National Institute of Allergy and Infectious Diseases, NIH - Volume 1: Frontiers in Research

von: Vassil St. Georgiev, Karl Western, John J. McGowan

Humana Press, 2008

ISBN: 9781597455695 , 530 Seiten

Format: PDF, OL

Kopierschutz: Wasserzeichen

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National Institute of Allergy and Infectious Diseases, NIH - Volume 1: Frontiers in Research


 

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)

511

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