Virus-Host Interactions: Methods and Protocols covers various aspects of virological research, such as biochemical approaches, including molecular interactions and regulatory mechanisms on the protein as well as the RNA level with a strong focus on the manifold possibilities to study protein-protein interactions, as well as cell biological and immunological methodologies. Viruses represent a reduced form of life that depends on host cells for propagation. To this end, viruses approach and penetrate cells and usurp cellular machineries for their own benefit. Recent technological improvements have enabled the systematic analysis of the virus-host interplay be it on the genomic, the transcriptomic, or proteomic level. In parallel, bioinformatic tools have emerged in support of the large datasets generated by these high-throughput approaches. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.
Authoritative and easily accessible, Virus-Host Interactions: Methods and Protocols will prove invaluable to professionals and novices with its well-honed methodologies and protocols.
Table of contents
1. A High-Throughput Yeast Two Hybrid Protocol to Determine Virus-Host Protein Interactions
Hannah Striebinger, Manfred Kögl, and Susanne M. Bailer
2. Analysis of Protein-Protein Interactions Using LUMIER Assay
Sonja Blasche and Manfred Koegl
3. Detection of Protein Interactions During Virus Infection by Bimolecular Fluorescence Complementation
Stefan Becker and Jens von Einem
4. Discovery of Host-Viral Protein Complexes During Infection
Daniell L. Rowles, Scott S. Terhune, and Ileana M. Cristea
5. Screening for Host Proteins with Pro- and Antiviral Activity Using High-Throughput RNAi
Samantha J. Griffiths
6. High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay by Metabolic Labelling of Newly Transcribed RNA using 4-thiouridine
Lars Dölken
7. Isolation and Characterization of Pathogen-Bearing Endosomes Enables Identification of New Cellular Cofactors and Analysis of Endosomal Escape
Konstanze D. Scheffer, Ruth Popa-Wagner and Luise Florin
8. Computational Analysis of Virus-Host Interactomes
Caroline C. Friedel
9. Interspecies Heterokaryon Assay to Characterize the Nucleocytoplasmic Shuttling of Herpesviral Proteins
Shuai Wang, Kezheng Wang, and Chunfu Zheng
10. Detection of Integrated Herpesvirus Genomes by Fluorescent in situ Hybridization (FISH)
Benedikt Kaufer
11. Fast Generation of Stable Cell Lines Expressing Fluorescent Marker Molecules to Study Pathogen Induced Processes
Jens Bernhard Bosse, Jessica Ragues, and Harald Wodrich
12. Determination of HSV-1 Infectivity Using a Luciferase Reporter Cell Line
Diana Lieber and Susanne M. Bailer
13. Generation of a Cell Line for Constitutive Expression of Host or Viral miRNAs
Diana Lieber
14. Applications for a Dual Fluorescent Human Cytomegalovirus in the Analysis of Viral Entry
Kerstin Laib Sampaio, Gerhard Jahn, and Christian Sinzger
15. High Temporal Resolution Imaging Reveals Endosomal Membrane Penetration and Escape of Adenoviruses in Real-Time
Ruben Martinez, Andrew M. Burrage, Christopher M. Wiethoff, and Harald Wodrich
16. Three-Dimensional Visualization of Virus Infected Cells by Serial Sectioning - An Electron Microscopic Study Using Resin Embedded Cells
Martin Schauflinger, Clarissa Villinger, and Paul Walther
17. 3D Tissue Model for Herpes Simplex Virus-1 Infections
Ina Hogk, Steffen Rupp, and Anke Burger-Kentischer
18. In vivo Visualization of Encephalitic Lesions in Herpes Simplex Virus Type 1 (HSV-1) Infected Mice by Magnetic Resonance Imaging (MRI)
Wali Hafezi and Verena Hoerr
19. Detection of Antigen-Specific T Cells Based on Intracellular Cytokine Staining Using Flow-Cytometry
Tina Schmidt and Martina Sester
20. Functional NK Cell Cytotoxicity Assays Against Virus Infected Cells
Rebecca J. Aicheler and Richard J. Stanton
21. Assessment of Natural Killer Cell Responses to Human Cytomegalovirus Infected Macrophages
Zeguang Wu, Giada Frascaroli, and Thomas Mertens
22. Analysis of Cell Migration During HCMV Infection
Stefania Varani and Giada Frascaroli
23. Gene Targeting in Mice: A Review
Hicham Bouabe and Klaus Okkenhaug
24. A Protocol for Construction of Gene Targeting Vectors and Generation of Homologous Recombinant ES Cells
Hicham Bouabe and Klaus Okkenhaug
25. Measurement of Mouse Cytomegalovirus Induced Interferon-? with Immortalized Luciferase Reporter Cells
Evgenia Scheibe, Stefan Lienenklaus, Tobias May, Vladimir Goncalves Magalhaes, Siegfried Weiss, and Melanie M. Brinkmann