Plant Virology Protocols

General Introduction.- Plant–Virus Interactions.- Role of Capsid Proteins.- Role of Plant Virus Movement Proteins.- Multiple Roles of Viral Replication Proteins in Plant RNA Virus Replication.- Role of Silencing Suppressor Proteins.- Role of Vector-Transmission Proteins.- Viral Nucleic Acid Sequence/Function Analysis.- In Vivo Analyses of Viral RNA Translation.- In Vitro Analysis of Translation Enhancers.- Identification of Plant Virus IRES.- Analysis of Geminivirus DNA Replication by 2-D Gel.- Begomoviruses: Molecular Cloning and Identification of Replication Origin.- Analysis of Viroid Replication.- Biochemical Analyses of the Interactions Between Viral Polymerases and RNAs.- In Situ Detection of Plant Viruses and Virus-Specific Products.- Detection of siRNAs and miRNAs.- Cloning of Short Interfering RNAs from Virus-Infected Plants.- Solution Structure Probing of RNA Structures.- RNA Encapsidation Assay.- Protein Analysis and Investigation of Protein Function.- Surface Plasmon Resonance Analysis of Interactions Between Replicase Proteins of Tomato Bushy Stunt Virus.- Biochemical Approaches for Characterizing RNA–Protein Complexes in Preparation for High Resolution Structure Analysis.- Probing Interactions Between Plant Virus Movement Proteins and Nucleic Acids.- Movement Profiles: A Tool for Quantitative Analysis of Cell-to-Cell Movement of Plant Viral Movement Proteins.- Analysis of siRNA-Suppressor of Gene Silencing Interactions.- Phosphorylation Analysis of Plant Viral Proteins.- Analysis of Interactions Between Viral Replicase Proteins and Plant Intracellular Membranes.- Membrane and Protein Dynamics in Virus-Infected Plant Cells.- Site-Directed Mutagenesis of Whole Viral Genomes.- Viral Protein–Nucleic Acid Interaction: South (North)-Western Blot.-Protein–Protein Interactions: The Yeast Two-Hybrid System.- NMR Analysis of Viral Protein Structures.- Localization of Viral Proteins in Plant Cells: Protein Tagging.- Microscopy/GFP/Protein Tagging/Infections Clones and Other Such Tools.- Construction of Infectious Clones for RNA Viruses: TMV.- Construction of Infectious cDNA Clones for RNA Viruses: Turnip Crinkle Virus.- Construction of Infectious Clones for DNA Viruses: Mastreviruses.- Construction of Infectious Clones of Double-Stranded DNA Viruses of Plants Using Citrus Yellow Mosaic Virus as an Example.- Insertion of Introns: A Strategy to Facilitate Assembly of Infectious Full Length Clones.- Analysis of Cell-to-Cell and Long-Distance Movement of Apple Latent Spherical Virus in Infected Plants Using Green, Cyan, and Yellow Fluorescent Proteins.- Agroinoculation: A Simple Procedure for Systemic Infection of Plants with Viruses.- Geminivirus: Biolistic Inoculation and Molecular Diagnosis.- Genomics, Host Factors and Plant Based Studies.- Expression Microarrays in Plant-Virus Interaction.- Genome-Wide Screens for Identification of Host Factors in Viral Replication.- Phosphorylation of Movement Proteins by the Plasmodesmal-Associated Protein Kinase.- Virus-Induced Gene Silencing as a Tool to Identify Host Genes Affecting Viral Pathogenicity.- Yeast Two-Hybrid Assay to Identify Host–Virus Interactions.