Plant Virology Protocols

Section 1 General Introduction 1. Plant virus interactions –Peter Palukaitis, John Carr and James Schoelz (EJ) 2. Role of capsid proteins – John Bol (EJ) 3. Role of plant virus movement proteins – Michael Taliansky, Lesley Torrance, Natalia O. Kalinina (EJ) 4. Multiple roles of viral replication proteins in plant RNA virus replication– Peter Nagy and Judith Pogany (PN) 5. Role of silencing suppressor proteins –Jozsef Burgyan (EJ) 6. Role of vector transmission proteins – Veronique Ziegler Graff, Veronique Brault (EJ) Section 2 Viral nucleic acid sequence/function analysis 7. In vivo analysis of Viral RNA translation- William Staplin, Allen Miller (PN) 8. In vitro analysis of translational enhancer –Aurelie Rakotondrafara, Allen Miller (YH) 9. Identification of plant virus IRES – Sek-Man Wong, Dora Chin-Yen Koh, DingXiang Liu (YH) 10. Analysis of geminivirus DNA replication by 2-D gel - Keith Saunders (YH) 11. Begomoviruses: Molecular cloning and identification of replication origin - Lilian H. Florentino, Anésia A. Santos, Francisco M. Zerbini, Elizabeth P. B. Fontes (YH) 12. Analysis of viroid replication - Ricardo Flores, María-Eugenia Gas, Diego Molina, Carmen Hernández, and José-Antonio Daròs (PN) 13. Biochemical Analyses of the Interactions Between Viral Polymerases and RNAs- Young-Chan Kim and C. Cheng Kao (PN) 14. In situ detection of plant viruses and virus-specific products - Andy Maule and Zoltan Havelda (PN) 15. Detection of siRNAs and miRNAs- Sakari Kauppinen, Zoltan Havelda (EJ) 16. Cloning of short interfering RNAs from virus infected plants - Thien X. Ho, Rachel Rusholme, Tamas Dalmay, and Hui Wang (YH) 17. Solution structure probing of RNA structures – Marc R. Fabian and K. Andrew White (PN) 18. RNA encapsidation assay - Padmanaban Annamalaiand A. L. N. Rao (GF) Section 3 Protein analysis and investigation of protein function 19. Surface plasmon resonance analysis of interactions between replicase proteins of tomato bushy stunt virus- KS. Rajendran and Peter Nagy (GF) 20. Biochemical approaches for characterizing RNA-protein complexes in preparation for high resolution structure analysis- Raúl C. Gomila and Lee Gehrke (PN) 21. Probing interactions between plant virus movement proteins and nucleic acids - Tzvi Tzfira, Vitaly Citovski (PN) 22. Movement profiles, a tool for quantitative analysis of cell-to-cell movement of plant viral movement proteins - Kateryna Trutnyeva, Pia Ruggenthaler, Elisabeth Waigmann (PN) 23. Analysis of siRNA-supressor of gene silencing interactions - Lóránt Lakatos and József Burgyán (EJ) 24. Phosphorylation analysis of plant virus proteins - Kristiina M. Mäkinen and Konstantin I. Ivanov (PN) 25. Analysis of interactions between viral replicase proteins and plant intracellular membranes- Hélène Sanfaçon and Guangzhi Zhang (PN) 26. Membrane and protein dynamics in virus-infected plant cells - Michael Goodin, Romit Chakrabarty, Sharon Yelton (PN) 27. Site-directed mutagenesis of whole viral genomes - Li liu, George Lomonossoff (YH) 28. Viral protein-nucleic acid interaction: South(North)-Western blot - Huanting Liu (YH) 29. Protein-protein interactions: yeast two hybrid system - Deyin Guo, Minna-Liisa Rajamäki, and Jari Valkonen (YH) 30. NMR analysis of viral protein structures - Andrew J. Dingley, Inken Lorenzen and Joachim Grötzinger (YH) 31. Localization of viral protein in plant cells: protein tagging –Sophie Haupt, Lesley Torrance (GF) Section 4 Microscopy/GFP/Protein tagging/infections clones and other such tools 32. Construction of infectious clones for RNA viruses -