Adenovirus Methods and Protocols: Volume 2: Ad Proteins and RNA, Lifecycle and Host Interactions, an

Ann E. Tollefson, Mohan Kuppuswamy, and William S. M. Wold TABLE OF CONTENTS Vol. II Topics: Ad proteins and RNA, lifecycle and host interactions, and phylogenetics 1. Analysis of the Efficiency of Adenovirus Transcription Cristina Iftode and S. J. Flint 2. The Use of In Vitro Transcription to Probe Regulatory Functions of Viral Protein Domains Paul M. Loewenstein, Chao-Zhong Song and Maurice Green 3. Preparation of Soluble Extracts from Adenovirus Infected Cells for Studies of RNA Splicing Oliver Mühlemann and Göran Akusjärvi 4. In Vitro Methods to Study RNA Interference During an Adenovirus Infection Gunnar Andersson, Ning Xu and Göran Akusjärvi 5. Simultaneous Detection of Adenovirus RNA and Cellular Proteins by Fluorescent Labeling In Situ Eileen Bridge 6. Study of Nucleolar Localization of Adenovirus Core Proteins David A. Matthews 7. Analysis of Adenovirus Infections in Synchronized Cells David A. Ornelles, Robin N. Shepard and Felicia D. Goodrum 8. Co-Immunoprecipitation of Protein Complexes Peter Yaciuk 9. Chromatin Immunoprecipitation (ChIP) to Study the Binding of Proteins to the Adenovirus Genome in Vivo Jihong Yang and Patrick Hearing 10. Assaying Protein-DNA Interactions In Vivo and In Vitro Using Chromatin Immunoprecipitation and Electrophoretic Mobility Shift Assays Pilar Perez-Romero and Michael J. Imperiale 11. Identifying Functional Adenovirus-Host Interactions Using Tandem Mass Spectrometry Anuj Gaggar, Dmitry Shayakhmetov, and Andre Lieber 12. The Use of Cell Microinjection for the in vivo Analysis of Viral Transcriptional Regulatory Protein Domains Maurice Green, Andrew Thorburn, Robert Kern and Paul M. Loewenstein 13. Determination of the Transforming Activities of Adenovirus Oncogenes Michael Nevels and Thomas Dobner 14. Human Adenovirus Type 12: Crossing Species Barriers toImmortalize the Viral Genome Walter Doerfler 15. Measurement of NK Cell Lytic Activity of Adenovirus-Infected or Adenovirus-Transformed Cells John M. Routes 16. A Flow Cytometric Assay for Analysis of NK Cell-Mediated Cytolysis of Adenovirus-Transformed Cells Graham Bottley, Graham P. Cook, and G. Eric Blair 17. Large Scale Purification and Crystallization of Adenovirus Hexon John J. Rux and Roger M. Burnett 18. Synthesis and Assay of Recombinant Adenovirus Protease Joseph M. Weber 19. Assay for the Adenovirus Proteinase- Purification of the Enzyme and Synthesis of a Fluorogenic Substrate Walter F. Mangel and William J. McGrath 20. Cofactors of the Adenovirus Proteinase: Measuring Equilibrium Dissociation Constants and Stoichiometries of Binding Walter F. Mangel and William J. McGrath 21. Characterization of the Adenovirus Fiber Protein Jeffrey A. Engler and Jeong Shin Hong 22. Phylogenetic Analysis of Adenovirus Sequences Balázs Harrach and Mária Benkö 23. Assessment of Genetic Variability Among Subspecies B1 Human Adenoviruses for Molecular Epidemiology Studies Adriana E. Kajon and Dean D. Erdman