HIV Protocols

I. Preparation of Virus Particles and Their Analysis 1. Methods for Viral RNA Isolation and PCR Amplification for Sequencing of Near Full-Length HIV-1 Genomes Kimdar Sherefa Kemal, Milan Reinis, Barbara Weiser, Harold Burger 2. Purification of HIV-1 Virions by Subtilisin Digestion or CD45 Immunoaffinity Depletion for Biochemical Studies David E. Ott 3. Calculating HIV-1 Infectious Titer Using a Virtual TCID50 Method Yong Gao, Immaculate Nankya, Awet Abraha, Ryan M. Troyer, Kenneth N. Nelson, Andrea Rubio, and Eric J. Arts II. Methods to Study HIV-1 Replication Section 1. Early Events 4. Cell-free Assays for HIV-1 Uncoating Christopher Aiken 5. Real-Time PCR Analysis of HIV-1 Replication Post Entry Events Jean L. Mbisa, Krista A. Delviks-Frankenberry, James A. Thomas, Robert J. Gorelick and Vinay K. Pathak 6. Analysis of 2-LTR Circle Junctions of Viral DNA in Infected Cells Dibyakanti Mandal and Vinayaka R. Prasad 7. HIV-1 Recombination: An Experimental Assay and a Phylogenetic Approach Michael D. Moore, Mario P.S. Chin, and Wei-Shau Hu 8. Methods of Preparation and Analysis of Intracellular Reverse Transcription Complexes Ariberto Fassati 9. Analysis of Viral and Cellular Proteins in HIV-1 Reverse Transcription Complexes by Co-immunoprecipitation Sergey N. Iordanskiy and Michael I. Bukrinsky 10. Isolation and Analysis of HIV-1 Preintegration Complexes Alan Engelman 11. Bisarsenical Labeling of HIV-1 for Real-Time Fluorescence Microscopy Nathalie J. Arhel and Pierre Charneau Section 2. Late Events 12. Methods for the Study of HIV-1 Assembly Abdul A. Waheed, Akira Ono and Eric O. Freed 13. Assembly of Immature HIV-1 Capsids using a Cell-Free System Jaisri R. Lingappa and Beth K. Thielen 14. Preparation of Recombinant HIV-1 Gag Protein and Assembly of Virus-like Particles in vitro Siddhartha A. K. Datta and Alan Rein 15. Methods for the Analysis of HIV-1 Nucleocapsid Protein Interactions with Oligonucleotides Andrew G. Stephen and Robert J. Fisher 16. Methods for Analysis of Incorporation and Annealing of tRNALys in HIV-1 Shan Cen, Fei Guo, and Lawrence Kleiman III. Specialized Approaches to Study HIV-1 Biology and Pathogenesis 17. Somatic Cell Genetic Analysis to Identify HIV-1 Host Restriction Factors Susana T. Valente and Stephen P. Goff 18. Rapid, Controlled and Intensive Lentiviral Vector-based RNAi Manuel Llano, Natassia Gaznick and Eric M. Poeschla 19. Reverse Two Hybrid Screening to Analyze Protein-protein Interaction of HIV-1 and Cellular Proteins Supratik Das and Ganjam V. Kalpana 20. Methods to Study Monocyte migration induced by HIV-infected cells Vasudev R. Rao, Eliseo Eugenin, Joan Berman and Vinayaka Prasad 21. Novel Mouse Models for Understanding HIV-1 Pathogenesis Aviva Joseph, Kaori Sango, Harris Goldstein IV. Immunological Studies of HIV Section 1. Mucosal Immunology 22. Mucosal Antibody Responses to HIV Zina Moldoveanu and Jiri Mestecky 23. Isolating Mucosal Lymphocytes from Biopsy Tissue for Cellular Immunology Assays Barbara L. Shacklett, J. William Critchfield and Donna Lemongello Section 2. Measuring T cell Responses via Flow Cytometry 24. Quantifying HIV-1-specific CD8+ T-cell Responses Using ELISPOT and Cytokine Flow Cytometry Barbara L. Shacklett, J. William Critchfield and Donna Lemongello 25. Multiparameter Flow Cytometry Monitoring of T cell Responses Holden T. Maecker Section 3. Antiviral Responses 26. Measuring HIV Neutralization in a Luciferase Reporter Gene Assay David C. Montefiori 27. Assessing the Antiviral Activity of HIV-1-specific cytotoxic T lymphocytes Otto O. Yang 28. Methods for Quantitating Antigen-specific T Cell Responses Using Functional Assays in Rhesus Macaques Rama Rao Amara V. Drug Resistant Viruses and Viral Evolution 29. Isolation of Drug-Resistant Mutant HIV Variants Using Tissue Culture Drug Selection Maureen Oliveira, Bluma G. Brenner, and Mark A. Wainberg 30. Virus Evolution as a Tool to Study HIV-1 Biology Ben Berkhout and Atze T. Das