Contents -- List of Contributors -- Chapter 1 Human Rhinovirus Cell Entry and Uncoating Renate Fuchs and Dieter Blaas -- Introduction -- Rhinovirus Receptor Groups and Subgenera -- Virus Structure -- The Receptors -- Virus-receptor Complexes -- HRV Entry: Endocytic Pathways and Selective Inhibitors -- Entry of Major Group HRVs -- Entry of Minor Group HRVs -- Conversion of Native Virus into Subviral Particles: Role of Receptors and Low pH -- Conversion of Major Group HRVs In Vitro -- Conversion of Major Group HRVs In Vivo -- Conversion of Minor Group HRVs In Vitro -- Conversion of Minor Group HRVs In Vivo -- Mechanism of Genome Uncoating: How is the Viral RNA Delivered into the Cytoplasm? -- Analysis of the Mechanism of Viral Genome Penetration into the Cytoplasm -- Penetration of Major Group HRVs -- Penetration of Minor Group HRVs -- HRV Uncoating at the Plasma Membrane -- Potential Mechanisms of RNA Egress -- What is Known of Receptor Expression and HRV Infection of the Airway Epithelium? -- Concluding Remarks -- Acknowledgments -- References -- Chapter 2 Role of Lipid Microdomains in Influenza Virus Multiplication Makoto Takeda -- Introduction -- Membrane Lipids Form Functional Microdomains -- Lipid Rafts and Viruses -- Influenza Virus Glycoproteins Intrinsically Associate with Rafts -- Raft-Association of Viral Glycoproteins Promotes Influenza Virus Replication -- HA Fusion and Lipid Rafts -- Rafts Function at the Process of Influenza Virus Assembly -- Concluding Remarks -- Acknowledgments -- References -- Chapter 3 Functions of Integrin α2 β1, A Collagen Receptor, in the Internalization of Echovirus 1 Varpu Marjomaki, Mikko Huhtala, Mikko Karjalainen, Timo Hyypia and Jyrki Heino -- Integrin α2 β1 is the Cellular Receptor for Echovirus 1 -- EV1 Binds to α2I Domain in the α2 β1 Integrin and Induces Clustering of the Receptor Molecules.

Clustering of α2 β1 Integrin Leads to Rapid Internalization of the Virus-Receptor Complexes -- EV1 Internalization and Integrin Signaling -- Internalized EV1 is Found in Caveosomes -- Open Questions -- References -- Chapter 4 Entry Mechanism of Murine and SARS Coronaviruses - Similarity and Dissimilarity Fumihiro Taguchi -- Introduction -- S Proteins of Coronaviruses -- Coronavirus Receptors -- Cell Entry Pathways of Coronaviruses -- Mechanism of Cell Entry -- Receptor-independent Entry Mechanism -- Concluding Remarks -- Acknowledgments -- References -- Chapter 5 Hepatitis Viruses, Signaling Events and Modulation of the Innate Host Response Syed Mohammad Moin, Anindita Kar-Roy and Shahid Jameel -- Genome Structure and Organization of Hepatitis Viruses -- Hepatitis A Virus -- Hepatitis B Virus -- Hepatitis C Virus -- Hepatitis D Virus -- Hepatitis E Virus -- The Interferon System -- Events in Virus-infected Cells -- Events in Uninfected Cells -- Regulation of Apoptosis -- Signaling Through the TNF Receptor Family -- Endoplasmic reticulum stress -- Reactive oxygen species (ROS) -- Cell Survival Strategies -- Regulation of the MAP Kinase Pathway -- Regulation of the PI3 Kinase/Akt (PKB) Pathway -- Regulation of the NF κB Pathway -- Conclusion -- Acknowledgments -- References -- Chapter 6 Virus-Cell Interaction of HCV Hideki Tani, Yasumasa Komoda, Chang-kwang Limn, Kensuke Suzuki, Kohji Moriishi, Tatsuo Miyamura and Yoshiharu Matsuura -- Introduction -- Initial Stage of HCV Infection -- HCV-LPs for HCV-cell Interaction -- Pseudotype Virus Systems for Characterization of HCV Infection -- 1) Glycosaminoglycans -- 2) hCD81 -- 3) LDLr -- 4) SR-BI -- 5) DC-SIGN and L-SIGN -- Acknowledgments -- References -- Chapter 7 RNA Replication of Hepatitis C Virus Hideki Aizaki and Tetsuro Suzuki -- Introduction -- Cell Culture Systems for HCV Replication.

Polyprotein Translation and Processing -- RNA Replication Model -- Host Factors Possibly Involved in HCV RNA Replication -- Future Perspectives -- References -- Chapter 8 Structure and Dynamics in Viral RNA Packaging Thorsten Dieckmann and Marta Zumwalt -- RNA-Protein Interactions in Viral RNA Packaging -- Packaging of Viral RNA -- The MS2 Phage -- The RNA Packaging Signal -- The Coat Protein -- The RNA-Coat Protein Complex -- Alfalfa Mosaic Virus -- Retroviruses -- The Nucleocapsid Protein -- The HIV-1 RNA Packaging Signal -- Complexes between the HIV-1 Ψ-site RNAs and the NC Protein -- Packaging of the Dimeric Genome -- RNA-Protein Interaction in Viral RNA Packaging: Present and Future -- Acknowledgements -- References -- Chapter 9 Rational Design of Viral Protein Structures with Predetermined Immunological Properties James Lara and Yury Khudyakov -- Strategies for Protein Design -- Focused Strategy: Mathematical Modeling -- Artificial Neural Networks -- Design of Biomolecules with Desired Antigenic and Immunogenic Properties with Artificial Neural Networks -- T-cell Epitope Prediction -- Artificial Peptide and Protein Design -- Other Computational Strategies for Design of Immunogens -- Evolutionary Algorithms (EAs) -- Probabilistic Graphical Models -- References -- Chapter 10 Bioinformatics Resources for the Study of Viruses at the Virginia Bioinformatics Institute Anjan Purkayastha, Oswald Crasta, J. Dana Eckart, Michael Czar, X. J. Meng, Joao Setubal and Bruno Sobral -- Introduction -- Bioinformatics Resource Centers -- The Pathogen Resource Integration Center (PATRIC) and Annotation and Curation of Microbial Genomic Data -- Genome Curation Process -- Pathogen Background Information -- Schema for Curation of Biological Data -- Genomic Analysis Tools -- The Scientific Community - Outreach and Feedback -- Viruses Curated at PATRIC.

The Genus Coronavirus -- The Caliciviridae Family -- Hepatitis A Virus -- Hepatitis E Virus -- Rabies Virus -- The Pathogen Portal Project (PathPort) -- Outreach Activities at PathPort -- Summary and Conclusion -- References -- Chapter 11 Virus Architecture Probed by Atomic Force Microscopy A. J. Malkin, Yu. G. Kuznetsov, M. Plomp and A. McPherson -- Introduction -- AFM Investigations of High-Resolution Structures of Viruses -- T =3 Icosahedral Viruses -- Herpes Simplex Virus-1 -- Paramecium Bursaria Chlorella Virus Type 1 -- Ty3 Retrotransposon Virus-like Particles -- Vaccinia Virus -- Visualization of Subviral Structures -- Herpes Virus -- Vaccinia Virus -- AFM Visualization of Virus-infected Cells -- Mouse Leukemic Virus-infected Cells -- Human Immunodeficiency Virus-infected Cells -- Acknowledgments -- References -- Chapter 12 Filovirus Assembly and Budding Takeshi Noda and Yoshihiro Kawaoka -- Introduction -- Virion Budding -- The VP40 Protein -- Assembly of VP40 and GP -- Use of Cellular Transport Pathways -- Nucleocapsid Assembly -- Conclusion -- Acknowledgments -- References -- Chapter 13 Challenges in Designing HIV Env Immunogens for Developing a Vaccine Indresh K. Srivastava and R. Holland Cheng -- Summary -- Introduction -- Role of Antibodies in Protection Against HIV -- Possible Steps for Immune Intervention -- Neutralizing Epitopes Relevant for Vaccine Development -- Carbohydrate-dependent Epitopes in gp120 -- Protective Efficacy of Neutralizing Monoclonal Antibodies in Passive Transfer -- Challenges in Inducing Antibodies of Approriate Specificity with Broadly Neutralizing Activity -- Strategies to Design Immunogens that may Induce Neutralizing Antibodies of Protective Specificities by Vaccination -- A. Structural Optimization to Target Conserved Neutralization Epitopes -- (i) Native trimers as immunogen.

(ii) Triggered Env: targeting conformational epitopes -- (iii) Rational design of Env immunogen -- Structure-based Targeted Deglycosylation -- Hyper-glycosylation for Focusing the Immune Response Toward Neutralizing Epitopes Recognized by b12 -- Directing the Immune Response Toward the CD4 Binding Site by Introducing Deletions in Bridging Sheet -- Structural Information on gp41 -- Current Structural Information that may be used for Designing new Immunogens -- B. Approaches to Overcome Genetic Diversity of HIV Env for Vaccine Development -- Multivalent vaccine approach -- Acknowledgments -- References -- Chapter 14 Insights into the Caliciviridae Family Grant Hansman -- Introduction -- Genome -- Genetic Analysis and Recombination -- Expression in Insect Cells and Virus-like Particles -- Capsid Structure -- VP1: N Terminus -- VP1: S Domain -- VP1: P1 Subdomain -- VP1: P2 Subdomain -- Subunits -- VP2 and VP3 -- Antigenicity -- Proteolytic and Replication -- References -- Chapter 15 Mathematical Approaches for Stoichiometric Quantification in Studies of Viral Assembly and DNA Packaging Peixuan Guo, Jeremy Hall and Tae Jin Lee -- Introduction -- Stoichiometry Quantification to Facilitate the Understanding on the Mechanism in Viral Assembly and DNA Packaging -- Stoichiometry Quantification to Facilitate the Application of Viral Materials in Nanoscience and Nanotechnology -- Hill Cooperativity Coefficient -- The use of Binomial Distribution for the Determination of Stoichiometry -- Principle -- Determination of the Stoichiometry, Z -- Determination of the X, the Copy Number of Mutant Sufficient to Block Individual Reaction -- Determination of Stoichiometry by Slopes of Log/Log Plot Curves for Concentration Versus Yield -- Principle -- Approaches -- Descending of Trimeric, Dimeric, and Monomeric Slopes of Log/Log Plot Curves.

Deduction of Equation for Stoichiometric Determination.