Preface... Contributors... xiii. Chapter 1 Plant Virus Interactions... 3 Peter Palukaitis, John P. Carr, and James E. Schoelz
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1 Contents Preface v Contributors xiii Section 1 General Introduction Chapter 1 Plant Virus Interactions Peter Palukaitis, John P. Carr, and James E. Schoelz Chapter 2 Role of Capsid Proteins John F. Bol Chapter 3 Role of Plant Virus Movement Proteins Michael Taliansky, Lesley Torrance, and Natalia O. Kalinina Chapter 4 Multiple Roles of Viral Replication Proteins in Plant RNA Virus Replication Peter D. Nagy and Judit Pogany Chapter 5 Role of Silencing Suppressor Proteins József Burgyán Chapter 6 Role of Vector-Transmission Proteins Véronique Ziegler-Graff and Véronique Brault Section 2 Viral Nucleic Acid Sequence/Function Analysis Chapter 7 In Vivo Analyses of Viral RNA Translation William R. Staplin and W. Allen Miller vii
2 viii Contents Chapter 8 In Vitro Analysis of Translation Enhancers Aurélie M. Rakotondrafara and W. Allen Miller Chapter 9 Identification of Plant Virus IRES Sek-Man Wong, Dora Chin-Yen Koh, and Dingxiang Liu Chapter 10 Analysis of Geminivirus DNA Replication by 2-D Gel Keith Saunders Chapter 11 Begomoviruses: Molecular Cloning and Identification of Replication Origin Lilian H. Florentino, Anésia A. Santos, Francisco M. Zerbini, and Elizabeth P.B. Fontes Chapter 12 Analysis of Viroid Replication Ricardo Flores, María-Eugenia Gas, Diego Molina, Carmen Hernández, and José-Antonio Daròs Chapter 13 Biochemical Analyses of the Interactions Between Viral Polymerases and RNAs Young-Chan Kim and C. Cheng Kao Chapter 14 In Situ Detection of Plant Viruses and Virus-Specific Products Andrew J. Maule and Zoltán Havelda Chapter 15 Detection of sirnas and mirnas Sakari Kauppinen and Zoltán Havelda Chapter 16 Cloning of Short Interfering RNAs from Virus-Infected Plants Thien X. Ho, Rachel Rusholme, Tamas Dalmay, and Hui Wang Chapter 17 Solution Structure Probing of RNA Structures Marc R. Fabian and K. Andrew White Chapter 18 RNA Encapsidation Assay Padmanaban Annamalai and A.L.N. Rao
3 Contents ix Section 3 Protein Analysis and Investigation of Protein Function Chapter 19 Surface Plasmon Resonance Analysis of Interactions Between Replicase Proteins of Tomato Bushy Stunt Virus K.S. Rajendran and Peter D. Nagy Chapter 20 Biochemical Approaches for Characterizing RNA Protein Complexes in Preparation for High Resolution Structure Analysis Raúl C. Gomila and Lee Gehrke Chapter 21 Probing Interactions Between Plant Virus Movement Proteins and Nucleic Acids Tzvi Tzfira and Vitaly Citovsky Chapter 22 Movement Profiles: A Tool for Quantitative Analysis of Cell-to-Cell Movement of Plant Viral Movement Proteins Kateryna Trutnyeva, Pia Ruggenthaler, and Elisabeth Waigmann Chapter 23 Analysis of sirna-suppressor of Gene Silencing Interactions Lóránt Lakatos and József Burgyán Chapter 24 Phosphorylation Analysis of Plant Viral Proteins Kristiina M. Mäkinen and Konstantin I. Ivanov Chapter 25 Analysis of Interactions Between Viral Replicase Proteins and Plant Intracellular Membranes Hélène Sanfaçon and Guangzhi Zhang Chapter 26 Membrane and Protein Dynamics in Virus-Infected Plant Cells Michael Goodin, Romit Chakrabarty, and Sharon Yelton Chapter 27 Site-Directed Mutagenesis of Whole Viral Genomes Li Liu and George P. Lomonossoff
4 x Contents Chapter 28 Viral Protein Nucleic Acid Interaction: South (North)-Western Blot Huanting Liu Chapter 29 Protein Protein Interactions: The Yeast Two-Hybrid System Deyin Guo, Minna-Liisa Rajamäki, and Jari Valkonen Chapter 30 NMR Analysis of Viral Protein Structures Andrew J. Dingley, Inken Lorenzen, and Joachim Grötzinger Chapter 31 Localization of Viral Proteins in Plant Cells: Protein Tagging Sophie Haupt, Angelika Ziegler, and Lesley Torrance Section 4 Microscopy/GFP/Protein Tagging/Infections Clones and Other Such Tools Chapter 32 Construction of Infectious Clones for RNA Viruses: TMV Sean N. Chapman Chapter 33 Construction of Infectious cdna Clones for RNA Viruses: Turnip Crinkle Virus Eugene V. Ryabov Chapter 34 Construction of Infectious Clones for DNA Viruses: Mastreviruses Margaret I. Boulton Chapter 35 Construction of Infectious Clones of Double-Stranded DNA Viruses of Plants Using Citrus Yellow Mosaic Virus as an Example Qi Huang and John S. Hartung Chapter 36 Insertion of Introns: A Strategy to Facilitate Assembly of Infectious Full Length Clones I. Elisabeth Johansen and Ole Søgaard Lund Chapter 37 Analysis of Cell-to-Cell and Long-Distance Movement of Apple Latent Spherical Virus in Infected Plants Using Green, Cyan, and Yellow Fluorescent Proteins Tsubasa Takahashi and Nobuyuki Yoshikawa
5 Contents xi Chapter 38 Agroinoculation: A Simple Procedure for Systemic Infection of Plants with Viruses Zarir E. Vaghchhipawala and Kirankumar S. Mysore Chapter 39 Geminivirus: Biolistic Inoculation and Molecular Diagnosis Anésia A. Santos, Lilian H. Florentino, Acássia B.L. Pires, and Elizabeth P.B. Fontes Section 5 Genomics, Host Factors and Plant Based Studies Chapter 40 Expression Microarrays in Plant Virus Interaction Kristina Gruden, Maruša Pompe-Novak, Špela Baebler, Hana Krečič-Stres, Nataša Toplak, Matjaž Hren, Polona Kogovšek, Lisa Gow, Gary D. Foster, Neil Boonham, and Maja Ravnikar Chapter 41 Genome-Wide Screens for Identification of Host Factors in Viral Replication Tadas Panavas, Elena Serviene, Judit Pogany, and Peter D. Nagy Chapter 42 Phosphorylation of Movement Proteins by the Plasmodesmal-Associated Protein Kinase Jung-Youn Lee Chapter 43 Virus-Induced Gene Silencing as a Tool to Identify Host Genes Affecting Viral Pathogenicity Xiaohong Zhu and S.P. Dinesh-Kumar Chapter 44 Yeast Two-Hybrid Assay to Identify Host Virus Interactions Stuart A. MacFarlane and Joachim F. Uhrig Index
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VIRUSES Many diseases of plants and animals are caused by bacteria or viruses that invade the body. Bacteria and viruses are NOT similar kinds of micro-organisms. Bacteria are classified as living organisms,
Supplementary Discussion 1: The mechanistic model of NIK1-mediated antiviral
doi:10.1038/nature14171 SUPPLEMENTARY DISCUSSION Supplementary Discussion 1: The mechanistic model of NIK1-mediated antiviral signaling 1. Stress-induced oligomerization of the extracellular domain of
Structure of viruses
Antiviral Drugs o Viruses are obligate intracellular parasites. o lack both a cell wall and a cell membrane. o They do not carry out metabolic processes. o Viruses use much of the host s metabolic machinery.
Dr. Ahmed K. Ali. Outcomes of the virus infection for the host
Lec. 9 Dr. Ahmed K. Ali Outcomes of the virus infection for the host In the previous few chapters we have looked at aspects of the virus replication cycle that culminate in the exit of infective progeny
WHY? Viruses are considered non-living because they do:
Viruses What is a Virus? Non-living particle WHY? Viruses are considered non-living because they do: NOT Carry out metabolism NOT Grow or develop NOT Replicate without the help of a living cell (host).
Islamic University Faculty of Medicine
Islamic University Faculty of Medicine 2012 2013 2 RNA is a modular structure built from a combination of secondary and tertiary structural motifs. RNA chains fold into unique 3 D structures, which act
Name Class Date. Infection in which a virus inserts its nucleic acid into the DNA of the host cell and is duplicated with the cell s DNA
Name Class Date 20.1 Viruses Lesson Objectives Explain how viruses reproduce. Explain how viruses cause infection. BUILD Vocabulary A. The chart below shows key terms from the lesson with their definitions.