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Главная Авторы Jane Flint Principles of Virology

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Principles of Virology

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Страница 1 Table of Contents List of Tables List of Illustrations Guide Pages Страница 7 VOLUME I Molecular Biology PRINCIPLES OF
Virology Страница 9Страница 10 About the Instructor Companion Website Страница 12 Acknowledgments About the Authors Key of Repetitive Elements 1 Foundations LINKS FOR CHAPTER 1 Luria’s Credo Viruses Defined Why We Study Viruses Viruses Are Everywhere PRINCIPLES Foundations Viruses Infect All Living Things BOX 1.1 BACKGROUND Some astounding numbers BOX 1.2 DISCUSSION The first animal virus discovered remains a scourge today Viruses Can Cause Human Disease Viruses Can Be Beneficial Viruses “R” Us Viruses Can Cross Species Boundaries Viruses Are Unique Tools To Study Biology Virus Prehistory Viral Infections in Antiquity The First Vaccines Microorganisms as Pathogenic Agents BOX 1.3 DISCUSSION Origin of vaccinia virus Discovery of Viruses BOX 1.4 DISCUSSION New methods amend Koch’s principles The Defining Properties of Viruses The Structural Simplicity of Virus Particles The Intracellular Parasitism of Viruses Organisms as Hosts Lessons from Bacteriophages Animal Cells as Hosts BOX 1.5 EXPERIMENTS The Hershey-Chase experiment BOX 1.6 BACKGROUND Properties of lysogeny shared with animal viruses Lytic versus Lysogenic Response to Infection Propagation as a Prophage Insertional Mutagenesis Gene Repression and Induction Transduction of Host Genes BOX 1.7 TERMINOLOGY The episome BOX 1.8 DISCUSSION Are viruses living entities? What can/can’t they do? Cataloging Animal Viruses The Classical System BOX 1.9 TERMINOLOGY Complexities of viral nomenclature Classification by Genome Type: the Baltimore System BOX 1.10 DISCUSSION Giant viruses discovered in amoebae A Common Strategy for Viral Propagation Perspectives REFERENCES Books STUDY QUESTIONS 2 The Infectious Cycle LINKS FOR CHAPTER 2 Introduction The Infectious Cycle The Cell PRINCIPLES The infectious cycle Entering Cells Viral RNA Synthesis Viral Protein Synthesis Viral Genome Replication Assembly of Progeny Virus Particles Viral Pathogenesis BOX 2.1 EXPERIMENTS In vitro assembly of tobacco mosaic virus Overcoming Host Defenses Cultivation of Viruses Cell Culture Types of Cell Culture BOX 2.2 BACKGROUND The cells of Henrietta Lacks BOX 2.3 EXPERIMENTS Zika virus blocks the neuronal road Evidence of Viral Reproduction in Cultured Cells BOX 2.4 TERMINOLOGY In vitro and in vivo Embryonated Eggs Laboratory Animals Assay of Viruses Measurement of Infectious Units Plaque Assay Fluorescent-Focus Assay BOX 2.5 METHODS Calculating virus titer from the plaque assay Infectious-Centers Assay Transformation Assay End-Point Dilution Assay Efficiency of Plating BOX 2.6 METHODS End-point dilution assays Measurement of Virus Particles Electron Microscopy Hemagglutination Centrifugation Measurement of Viral Enzyme Activity Serological Methods BOX 2.7 DISCUSSION Neutralization antigenic sites Fluorescent Proteins Fluorescence Microscopy Detection of Viral Nucleic Acids BOX 2.8 EXPERIMENTS Viral RNA is not infectious virus BOX 2.9 EXPERIMENTS Pathogen de-discovery Viral Reproduction: the Burst Concept The One-Step Growth Cycle BOX 2.10 METHODS How to read a phylogenetic tree One-Step Growth Analysis: a Valuable Tool for Studying Animal Viruses BOX 2.11 DISCUSSION Multiplicity of infection (MOI) Global Analysis DNA Microarrays Mass Spectrometry Protein-Protein Interactions Single-Cell Virology BOX 2.12 WARNING Determining a role for cellular proteins in viral reproduction can be quite difficult Perspectives REFERENCES Books Review Articles Papers of Special Interest STUDY QUESTIONS 3 Genomes and Genetics LINKS FOR CHAPTER 3 Introduction Genome Principles and the Baltimore System Structure and Complexity of Viral Genomes PRINCIPLES Genomes and Genetics BOX 3.1 BACKGROUND What information is encoded in a viral genome? BOX 3.2 TERMINOLOGY Important conventions: plus (+) and minus (–) strands DNA Genomes Double-Stranded DNA (dsDNA) (Fig. 3.2) Gapped DNA (Fig. 3.3) Single-Stranded DNA (ssDNA) (Fig. 3.4) RNA Genomes dsRNA (Fig. 3.5) BOX 3.3 BACKGROUND RNA synthesis in cells (+) Strand RNA (Fig. 3.6) (+) Strand RNA with a DNA Intermediate (Fig. 3.7) (–) Strand RNA (Fig. 3.8) What Do Viral Genomes Look Like? Coding Strategies What Can Viral Sequences Tell Us? The “Big and Small” of Viral Genomes: Does Size Matter? BOX 3.4 EXPERIMENTS Planaria and mollusks yield the biggest RNA genomes The Origin of Viral Genomes Genetic Analysis of Viruses BOX 3.5 EXPERIMENTS Origin of segmented RNA virus genomes Classical Genetic Methods Mapping Mutations Functional Analysis BOX 3.6 METHODS Spontaneous and induced mutations BOX 3.7 TERMINOLOGY What is wild type? Engineering Mutations into Viral Genomes Infectious DNA Clones BOX 3.8 TERMINOLOGY DNA-mediated transformation and transfection BOX 3.9 METHODS Synthesis of infectious horsepox virus from chemically synthesized DNA Types of Mutation Introducing Mutations into the Viral Genome Reversion Analysis BOX 3.10 TERMINOLOGY Operations on nucleic acids and proteins BOX 3.11 DISCUSSION Is the observed phenotype due to the mutation? RNA Interference (RNAi) Targeted Gene Editing with CRISPR-Cas9 Haploid Cell Screening Engineering Viral Genomes: Viral Vectors DNA Virus Vectors RNA Virus Vectors Perspectives REFERENCES Review Articles Papers of Special Interest STUDY QUESTIONS 4 Structure LINKS FOR CHAPTER 4 Introduction Functions of the Virion PRINCIPLES Structure Nomenclature Methods for Studying Virus Structure BOX 4.1 METHODS The development of cryo-electron microscopy, a revolution in structural biology Building a Protective Coat Helical Structures BOX 4.2 METHODS Nanoconstruction with virus particles Capsids with Icosahedral Symmetry General Principles BOX 4.3 BACKGROUND The triangulation number, T, and how it is determined BOX 4.4 EXPERIMENTS Viral chain mail: not the electronic kind Structurally Simple Capsids BOX 4.5 DISCUSSION Remarkable architectural relationships among viruses with double-stranded DNA genomes Structurally Sophisticated Capsids BOX 4.6 EXPERIMENTS A fullerene cone model of the human immunodeficiency virus type 1 capsid Other Capsid Architectures Packaging the Nucleic Acid Genome Direct Contact of the Genome with a Protein Shell Packaging by Specialized Viral Proteins Packaging by Cellular Proteins BOX 4.7 EXPERIMENTS A high-resolution view of an encapsidated viral genome Viruses with Envelopes Viral Envelope Components Envelope Glycoproteins BOX 4.8 DISCUSSION A viral membrane directly surrounding the genome Other Envelope Proteins Simple Enveloped Viruses: Direct Contact of External Proteins with the Capsid or Nucleocapsid Enveloped Viruses with an Additional Protein Layer Large Viruses with Multiple Structural Elements BOX 4.9 DISCUSSION A virus particle with different structures in different hosts Particles with Helical or Icosahedral Parts Bacteriophage T4 BOX 4.10 DISCUSSION The extreme pleomorphism of influenza A virus, a genetically determined trait of unknown function Herpesviruses Mimiviruses Alternative Architectures Poxviruses Pithoviruses Other Components of Virions Enzymes Other Viral Proteins Cellular Macromolecules Mechanical Properties of Virus Particles Investigation of Mechanical Properties of Virus Particles Stabilization and Destabilization of Virus Particles Perspectives REFERENCES Reviews Papers of Special Interest Websites STUDY QUESTIONS 5 Attachment and Entry LINKS FOR CHAPTER 5 Introduction Attachment of Virus Particles to Cells General Principles PRINCIPLES Attachment and entry BOX 5.1 TERMINOLOGY Is it a receptor or a coreceptor? Identification of Receptors for Virus Particles Virus-Receptor Interactions Nonenveloped Virus Receptor Binding Alternative Attachment Strategies Transmembrane Glycoproteins of Enveloped Viruses Mediate Attachment and Entry Cell Surface Lectins and Spread of Infection Entry into Cells Virus-Induced Signaling via Cell Receptors Routes of Entry Membrane Fusion Class I Fusion Proteins Alternative Fusion Triggers BOX 5.2 BACKGROUND Unusual triggers of retroviral fusion proteins The Membrane Fusion Process Class II Fusion Proteins BOX 5.3 EXPERIMENTS Membrane fusion proceeds through a hemifusion intermediate BOX 5.4 DISCUSSION Sex and the fusion protein Class III Fusion Proteins Intracellular Trafficking and Uncoating Movement of Viral and Subviral Particles within Cells Uncoating of Enveloped Virus Particles Release of Viral Ribonucleoprotein Uncoating by Ribosomes in the Cytoplasm Uncoating of Nonenveloped Viruses Disrupting the Endosomal Membrane Forming a Pore in the Endosomal Membrane Disrupting the Lysosomal Membrane Import of Viral Genomes into the Nucleus The Nuclear Pore Complex Nuclear Localization Signals Nuclear Import of RNA Genomes BOX 5.5 BACKGROUND Transport through the nuclear pore Nuclear Import of DNA Genomes Import of Retroviral Genomes BOX 5.6 DISCUSSION The bacteriophage DNA injection machine Perspectives REFERENCES Books Reviews Papers of Special Interest STUDY QUESTIONS 6 Synthesis of RNA from RNA Templates LINKS FOR CHAPTER 6 Introduction The Nature of the RNA Template Secondary Structures in Viral RNA PRINCIPLES Synthesis of RNA from RNA templates BOX 6.1 TERMINOLOGY What should we call RNA polymerases and the processes they catalyze? Naked or Nucleocapsid RNA The RNA Synthesis Machinery Identification of RNA-Dependent RNA Polymerases Three-Dimensional Structures of RNA-Dependent RNA Polymerases BOX 6.2 BACKGROUND Two-metal mechanism of catalysis by polymerases Mechanisms of RNA Synthesis Initiation De Novo Initiation Primer-Dependent Initiation Capping Elongation Functions of Additional Polymerase Domains RNA Polymerase Oligomerization Template Specificity Unwinding the RNA Template Role of Cellular Proteins Paradigms for Viral RNA Synthesis (+) Strand RNA Synthesis of Nested Subgenomic mRNAs (−) Strand RNA BOX 6.3 EXPERIMENTS Mapping gene order by UV irradiation Ambisense RNA Double-Stranded RNA Unique Mechanisms of mRNA and Genome Synthesis of Hepatitis Delta Virus BOX 6.4 EXPERIMENTS Release of mRNA from rotavirus particles BOX 6.5 BACKGROUND Ribozymes Do Ribosomes and RNA Polymerases Collide? Origins of Diversity in RNA Virus Genomes Misincorporation of Nucleotides Segment Reassortment and RNA Recombination RNA Editing BOX 6.6 DISCUSSION RNA recombination leading to the production of pathogenic viruses Perspectives REFERENCES Reviews Papers of Special Interest STUDY QUESTIONS {buyButton}

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