 Proteins adaptor, see Adaptor proteins AIF, 68:85, 87, 88 in apoptosis, 68:54, 74, 76, 85, 124 Auf-1, 68:33–34 AUUUA RNA-binding, 68:30–35 B cell linker, see B cell linker protein BLNK associating protein, 79:116–117 catalase-specific, RNA-binding, 68:25 complement regulatory protein, 79:166–167 cytokine and protooncogene mRNA-binding, 68:35 digestion of, by caspases, 68:60 a-fetoprotein, 79:298 heat shock, 68:197, 205 b-1,3-glucan-binding protein, 79:230–232 gram-negative binding protein, 79:230–232 interactions with mRNA, 68:22–23, 29–30 mitogen-actived protein kinase, 79:70–71 myelin basic, 68:389–391 non-AUUUA RNA-binding, 68:35–36 of permeability transition pore, 68:80 peptidoglycan recognition proteins, 79:229–230 prenylation of Ras GTPase

SUBJECT INDEX

C-terminal methylation of, 68:157–158, 171–172 heterotrimeric G, 68:164–165 Rab, 68:148, 158–162, 165–166, 172–174 Rac, 68:147, 169–170 Rap, 68:169–170 Ras, 68:146, 148–149, 163–164, 166–168 Rep, 68:161–162 Rho, 68:147, 171, 174, 177–178 Rho/Rac, 68:148–150, 168–169 Ras, 79:101–103 SH2-domain-containing leukocyte protein, see SH2domain-containing leukocyte protein signaling proteins, 79:110–113 SLP-76 coupling to downstream signaling, 79:113–116 thioester proteins, 79:236–237 Proteins, heat shock (HSPs), 82:76–77, 231 Proteins, high mobility group, 69:314 Proteins, lipidated, DRM-associated, 77:49–51 Proteins, SOCS -1, 82:7 -3, 82:7, 14 Proteoglycan (PG), 82:226 Proteolipid protein (PLP), multiple sclerosis and, 66:88, 90 Proteolysis 68:163 and DM-mediated peptide loading, 80:91–92 Ii, 80:73

159

cathepsin role, 80:87–88 Proteolytic enzymes, see Enzymes, proteolytic Proteolytic pathway alternate, 80:19–20 protein degradation, 80:2–3 Proteomics, intracellular bacteria immunization analysis, genome to antigen transition, 75:60–61 Prothrombin, 70:533–535 Protonophores, 68:80 Protooncogenes, 68:5–8, 19, 22, 27–29, 36; see also specific protooncogenes Proviral insertional mutagenesis, 81:109–110 Proximal interphalangeal (PIP), 82:217 Prp accumulations, 81:137 toxic form, 81:127 PrPC, 81:125–127, 130, 131, 134, 136, 140, 143, 147, 148, 150, 152–154, 156, 159 Sc PrP , 81:125–127, 130, 131, 134, 140, 150, 154, 160 PRR, see Pattern-recognition receptor PRRs, see Pattern recognition receptors PSA, see Antigens, prostate-specific Pseudogene, sPLA2-IIC as, 77:180 Pseudogout, inflammation in, 66:260 Psoriasis, 68:238, 357, 361; 73:428 PSTPIP, SH3 domain, 77:131 Psychodopygus spp., Leishmania host role, 74:277–281

160

SUBJECT INDEX

pTa chain, 69:23–25 PTK, see Protein tyrosine kinase; see Protein tyrosine kinases PU.1 gene, 69:80 PU.1, V(D)J recombination regulation, 78:203–204 Public health, 82:49 PUFAs, see Polyunsaturated fatty acids Pulmonary and activation-regulated chemokine (PARC), 81:22 PUM, see Mucin, polymorphic urinary Puromycin, aminopeptidase sensitive to, 80:45, 47 PVXCP, see Virus, potato X Pyknosis, 68:54 Pyogenic infection, 69:295 Pyrrolidine dithiocarbamate (PDTC), 82:23–24

Q Quantitative matrices algorithms based on, 66:81–82 peptide binding motifs by, 66:72–76

R RA, see Arthritis, rheumatoid Rab, 72:52–53 Rab proteins, 68:148, 158–162, 165–166, 172–174 Rabies virus, 69:369 Rabies virus, neutralization, 77:211 Rabies virus, outside immune system, 79:21–22

RAC protein, lymphocyte signaling role, actin polymerization regulation, 75:94–100 Rac proteins, 68:169–170 Rac-1, 72:23 Rac2, expression in Th1 cells, 80:135 Rad-1 factor, 73:521 Radiotherapy, 68:53 Raf-1 kinase characterization, 72:16 function, 72:22 RAG genes and GATA, 69:78–79 and HC allelic exclusion, 69:134–135 and LC gene rearrangement, 69:133, 152 and recombinational accessibility, 69:313–315, 316, 317 RAG proteins, see V(D)J recombination RAG-1, 72:118 RAG-2, 72:182 RAG1/2 regulation, 73:89–90 RAG-2, knockout mice, 77:150 Raji Burkitt’s lymphoma, 73:122 RANK, 81:347–348 RANK-L/TRANCE/ODF, 72:271–272 RANTES, 77:96; 81:4, 9, 11, 22, 29 Rap proteins, 68:169–170 Rap1, 72:5 Rapamycin, 68:9, 12, 333 Ras CD28 signaling, 72:49–51 cytokine receptor signaling, 72:25 function, 72:1–2 IRR activation, 72:3–5

SUBJECT INDEX

Cb1 role, 72:12–14 Grb2/Sos role, 72:8–11 PTK role, 72:5–8 Shc role, 72:8–11 SLP-76 role, 72:12–14 IRR signaling effectors, 72:15–18 negative factors, 72:23–25 transcription factors, 72:18–23 lymphocyte development, 72:64–66 regulation, 72:1–2 T cell anergy, 72:53–59 Ras protein, LAT coupling, 79:101–103 Ras proteins activation by GTPase cycle, 68:147–149 in apoptosis, 68:168 C-terminal events and, 68:163–164 cancer, and mutation of, 68:177 function in immune cells, 68:146, 164 growth inhibition and, 68:167 prenylation of, 68:150–152 Rho-Rac pathway, link to, 68:148–149 signaling pathway of, 68:146, 166–168 Ras superfamily, 68:145–157 Ras-GAP, 68:94 Ras/MAPK pathway, T cell signaling, 77:8 Rat, xenotransplantation from guinea pig, 79:156 from hamster, 79:156

161

wild-type rat, 79:157 Rats, 69:213, 421, 423 Rauscher virus, 68:194–195 Reactive oxygen intermediates (ROI), 82:22–24 Reactive oxygen species, in apoptosis, 68:64–65, 70–71, 77, 123 Receptor editing, 69:150–152, 155–156 Receptor specificity, 69:113 Receptor usage during mycobacterial entry into phagocytes, 81:80 Receptors Fc cell, 82:155–172, 221 high-affinity FceRI, 82:119–120 low-affinity FceRII, 82:119–120 NKG2A, 82:56–57 polymeric immunoglobulin (pIgR), 82:172–173 surface, 82:17–18 T cell, 82:51–52 Receptors, B cell (BCRs), 82:295 Receptors, TNF (TNFR), 82:300–301 Receptors, toll-like (TLR), 82:232–233 Recombinase activating gene, 70:1, 421–424 Recombination signal sequences, 69:143, 152–157, 312–313, 316–317 Recombination, see V(D)J recombination Recombinational accessibility biological consequences, 69:339–342

162

SUBJECT INDEX

Recombinational accessibility (continued) cis-acting sequences, 69:318–319, 321–337 coordinated interaction, 69:340 definition, 69:316 molecular basis, 69:319–321 nuclear DNA-binding factors, 69:339, 341 and plasma membrane, 69:339 and the 12/23-bp rule, 69:312 trans-regulatory factors, 69:338–339, 340 Reconstitution, thymus, aging and, 80:268–271 Recurrent spontaneous abortion (RSA), 81:229 Redox status, apoptosis and, 68:54, 64–65, 70–71, 88 Regulatory factor X (RFX) complex, 81:208 Regulatory tyrosine residues, Y551 and Y223, 77:130–132 Reiter’s syndrome, 68:238–239 Rel homology domains, 82:17 Rel-B, 72:280 Relish pathway, 79:244–247 Relish, Toll signaling, 78:3 Reoviruses antibody protection against, 77:238–239 neurally spreading, protection against, 77:243 Rep proteins, 68:161–162 Resistance, see Tolerance Respiratory burst, 68:169 Respiratory chain inhibitors, 68:80

Respiratory syncytial virus association with asthma, 77:285–286 effect of neutralizing antibody, 77:242 Respiratory syncytial virus, 73:381 Respiratory tracts, 82:109–110 Reth motif, 69:188–189 Retina, 68:161, 164 Retrovirus, 69:359–360 Retroviruses, 72:298–300 Retroviruses, antibody protection in vivo, 77:229–231 Reverse genetic approaches, 81:306–310 RF, see Rheumatoid factors Rhabdomyosarcoma cells, 68:105 Rhabdoviruses, antibody protection against, 77:231–232 Rheumatoid arthritis adjuvant, 73:213–214 animal studies on, 68:339, 340, 369–371 anti-CD4 therapy, 68:349–353 anti-CD5 therapy, 68:356–358 anti-CD7 therapy and, 68:358–359 anti-CD52 therapy and, 68:362–364 anti-IL6 therapy and, 68:344–345 anti-TNF-a therapy, 68:338–341 antigen-induced, 73:214 apoptosis induction therapy, 68:337 CD30 and, 68:115–116 CD51C trials in, 68:356–358 collagen-induced animal model, 73:211–213 human model, 73:230 cytokine production, 73:430–432

SUBJECT INDEX

cytokines and, 68:345–347 erosive versus non-erosive, 68:327 gene therapy, 68:337 HLA Class II peptide binding and, 66:85, 87 and ICAM-1, 68:369–371 interferon-g therapy, 68:346 interleukin-1 blockade and, 68:339, 341, 344 interleukin-2 targeting therapy, 68:359–360 juvenile, and oral collagen, 68:335 kallikrein in, 66:260 monoclonal antibody therapy, 68:336, 347–353 pristane-induced, 73:214 prognostic indicator for, 68:326–327 role of peptide transporter in, 68:238–239 susceptibility genotype, 68:315–332 synovial fluids, 73:383 T cell depletion, 73:314–315 Rheumatoid arthritis, 72:291 Rheumatoid arthritis, T cell responses against modified peptides in collagen-induced arthritis, 78:282 Rheumatoid factors (RF), 82:179–181, 218, 237–238 Rhinitis, 73:231 Rho CD28 signaling, 72:51–52 cell adhesion, 72:41–43 chemoattractant responses, 72:44–46

163

cytoskeleton reorganization, 72:27–34 hematopoietic cells regulation, 72:38–39 Vav integration, 72:34–35 integrin adhesion, 72:41–43 IRR signaling activation, 72:39–41 characterization, 72:25–26 p38 pathway, 72:68 SEK1 pathway, 72:68 selections, 72:43–44 Rho family GTPases, lymphocyte signaling, 75:98–100 actin polymerization, 75:99–100, 104 description, 75:98–99 Rho family members, differential effects on cell morphology, 77:9–10 RHO family, 72:34–35 Rho proteins, 68:147, 171, 174, 177–178 Rho/Rac proteins, 68:148–150, 160–161, 168–169 Rho, lipopolysaccharide signaling in macrophages, 78:17 Ribonucleases, 68:20, 31 Ribonucleotide reductase, 68:24–25, 35, 36 Ribosomes, 68:20, 24 Ricin B chain, 73:22 RIP proteins, 71:170–172 Risk–benefit ratio, in xenotransplantation, 79:189 RMA cells, 73:34 RML paradigm, 81:136 RNA-mediated gene silencing, 81:125

164

SUBJECT INDEX

RNAi, 81:310 Rodents, granulated metrial gland cells cell differentiation, 79:306–307 morphology and phenotypes, 79:302–305 origin, 79:300–302 overview, 79:299–300 ROG, repressor of GATA, 80:127 ROI, see Reactive oxygen intermediates Rossman fold, 69:260 Rosso, A., 82:7–9 Rotavirus, 69:359–360, 386; see also Adult diarrhea rotavirus Route of immunization, in active immunization models, 77:267, 270 RS/kde, 69:152–157 RS/kde element, B cell receptor editing, 74:93–94 RSS, see Recombination signal sequences RSV, see Respiratory syncytial virus RT-PCR analysis, 81:207, 285 Ruffini, P. A., 82:72 12/23 rule, B cell receptor editing, recombination signals, 74:90–91

S 11S REG, see PA28 19S complex, in formation of 26S proteasome, 80:10 20S proteasome catalytic subunits, 80:7–8 cleavages by, 80:33–35

complex with PA28, 80:12–13 immune subunits, 80:29 ring configuration, 80:6 26S proteasome ATP-dependent degradation, 80:6 cleavages by, 80:35–36 degradation of polyubiquitinated substrates, 80:9–10 formation, 80:10 S particles, 73:38–41 S-nitroso-N-acetypencillamine (SNAP), 82:25 Saccharomyces cerevisiae, 81:54, 266 Salmonella, 81:67 Salmonella dublin, 70:179–180 Salmonella spp., 71:107–108 Salmonella typhimurium, 81:65, 66, 79 Salmonellosis antigen carriers, 75:53–55 characteristics, 75:8–10 live mutant vaccines, 75:42–46 defined mutations, 75:43–46 undefined mutations, 75:42–43 SAPKS, see Stress-activated protein kinases SC, see Secretory component Scatter factor, see Hepatocyte growth factor Scavenger receptor, lipopolysaccharide binding, 78:12 Scavenger receptors, 81:56–57 Scavenger receptors, in insect immune response, 79:233–234 Scd1, 72:36–37 SCF, see Stem cell factor

SUBJECT INDEX

SCF, polyubiquitination dependent on, 80:4 Schistosoma mansoni, 70:186–187 Schistosoma mansoni, intratracheal delivery, 77:265–266 Schistosoma spp., 71:277 Schizosaccharomyces pombe, 68:56 SCID, see Severe combined immune deficiency; see Severe combined immunodeficient Sclerosis, systemic, 73:231 Scrapie, 81:123 SCW, see Arthritis; see Streptococcal cell wall SDF-1, 72:227–228; 81:6, 11, 19, 29–31 SDF-1, hematopoietic development role within lymphoid organs, 78:121–122 SDS-PAGE, see Sodium dodecyl sulfate-polyacrylamide gel electrophoresis SDS, see Sodium dodecyl sulfate Secondary lymphoid organs, 81:285–289 Secondary lymphoid tissue chemokine (SLC), 81:5 Secondary lymphoid tissues in zebrafish, 81:287–289 Secretory component (SC), 82:172–173 SEK1, 72:68 Selectins, 68:285 E-Selection, 72:225–227 L-Selection, 72:224–225, 232–233 P-Selection, 72:225–227 Selection ligands, T cell recruitment and, 80:150

165

Self–nonself discrimination, immune response in elderly, 80:266 Sema-K1, 81:192 Sema3a/H-SemaIII in immune cell migration, 81:192–193 Sema4A receptor, Tim-2 as, 81:189 Sema4A, 81:187–191, 194 expression, 81:187–188 in vitro activities, 81:189 in vivo activities, 81:189 structure, 81:187–188 Sema4D, 81:177–187 Sema7A, 81:192 Semaphorin family activities, 81:177 history, 81:173–174 in immune regulation, 81:173–198 members of, 81:174 overview, 81:173–177 structure, 81:174–176 see also CD100 Semaphorin receptors, 81:176–177 Semaphorin–receptor interactions, 81:175 Semaphorins cellular counterparts, 81:191–192 class I and II, 81:176 class III, 81:192–193 class III–VII, 81:176 class IV, 81:176–191 class V and VI, 81:176 classes, 81:176 derivation of term, 81:194 virus-encoded, 81:191–192 SemaVA, 81:191–192 SemaVB, 81:191–192

166

SUBJECT INDEX

Sendai virus, 69:387 processing pathway, 73:36–38 TCD8þ activation, 73:49 Sendai virus epitopes, 68:194, 196 Senescence, 73:180 cellular, impaired function, 80:247 immune system consequences of, 80:263–268, 272–273 controversies about, 80:271 Sensitization, allergic allergic immune response in, 82:111–114, 112 concept of, 82:106–111, 107 to cross-reactive allergens, 82:133 Sensitization, nickel, 73:222 Sensitized virus, neutralization with anti-antibody, 77:207 Separate lineage model, 71:17–18, 59–60 Sepsis 82:352–353 anticytokine therapies, 66:151 chemokines and, 66:104 interleukin-8, 66:104, 135–141 MCP-1, 66:141–142 cytokines and, 66:101–102, 103–104, 104 granulocyte colony-stimulating factor, 66:149–150 granulocyte–macrophage colony-stimulating factor, 66:150 IFNg and, 66:145–146 interleukin-2, 66:104, 150–151 interleukin-4, 66:144–145 interleukin-10, 66:142–145 interleukin-12, 66:146–147

leukemia inhibitory factor, 66:147–148 macrophage migration inhibition factor, 66:147–148 measurement, 66:104–105 TNF and interleukin-1, 66:104, 117–127, 150 defined, 66:101 IL-1b production, 73:432–434 IL-8 production, 73:432–434 immunointervention, 66:150–151 models for, 66:102–103, 117–121 pathogenesis, 66:150–151 chemokines, 66:135–142 cytokines, 66:104, 105–135, 142–151 Sepsis, ABCD chemokine role, 78:148 Septic shock, 68:12 Septic shock, contact cascade in, 66:235 Sequence-specific length polymorphisms (SSLP), 81:255 Sequential rearrangement model, 71:16–17 SEREX (serological identification of antigens by recombinant expression cloning), 82:58 Serine kinase receptor, transforming growth factor-b signaling, 75:116–119 TbR-I structure, 75:118–119 type I and II receptor characteristics, 75:116–117 type I subgroups, 75:117–118 Serine protease, 69:249–307 Serine proteases, 68:61, 62–64

SUBJECT INDEX

Serine threonine/PKB, 68:111–113 Serine-threonine kinases, 68:6, 93, 101, 121 Serine-threonine protein kinases, 68:120 Serine-threonine tyrosine kinases, 68:6, 93, 120–121, 122 Serine/threonine kinases, 70:38–39 Serine/threonine kinases, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:339–342 protein kinase C, 76:339–341 protein kinase D, 76:341–342 Serines, 82:251 Serpin, 69:289–291 Serpine mechanisms, 82:333, 334 non, 82:333–335, 335 Serpins, 73:83–84 Serum response element, 72:22 Serum response factor, 72:22 Serum response factor, activation, 77:32 Severe combined immune deficiency, 73:527 Severe combined immunodeficiency IL-2 defective, 70:59–60 IL-2 factors, 70:48–49 XSCID, 70:49–50 Severe combined immunodeficiency disease, 69:22–23, 32, 37, 197 Severe combined immunodeficient (SCID), 82:219, 299 SFV, see Virus, Semliki Forest SH2, see Src homology 2 domain SH2-domain-containing leukocyte protein, SLP-76

167

analog BLNK, 79:99–100 analog CLNK, 79:100 coupling to downstream signaling, 79:113–116 deficient mouse, 79:105–108 deficient T cells, 79:103–104 Gads association, 79:98–99 ITAM-coupled signaling, 79:98 in PLC-g1 activation, 79:118–120 SH3BP5, phosphorylation by Btk, 77:136 Shigella flexneri, 81:66 Shigella, 73:271; 81:67 Shigellosis, 73:437 SHIP, see Inositol 5-polyphosphate phosphatase; see Inositol polyphosphate 50 -phosphatase Grb2 interaction, 73:97–98 PtdIns regulation, 73:95 SHM, see Somatic hypermutations SHP-1, 69:221–223 B cell regulation PTK pathway, 73:112–113, 115 PTPase pathway, 73:112–113, 115 role, 73:110–112 CD22 binding, 73:107–108 SHP-1, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:334–335 SHP-2 B cell regulation CD22 binding, 73:107–108 FcgRIIB, 73:120–121 SHP-2, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:335

168

SUBJECT INDEX

Shwartzman reaction, 73:457 Sialoadhesin, 68:275–276 Sialomucins, 72:226–227 Sialylation, 82:252 ‘Sigma Chemical Co., 82:349 Signal end, 69:310–311, 314–315 Signal joint, 69:315, 342 Signal pathways and ITAMs, 69:202–207, 216–227 and Nef protein, 69:214–215 and pre-TCR complex, 69:32–35 and SHP-1, 69:221–223, 225–226 and SHP-2, 69:225–226 and thymocyte development, 69:70–72 Signal recognition particle, 70:369 Signal transducers and activators of transcription (STATs) -1, 82:3–5, 7–13 -2, 82:3–5 -3, 82:3–11 -4, 82:3–5 -5, 82:3–5, 8–11, 14 -6, 82:3–5 -7, 82:3–5 family members, 82:10–11, 15–17, 16 G-CSF and, 82:4–7 genes, 82:3 GM-CSF and, 82:7–11 IFN-c and, 82:11–14 IL-10 and, 82:13–14 JAK cascades, 82:4, 10, 16 other agents and, 82:14–17 Signal transduction 71:169–170 actin dynamics in, 77:30–34 B cell immune response regulation by

CD40-CD154-signaling, 76:86–145 activators and inhibitors, 76:80 AP-1 activation, 76:79, 87–92 CRE activation, 76:87, 92 functional outcomes, 76:126–136 adhesion, 76:129–130 antigen-presenting cell function, 76:130–131 apoptosis regulation, 76:134–136 cell survival and proliferation, 76:127–128 cytokine secretion, 76:131 IgH class switching, 76:133–134 immunoglobulin production regulation 76:131–134 NF-AT activation, 76:79, 88–92 NF-kb activation, 76:87, 92–93, 100–103, 116–121 overview, 76:61, 69 signaling cascades, 76:116–126 cAMP-mediated-signaling pathways, 76:144–145 ERK activation, 76:89–90, 120, 125–126 JAK–STAT pathways, 76:138–140 JNK activation, 76:90–91, 98–100, 120–124 NF-kb activation, 76:116–121 p38 activation, 76:92, 98, 100, 124–125 reverse-signaling through CD154, 76:145

SUBJECT INDEX

src activation, 76:140–143 tec family kinase activation, 76:140–143 ZAP-70 activation, 76:140–143 T cell collaboration, 76:69 TRAF adapter molecule discovery, 76:93–115 transcription factor activation, 76:87–93 B cells overview, 73:79–80 P13K, 73:92–93 PLC-g, 73:92–93 pleckstrin homology domains, 73:101–102 PTKs, 73:91–92 Ras pathway, 73:95–97 Vav guanine-nucleotide exchange factor, 73:100 BCR CD19, 73:118–119 CD22 regulation, 73:115 CD22-deficient mice in vivo, 73:108–109 description, 73:107–108 Lyn-deficient mice in vivo, 73:109–110 MAP kinases, 73:115–119 PTK pathway in vivo, 73:112–113, 115 SHP-1-deficient mice in vivo, 73:110–112 CD40 regulation apoptosis, 73:124–127 MAP kinase role, 73:128–129 overview, 73:122–124 P13K pathway, 73:129 PTK role, 73:127–128

169

TRNR factors, 73:129–132 CD95 regulation, 73:132–134 CDw150 regulation, 73:121–122 FcgRIIb, 73:120–121 Grb2-related molecules, 73:97–100 and control of secretion, 77:106–112 CpG-ODN cell response, 73:352–353 cellular uptake, 73:343–344 chloroquine effects, 73:346 CTL response, 73:353–354 lysosomotropic compounds, 73:344–345 stress kinase pathway, 73:345–346 cytokine receptors, 72:25 dendritic cells CD40/CD40L, 72:269–271 Fas/FasL, 72:272 OX40/OX40l, 72:271 RANK-L/TRANCE/ODF, 72:271–272 RANK/TRANCE-R/ osteoprotein, 72:271–272 TNF/TNF-R, 72:269 FcgRII, 72:154–158 high-affinity immunoglobulin E receptor FceRI, 76:325–344 calcium flux integration, 76:338–339 ITAM role, 76:327–328 lipid–protein interactions, 76:338–339 lipid rafts, 76:343–344 overview, 76:325–327, 344 phosphate transfer

170

SUBJECT INDEX

Signal transduction (continued) Bruton’s tyrosine kinase, 76:331–332 CD45 role, 76:333–334 LYN transfer kinase, 76:328–331 phosphate transfer kinases, 76:328–332 protein tyrosine phosphatases, 76:332–335 SHP-1 role, 76:334–335 SHP-2 role, 76:335 SYK role, 76:328–331 serine–threonine protein kinases, 76:339–342 protein kinase C, 76:339–341 protein kinase D, 76:341–342 signaling molecules LAT adapter protein, 76:335–336 SLP-76 adapter family, 76:336–337 VAV, 76:337–338 integrin, 72:335–337 IRR characterization, 72:2–3 Ras effectors, 72:15–18 Rho effectors, 72:39–41 transcription factors, 72:18–23 lipid rafts in, 77:19–21 T cell, actin cytoskeleton in, 77:33–34 Signal transduction pathways antigen receptor-mediated, 68:93–95 in apoptosis and apoptosis-resistance, 68:122

Bcl-2 and modules of, 68:107–111 Ras role in, 68:146–147, 166–168 resulting in permeability transition, 68:83 surface receptor to death effector, 68:89 Signal transduction, CD45 and, 66:1–56 Signal transduction, chemokine role, 74:144–146 Signal transduction, immune cells in old age, 80:262–263 Signaling calcium, downstream of Btk, 77:137–138 immunoreceptor, 77:54 raft membrane domains in, 77:66–73 IRR, raft perturbation effects, 77:71–73 T cell, see T cell signaling via GPI-anchored proteins and glycolipids, 77:63–65 Signaling cascades, as linear flow charts, 77:1–2 Signaling molecules, raft-associated, 77:55–66 Signaling pathways interleukin-12 receptors, 79:58–59 ITAM receptor, see Immunoreceptor tyrosine-based activation motif-coupled receptor signaling PLC-g1 activation, 79:118–120 proteins, LAT recruitment, 79:110–113

SUBJECT INDEX

SLP-76 antigen receptor coupling, 79:113–116 TEC tyrosine kinases, 79:120–121 g Silencer, 71:39 Silencers, 69:124, 147–148, 319, 333–334, 339 Silkworm, see Bombyx mori Simian immunodeficiency virus, 69:213–215; 73:315–316 SIN, see Virus, Sindbis SIV, see Simian immunodeficiency virus Skeletal muscle, macrophages in, 68:284 Skin lesions, 70:518 Skin, allergic reaction, contact activation, 66:259 Skin, macrophages in, 68:284 SLC/6Ckine, 72:228 SLE, see Systemic lupus erthematosus; see Systemic lupus erythematosus Sloan Kettering Cancer Center, 82:277 SLP-76, see SH2-domaincontaining leukocyte protein, 72:12–14 interaction with Gads, 77:147–148 SH2 containing, 77:7–8 SLP-76 adapter family, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:336–337 SMAC, see Supramolecular activation complex

171

Smad proteins, transforming growth factor-b signaling, 75:115–145 biological function, 75:125–126 cross-talk, 75:137–140 MAP kinase pathways, 75:138–139 nuclear steroid receptor, 75:140 Smad pathways, 75:137 STAT pathways, 75:139–140 cytoplasmic actions, 75:126–128 calmodulin interactions, 75:128 membrane anchoring, 75:126 nuclear transport, 75:127–128 oligomer formation, 75:127–128 expression regulation, 75:126 I-Smads, 75:135–137 expression regulation, 75:137 function, 75:135–136 in vivo functions, 75:142–143 embryogenesis, 75:142 immune function, 75:142–143 tumor development, 75:142–143 models C. elegans, 75:124 Drosophila, 75:124 human cancer, 75:140–143 Xenopus, 75:123–124 mutation biology, 75:141–142 nuclear actions, 75:128–135 AML interactions, 75:131–132 AP-1 complex interactions, 75:131 ATF-2 interactions, 75:131 CBFA interactions, 75:131–132

172

SUBJECT INDEX

Smad proteins, transforming growth factor-b signaling (continued) CBP transcriptional coactivator, 75:134 direct DNA binding, 75:128–129 Evi-1, 75:133 FASTs interactions, 75:130–131 interacting partners, 75:129–134 minor transcription factors, 75:132–133 MSG1, 75:135 p300 transcriptional coactivator, 75:134 PEBP2a interactions, 75:131–132 TGIF transcriptional corepressor, 75:134–135 transcriptional repressors, 75:133 overview, 75:115, 143–145 serine/threonine kinase receptors, 75:116–119 TbR-I structure, 75:118–119 type I and II receptor characteristics, 75:116–117 type I subgroups, 75:117–118 structure, 75:121–123 MH1 domain, 75:122–123 MH2 domain, 75:121–122 proline-rich linker region, 75:123 subclasses, 75:119–121 superfamily characteristics, 75:115–116

Small B-cell lymphoma (SBL), 81:104, 106 Small molecules, in interleukin-12 production, 79:80–81 SNAP, see S-nitroso-N-acetypencillamine SNARE hypothesis, 70:373 vesicle fusion, 70:382–383 SNAREs, 81:62, 68 SOCS-1, expression in activated Th cells, 80:121–122 Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), 82:6 Sodium dodecyl sulfate, 73:48 Soluble defense collagens, 81:53 Somatic diversification theory, 69:116 Somatic hypermutations (SHM), 82:295, 316, see also Hyper-IgM syndromes primary antibody repertoire in, 82:295–296 secondary repertoire in, 82:296–298 Somatostatin, 68:95 Sonication, 82:12 SOS, see Guanine nucleotide exchange factor Sox-4, 69:83 Sox-4, V(D)J recombination regulation, 78:208–209 Sp1, lipopolysaccharide signaling in macrophages, 78:20 SpA, see Protein, staphylococcus A Spatzel, Toll interaction, 78:2 Specific pathogen-free (SPF), 81:101

SUBJECT INDEX

Specificity, receptor, 69:113 SpH, see Protein, streptococcal H Sphingolipids amide and hydroxyl groups, 77:46 lateral assembly, 77:45 Sphingomyelin, 68:120–122, 168 Sphingomyelin, interaction with cholesterol, 77:47 Spleen 68:272, 275–276; 73:200–201 as major secondary lymphoid organ in teleosts, 81:285–287 prion infectivity in, 81:141–143 sympathetic innervation of, 81:144 in zebrafish, 81:287 Spleen, chemokine and receptor expression, 78:77–80 Splenic marginal zone lymphoma, 81:106–107 Splenocytes, 68:56, 239, 262–266, 273 Splenomegaly, 68:51 Spondylitis, ankylosing, 82:233 Spontaneous autoimmune disease, 70:165–166 Spontaneous B-lineage neoplasms, pathogenesis, 81:109–115 Spontaneous mouse B-cell neoplasms, 81:106–109 Src family kinases, 70:32–33 Src family kinases, regulation by CD45, 66:4, 23, 39–45 Src homology 2 domain, containing SLP-76, 77:7–8 Src homology 3 domain, Btk, 77:131–132, 135–136

173

Src kinases enzymatic activity regulation, 77:57–60 inner leaflet-anchored, 77:64 membrane anchored by multiple acylations, 77:55–56 palmitoylation, 77:56–57 src kinases, CD40-induced activation, 76:140–143 Src tyrosine kinase family, cellular response differentiation in B lymphocytes, 75:296–300 SRE, see Serum response element SRF, see Serum response factor SRP, see Signal recognition particle ST2, see T1 Stability, cytokine memory, 80:145–149 STAM protein, 70:40–41 Staphylococcus aureus, 68:351 STAT gene deficient mice, 71:152–155 family, 71:145–146 function cellular proliferation, 71:155–156 dimerization, 71:148–149 disease, 71:155–156 DNA binding, 71:149–150 nuclear localization, 71:149 receptor binding, 71:146–148 regulation, 71:156–157 SH2 domain, 71:146–148 transcriptional activation, 71:150–152 structure dimerization, 71:148–149 DNA binding, 71:149–150 nuclear localization, 71:149 receptor binding, 71:146–148

174

SUBJECT INDEX

STAT gene (continued) SH2 domain, 71:146–148 transcriptional activation, 71:150–152 STAT pathways, signaling cross-talk, 75:139–140 STAT proteins, JAK–STAT-signaling pathways, 76:138–140 Stat transcription factors description, 70:27–30 IL-2R, 70:27–30 IL-12R, 70:100–101 Stat6 BCL-6 competition with, 80:121 role in activation of IL-4 gene, 80:120 Stat6, T helper cell differentiation role, 78:241 STATs, see Signal transducers and activators of transcription Staurosporine, 68:69, 70, 71, 75 Stem cell factor, 69:67–69; 73:422–425 Stem cells, hematopoietic, 70:119–121; 72:338–339 Stochastic resonance, 69:420 Stochastic theories, aging, 80:244–245 Streptococcal cell wall, 73:186 Streptococcus pyogenes, 82:192, 194 Stress fiber formation, 68:150 Stress kinases, 68:101–107 Stress-activated protein kinases, 73:101–104 Stress, oxidative, 73:285–286 Stromal cell-derived factor-1 (SDF-1), 81:3

Stromal cells, CD40 engagement effects, 76:76 Strongyloides stercoralis, 70:187 Structure actin cytoskeleton, 77:23–24 lipid raft domains, in plasma membrane, 77:51–53 lipid rafts, 77:16–17 plasma membrane, fluid mosaic model, 77:45 sPLA2s, 77:164–167 Substance P, 68:11–12; 73:378 Superantigens, 68:97; 77:103–104 Superoxide production, 68:25, 85 Superoxide, Leishumania elimination mechanisms, 74:297–299 Suppressor of cytokine signaling-1, see SOCS-1 Suppressor-T cells, antigen-specific factors, 74:1–54 controversial issues, 74:17–33 biochemical identification, 74:26–33 cell identity, 74:17–18 nominal antigen-binding, 74:18–22 T cell receptor gene requirement, 74:23–26 T cell receptor relationship, 74:23–33 glycosylation inhibiting factor role, 74:33–51 antigen-primed B cells, 74:50–51 antigen-primed T cells, 74:48–50 cellular mechanisms, 74:5, 40–45

SUBJECT INDEX

I-J determinant association, 74:39–40 Immunoregulation mechanisms, 74:48–51 structural basis of bioactivity, 74:34–39 target cells, 74:45–48 T cell receptor derivative formation, 74:40–45 historical perspectives, 74:1–17 activity, 74:4–7 biochemical characteristics, 74:11–12 cell properties, 74:3–4 factor properties, 74:7–8 generation conditions, 74:1–3 I-J paradox, 74:14–17 monoclonal anti-suppressor T cell factors, 74:12–14 suppressor T cell cascade, 74:8–11, 54 overview, 74:1, 51–54 Supramolecular activation complex central and peripheral, 77:78–79 formation, 77:13–16 PKCu recruitment to, 77:33, 35 at T cell–APC contact, 77:21–22 Supramolecular activation complexes, lymphocyte signaling functions, 75:91–94 structure, 75:90–91 Surenhu, M., 82:72 Surface area, virus, antibody-coated, 77:215, 217 Surface molecules, human uNK cell studies, 79:308–309 Surrogate light chain, expression in XLA, 77:125–126 SV, see Sendai virus

175

Switch recombination, 80:186 Syk/Zap70 tyrosine kinase family, cellular response differentiation in B lymphocytes, 75:300–302 Syk, 69:196–197, 198–199, 200, 201–202, 208–209; 72:118, 122; 81:60 Syk, and Btk, integration via BLNK, 77:142–148 SYK, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:328–331 Sympathetic innervation of spleen, 81:144 Sympathetic nerves, 81:143–148 Synapse formation, 69:342 Syncytial virus, respiratory, 69:383–386 Synergy c-kit and gc, 69:7076 TNF-a with IFNg, 69:368 Synthetic mimotope peptides, 70:547 Systemic inflammatory response syndrome (SIRS), criteria for, 66:101, 123 Systemic lupus erthematosus (SLE), 82:171–172 Systemic lupus erythemalosus induction, complement deficiency role, 74:78–82 receptor editing role, 74:113–114 Systemic lupus erythematosus 71:167 animal studies of, 68:337, 377–378 CD30 and, 68:115–116

176

SUBJECT INDEX

Systemic lupus erythematosus (continued) CD4 monoclonal antibody and, 68:352 CD51C studies on, 68:357 cytokine production, 73:432 immune complexes, 73:331 and tumor necrosis factor, 68:338 Systemic lupus erythematosus, complement deficiency, 76:227–299 animal models autoimmunity, 76:297–298 B-deficient mouse, 76:278 C2-deficient mouse, 76:278 C3-deficient mouse, 76:278–279 C4-deficient mouse, 76:278–279 C1q-deficient mouse, 76:277–278 CR1-deficient mouse, 76:227, 278–279 CR2-deficient mouse, 76:278–279 other nonhuman species, 76:279 apoptosis, 76:283–292 anti-C1q autoantibody development, 76:292 apoptotic cell clearance, 76:287–288, 290–291 autoantigen source, 76:285–287 complement role, 76:290–291 immune response, 76:288–290

association hypotheses, 76:283–297 apoptosis, 76:283–292 complement role in humoral immune response, 76:294–297 complement role in immune complex clearance, 76:292–294 autoantibody production to C1q, 76:281–283 complement null alleles, 76:259–272 C2 null alleles, 76:269–272 C4 null alleles, 76:265–269 complement receptor type 1, 76:273–276 acquired numbers reduction, 76:274–276 inherited numerical polymorphisms, 76:273–274 inherited structural polymorphisms, 76:276 genetic deficiencies, 76:228–259 acquired complement deficiency, 76:259 ascertainment artifacts, 76:257–259 C2 deficiency, 76:243–251 C3 deficiency, 76:251–252 C4 deficiency, 76:238–243 C1q deficiency, 76:227–237 C1r deficiency, 76:238 C1s deficiency, 76:238 homozygous classical pathway deficiency, 76:228–229

SUBJECT INDEX

mannose-binding lectin deficiency, 76:252–257 terminal pathway component deficiency, 76:252 inflammation, 76:279–281 overview, 76:227–228, 298–299

T T. acidophilum, 68:200 T-bet reversal of Th2 cytokine memory, 80:149 for Th1 cytokine memory, 80:128–129 T cell activation, 78:127 antigen recognition, see Major histocompatibility complex molecules B cell encounters and chemokines, 78:141–143 CD8þ cells autoimmune diabetes role, 78:236 cytokine production, 78:236 DNA microarray studies of differentially-expressed genes humans, 78:252 mice, 78:252–253 overview, 78:250–251 table of genes, 78:251 subsets, 78:236 virus response, 78:236–237 compartmental homing within secondary lymphoid organs

177

microarchitecture formation role lymphotoxins and receptors, 78:131–133 tumor necrosis factor and receptor, 78:131–133 T cell-rich areas, 78:130 effector subsets, 78:233–234 eosinophil interactions, 78:298–299, 315–316 gastrointestinal cell characteristics, 78:318–319 memory/effector cell migration, see also T helper cell CCR4 role, 78:146–147 CCR6 role, 78:146–147 CCR7 role, 78:145–147 features of cells, 78:143–145 secondary lymphoid organs, 78:145 NK1 cell function, 78:237–238 overexpression effects on lamina propria eosinophils, 78:305–309 gd T cell function, 78:238 ab T cell recognition of antigens, 78:284 V(D)J rearrangements, see V(D)J recombination T cell antigen receptor, LAT interaction, 79:101–103 T cell cytokine receptor, for Th1 differentiation, 80:118–119 T cell hybridomas, 68:78–80, 97 T cell line-adapted HIV-1 isolates, 77:212–213 T cell receptor complex, expressed by CD4þ T helper lymphocytes, 77:3–4 engagement, 77:34–35

178

SUBJECT INDEX

T cell receptor (continued) recruitment into DRMs, 77:70–71 TCR–peptide–MHC complex, 77:15–16 T cell receptor, antigen-specific suppressor-T cell factor relationships controversial issues biochemical identification, 74:26–33 cell identity, 74:17–18 factor relationship, 74:23–33 gene requirement, 74:23–26 nominal antigen-binding, 74:18–22 glycosylation inhibiting factor role, 74:40–45 overview, 74:1, 51–54 T cell receptors, see also Pre-T cell receptors CD3 contribution, 72:116–117 antagonists, and autoimmune disease, 68:386–387 anti-idiotypic antibodies to, 80:218 CD3b chain components, 72:113–114 CD3e chain components, 72:112–113 CD3g chain components, 72:114 CD3 and, 68:16, 34, 93–96, 100–101, 266 and CD28 costimulation, 68:12 and CD4, 68:381–385 cell survival, 72:131–138 ab chain sensors, 72:128–131 b chain

allelic exclusion, 72:127–128 components, 72:109, 111 gd chain, 72:124–127 costimulation, interference with, 68:381–385 FceRIg components, 72:115–116 and IL-4R, concomitant signaling, 80:142 immunoreceptor tyrosine-based activation motifs, 76:326–328 major histocompatibility complex class I and II interactions, 76:1–5, 19–20, 42 mutations, 72:138–140 naive T-cell activation requiring, 80:249–251 pre-TCR apoptosis checkpoint, 76:190–192 pTa chain components, 72:111–112 maturation independent of, 72:122–124 Ras pathway and, 68:166–168 restimulation of polarized Th2 cells, 80:147 and rheumatoid arthritis susceptibility, 68:322–324 self-recognizing, 68:89–91 signals, in induction of cytokine memory, 80:133–138 stimulation duration, 80:155 and thymocyte deletion, 68:68–69 transgenic H-Y, 68:97, 99 T cell signaling actin cytoskeleton and, 77:2 formation of SMAC, 77:13–16 PI3K and lipid metabolism, 77:9

SUBJECT INDEX

PLC-g1 pathway, 77:8 Ras/MAPK pathway, 77:8 recruitment of PTKs and adapter molecules, 77:4–8 TCR complex, 77:3–4 Vav/Rac pathway, 77:9–13 T cell-mediated killing, 68:27 T cells, see also Cytotoxic T lymphocytes; T helper cells activation linker, 72:11–12 activation, 68:8–9, 16–17 activation, architecture of, 77:77–79 active suppression role, 73:170–171 anergy Rap1-induced, 72:5 Ras induced, 72:53–59 anergy, 69:209–211 antigen-receptor signaling in, 68:111 antigenic spreading, 70:546 apoptosis in, 68:51–144 apoptosis, 76:179–205 caspase role, 76:179–180, 184–186 cell development peripheral lymphoid organs, 76:195–199 positive and negative selection, 76:192–195 pre-TCR checkpoint, 76:190–192 tumor necrosis factor-R family role, 76:199–200 immune system function, 76:189–190, 288–290 overview, 76:179, 205 regulation

179

Apaf-1 signals, 76:184–186 Bcl-2 family, 76:184–189 caspase 9 signals, 76:184–186 death receptor signals, 76:180–184 transcriptional control, 76:188–189 as apoptosis inducers, 68:53 B cell activation, in viral infections, 79:16–17 bacterial invasions conventional, 71:307, 310–312 unconventional, 71:313–317 Bcl-2, and mitochondrial function of, 68:75 and cancer, 69:215 and CD8 expression, 69:195 CD 45 and, 68:98–101 CD28 signaling Ras role, 72:49–51 Rho role, 72:51–52 CD4 monoclonal antibody and, 68:348 CD4/CD8 as cell surface markers, 71:5–8 g thymocytes, 71:12 CD45 and, 66:32–36 monoclonal antibody studies, 66:6–12 CD45-deficient, 66:18–22 CD4þ activation administration, 70:314–319 APC targeting, 70:321–323 dosage, 70:314–319 location, 70:314–319 MHC II molecules, 70:317–321

180

SUBJECT INDEX

T cells (continued) Th cells, 70:324–327 B cell priming, 70:325–326 characterization, 70:330 effector functions cytokines, 70:332–334 cytomegalovirus, 70:347–348 hepatitis B virus, 70:340–341 herpes simplex virus, 70:348–349 HIV, 70:339–340 influenza, 70:341–344 kinetics, 70:332 LCMV, 70:336, 338–339 measles virus, 70:344 mechanism, 70:330–331 mouse mammary tumor virus, 70:350–351 picornaviruses, 70:349–350 poxviruses, 70:344–346 vesicular stomatitis virus, 70:346–347 function, 70:313–314 overview, 70:351–352 presentation, 70:314–319 soluble antigens MHC class II, 70:317–319 CD4þ, in passive transfer models, 77:277–278 CD8þ and, 68:191, 193–194 CD95/CD95L system, 71:166–167 chemokine relationship memory T lymphocytes, 74:132–137 naive T lymphocytes, 74:132–137 progenitors, 74:142–144

receptors, 74:129–132 T helper cells, 74:137–139 clones, transfer of, 77:278–279 costimulation through CD28, 77:22–23 CpG DNA role, 73:353–354 and CpG motifs, 69:372–373 cytokine memory in, 80:148–149 cytokine secretion, 80:116 cytoskeletal defects in, 68:169 deficient for NFATp, 80:137–138 deletions, 71:229, 231–232 dendritic cell interaction cytokine role, 72:282 T cell priming, 72:282–283 in vivo association, 72:281–282 depletion HIV-1-induced, 73:320–322 recovery rates, 73:313–315 thymus relation, 73:322 development CD3 function, 72:103, 105–106 integrin function, 72:340–343 mouse model, 72:106–109 development, 70:42–47 development, apoptosis role peripheral lymphoid organs, 76:195–199 positive and negative selection, 76:192–195 pre-TCR checkpoint, 76:190–192 tumor necrosis factor-R family role, 76:199–200 differentiation of, 68:17, 89–91 differentiation programs, cytokine memory as part of, 80:149–154 division

SUBJECT INDEX

Ki67 mAb expression humans, healthy, 73:316–319 humans, HIV-infected, 73:319–320 effector functions, regulation, 80:152–154 elimination of, and rheumatoid arthritis, 68:353–358 endosome access, 73:11 epitopes, computational identification, 66:77–84 ERK activation, 72:16–17 Fc receptors in, 68:278–279 FV receptors and, 68:258–266 germinal center reaction initiation, 76:70, 74, 132 glycolipid presentation, 71:303–306 GM-CSF production and, 68:8, 258 growth IL-2R, 70:63–64 HIV-1 depletion, 73:301–303 HLA class II expression in, 68:16–17 homeostasis of, 68:91–93 idiotypic activation or suppression, 80:211–219 IL-12 induced, 70:107–108 IL-12-induced, 70:131–133 IL-18 effects, 70:287–289 IL-18 expression, 70:294–295 IL-18R expression, 70:296–297 immune response regulation activators and inhibitors, 76:80 B cell collaboration, 76:69 humoral immune responses

181

T cell-dependent responses, 76:70–75 T cell-independent responses, 76:75–76 Ig secretion regulation, 76:131–133 inhibition of activation signals, 69:225–226 interleukin-12 induction, 79:65–66 interleukin-12/NK effect on human, 68:10 and interleukins, 68:13, 14 in vivo role, 73:16–17 and ITAMs, 69:202–205 LAT-deficient lines, 79:101–103 LAT role, 73:96–97 in xenotransplantation gamma–delta T cells, 79:142–143 NK/T cells, 79:142–143 tolerance, 79:174 ab lineage cell culture studies, 71:52–53 competitive rearrangement model, 71:57, 59 consensus model, 71:54–57 data integration, 71:60–63 DP thymocyte representation, 71:46–49 gd interaction, 71:98–104 notch role, 71:50–51 separate lineage model, 71:59–60 a/g lineage competitive rearrangement model, 71:17, 19 development, 71:14–16 function, 71:2 identification, 71:1–5

182

SUBJECT INDEX

T cells (continued) maintenance, 71:18 selection, 71:3–4 separate lineage model, 71:17–18 sequential rearrangement model, 71:16–17 TCR gene rearrangements general considerations, 71:19 models, 71:34–35 molecular analysis, 71:20–22 TCRa locus, 71:32–34 TCRb locus, 71:28–32 TCRd locus, 71:24–27 TCRg locus, 71:22–24 gd lineage activation, 71:91–92 antibody responses, 71:95–98 bacterial invasions, 71:306–307, 313–314 B cell stimulation, 71:93–95 cutaneous hypersensitivity, 71:111–112 development, 71:78–83 distribution, 71:78–83 evolution, 71:123–124 ab interaction, 71:98–104 inflammation, 71:108–111 ligand recognition HSV-specific, 71:90–91 MHC-specific, 71:89–90 sTCR constructs, 71:92–93 macrophages, 71:102–105 molecule stimulation, 71:87–89 NK cells, 71:101–102 origin, 71:78–83

overview, 71:77–78 pathogen response, 71:105–108 selection, 71:85–87 structure specificity, 71:83–85 tissue specificity, 71:80–83 tolerance antigens, 71:112–117 epithelial homeostasis, 71:122–123 pregnancy, 71:120–122 tissue grafts, 71:117–120 wound healing, 71:122–123 waves, 71:79–81 major histocompatibility complex molecules and, 68:89–91 maturation, 80:249 memory responses, 73:24–25 memory, 68:91–92, 285, 356; 79:30–31; see Memory T cells memory, recirculation, 72:344–345 mRNA regulation and function of, 68:1–50 naive, 80:249–251 naive, recirculation, 72:344 negative selection, 71:238–239 NK1 IL-12-induced, 70:133–134 pAPC triggering, 73:15 peptides from intruders and, 68:191, 230 peripheral CD95 apoptosis, 71:182–184 deletion, 71:168–169 tolerance anergy, 71:243–248 deletion, 71:242–243 exhaustion, 71:242–243

SUBJECT INDEX

immune deviation, 71:248 partial signaling, 71:243–248 recirculation, 71:240–242 regulation, 71:248–250 pokeweed mitogen effect on, 68:5 polarized, and cytokine memory plasticity, 80:146 priming, 73:42–44 product, mathematical model, 73:323–324 production BrdU labeling, 73:315–316 division rates, 73:312–313 total body number, 73:310–312 turnover, 73:309–310 progenitor renewal HIV-1 infection bone marrow function, 73:306–307 development, 73:307 impact, 73:305–306 thymic function, 73:307–308 human, 73:304–305 mice, 73:303–304 normal, 73:303–304 progenitor, 69:6 proliferation, 70:10–13 protooncogene levels, 68:5 Raf-1 activation, 72:16–17 Ras pathway in, 68:166–168 regulation, 70:394–396 response, 73:1–2, 17 self-reactive, 68:93, 321 sensitivity, 71:4–5 shape regulation, 72:43–44

183

signal transduction, actin cytoskeleton in 77:33–34 SLP-76-deficient lines, 79:103–104 specific antigen recognition, 68:89, 93 suppressor T cells, see Suppressor-T cells SV, 73:49 Th1 response, 73:348–349 Th2 response, 73:350–351 thymic development, 71:3 transferrin receptors in, 68:16 triggering, 73:1–3 tumor eradication and, 68:257–258 tumor necrosis factor and, 68:14 tumor recognition escape, 74:181–245 human leukocyte antigen I, polymorphism, 74:226–228 immunogenicity inadequacy, 74:236–241 antigen-presenting cell-helper T cell interactions, 74:241 antigen-presenting cell role, 74:239–241 human leukocyte antigen II expression, 74:238–239 immunological alternatives, 74:241–245 mechanisms, 74:190–195 microenvironmental inhibitory signals, 74:229–236 apoptitic signal surface expression, 74:234–236 cytokines, 74:229–236

184

SUBJECT INDEX

T cells (continued) overview, 74:181–190 tumor cells as targets, 74:195–226 cytotoxic T lymphocyte activity reduction, 74:202–203 down regulation, 74:195–204, 204–214 human leukocyte antigen I role, 74:204–214, 214–226 processing defects, 74:214–226 tumor-associated antigen loss, 74:195–204 tyrosine phosphorylation in, 69:215 and V(D)J gene arrangement, 69:316–317, 318–319 and viral vectors, 69:354–356 and ZAP-70, 69:197–198, 216 vaccination with, 68:387–389 viral response, 73:3–4 T cells, see also specific types activation, T-cell receptor crossreactivity role in autoimmune disease, 75:209–217 low affinity ligands, 75:211–214 peripheral T-cell tolerance, 75:214–217 T-cell antagonism, 75:211–217 antigen processing, see Antigens cancer immunotherapy, see Cancer cytotoxic T lymphocytes

cancer immunity, 75:236–240, 247–248, 256 host adjuvant use, 75:33–34 protection correlates, 75:25–26 purging useless cells, 75:218–220 signaling, cytoskeleton role, 75:89–110 actin cap effective molarity regulation, 75:110 function, 75:91–94 proximity regulator role, 75:110 structure, 75:90–91 actin cytoskeleton regulation, 75:105–107 actin polymerization regulation current view, 75:94–95 nucleus signal propagation, 75:108–110 RAC role, 75:94–100 Rho family GTPases role, 75:99–100, 104 WASP role, 75:92–94, 104–107 BAF chromatin-remodeling complex, 75:109–110 guanine nucleotide exchange factors, Vav family, 75:95–98 ligand-induced actin-dependent assemblies, functions, 75:91–94 overview, 75:89–94 Rho family GTPases, 75:98–100

SUBJECT INDEX

actin polymerization, 75:99–100, 104 description, 75:98–99 supramolecular activation complexes functions, 75:91–94 structure, 75:90–91 WASP actin regulation, 75:92–94, 104–107 cytoskeleton regulation, 75:105–107 structure, 75:102–104 Vav-deficient mouse phenotype compared, 75:107–108 Wiskott-Aldrich syndrome, 75:100–104 tolerance, 75:214–217 autoimmune disease resistance, 75:216–217 immunoglobulin-derived peptide antagonists role, 75:215–216 vaccinology host adjuvant use, 75:33–34 intracellular bacteria protection role, 75:6–7 memory, 75:23–25 protection correlates, 75:25–26 T-cell antigen receptor (TCRs), 81:329 T-cell development, 81:254, 280–282 T-cell differentiation, T-cell-derived CD100 in, 81:186–187 T-cell genes, 81:255 T-cell lymphomas, 81:99, 238–239

185

T-cell lymphopoiesis, 81:276 T-cell ontogeny in zebrafish, 81:280–283 T-cell receptor a (TRCa), 81:134 T-cell receptor, crossreactivity, autoimmune disease role, 75:209–226 cytokine checkpoints, 75:223–226 low affinity ligands, 75:211–214 overview, 75:209 peripheral purging of useless T cells, 75:218–220 peripheral T-cell tolerance, 75:214–217 T-cell antagonism, 75:211–217 viral-derived peptide agonists, 75:220–223 T-cell receptor genes in teleosts, 81:280 T-cell receptors antigen, 70:387–389 evolution emergence, 70:425–430 jawed vertebrates, 70:430–433 species comparisons, 70:441–451 T-cell receptors (TCRs), 81:47, 272, 273, 279, 280, 330, 350, 356, 357 4-1BB, T-cell response in cancer, 75:252–253, 256 T-cell subsets, 81:46 T-cell-derived CD100 in T-cell differentiation, 81:186–187 T-cell-receptor a assembly, 69:117 enhancers, 69:326–328, 340 amd IL-7, 69:338

186

SUBJECT INDEX

T-cell-receptor a (continued) and LCR, 69:336–337, 339 and V(D)J gene arrangement, 69:317 T-cell-receptor b and allelic exclusion, 69:38–44, 117 assembly, 69:117 enhancer, 69:323–326, 339 and IL-7, 69:338 and signal transduction, 69:45–57 and V(D)J gene arrangement, 69:317, 318–319, 326 T-cell-receptor d, 69:317, 318–319, 328, 338, 340 T-cell-receptor g1, 69:337, 338–339 T-cell-receptor z, 69:210–211, 215–216, 225–226 T-cell-receptors, see also Pre-T-cell receptor and ITAMs, 69:186, 201, 202–205, 207–208 structure of, 69:188–189 T-cells, 81:1, 5–7, 134, 275 antigen-specific, CD100/Sema4D in in vivo generation, 81:187 regulatory, 81:330–331 subsets, 81:339–340 self-reactive, 81:329, 330 subpopulation, 81:330 T early a, 69:334–336, 339, 340–341 T helper cell antibody production role, 78:238–239 chemokine and receptor expression

CCR3, 78:82, 245–246 CCR4, 78:82–83, 246 CCR5, 78:81–82, 244–245 CCR7, 78:83–84, 244 CCR8, 78:83 CXCR3, 78:81–82, 244 CXCR5, 78:84–85, 239, 247–248 follicular T helper cell migration, 78:247–248 inhibitors of receptors, 78:246–247 intervention therapy, 78:92 overview, 78:242–244 receptor expression by cell type, 78:80–81 Th1 responses, 78:244–245 Th1/Th2 polarization role, 78:90, 140–141, 246 Th2 responses, 78:245–246 classification by cytokine production, 78:80, 91, 140, 234–235 differentiation factors antigen dose, 78:240 interleukin-1, 78:240 interleukin-4, 78:239–240 interleukin-12, 78:239–240 interleukin-18, 78:240 transcription factors c-Maf, 78:241 GATA-3, 78:241 identification, 78:240–241 Stat6, 78:241 Th1 factors, 78:241–242 DNA microarray studies of differentially-expressed genes humans, 78:252 mice, 78:252–253

SUBJECT INDEX

overview, 78:250–251 table of genes, 78:251 functions of secreted cytokines, 78:234–236 molecules distinguishing effector function ICOS, 78:248–249 interleukin-18 and receptor, 78:249–250 T1, 78:249 tetraspans, 78:250 T helper cells activation, 70:324–327 autoimmunity, 70:157–158 and CD4 expression, 69:195 chemokine relationship, 74:137–139 differentiation, 70:141–143, 141–146 effector functions, 70:330–336 effector, transfer of, 77:279 generation, 70:134–136 IL-12 role, 70:134–140 NK cells role, 70:139–140 IL-18 effect, 70:289–291 leishmaniasis adaptive immune response antigen presentation, 74:285–286 elimination, 74:300 induction, 74:288–290, 302 development cytokine role, 74:290–291 interleukin-4 role, 74:291–294 polarization, 70:140–141 stability, 70:136–138 Th1 cytokines, proinflammatory effects 77:279–280

187

TH2, 69:363 Th2, inflammation mediated by, 77:280–282 tumors, T-cell recognition escape, antigen-presenting cell interactions, 74:241 T-helper 1 cells, 81:50 T-helper 3 cells, 81:339 T-helper 1 cytokines, 81:71 T lymphocytes, in GMG cell–NK cell relationship, 79:303, 305 T lymphoma cells, murine, 68:7, 193, 195 T-lymphocytes, 81:1, 47 T-lymphopenia, organ-specific autoimmunity induced by, 81:331–336 T1/ST2, selective expression on T cells, 80:152–153 T1, T helper cell function, 78:249 T10 clone, 71:90 T22 clone, 71:90 TACO (tryptophan aspartate-containing coat protein), 81:76–85 Tacrolimus, 69:358 Taiwan, 82:49 TAK1, interleukin-1 receptor signaling, 78:4–5 TANK, immune response regulation, I-TRAF/TANK, 76:109–114 TAP, see Peptide transporter; see Transporter associated with antigen processing mobility, 80:23 peptides transported via, 80:43–44

188

SUBJECT INDEX

TAP1 deficient cells, 73:22 expression, 73:12 function, 73:6–9 TAP2 deficient cells, 73:22 expression, 73:12 function, 73:6–9 TAPA-1, 69:88 Tapasin, 68:207–208 Target of rapamycin, 70:39–40 Target tissues, differential T cell recruitment to, 80:150–152 Targeting Btk to membrane, 77:132–134 LAT into DRM, 77:61 Targeting Induced Local Lesions In Genomes (TILLING), 81:306–308, 315 Taxol binding proteins, 78:26–27 lipopolysaccharide mimetic activity, 78:26 TLR4 binding, 78:26 Tcf-1, 69:82–83 TCL1, 81:115 TCR/CD3 receptor complex, 68:93–97, 100–101, 266 TCR, see T cell receptor; see T cell receptors; see T-cell-receptors; see T cell antigen receptor Tdt-mediated dUTP nick end-labeling (TUNEL), PCD and, 77:309–310 TdT, see Terminal deoxynucleotidyl transferase TEA, see T early a TEA element, immunoglobulin heavy chain gene assembly role, 78:196

Tec homology domain, 77:124 Btk, 77:136 tec kinases, CD40-induced activation, 76:140–143 Tec tyrosine kinase family, cellular response differentiation in B lymphocytes, 75:302–304 TEC tyrosine kinases, in SLP-76 signaling, 79:120–121 Technology, molecular, 82:57 Teleosts, 81:254 B-cell development in, 81:282–285 immunoglobulin genes in, 81:282–284 innate immunity, 81:257–272 spleen as major secondary lymphoid organ in, 81:285–287 T-cell receptor genes in, 81:280 Telomerase reverse transcriptase (hTERT), 82:61 Telomeres aging and, 80:245 shortening, 80:271 TEPITOPE (software), T cell epitope prediction, 66:82–84, 86, 90–91 TEPs, see Thioester proteins Terminal deoxynucleotidyl transferase, 69:315; 80:186 Tetracycline, as mRNA promoter, 68:3 Tetraspans, T helper cell function, 78:250 TFII-I pathway, downstream of Btk, 77:141–142 tg, see Transgenic mouse models TGF-b, 81:343–345, 355

SUBJECT INDEX

TGF, see Tumor growth factor TgI4.4 clone, 71:90–91 TGIF transcriptional corepressor, transforming growth factor-b signaling, 75:134–135 Th1 cytokine memory stabilization, 80:148–149 T-bet for, 80:128–129 differentiation, instructive cytokines for, 80:117–119 program description, 80:115–116 transcription factors, CIITA, 80:129–130 Th2 cytokine memory GATA-3 for, 80:123–125 reversal, 80:149 differentiation, instructive cytokines for, 80:119–122 IL-4 memory in, 80:147 induction of development by dendritic cells, 80:131–132 program description, 80:115–116 transcription factors c-Maf, 80:127 JunB, 80:128 Th2-like cytokines, basophils and, 77:100 Thalidomide, 68:13 Theiler’s virus, 70:349–350 Thermoplasma acidophilum, 68:200 Thimet oligopeptidase antigen presentation inhibited by, 80:45–46 in catabolic pathway, 80:17–18

189

Thioester proteins, in immune responses, 79:236–237 Threonine kinase receptor, transforming growth factor-b signaling, 75:116–119 Threonine protein kinases, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:339–342 Threonines, 82:251, 252 Thrombomodulin, downregulation of, 66:111 Thromboregulation, in xenotransplantation, 79:152–153 Thromboregulatory factors, in xenotransplantation, 79:170 Thrombosis antiprothrombin-link, 70:534 deep venous APS-associated, 70:515 glomerular capillary, 70:516 b2-glycoprotein I link, 70:539–540 mesenteric vessels, 70:517 Thrombosis, CD40/ CD154-mediated regulation, 76:76–78 Thrombospondin domains, 81:174 Thrombotic diathesis, in xenotransplantation, 79:152 Thymic development, 81:273–279 Thymic epithelial cells (TECs), 81:275, 278 Thymic generation of Treg cells, 81:350–353 Thymic organogenesis, 81:276 phylogeny, 81:273–275 in zebrafish, 81:277–279

190

SUBJECT INDEX

Thymic rudiment formation, 81:277–279 Thymic stromal cell-derived lymphopoietin, 69:77 Thymocytes adhesion molecule mutations, 69:84–88 antigen-specific activation of, 68:95–96 apoptosis in, 68:78–80, 90–91 and B cells, 69:18 Bcl-2, and mitochondrial function of, 68:75 CD4/CD8 scheme, 71:12 CD45 and, 68:99–100 CD81 effect, 69:88 CD8þ and, 68:97 chromatin condensation in rat, 68:56 and cytokines, 69:57–77 and dendritic cells, 69:19–20 development assays, 69:3–6 development pathways, 69:27–38, 70–76 differentiation and selection of, 68:17–18, 89–91, 106–107 differentiation, 69:79 DN heterogeneity, 71:8–11 DP gene-targeted mice, 71:44–45 ab lineage representation, 71:46–49 transgenic mice, 71:40–41 etoposide effect on, 68:62 glucocorticoid-treated, 68:52, 56, 57, 61–62, 68–69 immature, and thymic stromal cells, 68:95 ISP stage, 71:32

major histocompatibility complex and, 68:89–91, 97 mitochondrial transmembrane potential, 68:91 modes of action, 69:29–32 and myeloid cells, 69:18–19 and NK cells, 69:14–18 non pre-TCR development, 69:32–38 notch role, 71:50–51 origin of, 69:6–8 positive and negative selection, 68:89–91 pre-TCR role in development, 69:20–32 progenitor populations, 69:9–14 with self-recognizing T cell receptors, 68:89–91 signaling pathways, 69:70–72 sphingomyelinase and, 68:120 T cell receptors and, 68:68–69, 95–97 thymic stromal cells and, 68:95 transcription factors, 69:77–84 and zinc finger-containing transcription factor, 69:56–57 Thymocytes development, 72:341–342 Thymopoiesis, 71:5–8 Thymopoiesis, ectopic, 69:61 Thymosins, buffering of G-actin pool, 77:27 Thymus 68:17, 115, 239; 69:73–76, 87; 80; see also Thymocytes atrophy, cytokines and, 80:269–270

SUBJECT INDEX

chemokine and receptor expression, 78:75–77, 121–123 development, 73:322 function decline, age-related, 73:305 T cell renewal, 73:307–308 hematopoietic stem cell homing, 78:119–121 intact function, and immune reactivity, 80:268–269 involution, T cell maturation and, 80:249 lineage divergence, 71:53–54 lymphomas AKR mice, 73:514–515 generation immunobiology, 73:513–514 PLCs, 73:515 preventive therapy, 73:525–529 RadLV-induced, 73:520–525 organ culture, fetal, 73:307 pTa-deficient, 71:47–48 TECK and thymocyte migration, 78:122–123 tissue engineering, 80:270–271 tolerance clonal deletion, 71:229–232 negative selection APC, 71:232–234 cell surface receptors, 71:234–236 clonal deletion, 71:237–240 signaling, 71:236–237 Thymus and activation-regulated chemokine (TARC), 81:6 Thymus development beyond larval stage, 81:279

191

Thymus expressed chemokine (TECK), 81:6 Thymus, xenotransplantation, 79:182–184 Thymus-dependent antigen, humoral immunity enhancement, 74:65–67 Thyroid disease, 68:346, 371 Thyroid hormone replacement, 73:231 Thyroiditis, 73:222 Tick-borne encephalitis, antibody protection against, 77:235–236 TILLING (Targeting Induced Local Lesions In Genomes), 81:306–308, 315 Tim protein family, 81:190–191 Tim-2, 81:194 as Sema4A receptor, 81:189 structure, 81:190 Tissue destruction, autoimmune, 68:368, 378 Tissue engineering, thymic organoid, 80:270–271 Tissue expression sPLA2-IIA, 77:169–170 sPLA2-IIE, 77:180 Tissue factor pathway inhibitor (TFPI), 66:132 Tissue grafts, 71:117–120 Tissue-specific expression systems, gene transfer, 77:283–285 TLR, see Receptors, toll-like TLR9, see Toll-like receptor 82:9 TLRs, see Toll-like receptors TN thymocytes, 70:46 TNF, see Tumor necrosis factor TNF receptors, 66:107–108, 116

192

SUBJECT INDEX

TNFa, see Tumor necrosis factor a TNF-b, see Tumor necrosis factor b TNFR, see Receptors, TNF Tolerance, see Oral tolerance B cell activation, 75:286–287 B cell receptor editing developmental block association, 74:104–106 disease association, 74:113–114 transgenic models, 74:100–102 complement role, see Complement peripheral T cell anergy, 71:243–248 deletion, 71:242–243 exhaustion, 71:242–243 immune deviation, 71:248 partial signaling, 71:243–248 recirculation, 71:240–242 regulation, 71:248–250 gd T cells antigens, 71:112–117 epithelial homeostasis, 71:122–123 pregnancy, 71:120–122 tissue grafts, 71:117–120 wound healing, 71:122–123 T-cell activation, 75:214–217 autoimmune disease resistance, 75:216–217 immunoglobulin-derived peptide antagonists role, 75:215–216 thymus clonal deletion, 71:229–232

negative selection APC, 71:232–234 cell surface receptors, 71:234–236 signaling, 71:236–237 Tolerance, antigen-specific, 68:389–395 Toll Dif signaling, 78:3 domains, 78:2 Dorsal activation, 78:2–3 18W homology, 78:3 receptor human homologs, see Toll-like receptors innate immunity role in Drosophila, 78:2–4 interleukin-1 receptor signaling homology, 78:7 Relish signaling, 78:3 Spatzel interaction, 78:2 Toll-like receptor 9 (TLR9), 82:67 Toll-like receptors (TLRs) 81:55–56, 148–149 classification and discovery, 78:7–8, 35 dendritic cell expression of TLR3, 78:8 gene loci, 78:7–8 host resistance role in microbial infection, 78:34–35 interleukin-1 receptor signaling homology, 78:9 microbial cell wall component recognition CpG motifs, 78:33–34 Gram-positive bacteria, 78:30–31

SUBJECT INDEX

heat shock protein response, 78:32–33 lipoproteins, 78:2 mycobacteria, 78:31 zymosan, 78:32 regulation of expression, 78:9 TLR2 lipopolysaccharide signaling, 78:29–30 TLR4 lipopolysaccharide signaling, 78:21–24 Taxol binding, 78:26 Toll-like receptors, immune response, 79:234–235 Tosoplasma gondii, 81:68 Toxic effector molecules, 71:278–281 Toxins, 68:53, 122, 359–361 Toxoplasma gondii, 70:183 Trachael eosinophilia, 73:222 TRAF adapter molecule immune response regulation apoptosis regulation, 76:134–136 CD40 event mediation, 76:115–145 functional outcomes, 76:126–136 signaling cascades, 76:116–126 discovery, 76:93–115 expression regulation, 76:114–115 functional outcomes, 76:126–136 adhesion, 76:129–130 antigen-presenting cell function, 76:130–131 apoptosis regulation, 76:134–136

193

cell survival and proliferation, 76:127–1 cytokine secretion, 76:131 IgH class switching, 76:133–134 immunoglobulin production regulation, 76:131–134 I-TRAF/TANK, 76:109–114 MAPK activation, 76:97–100 NF-kb activation, 76:100–103 signaling cascades, 76:116–126 cAMP-mediated-signaling pathways, 76:144–145 ERK activation, 76:89–90, 120, 125–126 JAK–STAT pathways, 76:138–140 JNK activation, 76:90–91, 98–100, 120–124 NF-kb activation, 76:116–121 p38 activation, 76:92, 98, 100, 124–125 reverse-signaling through CD154, 76:145 src activation, 76:140–143 tec family kinase activation, 76:140–143 ZAP-70 activation, 76:140–143 structure–function relationship, 76:95–104 TRAF–CD40 association, 76:65, 104–109 properties, 76:93–94 TRAF, see Tumor necrosis factor-receptor-associated factors

194

SUBJECT INDEX

TRAF6, interleukin-1 receptor signaling, 78:4–7 TRAIL characterization, 73:286–287 FasL and, 73:287 trans-regulatory factors, 69:338–339, 340 Transcription B cell differentiation regulation via IgH 30 region, 75:331–334 CD154 expression regulation, 76:78–79, 83–86 CD40 expression regulation, 76:78–79, 82–83 CRE transcription, 76:92 and HMG box family, 69:82–84 lymphocyte apoptosis regulation by Bcl-2 family proteins, 76:188–189 major histocompatibility complex class II expression regulation, 75:171–172 MIC genes, 76:15–18 mechanisms, 76:16–18 transcripts, 76:15–16 mutations, and thymocyte development, 69:77–84 of k loci, 69:137–138 regulation enhancers, 69:124–128, 136–137 LCR, 69:124 MARs, 69:124 and olfactory system, 69:439–440 promoters, 69:124 silencers, 69:124

Transcription factors AP-1 family of, 82:31–32 C/EBP family of, 82:30–31 Ets family of, 82:28–30 in neutrophil activation, 82:28–34 Transcription factors, B cell immune response regulation by CD40-signaling AP-1 activation, 76:79, 87–92 CRE activation, 76:87, 92 NF-AT activation, 76:79, 88–92 NF-kb activation, 76:87, 92–93, 100–103, 116–121 Transcription factors, NF-kB family components, 82:18–22 HIGM and, 82:304–305 regulation of, 82:24–25 ROI and, 82:22–24 role of, 82:25–28, 27 Transcription, interleukin-12 p35 gene control, 79:71–72 Transcription, role in Ig hypermutation, 80:187–188 Transcriptional factor, PU.1, 79:69–70 Transcriptional repressors, transforming growth factor-b signaling, 75:133 Transcytosis FcRn and, 82:165–166, 167, 169–171 IgG and, 82:166–169, 167, 169 Rc receptors in, 82:165, 166 therapeutic implications of, 82:171–172 Transepithelial enteric passage of prions, 81:131–133

SUBJECT INDEX

Transepithelial transport of prions via M-cells, 81:132 Transferrin receptor, cross-linked, 77:22 Transferrin receptors, 68:15–16, 24, 297 Transforming growth factor ligation of receptor, and apoptosis, 68:53 transforming growth factor a, 68:17 transforming growth factor b, 68:6, 24–25, 36, 377, 378 Transforming growth factor-b, Smad protein signaling, 75:115–145 biological function, 75:125–126 cross-talk, 75:137–140 MAP kinase pathways, 75:138–139 nuclear steroid receptor, 75:140 Smad pathways, 75:137 STAT pathways, 75:139–140 cytoplasmic actions, 75:126–128 calmodulin interactions, 75:128 membrane anchoring, 75:126 nuclear transport, 75:127–128 oligomer formation, 75:127–128 expression regulation, 75:126 I-Smads, 75:135–137 expression regulation, 75:137 function, 75:135–136 in vivo functions, 75:142–143 embryogenesis, 75:142 immune function, 75:142–143

195

tumor development, 75:142–143 models C. elegans, 75:124 Drosophila, 75:124 human cancer, 75:140–143 Xenopus, 75:123–124 mutation biology, 75:141–142 nuclear actions, 75:128–135 AML interactions, 75:131–132 AP-1 complex interactions, 75:131 ATF-2 interactions, 75:131 CBFA interactions, 75:131–132 CBP transcriptional coactivator, 75:134 direct DNA binding, 75:128–129 Evi-1, 75:133 FASTs interactions, 75:130–131 interacting partners, 75:129–134 minor transcription factors, 75:132–133 MSG1, 75:135 p300 transcriptional coactivator, 75:134 PEBP2a interactions, 75:131–132 TGIF transcriptional corepressor, 75:134–135 transcriptional repressors, 75:133 overview, 75:115, 143–145 serine/threonine kinase receptors, 75:116–119 TbR-I structure, 75:118–119

196

SUBJECT INDEX

Transforming growth factor-b, Smad protein signaling (continued) type I and II receptor characteristics, 75:116–117 type I subgroups, 75:117–118 structure, 75:121–123 MH1 domain, 75:122–123 MH2 domain, 75:121–122 proline-rich linker region, 75:123 subclasses, 75:119–121 superfamily characteristics, 75:115–116 Transforming growth factors TGR-a, 73:418–419 TGR-b, 73:419–420 VEGF expression, 73:420–421 Transgenic (tg) mouse models, 82:56, 266–268, see also MET Transgenic mice DEC, 71:38–39, 42–43 G8, 71:40–43 TCRab, 71:35–37 TCRgd, 71:37–43 Transgenic mice expressing transgenic TCRs, 81:350 Transgenic models, gene transfer systems, 77:282–283 Transgenics, immune tolerance models, in vivo, B cell receptor editing, 74:100–102 Transient gene knockdown using morpholinos, 81:309–310 Transient gene transfer models, allergen challenge, 77:284–285

Transmissible spongiform encephalopathies (TSEs), 81:123, 124, 126, 148, 159 Transplantation, 73:222–223 Transplants, 69:367 Transporter associated with antigen processing, 69:382, 387 Transporter of antigenic peptides, 70:390–391 Treg cells abnormality in autoimmune disease, 81:335–336 alloantigen-specific, 81:354 antigen specificity required for suppressor effector functions of, 81:356–359 CD25 marker for, 81:337–338 cell surface markers, 81:338–339 chemokines in migration/ recruitment, 81:348–349 de novo generation, 81:356 generation/maintenance, 81:360–362 maintenance in periphery, 81:359–360 molecular basis of functions, 81:343–349 peripheral generation, 81:354–356 in spontaneous models of autoimmunity, 81:335 thymic generation, 81:350–353 tissue-specific, 81:357 Trehalose dimycolate (TDM), 81:75 Trichuris muris, 70:187 Trigger mechanism, 71:269 Trimming by aminopeptidases, 80:18 peptides

SUBJECT INDEX

in cytoplasm, 80:40–43 in endoplasmic reticulum, 80:43–44 Tripeptidyl peptidase II inhibitors, apoptosis induced by, 80:20 Trophoblast cells, 79:315–317 Tropism, viral sensitivity, 79:23–24 Trypanosoma cruzi, 70:183–184 TSG-6, 66:111–112 TSICSLYQLE (peptide), 66:88 TSLP, see Thymic stromal cell-derived lymphopoietin Tuberculosis 81:70 BCG vaccines, 75:29, 46–47 characteristics, 75:3, 7–8 DNA vaccines, 75:39–41 a-Tubulin, 72:31–32 Tumor cell-lines, HLA-G expression by, 81:238–243 Tumor growth factor (TGF), 82:2, 53 Tumor growth factor-b, 73:165–167 Tumor necrosis factor (TNF) 82:2 -a, 82:219, 225 anti-TNF, 66:124, 132, 150 biochemistry, 66:105–107 cardiomyocytes and, 66:114 circulating levels, 66:104–107 CD154, see CD154 CD40, see CD40 and cytokine stimulation, 68:12 and encephalomyelitis, 68:373–374 in endotoxemia, 66:114–116 granuloma formation, 71:320 immune response effects, 76:72 inappropriate responses, 71:321 induced apoptosis, 71:178–179

197

induction, 71:275 in vitro effects, 66:110–112 in vivo effects, 66:112–114 lymphopoeisis, 71:321–322 neutrophils and, 66:111 platelet activation, 76:77 properties, 76:64 receptors, 66:107–108, 116 regulation, 66:108–110 sepsis and, 66:104, 126–127, 150 animal models, 66:117–121 clinical, 66:121–124 treatment, 66:124–126 sphingomyelinases, ceramide and, 68:120–122 superfamily, 82:299–300 T cell proliferation, 76:199–200 and TCR/CD3-triggered thymocyte apoptosis, 68:91–92 Tumor necrosis factor, Leishmonia elimination mechanisms, 74:297–299 Tumor necrosis factor (TNF), lymphocyte compartmental homing role within secondary lymphoid organs, 78:131–133 Tumor necrosis factor a, 69:77, 367–371, 379 Tumor necrosis factors, 69:379 Tumor necrosis factor family autoimmune disease generation role, 75:223–226 T-cell responses in cancer, 75:249–253 Tumor necrosis factor-a, 79:75–77 Tumor necrosis factor-a; see also Tumor necrosis factor; Tumor necrosis factor receptor

198

SUBJECT INDEX

Tumor necrosis factor-a (continued) Actinomycin D and mRNA of, 68:19 in activated murine T cell clones, 68:14 apoptotic effect in thymocytes, 68:114 AU-A protein and, 68:34 in collagen II arthritis, 68:377 in Crohn’s disease therapy, 68:342 effect on interleukin-1 mRNA, 68:11 ligation of, and apoptosis, 68:53, 72 mRNA regulation in, and T cell activation, 68:8–9 NF-kB activation and, 68:119–120 produced by T cells with Fv receptor, 68:258 and rheumatoid arthritis, 68:338–342 in systemic lupus, 68:338 Tumor necrosis factor-a (TNF-a), 81:4, 73, 130, 238–243, 259 Tumor necrosis factor-a (TNF-a) receptor family molecules, 81:347–348 Tumor necrosis factors receptor families CD40 signaling, 73:129–132 description, 73:80, 83–84 TNF-a characterization, 73:390–391 CpG effects, 73:336–338 inflammatory disease implications, 73:275–277 LPS expression, 73:392–393

ODN effects, 73:342 PMN expression, 73:391–392, 394–397 prelymphoma cells, 73:527 Tumor necrosis factor receptor, and apoptosis in thymocytes, 68:114–116 Tumor necrosis factor-receptorassociated factors, 79:241–242 Tumor necrosis factors dendritic cells generation, 72:269–277 maturation, 72:279–280 signaling, 72:269–272 Tumor-associated antigen, tumors escape from T-cell recognition down regulation, 74:195–204 loss, 74:195–204 masking, 74:203–204 mechanisms, 74:190–195 mimics, 74:202–203 overview, 74:181, 186 Tumor-associated antigens, 81:330 Tumor-infiltrating lymphocytes, 69:215 Tumorigenesis, AT characterization, 72:179 dissecting, 72:181–185 Tumor(s), 82:49; see also Vaccines, tumor breast, 82:279–280 cells, 82:65–66, 255, 258–260 DC-tumor cell, 82:275 families, 82:60 immunology, 82:249 metatasis, 82:258 pancreatic, 82:268–269 resurgence of, 82:54

SUBJECT INDEX

types of, 82:53, 56–57 vaccines, 82:68–69 virus-associated, 82:52 Tumors, 70:187–193; see Cancer; see also Carcinoma; Lymphoma and adoptive immunity, 68:257–269 CD30 and, 68:115 cells, SCF effects, 73:422 CpG DNA effects, 73:349–350 cytokine role in vivo, 73:472–473 FTase inhibitors and, 68:177–179 loss of TAP expression in human, 68:236–238 lymphocyte-derived, 68:51 macrophages, binding to, 68:284 propagation, HGF, 73:421 VEGF effects, 73:420–421 Tumors, T-cell recognition escape, 74:181–245 human leukocyte antigen I, polymorphism, 74:226–228 immunogenicity inadequacy, 74:236–241 antigen-presenting cell–helper T cell interactions, 74:241 antigen-presenting cell role, 74:239–241 human leukocyte antigen II expression, 74:238–239 immunological alternatives, 74:241–245 mechanisms, 74:190–195 microenvironmental inhibitory signals, 74:229–236 apoptitic signal surface expression, 74:234–236

199

cytokines, 74:229–236 overview, 74:181–190 tumor cells as targets, 74:195–226 cytotoxic T lymphocyte activity reduction, 74:202–203 down-regulation, 74:195–204 human leukocyte antigen I loss or down regulation, 74:204–214 processing defects, 74:214–226 tumor-associated antigen loss, 74:195–204 masking, 74:203–204 mimics, 74:202–203 Tweady, D. J., 82:24 Txk transcription factor, Th1, 80:129 Tyrosine kinase, cellular response differentiation in B lymphocytes, 75:283–308 activation–cellular response connection, 75:304–307 development regulation, 75:284–288 heavy chain selection of preB cells, 75:284–286 mature B cell activation, 75:287–288 mature B cell maintenance, 75:288 tolerance induction of immature B cells, 75:286–287 immunoglobulin-a and -b coreceptors, 75:292–295 overview, 75:283–284, 307–308

200

SUBJECT INDEX

Tyrosine kinase, cellular response differentiation in B lymphocytes (continued) receptor response mechanisms, 75:288–292 B cell response differences, 75:291–292 stage-specific differences, 75:289–291 tyrosine kinase families, 75:295–304 Btk of the Tec family, 75:302–304 Src family, 75:296–300 Syk of the Syk/Zap70 family, 75:300–302 Tyrosine kinases, 68:6, 17; 69:47–49, 51–52, 133; 70:34–35; see also Protein tyrosine kinases, C-kit, 69:67–69 Tyrosine kinases, PLC-g1 interaction, 79:103–104 Tyrosine phosphatase, 69:49–50 Tyrosine phosphatases, 70:33–34 Tyrosine phosphorylation, 68:17, 93; 71:148–149 Btk, 77:129–132 PLCg, 77:144–145 Tyrosine residues, 69:189, 191–192, 211, 221–222 Tyrosine-based activation motif, 69:188–189 Tyrosine-based activator (ITAM), 82:156 Tyrosine-based inhibitor (ITIM), 82:156

U U-rich sequence-binding proteins, 68:34 Ubiquitin system, 68:204 Ubiquitin, conjugation, and protein degradation, 80:3–6 Ubiquitination, in antigen presentation, 80:25–26 Ulcerative colitis, 72:213 Ultraviolet light, 68:27, 102, 103, 105 UNG, see Gene(s) uNK cells, see Uterine natural killer cells Uterine natural killer cells human, 79:307–310 mammalian species, 79:310 in pregnancy colony stimulating factor-1 production, 79:311–312 cytolytic activity, 79:315–318 epidermal growth factor production, 79:312 interferon-g production, 79:313–314 interleukin-1 production, 79:312–313 leukemia inhibitory factor production, 79:313 uteroplacental unit, 79:318–321 rodent GMG cell relationship cell differentiation, 79:306–307 morphology and phenotypes, 79:302–305 origin, 79:300–302 overview, 79:299–300

SUBJECT INDEX

Uteroplacental unit, 79:318–321 Uterus, changes during pregnancy, 79:298–299 Uveitis oral tolerance, 73:231 tolerance models, 73:216–217 Uveitis, experimental autoimmune, 68:371 Uveoretinitis, experimental, 70:162

V Viral inhibition Vaccination(s) active, 82:52–54 anti-MUC1, 82:257 booster, 82:80–83 for cancer, 82:53–54 children and, 82:49 preventive, 82:49 strategies, 82:61–84 therapeutic, 82:49 Vaccination, DNA, 69:362–364 Vaccination, in elderly, 80:265–266, 272 Vaccination, T cell receptor peptide, 68:387–389 Vaccinations, 70:148–151 Vaccine design, and neutralizing antibodies, 77:247–248 Vaccines adjuvants, 71:331–333 alphavirus-based cancer, 82:79–80 cancer treatment, 75:235–236 DC-based, 82:271–276 DNA, 73:340–341; 82:66–69, 67, 74–75, 78–79, 271

201

gentle fusion, 82:69–71 hepatitis B, 82:49 intracellular bacteria immunization, 75:1–63 animal models, 75:5–6 bacteria characteristics, 75:12–26 acquired immune response, 75:15–20 antigen-processing pathways, 75:14–15 innate immune response, 75:13–14 memory, 75:23–25 mucosal immunity, 75:20–23 quantitative correlates of protection, 75:25–26 genome to antigen transition, 75:59–61 DNA microarrays, 75:59–60 genome microarrays, 75:59–60 proteomics, 75:60–61 vaccinomics, 75:61 immunotherapy, see Immunotherapy infectious disease characteristics, 75:7–12 chlamydial infections, 75:11–12 listeriosis, 75:10–11, 38–39 salmonellosis, 75:8–10 tuberculosis, 75:3, 7–8 nomenclature, 75:3–5 overview, 75:1–7, 61–63 T cells role, 75:6–7 vaccine characteristics, 75:26–59

202

SUBJECT INDEX

Vaccines (continued) adjuvant vaccines, 75:31–33 antigen carrier role, 75:49–55 antigen physicochemistry, 75:27–28 attenuated mutations, 75:47–48, 53 BCG mutations, 75:46–47 conserved versus specific proteins, 75:28–30 defined mutations, 75:43–46 dendritic cells, 75:34–35 DNA delivery vectors, 75:58–59 DNA vaccines, 75:35–41 heat shock proteins, 75:29, 33–34 host adjuvants, 75:33–35 live vaccines, 75:41–49 M. tuberculosis mutations, 75:46–47 phagosomal escape function transfer, 75:56–58 protective antigen features, 75:27–31 r-carrier compartmentalized expression of antigens, 75:55–56 recombinant bacterial carrier expression, 75:30–31 Salmonella mutants, 75:42–46 undefined mutations, 75:42–43 MUC1, 82:269–275, 276–281, 282–284, 283 naked DNA, 71:333–335 peptide, 82:269–271

prophylactic allergy, 82:142 protective antigens, 71:328–329 recombinant vaccinia virus, 82:276 RNA, 82:83–84 strains, 71:329–331 strategies, 71:326–328 subunit, 71:331–333 TCD8þ eliciting, 73:25 VP22-E7, 82:74 Vaccines, antibody neutralization, 79:32–33 Vaccines, tumor active vaccination and, 82:52–54 DNA, 82:68–71, 74–75, 78–79 evasion/tolerance of, 82:55–58 gene-based, 82:66 glycloproteins/proteins as, 82:61–64 introduction to, 82:49–58 passive immunotherapy and, 82:49–52 peptides and, 82:64–66 RNA vaccines and, 82:83–84 strategies for, 82:61–84 tumor antigens and, 82:58–61, 60 Vaccinia virus, 69:361, 378, 379–380; 71:106 Vaccinia, 70:344–346 Vancurova, I., 82:22 Vanin-1, 69:87–88 Variable domain, in heavy-chain antibody H chain, 79:266–269 Variant Creutzfeldt–Jakob disease (vCJD), 81:124, 137 Variola virus, 69:379–380 Vascular cell adhesion molecules inflammatory response, 72:351–353

SUBJECT INDEX

integrin ligand domains, 72:331–332, 334 lymphocyte homing, 72:220–221 Vascular endothelial growth factor, 73:420–421 Vascular inflammation, 69:354 Vascular permeability, 82:331–332 regulation of, 82:345–349, 348 Vasculitis, 68:352, 364 Vasoactive intestinal peptide, 79:81 Vasodilator-stimulated phosphoprotein (VASP), 81:68 Vav G protein regulation, 72:68–69 Ras activation, 72:12–14 Rho signals, 72:34–35 Vav guanine-nucleotide exchange factor, 73:101–102 Vav protein family, lymphocyte signaling characteristics, 75:95–98 activation mechanisms, 75:97 signaling mechanisms, 75:97–98 Vav1 structure, 75:96 WASP-deficient mouse phenotype compared, 75:107–108 Vav/Rac pathway, T cell signaling, 77:9–13 VAV, high-affinity immunoglobulin E receptor FceRI signal transduction, 76:337–338 VCAM, 69:354 V(D)J gene rearrangement, 69:144–145 and chromatin, 69:317 Ig assembly theories, 69:116–120

203

in immunoglobulins, 69:119–129 instability, 69:310–311 interlocus, 69:311 intralocus, 69:312 joins, productive and nonproductive, 69:312 in nonlymphoid cells, 69:316 phases, 69:313–316 products of, 69:310–311 and RAG genes, 69:313–315, 316 and recombinational accessibility, 69:309–352 regulation, 69:316–318 and TdT, 69:315 and XRCC4 gene, 69:315 V(D)J rearrangements, 79:3 V(D)J recombination, 72:182–185; 77:313–314 antigen receptor loci structure, 78:170, 172 transcriptional control elements and sterile transcripts, 78:172–174 chromatin structure and accessibility DNA methylation of CpG motifs hypomethylation and transcription, 78:184–186 Igk locus methylation, 78:185 methyl cytosine binding protein function, 78:183–184 methyltransferases, 78:184 DNase sensitivity and recombination, 78:186–188

204

SUBJECT INDEX

V(D)J recombination (continued) b-globin locus transcription cis-acting elements as assembly platforms, 78:182–183 histone acetylation, 78:187–188 linking model, 78:193 looping model, 78:192 model for V(D)J recombination, 78:179 organization and expression, 78:182 heterochromatin versus euchromatin, 78:181 high-mobility group protein effects on RAG cleavage, 78:188–189 histone acetylation, 78:188 interchromatin granules and splicing factors, 78:181 nucleosome remodeling complexes, 78:189–190 structure, 78:179 promoter exposure, 78:189 sterile transcripts, 78:190–191 transcription site visualization, 78:182 developmental pattern of recombination events, 78:172 DNA recognition and cleavage by RAG proteins, 78:174–176 end processing and joining, 78:176–177 errors in lymphoid malignancy, 78:170

immunoglobulin heavy chain gene assembly and cis-acting control elements D-to-J rearrangement, 78:194–196, 199–200 KI/KII region, 78:197 MARs knockout effects, 78:194, 196–197 ordered rearrangement and allelic exclusion, 78:199–201 overview, 78:193–194 PDb1 element, 78:195–196 PDQ52 element, 78:194–195, 209 TEA element, 78:196 V-to-DJ recombination, 78:197–200 V-to-J recombination, 78:196–197 overview, 78:169 RAG protein expression regulation, 78:177–179 recombination signal sequences accessibility modeling, 78:213–215 chromatin unfolding for access, 78:181, 189 recognition, 78:172 restrictions on productive interactions, 78:211–213 substrate matching, 78:213 synapsis of endogenous sequences, mechanisms, 78:209–211 transcription and recombination dependence, 78:191 12/23 rule, 74:90–91; 78:212

SUBJECT INDEX

regulation BSAP, 78:206–207 E2A, 78:201–203 early B cell factor, 78:206 ETS proteins, 78:203–204 Igb, 78:208 Ikaros, 78:208 interleukin-7 receptor, 78:207 mE3-binding proteins, 78:204–205 Oct1, 78:205–206 Oct2, 78:205–206 overview, 78:170 PU.1, 78:203–204 Sox-4, 78:208–209 T cell development, 78:120, 169 V(D)J recombination, B cell receptor editing, 74:89–114 12/23 rule, 74:90–91 allelic exclusions, 74:96–100 feedback suppression of recombination, 74:98 immunoglobulin-L chain, 74:99–100 mechanisms, 74:97–98 selective factors, 74:97–98 stochastic factors, 74:97 antigen-reactive B cells, 74:108–110 antigen receptor gene assembly, 74:89–90 clonal versus receptor selection, 74:89 developmental stage specificity, 74:107–108 editing analysis, 74:102–104 gene-targeted antibody gene mouse, 74:102–104 immunoglobulin genes, 74:91–92

205

in vivo monitoring, 74:100–102 locus specificity, 74:106–107, 110–111 mature B cells, 74:108–110 overview, 74:89, 114 quasi-ordered rearrangements, 74:95–96 receptor diversification, 74:108 receptor revision, 74:108–111 receptor selection concept problems, 74:112–114 allelic inclusion, 74:113 disease applications, 74:113–114 need, 74:113 rearrangement possibilities, 74:112 receptor versus clonal selection, 74:89 recombination signals, 74:90–91 recombinational accessibility, 74:94–95 secondary rearrangements, 74:92–94 RS/kde element, 74:93–94 tolerance developmental block association, 74:104–106 transgenic models, 74:100–102 V(D)J recombination machinery, 81:254 Vectors administration, 69:362, 364–365 and antigen presentation, 69:382–387 and CpG motifs, 69:372–375 and cytokines, 69:366–371, 386 effects on immune system, 69:375–387

206

SUBJECT INDEX

Vectors (continued) gene transfer products, immunity to, 69:362–366 and local versus systemic immunosuppression, 69:365–366 temperature-sensitive, 69:366 viral, 69:354–361 Vectors, bacterial DNA delivery, 75:58–59 VEE, see Venezuelan equine encephalitis VEGF, 81:193; see Vascular endothelial growth factor VEGF-R, 81:265 Venezuelan equine encephalitis (VEE), 82:79 Venezuelan equine encephalomyelitis virus, 77:232–233 Venoocclusive disease, hepatic, 70:517 Ventricular zone cerebral cortex, 77:303–304 neuroblast programmed cell death, 77:309–313 Vertebrates, immune response, 79:226 Very low density lipoprotein, 69:366 Vesicle fusion, 70:382–383 Vesicular stomatitis virus antibody protection against, 77:231–232 neutralization, 77:209 Vesicular stomatitis virus, 70:346–347 Vesicular traffic, principles and components of, 81:62–64 Vesicular transport, 68:174

VESPR/CD232/plexin-C1, 81:192 VHH-D-J genes, 79:272–274 VHH genes antigen-binding loop structures, 79:286–289 antigen-specific, isolation immune libraries, 79:281–284 monoclonal VHH, 79:277–281 polyclonal VHH, 79:276–277 biotechnological role, 79:289–290 overview, 79:270–272 structure, 79:285 VL-side conformation, 79:285–286 Vinblastine, 68:110 Vincristine, 68:110, 224 Vinyl sulfones dendritic cells treated with, 80:90 inhibitors of cysteine proteases, 80:82–85 VIP, see Vasoactive intestinal peptide Viral inhibition CD8þ cells, 66:273–275, 281 cell-mediated effects, 66:286–287 cytolysis, 66:283–286, 287–291 HIV-1 specific lytic activity, 66:275–277, 283–286 mechanism, 66:280–291 chemokines and, 66:281–282 interleukin-16, 66:283 Virions HIV-1, 77:213

207

SUBJECT INDEX

host cell-derived proteins incorporated into, 77:222 neutralization, by coating with complement, 77:210 particles, antibody coating of, 77:214–219 Virolysis, complement-mediated, 77:225–226 Virosomes, 73:42–44 Virulence, pathogenicity compared, 75:3 Virus-encoded semaphorin protein receptor (VESPR), 81:177 Virus-like particles, 73:38–42 Virus, Epstein-Barr (EBV), 82:50–51, 57 Virus, herpes simplex (HSV-1), 82:195–196 Virus, human papilloma (HPV), 82:63 Virus, potato X (PVXCP), 82:70 Virus, Semliki Forest (SFV), 82:79 Virus, Sindbis (SIN), 82:79 Viruses, 72:295–298 B cell unresponsiveness, 79:18–19 infections, T-cell-dependent B cell activation, 79:16–17 neutralization immunosuppression, 79:22–23 infection enhancement, 79:22 outside immune system, 79:21–22 neutralizing antibody response, 79:3–4 hepatitis B virus, 79:26 hepatitis C virus, 79:26 HIV, 79:26–27 influenza virus, 79:25–26

lymphocytic choriomeningitis virus, 79:27 sensitivities, antibody neutralization vs. tropism, 79:23–24 Viruses, see also specific virus as apoptosis inducers, 68:53 caspase inhibitors in, 68:60 and cytotoxic T cells, 68:53 peptide transport inhibition by, 68:234–235 and T cell death, 68:93 Viruses, see also specific viruses and adhesion molecules, 69:386 and complement system, 69:295 and cytokines, 69:386 mimicry, 69:212–215 as vectors, 69:354–361, 375–387 Viruses, alpha, 82:79–80, 83–84 Viruses, antigen expression in human cancer, 75:235–240, 256 Viruses, inactivated, 73:23–24 Viruses, reduction of antigen presentation, 80:50 Vitronectins, 82:343 VLDL, see Very low density lipoprotein VLP, see Virus-like particles Vomeronasal organ, 69:427–428 von Pirquet, Clemens, 82:105 von Willebrand factor, 79:170 VP-16, 68:62, 105, 224

W WASP, see Wiskott–Aldrich syndrome protein Waves, see Ontogenetic waves

208

SUBJECT INDEX

WEHI-231 cells, 73:125–126 West Nile virus, 69:386 Western equine encephalitis virus, neutralization, 77:201 Wilson’s disease, 73:284–285 Wiskott–Aldrich signaling protein, lymphocyte signaling actin regulation, 75:92–94, 104–107 cytoskeleton regulation, 75:105–107 structure, 75:102–104 Vav-deficient mouse phenotype compared, 75:107–108 Wiskott–Aldrich syndrome, 75:100–104 Wiskott-Aldrich syndrome, 68:169; 72:63–64 Wiskott Aldrich Syndrome Protein (WASP), 81:58, 68 Wiskott–Aldrich syndrome protein, 77:11–13, 75, 130–131, 141 Women, 82:260–261 Worm models, allergic airway disease, 77:266 Wound healing cytokine role in vivo, 73:474–475 HGF production, 73:421 LDGF production, 73:423 TGR-a production, 73:418–419

X Xenopus, transforming growth factor-b signaling by Smad proteins, 75:123–124

X-linked agammaglobulinemia bone marrow pre-B cells, 77:125–127 Btk defect causing, 77:124–125 X-linked agammaglobulinemia, 72:159–160 X-linked lymphoproliferative disease, 73:122 X-ray crystallography, 82:166, 179, 193 Xenograft rejection acute humoral, see Acute humoral xenograft rejection humorally mediated, 79:134–135, 150 Xenotransplantation acquired cellular responses, 79:148–150 allogeneic hematopoietic cells, 79:177–180 coagulation disturbances clotting, 79:155 disordered thromboregulation, 79:152–153 disseminated intravascular coagulation, 79:153 fibrinolytic abnormalities, 79:154–155 natural anticoagulants, 79:153–154 platelet agonists, 79:152 platelets, 79:155 prevention, 79:169–171 regulators, 79:153–154 thrombotic diathesis, 79:152 xenogenic molecular incompatibilities, 79:153 concordant vs. discordant, 79:133

209

SUBJECT INDEX

early attempts, 79:130 endothelial cell activation AXHR, 79:151–152 HAR, 79:150 ethical issues, 79:188–190 future research, 79:190–192 genetic engineering donor modification, 79:166–169 recipient modification, 79:164–165 heart, 79:130–131 humoral responses acquired, 79:135–142 innate, 79:134–135 overview, 79:133–134 immunosuppression accomodation, 79:160 antidiotypic antibodies, 79:159 anti-Gal antibodies, 79:157–161 cellular response, 79:163–164 complement, 79:161–162 human immunoglobulin, 79:159 induced antibody response, 79:162–163 infectious agents, 79:187–188 innate cellular responses gamma–delta T cells, 79:142–143 macrophages, 79:146–148 monocytes, 79:146–148 natural killer cells, 79:143–146 neutrophils, 79:148 NK/T cells, 79:142 kidney, 79:130

liver, 79:131 mixed hematopoietic cell chimerism, 79:171–177 models, 79:155–157 necessity, 79:129–130 pharmacotherapy, 79:181–182 physiological barriers, 79:184–187 pig donor, 79:131–133 pig-to-primate model, 79:180–181 thymus, 79:182–184 xenogeneic hematopoietic cells, 79:177–180 XID mouse, B cell defects, 77:127–128 XLA, see X-linked agammaglobulinemia XLP, see X-linked lymphoproliferative disease XRCC4 gene, 69:315

Y Yang, M. F., 82:72 Yarden, Y., 82:7–9 Yeast a-mating factor, 68:151 endoplasmic reticulum protein in, 68:198 genes for prenyltransferases of, 68:152 methylation in, 68:157 prenylated proteins in, 68:175 proteasomes of, 68:200–201 Ras2 and adenylyl cyclase, 68:164 Yersinia entercolitica, 81:66

210

SUBJECT INDEX

Yersinia pseudotuberculosis, 81:79 Yersinia, 81:65 Yolk sac, 81:262–264 YxxL-motif, 69:188–189

Z ZAP-70 69:197–198; 71:237 CD3 complex, 72:57 characterization, 72:118 recruitment, 72:121–122 ZAP-70 kinases, CD40-induced activation, 76:140–143 ZAP-70, LAT and, 77:6–7 Zebrafish, 69:441 advantages in studying immune system, 81:254–256 attraction of early macrophages to wounds, 81:267 autonomous immune function of early macrophages, 81:265–267 B-cell development in pancreas, 81:284–285 B-cells, 81:255 characteristics and life cycle, 81:295–296 in development of immune system, 81:253–328 early macrophages, 81:261 embryo, 81:261–262, 301 hematopoietic regions, 81:262 expression of genes involved in T-cell lymphopoiesis and thymic organogenesis, 81:276 expression of Hox-11 in larvae, 81:288

F2 genetic screen design, 81:300 functional characteristics of early macrophages, 81:264–265 gene-targeting strategies, 81:308–309 genetic mutations, 81:298–299 genomics, 81:312–314 GFP transgenes to define zebrafish blood lineages, 81:291–294 granulocytes, 81:267–268 hematopoiesis in, 81:290 hematopoietic cell transplantation (HCT), 81:291 impact on immunology, 81:314–315 innate immune system, 81:260–268 innate immunity, 81:268 lineage separation by light scatter characteristics, 81:289–291 lymphoid library, 81:282 M-CSF receptor, 81:265 mapping and positional cloning, 81:255 natural killer (NK) cells in, 81:268–272 phenotypic characterization, 81:289–295 rostral-most lateral mesoderm, 81:263 screens for lymphoid mutants, 81:305–306 secondary lymphoid tissues, 81:287–289 spleen, 81:287

SUBJECT INDEX

T-cell ontogeny, 81:280–282 target-selected mutagenesis, 81:307 TCRa genes, 81:280 thymic organogenesis, 81:277–279 as vertebrate model system for forward genetic screens, 81:295–305 Zebrafish Genome Project (ZGP), 81:270, 271

ZFIN database, 81:312 Zinc, 68:55, 56, 156, 157 Zinc finger proteins, 68:32 Zinc finger transcription factor, 69:56 Zipper mechanism, 71:269 Zymogen, 69:276, 286 Zymogens, protease, 82:340 Zymosan, 82:227–228 Zymosan, Toll-like receptor recognition, 78:32

211

CONTRIBUTOR INDEX

Boldface numerals indicate volume number

A

Bernstein, Ralph M., 70:417 Bertocci, Barbara, 80:183 Bierer, Barbara E., 77:1 Bolland, Silvia, 72:149 Born, Willi, 71:77 Botto, M., 76:227 Brandt, Eric B., 78:291 Breedveld, F. C., 68:333 Briskin, Michael, 72:209 Brocker, Thomas, 68:257 Bromberg, Jonathan S., 69:353 Bryant, Paula Wolf, 80:71 Bucala, Richard, 66:197 Burkhardt, H., 68:333 Burmester, G. R., 68:333 Burton, Dennis R., 77:195 Butcher, Eugene C., 72:209

Aarden, Lucien A., 66:101 Aguzzi, Adriano, 81:123 Akira, Shizuo, 78:1 Alajez, Nehad M., 82:249 Alt, Frederick W., 69:113; 75:89 Altman, Amnon, 72:1 Amemiya, Chris T., 81:253 Andersen, Mads Hald, 78:267 Aoufouchi, Said, 80:183 Ardouin, Laurence, 72:103 Arlaud, Ge´rard J., 69:249

B Baba, Yoshihiro, 77:123 Bachmann, Martin F., 79:1 Baggiolini, Marco, 74:127 Bahram, Seiamak, 76:1 Ball, T., 82:105 Banchereau, Jacques, 72:255 Bauch, Angela, 75:89 Bell, Dianas, 72:255 Bennink, Jack R., 73:1 Benoist, Christophe, 82:217

C Cady, Carol, 71:77 Cai, Shenghe, 82:331 Cantor, Harvey, 75:209 Carlos, Casey A., 82:249 Carosella, Edgardo D., 81:199 Carroll, Michael C., 74:61 213

214

CONTRIBUTOR INDEX

Cassatella, Marco Antonio, 73:369 Catic, Andre´ , 81:253 Ceredig, Rhodri, 71:1 Chattopadhyay, Sisir K., 81:97 Chaveau, Christine, 75:317 Chess, Andrew, 69:437 Chtanova, Tatyana, 78:233 Chun, Jerold, 77:297 Ciurea, Adrian, 79:1 Clark, Dawn R., 73:301 Clark, Edward A., 73:79 Cogne´ , Michel, 75:317 Collins, Helen L., 71:267 Cooper, David K. C., 79:129 Coutts, Stephen M., 70:507 Coyle, Anthony J., 77:263 Crabtree, G. R., 75:89 Craxton, Andrew, 73:79

D Dahan, Auriel, 80:183 Damme, Jo Van, 81:1 Dausset, Jean, 81:199 Davis, III, Alvin E., 82:331 de Smet, Annie, 80:183 de Boer, Rob J., 73:301 Debruyne, Lisa, 69:353 Deckert, Marcel, 72:1 Decourt, Catherine, 75:317 Delbos, Fre´ de´ ric, 80:183 Desmyter, Aline, 79:261 Dijke, Peter ten, 75:115 Durandy, Anne, 82:295

F Faili, Ahmad, 80:183 Faria, Ana, 73:153 Fehling, Hans Jo¨ rg, 69:1; 71:1 Fehr, Thomas, 79:1 Ferrier, Pierre, 69:309 Ferrone, Soldano, 74:181 Fiebiger, Edda, 80:71 Finn, Olivera J., 82:249 Fischer, Alain, 82:295 Flatter, Eric, 80:183 Focke, M., 82:105 Fredrickson, Torgny N., 81:97 Frey, Ste´ phane, 80:183

G Gatfield, John, 81:45 Ghebrehiwet, Berhane, 66:225 Ghetie, Victor, 82:155 Gilfillan, Susan, 71:1 Gillet, Anne, 72:103 Ginsberg, Mark H., 72:325 Goldberg, Alfred L., 80:1 Gonzalo, Jose-Angel, 77:263 Gordon, Siamon, 68:271 Gorman, James R., 69:113 Grammer, Amrie C., 76:61 Grubeck-Loebenstein, B., 80:243 Grusby, Michael J., 71:145 Gutierrez Ramos, Jose-Carlos, 77:263

H E Edmunson, Allen B., 70:417 Elliott, Tim, 78:267

Ha¨mmerling, Gu¨nter J., 68:191 Hack, C. Erik, 66:101 Hammer, Juergen, 66:67

215

CONTRIBUTOR INDEX

Harder, Thomas, 77:45 Harris, Lisa J., 72:191 Hartley, Janet W., 81:97 Haurum, John S., 78:267 Heldin, Carl-Henrik, 75:115 Hempel, William M., 69:309 Hengartner, Hans, 70:313; 79:1 Herbomel, Philippe, 81:253 Hess, Ju¨ rgen, 75:1 Hesslein, David G. T., 78:169 Hicklin, Daniel J., 74:181 Hoey, Timothy, 71:145 Hogan, Simon P., 78:291 Hori, Shohei, 81:329 Hsu, Victor W., 70:369 Hsueh, Robert C., 75:283 Hunziker, Lukas, 79:1

Kaplan, Allen P., 66:225 Karjalainen, Klaus, 68:257 Kashiwamura, Shin-ichiro, 70:281 Kastrup, Ingelise Bjerring, 78:267 Kaufmann, Stefan H. E., 71:267; 75:1 Kawabata, Kenji, 71:211 Kettel, Jessica C., 82:249 Khamlichi, Ahmed Amine, 75:317 Kikutani, Hitoshi, 81:173 Kinet, Jean-Pierre, 76:325 Kraft, D., 82:105 Krammer, Peter H., 71:163 Krilis, Steven A., 70:507 Kroemer, Guido, 68:51 Kudo, Ichiro, 77:163 Kumanogoh, Atsushi, 81:173

I Imai, Toshio, 78:57 Isakov, Noah, 69:183 Ishii, Yasuyuki, 74:1 Ishizaka, Kimishige, 74:1

J Jaee, Elizabeth M., 74:181 Jiang, Aimin, 73:79 Jones-Carson, Jessica, 71:77 Joseph, Kusumam, 66:225 Justement, Louis B., 66:1

K Kalden, J. R., 68:333 Kalinke, Ulrich, 79:1 Kandiah, David A., 70:507

L Lo¨ hning, Max, 80:115 Lachmann, P. J., 76:227 Lagaudrie`re -Gesbert, Ce´ cile, 80:71 Lahn, Michael, 71:77 Lamarre, Alain, 79:1 Lange, Hans, 80:203 Larson, Steven B., 72:191 Laskay, Tama´ s, 74:275 Le Discorde, Magali, 81:199 Le Maoult, Joe¨ l, 81:199 Leduc, Isabelle, 69:309 Lemke, Hilmar, 80:203 Lennon-Dume´ nil, Ana-Maria, 80:71 Lichtenstein, Lawrence M., 77:93 Lin, Shih-Yao, 72:103

216

CONTRIBUTOR INDEX

Linhart, B., 82:105 Lipsky, Peter E., 76:61 Litman, Gary W., 81:253 Liu, Chau-Ching, 79:297 Liu, Dongxu, 82:331 Lloyd, Clare M., 77:263 Lobell, Robert B., 68:145 Loetscher, Pius, 74:127

Momburg, Frank, 68:191 Monach, Paul A., 82:217 Moreau, Philippe, 81:199 Morse, Herbert C., 81:97 Moser, Bernhard, 74:127 Mothes, N., 82:105 Mukasa, Akiko, 71:77 Murakami, Makoto, 77:163 Murphey, Ryan D., 81:253 Muyldermans, Serge, 79:261

M Ma, Averil, 70:245 Ma, Xiaojing, 79:55 MacGlashan, Jr., Donald W., 77:93 Mackay, Charles R., 78:233 Malissen, Bernard, 72:103 Malissen, Marie, 72:103 Malter, James S., 68:1 Marchalonis, John J., 70:417 Marincola, Francesco M., 74:181 Marquis, David M., 70:507 Mathieu, Noelle, 69:309 Mathis, Diane, 82:217 Matthews, Sharon A., 76:325 McCarty, Tom, 81:97 McCoy, Kathy D., 79:1 McDonald, Patrick P., 82:1 McKnight, Andrew J., 68:271 McPherson, Alexander, 72:191 Medema, Jan Paul, 75:235 Melchers, Fritz, 78:111 Melief, Cornelis J. M., 75:235 Metz, Christine N., 66:197 Miedema, Frank, 73:301 Minn, Andy J., 70:245 Mishra, Anil, 78:291 Miyazono, Kohei, 75:115

N Nadler, Monica J. S., 76:325 Nagasawa, Takashi, 71:211 Naghashfar, Zohreh, 81:97 Nakanishi, Kenji, 70:281 Nakano, Tatsumi, 74:1 Narayana, Sthanam V. L., 69:249 Nelson, Brad H., 70:1 Nemazee, David, 74:89 Nepom, Gerald T., 68:315 Newton, Kim, 76:179 Nezlin, Roald, 82:155 Nguyen, Viet Khong, 79:261 Niederberger, V., 82:105 Nomiyama, Hisayuki, 78:57 Norbury, Christopher C., 73:1

O O’Brien, Rebecca, 71:77 Ochsenbein, Adrian F., 79:1 Oringa, Rienk, 75:235 Okamura, Haruki, 70:281 Ossendorp, Ferry, 75:235 Otipoby, Kevin L., 73:79 Oxenius, Annette, 70:313

217

CONTRIBUTOR INDEX

P Parren, Paul W. H. I., 77:195 Patton, E. Elizabeth, 81:253 Penn, Dustin, 69:411 Penninger, Josef M., 68:51 Peters, Peter J., 70:369 Pickering, M. C., 76:227 Pieters, Jean, 75:159 Pieters, Jean, 81:45 Pinaud, Eric, 75:317 Ploegh, Hidde L., 80:71 Posey Morley, Celeste S., 77:1 Potts, Wayne, 69:411 Proost, Paul, 81:1

Q Qi, Chen-Feng, 81:97 Qin, Lihui, 69:353

R Radbruch, Andreas, 80:115 Raupach, Ba¨ rbek, 75:1 Ravetch, Jerey V., 72:149 Reddigari, Sesha, 66:225 Reed, John C., 73:265 Revy, Patrick, 82:295 Reynaud, Claude-Agne`s, 80:183 Rice, Jason, 82:49 Richter, Anne, 80:115 Robson, Simon C., 79:129 Rock, Kenneth L., 80:1 Rodewald, Hans-Reimer, 69:1 Rolink, Antonius G., 78:111

Rose, David M., 72:325 Rossi, Ve´ ronique, 69:249 Rothenberg, Marc E., 78:291 Rott, Lusijah, 72:209 Rouas-Freiss, Nathalie, 81:199

S Sachs, David H., 79:129 Sakaguchi, Shimon, 81:329 Sali, Andrej, 70:507 Saric, Tomo, 80:1 Schaible, Ulrich E., 71:267; 75:1 Schaniel, Christoph, 78:111 Schatz, David G., 78:169 Scheuermann, Richard H., 75:283 Schluter, Samuel F., 70:417 Schroeder, John T., 77:93 Shen, Shanxiang, 70:417 Sheng, Yonghua, 70:507 Shibayama, Yoji, 66:225 Shimizu, Yoji, 72:325 Silverberg, Michael, 66:225 Sinigaglia, Francesco, 66:67 Snapper, Scott B., 75:89 Solbach, Werner, 74:275 Spitzauer, S., 82:105 Stevenson, Freda K., 82:49 Stockinger, Brigitta, 71:229 Storck, Se´ bastien, 80:183 Strasser, Andreas, 76:179 Struyf, Sofie, 81:1 Sturniolo, Tiziana, 66:67 Sugie, Katsuji, 74:1 Swain, Rachel E., 70:245 Swoboda, I., 82:105 Sykes, Megan, 79:129

218

CONTRIBUTOR INDEX

T Tachibana, Kazunobu, 71:211 Takahashi, Takeshi, 81:329 Taylor, P. R., 76:227 Thielens, Nicole M., 69:249 Thijz, Lambertus G., 66:101 Thompson, Craig B., 70:245 Toes, Rene´ E. M., 75:235 Torrey, Ted A., 81:97 Traver, David, 81:253 Trede, Nikolaus S., 81:253 Trinchieri, Giorgio, 70:83 Trinchieri, Giorgio, 79:55 Tripathi, Raj Kamal, 69:309 Tsukada, Satoshi, 77:123 Tsutsui, Hiroko, 70:281 Turner, Helen, 76:325

V Valenta, R., 82:105 van der Burg, Sjoerd H., 75:235 Victoria, Edward J., 70:507 Vlad, Anda M., 82:249 Volanakis, John E., 69:249 Vrtala, S., 82:105

Weiner, Howard L., 73:153 Weiss, Arthur, 79:93 Weller, Sandra, 80:183 Westritschnig, K., 82:105 Wick, G., 80:243 Willerford, Dennis M., 70:1 Williams, Marna, 72:209 Williams, Michael J., 79:225 Wolthers, Katja C., 73:301

X Xu, Yang, 72:179 Xu, Yuanyuan, 69:249

Y Yablonski, Deborah, 79:93 Yang, Otto O., 66:273 Yefenof, Eitan, 73:511 Yewdell, Jonathan W., 73:1 Yoder, Jerey A., 81:253 York, Ian A., 80:1 Yoshie, Osamu, 78:57 Yoshimoto, Tomohiro, 70:281 Young, James W., 72:255 Young, John Ding-E, 79:297 Youngman, Kenneth, 72:209

W Wagner, Hermann, 73:329 Walker, Bruce D., 66:273 Walport, M. J., 76:227 Watanabe, Dai, 77:123 Weill, Jean-Claude, 80:183

Z Zhu, Delin, 82:49 Zinkernagel, Rolf M., 70:313; 79:1 Zon, Leonard I., 81:253