Problems 433

CHAPTER 22 The Molecular Genetics of Viruses 435

Mutations in genes and resulting changes to proteins 437 Analysis of mutations 438 Complementation 438 Recombination 439 Isolation of mutants 440 Selection 440

HSV thymidine kinase - a portable selectable marker 440 Screening 441 A tool kit for molecular virologists 441 Viral genomes 441

Locating sites of restriction endonuclease cleavage on the viral genome — restriction mapping 442 Cloning vectors 443

Cloning of fragments of viral genomes using bacterial plasmids 444 Cloning using phage A 449

Cloning single-stranded DNA with bacteriophage M13 451 DNA animal virus vectors 451 RNA virus expression systems 453 Defective virus particles 454 Directed mutagenesis of viral genes 454

Site-directed mutagenesis 456 Generation of recombinant viruses 456 Bacterial artificial chromosomes 458 Questions for Chapter 22 461

CHAPTER 23 Molecular Pathogenesis 463

An introduction to the study of viral pathogenesis 463 Animal models 464

Choosing a model: natural host vs. surrogate models 464 Development of new models: transgenic animals 464 Hybrid models: the SCID-hu mouse 464 Considerations regarding the humane use of animals 465 Methods for the study of pathogenesis 466 Assays of virulence 466 Analysis of viral spread within the host 467 Resolving the infection to the level of single cells 470 Characterization of the host response 470 Immunological assays 470

Use of transgenic mice to dissect critical components of the host immune response that modulate the viral infection 471 Question for Chapter 23 471

CHAPTER 24 Viral Bioinformatics and Beyond 473

Bioinformatics 473

Bioinformatics and virology 473 Biological databases 474

Primary databases 474 Secondary databases 475 Composite databases 475 Other databases 476 Biological applications 476 Similarity searching tools 476 Protein functional analysis 478 Sequence analysis 478 Structural modeling 478 Structural analysis 478 Systems biology and viruses 479 Viral internet resources 481 Questions for Chapter 24 484

CHAPTER 25 Viruses and the Future - Problems and Promises 485

Clouds on the horizon — emerging disease 485 Sources and causes of emergent virus disease 488 The threat of bioterrorism 489 What are the prospects of using medical technology to eliminate specific viral and other infectious diseases? 490 Silver linings — viruses as therapeutic agents 490 Viruses for gene delivery 491 Using viruses to destroy other viruses 493 Viruses and nanotechnology 493 The place of viruses in the biosphere 494 Why study virology? 494 Questions for Chapter 25 495 Problems for Part V 497 Additional Reading for Part V 499

APPENDIX Resource Center 501

Books of historical and basic value 501 Books on virology 501

Molecular biology and biochemistry texts 503 Detailed sources 503 Sources for experimental protocols 503 The Internet 504 Virology sites 504

Important websites for organizations and facilities of interest 505

Technical Glossary 507 Index 533

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