The application of modern methods in molecular biology and biotechnology to the study of human, animal, and plant viruses continues to revitalize the age-old discipline of virology. DNA Viruses: Methods and Protocols not only describes innovative approaches to solving important problems in modern virology, but also provides methodologies that can be equally applied to numerous other biological systems. In order to emphasize the various methodological approaches as they are applied to important questions in virology, this book is divided up into nine sections. These sections include: viral detection, structure, entry, gene expression, replication, pathogenesis, complex cellular models, recombinant genetics, and computational/systems approaches towards virology.
Part I. Viral Detection; 1. Viral Detection; Feng Wang-Johanning and Gary L. Johanning; 2. Quantitative detection of Epstein-Barr virus DNA in clinical specimens by rapid real-time PCR targeting a highly conserved region of EBNA-1; Servi J.C. Stevens, Sandra A. W. M. Verkuijlen and Jaap M. Middeldorp; 3. Profiling of Epstein-Barr virus latent RNA expression in clinical specimens by gene-specific multi-primed cDNA synthesis and PCR; Servi J. C. Stevens, Antoinette A. T. P. Brink, and Jaap M. Middeldorp; 4. Quantitative Detection of Viral Gene Expression in Populations of EBV-Infected Cells In Vivo; Donna R. Hochberg and David A. Thorley-Lawson; 5. Identifying the needle in the haystack: Detection and quantification of the rare latently infected cell undergoing herpes simplex virus transcriptional activation in the nervous system; N. M. Sawtell; 6. Reporter Cell Lines for the Detection of Herpes Simplex Viruses; Szu-Hao Kung; Part II. Virus Structure and Imaging; 7. Unraveling the Architecture of Viruses by High Resolution Atomic Force Microscopy; Alexander J. Malkin, Marco Plomp, and Alexander McPherson; 8. Studying the structure of large viruses with multiresolution imaging; Carmen San Martin; 9. Herpes simplex virus-cell interactions studied by low fading contrasted immunofluorescence; Helle Lone Jensen and Bodil Norrild; 10. Herpes simplex virus-cell interactions studied by immunogold cryosection electron microscopy; Helle Lone Jensen and Bodil Norrild; 11. FTIR Microscopy Detection of Cells Infected with Viruses; Vitaly Erukhimovitch, Marina Talyshinsky, Yelena Souprun, and Mahmoud Huleihel; Part III. Virus Entry; 12. The JC Virus-like particle overlay assay; Hirofumi Sawa and Rika Komagome; 13. Analysis of Fusion Using a Virus-Free Cell Fusion Assay; Marisa P. McShane and Richard Longnecker; 14. Pseudovirions as Specific Tools for Investigation of Virus Interactions with Cells; Martin Sapp and Hans-Christoph Selinka; Part IV. Gene Expression; 15. Simultaneous In Situ Detection of RNA, DNA, and Protein Using Tyramide-Coupled Immunofluorescence; Brian A. Van Tine, Thomas R. Broker, and Louise T. Chow; 16. Identification and Characterization of Herpesviral Immediate-early Genes; Yan Yuan; Part V. Replication and Genome Maintenance; 17. Methods for Measuring the Replication and Segregation of Epstein-Barr Virus - Based Plasmids; Priya Kapoor and Lori Frappier; 18. DNA Affinity Purification of Epstein-Barr Virus OriP-Binding Proteins; Constandache Atanasiu, Larissa Lezina, and Paul M. Lieberman; Part VI. Pathogenesis; 19. Pre-B Cell Colony Formation Assay; Masato Ikeda and Richard Longnecker; 20. Use of Luciferase Real Time Bioluminescence Imaging for the Study of Viral Pathogenesis; Gary D. Luker and David A. Leib; Part VII. Complex Cell Systems; 21. Culturing primary and transformed neuronal cells for studying pseudorabies virus infection; Toh Hean Ch'ng, Enrique Alexander Flood, and Lynn William Enquist; 22. Methods for studying the human papillomavirus type 31 life cycle using tissue culture models; Frauke Fehrmann and Laimonis A. Laimins; Part VIII. Recombinant Genetics; 23. Molecular Genetics of Herpesviruses: A Recombinant Technology Approach; Jason S. Knight, Subhash C. Verma, Ke Lan, and Erle S. Robertson; 24. Molecular Genetics of DNA viruses-recombinant virus technology; Bernhard Neuhierl and Henri-Jacques Delecluse; 25. Genetic Analysis of Cytomegalovirus by Shuttle Mutagenesis; Manfred Lee and Fenyong Liu; 26. Construction of a gene inactivation library for Bovine herpesvirus 1 using infectious clone technology; Timothy J. Mahony, Fiona M. McCarthy, Jennifer L. Gravel, and Peter L. Young; 27. Selective silencing of viral gene E6 and E7 expression in HPV-positive human cervical carcinoma cells using small interfering RNAs