National Institute of Allergy and Infectious Diseases, NIH (eBook)

Dedication 6
Preface 7
Acknowledgments 9
Table of Contents 11
Contributors 15
Part I: Introduction 20
National Institute of Allergy and Infectious Diseases (NIAID): An Overview 21
Part II: Microbiology and Infectious Diseases 28
Section 1: Emerging and Re-Emerging Infections 29
Chapter 1 31
Biotools for Determining the Genetics of Susceptibility to Infectious Diseases and Expediting Research Translation Into Effective Countermeasures 31
1.1 Introduction 31
1.1.1 A Genetically Diverse, Genomically Well Defined Reference Mouse Panel Afford an Ideal Model for a Systems Biology Approach to Infectious Diseases 31
1.1.2 Studies on the Genetics of Susceptibility to Invasive Group A Streptococcal (GAS) Sepsis Illustrate the Utility of RI Mice in Infectious Disease Research 33
References 34
Chapter 2 37
Spore Surface Components and Protective Immunity to Bacillus anthracis 37
2.1 Introduction 37
2.1.1 Spore Surface Structure 37
2.2 Spores and Host Interaction 38
2.3 Spores and Protective Immunity 39
References 41
Chapter 3 43
New Candidate Anthrax Pathogenic Factors 43
3.1 Introduction 43
3.2 History of Anthrax Toxins Discovery 43
3.3 Genetic Evidence of LT Role 44
3.4 LT Potential in Animals and Cell Culture 45
3.5 Anti-LT Therapy in Anthrax 45
3.6 Spore Resistance in the Host, a New Function of LT 46
3.7 Anthrax Apoptosis, Life-Critical Organs, and Inflammation 47
3.8 Candidate New Pathogenic Factors 48
3.9 Anthrax Hemolysins 49
3.10 Anthrax Proteases Other Than LT 49
3.11 Non-cytotoxic Pathogenic Mechanisms 50
3.12 Conclusion 51
References 51
Chapter 4 55
Ehrlichiae and Ehrlichioses: Pathogenesis and Vector Biology 55
4.1 Introduction 55
4.2 Genomic Studies and Potential Virulence Factors 55
4.3 Ehrlichial Monocyte Entry, Developmental Stages, Differential Outer Membrane Protein Expression, and Manipulation of Host Defenses 57
4.4 Clinical Manifestations and Pathology of HME 59
4.5 Current Status of Animal Models 59
4.6 Characteristics of the Protective and Detrimental Immune Responses to Ehrlichiae 61
4.7 Tick Vectors, Ecology, and Ehrlichial Transmission 61
4.8 Conclusions 61
References 62
Chapter 5 65
Multiple Locus Variable Number Tandem Repeat (VNTR) Analysis (MLVA) of Brucella spp. Identifies Species-Specific Markers and Insights into Phylogenetic Relationships 65
5.1 Introduction 65
5.2 Materials and Methods 66
5.2.1 DNA Preparation 66
5.2.2 Identification of VNTR Sequences 66
5.2.3 PCR Screening for Variability 66
5.2.4 MLVA Design and Multiplex PCR Conditions 66
5.2.5 Automated Genotype Analysis 67
5.2.6 Brucella Isolates 67
5.2.7 Phylogenetic Analysis 67
5.3 Results 68
5.3.1 Identification of VNTR Sequences 68
5.3.2 PCR Screening for Variability 68
5.3.3 MLVA 68
5.3.4 VNTR Marker Diversity 68
5.3.5 Brucella Genotypes and Species-Specific Alleles 68
5.3.6 Brucella Genetic Relationships 68
5.4 Discussion 69
References 71
Chapter 6 73
Expression of the MtrC-MtrD-MtrE Efflux Pump in Neisseria gonorrhoeae and Bacterial Survival in the Presence of Antimicrobials 73
6.1 Overview of Neisseria gonorrhoeae , Epidemiology, Antibiotic Resistance, and Resistance to Host Defenses 73
6.2 Efflux Pumps Possessed by N. gonorrhoeae 74
6.2.1 Discovery of Bacterial Efflux Pumps 74
6.2.2 Neisserial Efflux Pumps 74
6.2.3 The MtrC-MtrD-MtrE Efflux Pump System 75
6.3 Regulation of Efflux Pumps and Other Genes Possessed by N. gonorrhoeae 75
6.3.1 Cis -Acting Control Elements Important in Regulating Control of the mtr Locus 75
6.3.1.1 Regulatory Properties of a 13-bp Inverted Sequence 76
6.3.1.2 CE Positioned Upstream of mtrCDE 76
6.3.2 Trans-acting Regulatory Proteins That Control mtrCDE Expression 76
6.3.2.1 DNA-binding and Transcriptional Regulatory Properties of MtrR 76
6.3.2.2 Transcriptional Regulatory Properties of MtrA 77
6.4 Biologic Functions and Significance of the Gonococcal MtrC-MtrD-MtrE Efflux Pump 77
6.4.1 Export of Antibiotics by MtrC-MtrD-MtrE and Clinical Relevance 78
6.4.2 Export of an Over-The-Counter Biocide/ Spermicide N-9 78
6.4.3 Export of Host-Derived Antimicrobials 78
6.4.4 Evidence that the MtrC-MtrD-MtrE Efflux System is Important in Gonococcal Pathogenicity 78
6.5 Conclusions and Future Studies 79
References 80
Section 2: Tuberculosis 83
Chapter 7 85
What can Mycobacteriophages Tell Us About Mycobacterium tuberculosis ? 85
7.1 Introduction: The Challenges of Studying Mycobacterium tuberculosis 85
7.2 The Big Wide World of Bacteriophages 85
7.3 Insights into Mycobacteriophage Genomes 85
7.4 Mycobacteriophage Morphologies 86
7.5 Mycobacteriophage Genetic Mosaicism 86
7.6 How is Genetic Mosaicism Generated? 88
7.7 All in the Phamily 88
7.8 Acquisition of Host Genes by Mycobacteriophages 88
7.9 Development of Mycobacteriophage-based Genetic Tools 89
7.10 Integration-proficient Plasmid Vectors 89
7.11 Development of tRNA Suppressors 90
7.12 Immunity-based Selectable Markers 90
7.13 Recombineering 91
7.14 Physiological Consequences of Phage Integration 91
7.15 Conclusion 92
References 92
Chapter 8 95
Clinical Mycobacterium tuberculosis Strains Differ in their Intracellular Growth in Human Macrophages 95
8.1 Introduction 95
8.2 TB Infection and Disease 95
8.3 Strain-specific MTB Pathogenesis 95
8.3.1 Murine Models of Virulence 95
8.3.2 Macrophage Models of Virulence 96
8.4 Virulence Assessment of Household Transmitted Isolates 97
8.5 Virulence Assessment of Strains of the Beijing Family 97
8.6 Summary 98
References 98
Chapter 9 101
Mechanisms of Latent Tuberculosis: Dormancy and Resuscitation of Mycobacterium tuberculosis 101
9.1 Introduction 101
9.2 In Vitro Models of Mycobacterial Dormancy 101
9.2.1 Semi-anaerobic Model of Non-culturability in M. tuberculosis 101
9.2.2 Growth Under Unbalanced Conditions 102
9.2.3 Mycobacterial NC Forms: Features and Characteristics 102
9.3 Resuscitation-promoting Factor (Rpf) 103
9.3.1 Mechanisms of Rpf Action 103
9.4 Conclusion 105
References 106
Chapter 10 109
Separating Latent and Acute Disease in the Diagnosis of Tuberculosis 109
10.1 Introduction 109
10.2 Antigenics and Genomics: The Key to Improved TB Diagnosis 109
10.3 What Can We Learn From the Magnitude of the Immune Response? 110
10.4 What Can We Learn From the Nature of the Immune Response? 111
10.5 What Can We Learn From the Specificity of the Immune Response? 112
10.6 Conclusions 114
References 115
Chapter 11 119
Mutant Selection Window Hypothesis: A Framework for Anti-mutant Dosing of Antimicrobial Agents 119
11.1 Introduction 119
11.2 Mutant Prevention Concentration 119
11.3 Mutant Selection Window Hypothesis 120
11.4 Stepwise Accumulation of Resistance Mutations 121
11.5 Extension of the Selection Window to Dynamic Systems 121
11.6 Clinical Test of the Window Hypothesis 121
11.7 Correction for Lethal Agents 122
11.8 Concluding Remarks 122
References 122
Section 3: Avian Influenza 125
Chapter 12 127
The NIAID Influenza Genome Sequencing Project 127
12.1 Background 127
12.2 Purpose and Process 127
12.2.1 How to Collaborate With the NIAID Influenza Genome Sequencing Project 128
12.3 Progress To Date 128
12.3.1 Seasonal Human Influenza Virus Collections 128
12.3.2 Avian and Other Animal Virus Collections 129
12.3.3 Scientific Insights 129
12.4 The Future 130
References 131
Chapter 13 133
Lessons From the 1918 Spanish Flu Epidemic in Iceland 133
13.1 Introduction 133
13.2 Materials and Methods 133
13.2.1 Historical and Medical Data 133
13.2.2 Birth Data 133
13.2.3 Statistics 133
13.3 Description of the Epidemic by the Lay Press 133
13.3.1 Arrival of the Flu: Early News 133
13.3.2 Responses by the Health Authorities 134
13.3.3 The Shock and its Aftermath 134
13.4 Description of the Epidemic According to Health Report of the CMO 134
13.4.1 Index Cases and Early Spread of the Epidemic 134
13.4.2 Incubation Period, Attack Rate, and Case Fatality 134
13.4.3 Responses and Quarantine Measures 136
13.5 Dr. Thoroddsen’s Description of the Epidemic 136
13.5.1 Rise and Fall Within 40 Days 136
13.5.2 Characteristics of the Illness 137
13.5.3 The Spanish Flu in Perspective 139
13.6 Summary and Lessons Learned 139
References 140
Chapter 14 141
Control of Notifiable Avian Influenza Infections in Poultry 141
14.1 Introduction 141
14.2 Prevention of AI 142
14.3 Vaccination for AI 142
14.4 Emergency Vaccination 143
14.5 Vaccination Versus Pre-emptive Culling 144
14.6 Prophylactic Vaccination 145
14.7 Conclusions 145
References 146
Chapter 15 149
Understanding the Complex Pathobiology of High Pathogenicity Avian Influenza Viruses in Birds 149
15.1 Introduction 149
15.2 Pathobiology Concepts 149
15.2.1 Ecology and Epidemiology 149
15.3 Critical Virus Factors in Infection and Virulence 150
15.4 Pathogenesis of HPAI Virus Infections in Chickens 150
15.5 Pathobiology of HPAI 152
15.5.1 Gallinaceous Poultry 152
15.5.2 Pathobiology Groups 152
15.5.3 Domestic Ducks and H5N1 HPAI Viruses 154
15.5.4 Other Species of Birds 155
15.6 Summary 157
References 157
Section 4: Prophylactics and Therapeutics for Infectious Diseases 161
Chapter 16 163
Development of Prophylactics and Therapeutics Against the Smallpox and Monkeypox Biothreat Agents 163
16.1 Introduction 163
16.2 Human Poxvirus Diseases 163
16.2.1 Smallpox 163
16.2.1.1 History 163
16.2.1.2 Clinical Disease 164
16.2.1.3 Person-to-Person Transmission 164
16.2.1.4 VARV as a Potential Biothreat Agent 165
16.2.2 Human Monkeypox 165
16.2.2.1 History 165
16.2.2.2 Clinical Disease 166
16.2.2.3 Person-to-Person Transmission of MPXV 166
16.2.2.4 Human Monkeypox: An Emerging Infectious Disease 166
16.2.2.4.1 Increasing Geographic Range 166
16.2.2.4.2 Increasing Incidence of Disease 166
16.3 Recognition of the Threat of Bioweapons and Emerging Infectious Diseases 167
16.4 Historic Prophylactic and Therapeutic Treatments for Human Poxvirus Diseases 168
16.4.1 Smallpox Vaccines 168
16.4.1.1 Traditional Vaccines: Live, Animal Passaged and Virulent 168
16.4.1.2 Type and Frequency of Complications 168
16.4.1.3 Contraindications to Vaccination 168
16.4.2 Vaccinia Immune Globulin (VIG) 168
16.4.3 Antivirals 168
16.5 New Risks Require New Treatment Modalities 169
16.6 A New Paradigm for Licensure of Human Poxvirus Vaccines and Drugs 169
16.6.1 Animal Efficacy Rule 169
16.6.2 Historic Animal Models for Preclinical Evaluation of Human Orthopoxvirus Vaccines and Drugs 170
16.6.2.1 Vaccinia Virus in Mice 170
16.6.2.2 CPXV in Mice 170
16.6.3 New Models for Preclinical Evaluation of Human Orthopoxvirus Vaccines and Drugs 171
16.6.3.1 Mousepox: ECTV in Mice 172
16.6.3.2 Rabbitpox: VACV in Rabbits 172
16.6.3.3 Monkeypox: MPXV in Non-human Primates 173
16.6.4 New Drug Applications and New Biological Licenses for Therapeutic and Prophylactic Treatments of Human Orthopoxvirus Infections 173
16.6.4.1 New Vaccines 173
16.6.4.1.1 Acambis 2000 Vaccine 174
16.6.4.1.2 MVA Vaccine 174
16.6.4.2 New Antivirals 174
16.6.4.2.1 CMX001 174
16.6.4.2.2 ST-246 175
16.6.5 Financing Development of Products for Human Orthopoxvirus Infections That Have No Commercial Market 175
References 175
Chapter 17 181
The Hierarchic Informational Technology for QSAR Investigations: Molecular Design of Antiviral Compounds 181
17.1 Introduction 181
17.2 Materials and Methods 182
17.2.1 Simplex Representation of Molecular Structure (SiRMS) 182
17.2.1.1 1D Models 182
17.2.1.2 2D Models 183
17.2.1.3 3D Models 184
17.2.1.4 4D Models 184
17.2.2 The Whole-Molecule Parameters 184
17.2.3 Statistical Processing 185
17.2.3.1 Validation of QSAR 185
17.2.3.2 Automatic Variable Selection (AVS) Strategy in PLS 185
17.2.3.3 Removal of Highly Correlated Descriptors 185
17.2.3.4 Trend-Vector Procedure 185
17.2.3.5 Genetic Algorithm 186
17.2.4 Estimation of Factors Determining the Interaction With the Biological Target 186
17.2.5 Inverse Task Solution: Molecular Design of Novel Compounds with Given Level of Activity 186
17.2.6 Virtual Screening of Activity: Estimation of Domain Applicability of PLS Models 186
17.2.7 Comparison of HIT with Other QSAR Methods 187
17.2.8 Investigation of Anti-influenza Activity 3,4 187
17.3 Results and Discussion 189
17.4 Conclusion 191
References 195
Chapter 18 197
Antivirals for Influenza: Novel Agents and Approaches 197
18.1 Introduction 197
18.2 NA Inhibitors 199
18.2.1 Intravenous Zanamivir 199
18.2.2 Peramivir 199
18.2.3 A-315675 200
18.2.4 Long-acting NA Inhibitors 200
18.2.4.1 Multivalent LANIs 200
18.2.4.2 CS-8958 201
18.3 Nucleoside Analogs 201
18.3.1 T-705 201
18.3.2 Viramidine and Ribavirin 201
18.4 HA and Attachment Inhibitors 202
18.4.1 DAS 181 202
18.4.2 Cyanovirin-N 202
18.4.3 Entry Blocker (EB) 203
18.5 Protease Inhibitors 203
18.6 Serotherapy 203
18.7 RNA Interference 204
18.8 Interferons 204
18.9 Host Cellular Targets 204
18.10 Combination Chemotherapy 205
References 205
Chapter 19 211
Anti-Infectious Actions of Proteolysis Inhibitor epsilon-Aminocaproic Acid (epsilon-ACA) 211
19.1 Introduction 211
19.2 Materials and Methods 211
19.3 Results and Discussion 212
References 216
Chapter 20 217
A New Highly Potent Antienteroviral Compound 217
20.1 Introduction 217
20.2 Oxoglaucine 217
Section 5: Russian Perspectives in Emerging and Re-Emerging Infections Research 221
Chapter 21 223
Reduction and Possible Mechanisms of Evolution of the Bacterial Genomes 223
21.1 Introduction 223
21.2 Examples of Genome Reduction 223
21.3 Traditional View on the Mechanism of Genomes’ Reduction 225
21.4 Facts that Cannot be Explained by the Universally Recognized Concept of Genome Reduction 225
21.5 Molecular Mechanisms of Genomic Rearrangements 226
21.5.1 Types of Recombination Sites: RNA, Integrons 226
21.5.2 The Role of Movable Elements and Repeats 226
21.5.3 Scenario of Rearrangements 227
21.6 Polynucleotide (Pn)-selection 227
21.7 Pulsing Genome Hypothesis 229
21.7 Do Any Indications of Genome Pulsing Exist? 229
21.8 Conclusion 229
References 230
Chapter 22 233
Interaction of Yersinia pestis Virulence Factors with IL-1R/TLR Recognition System 233
22.1 Introduction 233
22.2 V Antigen Y. pestis (LcrV) 233
22.2.1 LcrV Is a Short- and Long-term Weapon of Y. pestis 233
22.2.2 LcrV of Y. pestis Has Two Binding Sites for Interaction With TLR2 and Receptor-bound Human IFN-gamma 233
22.2.3 Apoptosis Induction in Human Thymocytes by LcrV 68–326 and Human IFN-gamma 235
22.3 Capsular Antigen F1 (Caf1) 235
22.3.1 Biogenesis of Y. pestis Capsule 235
22.3.1.1 Caf1 Biosynthesis and Dimer Formation in the Bacterial Periplasm: Caf1 Dimer is a Minimal Building Block of Capsule 235
22.3.1.2 Hydrodynamic Properties of Caf1 237
22.3.1.3 Caf1 Dimer is a Minimal Cooperative Block of Y. pestis Capsule 238
22.3.1.4 Role of Tyrosine Residues in the Caf1 Dimer Formation 238
22.3.1.5 Spatial Organization of the Capsule 239
22.3.1.6 Theory of Y. pestis Capsule Melting in Aerosol Microdroplets 239
22.3.2 Interaction of Caf1 Dimer With IL-1R on Target Cells and Soluble IL-1beta 240
22.4 Plasminogen Activator (Pla) 240
22.4.1 Interaction of Pla With Human Cells 240
22.4.2 Synergistic Protection of Mice Against Y. pestis by LcrV and Pla 240
22.5 Conclusion 241
References 241
Chapter 23 245
IS481-Induced Variability of Bordetella pertussis 245
23.1 Introduction 245
23.2 The Transposition of IS481 in E. coli Cells 245
23.3 The Transposition of IS481 in B. pertussis Cells 246
23.4 IS481 Transposition in B. pertussis Cells is bvg -Depends Process 247
23.5 IS Transposition is Mechanism for Phase Variation in Bordetella 248
References 248
Chapter 24 251
Microarray Immunophosphorescence Technology for the Detection of Infectious Pathogens 251
24.1 Introduction 251
References 257
Chapter 25 259
Development of Immunodiagnostic Kits and Vaccines for Bacterial Infections 259
25.1 Introduction 259
25.1 Immunoreagents for Immunodiagnostic Kits 259
25.1.1 Polyclonal, Monoclonal, 259
25.1.1.1 Polyclonal Abs (PAbs) 259
25.1.1.2 Monoclonal Abs (MAbs) 260
25.1.1.3 Anti-idiotypic (Anti-Id) Abs 261
25.1.2 Abs With Desired Specificity Obtained Using Other Immunological Approaches (Directed Immunogenesis) 261
25.1.2.1 The Use of Inbred Biomodels With Certain Genotypes Providing Induction of Abs to Some Desired Antigens/Epitopes of a Complex Immunizing Agent and Tolerance to the Others 261
25.1.2.2 Inoculation of Cross-Reactive Immunizing Agents to Newborn Mice Following Injection of the Antigen to 6- to 8-Week-Old Mice 261
25.1.3 Murine Immune Ascitic Fluids as a Source for Obtaining Different Kinds of Abs 262
25.2 Prospects for New Vaccine Development 262
25.2.1 Vaccines Against Pathogens With Extracellular and Intracellular Life Cycles 263
25.2.2 Vaccines With Decreased Reactogenicity and Increased Immunogeneity 264
25.2.2.1 Organisms With Mutation in the Genes of Lipid A: Toxic Part of Bacterial LPS 264
25.2.2.2 Anti-idiotypic Vaccines 264
25.3 Methods for the Control of Biosynthesis of Protective Antigens for Vaccines During Their Manufacture 265
References 265
Section 6: Perspectives in Emerging and Re-Emerging Infections-Research in Central Asia and Caucasus 267
Chapter 26 269
Research in Emerging and Re-emerging Diseases in Central Asia and the Caucasus: Contributions by the National Institute of Allergy and Infectious Diseases and the National Institutes of Health 269
26.1 Introduction 269
26.2 Research Grants 269
References 270
Chapter 27 271
Disease Surveillance in Georgia: Benefits of International Cooperation 271
27.1 Introduction 271
27.2 Surveillance System in Georgia 271
27.3 The National Center for Disease Control and Medical Statistics (NCDC) of Georgia 271
References 273
Chapter 28 275
Epidemiology (Including Molecular Epidemiology) of HIV, Hepatitis B and C in Georgia: Experience From U.S.-Georgian Collaboration 275
28.1 Introduction 275
28.2 Completed Projects 275
28.3 Major Epidemiology Findings 275
28.4 Molecular Epidemiology of HIV 276
28.5 Epidemiology of HCV 278
28.6 Other Accomplishments of the US-Georgian Collaboration 279
Chapter 29 281
The National Tuberculosis Program in the Country of Georgia: An Overview 281
29.1 Background 281
29.2 Methods 281
29.2.1 The Infrastructure of the NTP 281
29.2.2 Political Commitment and Financing 281
29.2.3 Diagnosis of TB 281
29.2.3.1 Laboratory Diagnostic Facilities 282
29.2.4 Tuberculosis Treatment 282
29.2.4.1 Directly Observed Treatment (DOT) 282
29.2.5 Monitoring and Evaluation System 282
29.2.5.1 Permanent Reporting System 282
29.2.5.2 Supervision 282
29.3 Results and Future Plans 283
29.3.1 Administrative/Budgeting Measures 283
29.3.1.1 Political Commitment and Financing 283
29.3.1.2 Partner and Donor Organizations 283
29.3.2 TB Case Finding 283
29.3.2.1 Laboratory Network Optimization 283
29.3.2.1.1 Culture Examination and DST 284
29.3.3 TB Treatment 284
29.3.3.1 DOT 284
29.3.3.2 DR-TB Treatment 284
29.3.3.3 Regular Drug Supplies 284
29.3.4 Permanent Reporting System 284
29.3.5 TB Control in the Penitentiary System 285
29.3.6 Scientific Research on TB in Georgia in the Context of Global Goals 285
29.4 Conclusion 285
References 285
Part III: Human Immunodeficiency Virus and AIDS 287
Chapter 30 289
Virus Receptor Wars: Entry Molecules Used for and Against Viruses Associated with AIDS 289
30.1 Introduction 289
30.2 HIV Entry and Neutralization of Infection 290
30.2.1 The Entry Mechanism of HIV 290
30.2.2 The HIV Neutralizing Antibody Problem 291
30.2.3 A Novel Bifunctional HIV-neutralizing Protein Based on Sequential Receptor Interactions 291
30.3 KSHV Entry and Receptor Identification 292
30.3.1 Entry Mechanisms of Herpesviruses 292
30.3.2 Identification of KSHV Receptor by Functional cDNA Library Screening 292
30.3.3 Potential Significance of xCT for KSHV Pathogenesis 294
30.4 Conclusions 294
References 294
Chapter 31 297
HIV Latency and Reactivation: The Early Years 297
31.1 HIV as a Retrovirus: A New Pathogenic Entity 297
31.2 Surrogate Model Systems for Studying HIV Infection In Vitro 298
31.3 Cytokines as Physiological Factors Controlling HIV Latency and Replication 300
31.4 Cytokine-mediated Modulation of HIV Replication: From Cell Lines to Primary Cells Infected In Vitro or In Vivo 301
31.5 Conclusions and Perspectives 303
References 303
Chapter 32 307
HIV-1 Sequence Diversity as a Window Into HIV-1 Biology 307
32.1 Overview 307
32.2 Complexity of Newly Transmitted Virus 307
32.3 Compartmentalization and HIV-associated Dementia 308
32.4 Source of Compartmentalized Virus in the CNS 309
32.5 Evolution of CCR5 Usage to CXCR4 Usage 309
32.6 CCR5 and CXCR4 Usage Differences Between Subtype B and Subtype C HIV-1 310
32.7 Neutralizing Antibodies Against HIV-1 Env 311
32.8 Conclusion 311
References 312
Chapter 33 317
Human Monoclonal Antibodies Against HIV and Emerging Viruses 317
33.1 Introduction 317
33.2 HIV 318
33.2.1 Anti-HIV Antibodies Elicited by Infection or Immunization 318
33.2.2 HIV-1-neutralizing hmAbs Against the Env 318
33.2.3 Evidence That Antibodies Can Affect HIV-1 Replication in Humans 319
33.2.4 Developing Antibodies With Improved Neutralizing Activity 319
33.2.5 Conclusions (HIV) 319
33.3 SARS-CoV 320
33.3.1 NiV and HeV 321
33.3.2 Conclusions (SARS-CoV and Henipaviruses) 322
References 323
Chapter 34 327
Biological Basis and Clinical Significance of HIV Resistance to Antiviral Drugs 327
34.1 Introduction 327
34.2 Generation of HIV-1 Drug Resistance 327
34.3 Inhibitors of RT 329
34.4 PR Inhibitors 330
34.5 ARV Drug Resistance in Non-B Subtypes of HIV-1 Group M 331
34.6 Transmission of HIV Drug-Resistance 331
34.7 Conclusion 333
References 333
Chapter 35 337
NIAID HIV/AIDS Prevention Research 337
35.1 HIV/AIDS Pandemic 337
35.2 HIV/AIDS Prevention Research 338
35.3 National Institute of Allergy and Infectious Diseases (NIAID) HIV Prevention Research 340
35.4 Conclusion 342
References 342
Chapter 36 345
Epidemiological Surveillance of HIV and AIDS in Lithuania 345
36.1 Introduction 345
36.2 HIV Epidemiological Situation 345
36.3 General Overview 345
36.4 AIDS Cases 348
36.5 HIV/TB Co-infection in Lithuania 350
36.6 HIV Outbreak in Alytus CF 350
36.6.1 State Mental Health Center, Lithuanian AIDS Center, and Prison Department Data, 2005 350
36.6.2 Prison Department Data, 2005 350
36.7 HIV Transmission Through Sexual Contacts 351
36.8 Homosexual Transmission 352
36.9 Heterosexual Transmission 353
36.10 SWs 353
36.11 IDU 353
36.12 Mother-to-Child Transmission 354
36.13 Conclusions 354
References 355
Part IV: Immunology and Vaccines 357
Section 1: Immunomodulation 359
Chapter 37 361
TACI, Isotype Switching, CVID, and IgAD 361
37.1 APRIL, BAFF, and Their Receptors 361
37.2 Isotype Switching 362
37.3 CVID and IgAD 362
37.4 Mutations in TACI Result in CVID and IgAD 363
37.5 Mechanisms of B-cell Deficiency in Patients with TACI Mutations 364
37.6 Penetrance of TACI Mutations 364
37.7 Conclusion and TherapeuticImplications 365
References 365
Chapter 38 367
A Tapestry of Immunotherapeutic Fusion Proteins: From Signal Conversion to Auto-stimulation 367
38.1 Introduction 367
38.2 Costimulator and Coinhibitor Paints 368
38.3 Trans Signal Converter Proteins (TSCP) 369
38.4 Cis Loop-Back Proteins (CLAP) 370
38.5 Mining the Fusion Protein Concept 371
References 371
Chapter 39 375
A Role for Complement System in Mobilization and Homing of Hematopoietic Stem/Progenitor Cells 375
39.1 Introduction 375
39.2 The Role of C in Stem Cell Trafficking 375
39.2.1 Retention, Mobilization, and Engraftment of HSPCs 375
39.2.1.1 Retention of HSPC in BM 375
39.2.1.2 Mobilization of HSPC to PB 376
39.2.1.3 Homing of HSPC After Transplantation 377
39.2.2 Role of C in Inflammation and Tissue Injury 377
39.2.3 C3 is Secreted by BM Stroma Cells and Activated/Cleaved During Marrow Injury 377
39.2.4 C3aR Increases Incorporation of CXCR4 Into Membrane Lipid Rafts and This Increases Responsiveness of the CXCR4 Receptor to an SDF-1 Gradient 378
39.2.5 CR3 Tethers Hematopoietic Progenitor Cells (HPC) to iC3b Deposits on Irradiated Stroma 379
39.2.6 The Need for New Strategies to Improve Mobilization, Homing, and Expansion of HSPC 379
39.3 Conclusion 380
References 380
Chapter 40 383
Post-translational Processing of Human Interferon- gamma Produced in Escherichia coli and Approaches for its Prevention 383
40.1 Introduction 383
40.2 Experimental Procedures 384
40.2.1 Purification of rhIFN-gamma 384
40.2.2 Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) 384
40.2.3 Liquid Chromatography/Electrospray Ionization-Mass Spectrometry (LC/ESI-MS) 384
40.2.4 Gel Filtration Chromatography 384
40.2.5 Kynurenine Bioassay 384
40.2.6 Fluorescence Measurements 385
40.3 Results and Discussion 385
40.3.1 Post-translational Processing of rhIFN-gamma 385
40.3.2 Are rhIFN-gamma Covalent Dimers Biologically Active? 385
40.3.3 Inhibition of Glycation and Stabilization of rhIFN-gamma 387
40.4 Conclusions 389
References 389
Section 2: Autoimmunity 393
Chapter 41 395
B-cell Dysfunctions in Autoimmune Diseases 395
41.1 B Lymphocytes Play Multiple Roles in the Autoimmune Pathologic Process 395
41.2 Multiple Mechanisms Contribute to B-cell Tolerance to Self 396
41.3 Regulation of B-cell Survival 397
41.4 B-cell Longevity and Autoimmunity 398
41.5 B-cell Survival in Human Systemic Autoimmune Disease 398
41.6 Autoimmunity and BcR-mediated Signaling 398
41.7 Therapeutic Implications 399
References 400
Chapter 42 403
A Model System for Studying Mechanisms of B-cell Transformation in Systemic Autoimmunity 403
42.1 Introduction: Evidence for a Strong Association Between Systemic Autoimmunity and B-cell Lymphoma 403
42.2 Evidence to Support a Role for Sustained Ag Drive in Lymphoma Etiology 404
42.3 IL-10 and BAFF as Potential Links Between B-cell Hyperactivity, Systemic Autoimmunity and B-cell Transformation 404
42.4 FasL-deficient Mice as a Model System for Studying Relationships Between Systemic Autoimmunity and B-cell Lymphomagenesis 405
42.5 Activated CD21/CD23lo B Cells are the Likely Precursors of PL 406
42.6 IL-10 Is Not Essential for the Development of Autoimmunity or B-cell Lymphomas in gld Mice 409
42.7 Conclusions 411
References 411
Chapter 43 415
Breach and Restoration of B-cell Tolerance in Human Systemic Lupus Erythematosus (SLE) 415
43.1 Introduction 415
43.1.1 B Cells as Central Pathogenic Players in SLE 415
43.1.2 B-cell Tolerance as a Critical Factor in Autoimmunity 415
43.1.3 Experimental Approaches to the Study of Human B-cell Tolerance 416
43.1.4 B-cell Depletion in the Treatment of SLE 417
43.1.5 Restoration of B-cell Tolerance After Prolonged B-cell Depletion 420
43.2 Discussion 420
References 422
Section 3: Infection and Immunity 425
Chapter 44 427
Dendritic Cells: Biological and Pathological Aspects 427
44.1 Introduction 427
44.2 DC Biology 427
44.2.1 Activation of DCs and Launching of Protective Immunity 427
44.2.1.1 Activation of DCs by Microbial Components 428
44.2.1.2 Activation of DCs by Products of Dying Cells 429
44.2.1.3 DCs as Choreographers of the Immune System 429
44.2.1.4 Activation of DCs by Innate Immune Cells and Tissue Environment 430
44.2.1.5 DC Interaction With Adaptive Immune Cells 431
44.2.2 Maintenance of Tolerance by DCs 431
44.3 DC Subsets 431
44.3.1 Myeloid DC subsets 432
44.3.2 Blood DC Subsets 433
44.3.3 DC Subsets Regulate B-cell Responses 434
44.4 DCs in Diseases 434
44.4.1 DCs in Autoimmunity 434
44.4.2 DCs and Allergy 434
44.4.3 DCs and Infection 435
44.4 DCs and Cancer 435
44.5 Design of Vaccines Through DC Biology 435
44.5.1 Ex Vivo DC-based Vaccines 436
44.5.2 Targeting DCs In Vivo 436
44.6 Conclusion 436
References 436
Chapter 45 447
Immunomic and Bioinformatics Analysis of Host Immunity in the Vaccinia Virus and Influenza A Systems 447
45.1 Introduction 447
45.2 Demonstrating the Success of Bioinformatics-based Epitope Predictions Using VACV as a Model Pathogen 447
45.2.1 Validation of Bioinformatics-based Epitopeprediction in the H-2b Murine Model System 448
45.2.2 Identification of HLA-restricted Class I VACV-specific Epitopes 448
45.2.2.1 VACV-specific CD8+ T-cell Epitope Identification in HLA-transgenic Mice 448
45.2.2.2 VACV-specific CD8 + T-cell Epitope Identification in Human Vaccines 449
45.2.3 Structural Features of the Antigens Recognized by Cellular Immunity 449
45.3 Immune Epitope Database and Analysis Resource (IEDB) and Mapping the Known Immune Responses Against Influenza A Virus 449
45.3.1 The IEDB 449
45.3.2 Populating and Querying the Database and its Associated Analysis Resource 450
45.3.3 An Analysis of the Influenza A Data Available in the Scientific Literature 450
45.4 Conclusion 451
References 452
Chapter 46 453
Immunoreactions to Hantaviruses 453
46.1 What Are Hantaviruses? 453
46.2 Cell Receptors 453
46.3 The Struggle Between Cells and Hantaviruses 454
46.3.1 Monocytes/macrophages 454
46.3.2 Dendritic Cells (DCs) 454
46.3.3 Endothelial Cells 455
46.4 Apoptosis 458
46.5 Conclusion 459
References 460
Chapter 47 463
Innate Immunity to Mouse Cytomegalovirus 463
47.1 Introduction 463
47.2 Macrophages and DCs as Components of the Innate Immunity to MCMV 463
47.3 NK cells and Their Receptors 465
47.4 NK Cells in MCMV Infection: Resistant and Sensitive Mouse Strains 468
47.5 CMV Strategies to Evade NK Responses 468
47.5.1 MCMV Downregulation of NKG2D Ligands 470
47.6 Conclusion 470
References 471
Section 4: Vaccines 475
Chapter 48 477
Research and Development of Chimeric Flavivirus Vaccines 477
48.1 An Introduction to Flaviviruses 477
48.1.1 Flavivirus Overview 477
48.1.1.1 YF 477
48.1.1.2 Japanese Encephalitis (JE) 477
48.1.1.3 Dengue Virus (DV) 477
48.1.1.4 West Nile 478
48.1.2 Wanted: New and Better Vaccines 479
48.1.2.1 YF Vaccine as Exemplar 479
48.1.2.2 JE Vaccines 479
48.1.2.3 Dengue Vaccines in Development 479
48.1.2.4 WN vaccines in development 480
48.1.2.5 CV Vaccines 480
48.2 Construction of Chimeric Flaviviruses 480
48.3 Preclinical Testing of Chimeric Flaviviruses 481
48.3.1 Safety Testing in Animal Models 481
48.3.1.1 Neurovirulence 481
48.3.1.2 Neuroinvasiveness 482
48.3.1.3 Extraneural pathology 482
48.3.1.4 Viremia 482
48.3.2 Efficacy Testing in Animal Models 483
48.3.2.1 Immunogenicity 483
48.3.2.2 Protection 483
48.3.3 Genetic Stability and Vector Tropism 484
48.3.3.1 Genetic Stability 484
48.3.3.2 Recombination Studies 484
48.3.3.3 Vector Transmission 485
48.4 Clinical Development 485
48.4.1 CV-JE 485
48.4.2 CV-DV 486
48.4.3 CV-WN02 487
48.5 Conclusions 487
References 487
Chapter 49 491
Correlates of Immunity Elicited by Live Yersinia pestis Vaccine 491
49.1 Introduction 491
49.2 Results and Discussion 491
49.2.1 Experimental Outline for Immunization in the Murine Model 491
49.2.2 Murine Humoral Responses 492
49.2.3 Murine T-cell-mediated Responses 493
49.2.4 Human Humoral Responses 494
49.2.5 Human T-cell-mediated Responses 495
49.3 Conclusions 497
References 497
Part V: Building A Sustainable Personal Research Portfolio 499
Chapter 50 501
Strategies for a Competitive Research Career 501
50.1 Introduction 501
50.2 Secure Complementary Funding 501
50.3 Identify and Seek Collaborative Opportunities 501
50.4 Identify and Seize Training Opportunities 502
50.5 Gain Access to Research Administration Infrastructure 503
50.6 Overview of the Essential Components for Building a Sustainable Research Portfolio and Biomedical Research Career 503
Chapter 51 505
Selecting the Appropriate Funding Mechanism 505
51.1 Introduction 505
51.2 Investigator-Initiated Research (Unsolicited Applications) 506
51.2.1 Research Grants (R Series) 506
51.2.2 NIH Research Training and Research Career Development Opportunities (F, K, and T series) 507
51.3 Program Project/Center Grants (P series Solicited or Unsolicited Applications)
51.4 Responding to an Institute-Specific FOAs (Solicited Applications) 511
51.5 Support for International Research 512
Chapter 52 515
Preparing and Submitting a Competitive Grant Application 515
52.1 Introduction 515
52.2 Why Applications Succeed or Fail in the Peer-Review Process 515
52.3 Developing a Competitive and Successful Application 516
52.3.1 Strategies for Success 516
52.3.2 Checklists for the Application Process 516
52.3.3 Advice for New Investigators 517
52.4 The Review Criteria 517
52.4.1 Significance 517
52.4.2 Approach 517
52.4.3 Innovation 517
52.4.4 Investigator 517
52.4.5 Environment 518
52.5 Submission of the Application 518
52.6 Overview of the NIH Peer-Review System 518
52.6.1 COI and Confidentiality 519
50.6.2 NIAID Scientific Review Staff Roles 519
52.7 What Happens During a Review Meeting 519
52.7.1 Streamlining 520
52.7.2 Assigning Priority Scores 520
52.7.3 Budget Recommendations 520
52.7.4 Post-Review 520
52.8 Conclusion 520
52.9 Additional Resources 520
52.9.1 Registration and Application Submission Process Details 520
52.9.1.1 Registration 520
52.9.1.2 Pre-Application 521
52.9.1.3 The Application Process 521
52.9.2 DHHS, NIH Regulations, Policies and Offices that Affect the Submission, Evaluation, and Management of Awards 522
Chapter 53 525
Identifying Research Resources and Funding Opportunities 525
53.1 Introduction 525
53.2 Glossary of Terms 525
53.3 Literature Searching and Other Database Resources 525
53.3.1 Medical Genetics Resources: 526
53.4 Additional NIH/NIAID Research Resources and Networks 527
53.5 National/International Funding Resources 531
Index 537
Color Plates 549