Description
Book SynopsisThis volume explores the latest methods used by researchers to study the detection, characterization, and various aspects of viroids. The chapters in this book are organized into seven parts and cover topics such as detection methods based on the biology of viroids; detection techniques based on electrophoresis and hybridization techniques; PCR-based techniques that provide high degrees of sensitivity; emerging area of nucleic acid sequence-based technology; and emerging techniques in viroid research such as RNA silencing, splicing, and viroid structure. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and comprehensive, Viroids: Methods and Protocols is a valuable resource for researchers and gradua
Table of Contents
Preface…
Table of Contents…
Contributing Authors…
Part I Biological Techniques
1. Study and Detection of Citrus Viroids in Woody Hosts
Robert R. Krueger and Georgios Vidalakis
2. Detection and Characterization of Viroids via Biological Assays on Herbaceous Hosts
Rosemarie W. Hammond
3. Analysis on RNA Motif-Based RNA Trafficking in Plants
Heather N. Smith, Junfei Ma, and Ying Wang
4. Isolation and Transfection of Citrus Protoplasts with Citrus Exocortis Viroid
Subhas Hajeri, James Ng, Jude Grosser, and Georgios Vidalakis
Part II Electrophoresis and Hybridization Techniques
5. High-Throughput RNA Extraction from Citrus Tissues for the Detection of Viroids
Tyler Dang, Fatima Osman, Jinbo Wang, Tavia Rucker, Sohrab Bodaghi, Shih-hua Tan, Deborah Pagliaccia, Irene Lavagi-Craddock, and Georgios Vidalakis
6. Extraction and Purification of Viroids from Herbaceous Hosts
Rosemarie W. Hammond
7. Detection of Viroids by sPAGE Gel Electrophoresis
Núria Duran-Vila
8. Two-Dimensional Polyacrylamide-Gel Electrophoresis Analysis of Viroid RNAs
José-Antonio Daròs
9. A Simplified Dot-Blot Hybridization Protocol for Potato spindle tuber viroid Detection in Solanaceae
Oxana Kekstidou, Christina Varveri, and Nikon Vassilakos
10. Gel Blot Hybridization for Viroids
Pedro Serra
11. Tissue Print Hybridization for Detection and Characterization of Viroids
Maria S. Kaponi, Teruo Sano, and Panayota E. Kyriakopoulou
12. Fluorescein-Based Electrophoretic Mobility Shift Assay
Shachinthaka D. Dissanayaka Mudiyanselage and Ying Wang
Part III PCR Techniques
13. Detection of Viroids by RT-PCR
Nerida J. Donovan, Grant A. Chambers, and Mengji Cao
14. Detection of Viroids using RT-qPCR
Subhas Hajeri, Georgios Vidalakis, and Raymond Yokomi
15. Multiplex RT-PCR
Francesco Faggioli and Marta Luigi
16. Real-Time Detection of Viroids using Singleplex and Multiplex Quantitative Polymerase Chain Reaction
Fatima Osman and Georgios Vidalakis
17. Reverse Transcription-Loop Mediated Isothermal AMPlification (RT-LAMP) at the Service of Viroid Detection
Iraklis N. Boubourakas and Panayota E. Kyriakopoulou
18. SYBR ® Green RT-qPCR for the Universal Detection of Citrus Viroids
Georgios Vidalakis, Jinbo Wang, Tyler Dang, Tavia Rucker, Sohrab Bodaghi, Shi-hua Tan, Irene Lavagi-Craddock, Alexandra Syed, Gerardo Uribe, Yi Hsieh, and Joana Carbajal-Moreno
19. Detection of Avocado sunblotch and Other Viroids using RNA Filter Paper Capture and RT-PCR
Deborah M. Mathews, Sohrab Bodaghi, James A. Heick, and J. Allan Dodds
Part IV Cloning and Sequencing Techniques
20. Cloning and Sequencing of Viroids
Rosemarie W. Hammond
21. QuantiGene Plex Assay: A Method for High-Throughput Multiplex Citrus Viroid Detection and Identification
Tyler Dang, Jinbo Wang, Tavia Rucker, Sohrab Bodaghi, Irene Lavagi-Craddock, and Georgios Vidalakis
22. Culture-Independent Discovery of Viroids by Deep Sequencing and Computational Algorithms
Ali Raza, Shou-Wei Ding, and Qingfa Wu
23. An In Silico Detection of a Citrus Viroid from Raw High Throughput Sequencing Data
Tyler Dang, Andres Espindola, Georgios Vidalakis, and Kitty Cardwell
Part V RNA Silencing Techniques
24. Detection of Viroid RNA and vd-siRNA in N. benthamiana Plants: Northern Blot Analyses for Viroid and vd-siRNAs
Konstantina Katsarou, Nikoleta Kryovrysanaki, and Kriton Kalantidis
Part VI Splicing Techniques
25. Production of Recombinant RNA in Escherichia coli Using Eggplant Latent Viroid as a Scaffold
Beltrán Ortolá and José-Antonio Daròs
Part VII Structural Analysis
26. Predicting the Structure of a Viroid
Gerhard Steger
Subject Index List…
