Antiviral RNAi: Concepts, Methods, and Applications

ISBN-13: 9781493958252 / Angielski / Miękka / 2016 / 425 str.

Ronald P. van Rij

Opis

Here is a collection of protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as for development and optimization of RNAi-based antiviral drugs. The methods here can also be applied outside the context of a virus infection.

Recenzje

From the reviews:

"This well-illustrated book details the necessary protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as the development and optimization of RNAi-based antiviral drugs. The book is intended for both novice and experienced researchers ... . It also will be of immense help to graduate students, physicians who treat patients with infectious diseases, and other researchers interested in the field of antiviral RNAi. ... a well-illustrated and authoritative resource on important basic concepts in the field of antiviral RNAi." (Omer Iqbal, Doody's Review Service, July, 2011)

Spis treści

Part I: General Introduction

                                     

1. Defense and counter-defense in the RNAi-based antiviral immune system in insects           

Joël T. van Mierlo, Koen W.R. van Cleef, and Ronald P. van Rij                            

 

2. RNAi and cellular miRNAs in infections by mammalian viruses

Joost Haasnoot and Ben Berkhout                            

 

3. Viral miRNAs       

Karlie Plaisance-Bonstaff, and Rolf Renne                           

 

4. Progress in RNAi-based antiviral therapeutics 

Jiehua Zhou and John J. Rossi                                   

 

5. Chemical modification of small interfering RNA         

Jesper B. Bramsen and Jørgen Kjems                        

           

 

Part II: Viral small RNAs

 

6. Viral small RNA cloning and sequencing          

Valérie Gausson and Maria-Carla Saleh                    

           

7. Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets        

Christophe Antoniewski                                

 

8. Computational prediction of viral miRNAs      

Adam Grundhoff                               

 

9. Detection of Viral microRNAs by Northern Blot Analysis      

Lydia V. McClure, Yao-Tang Lin, and Christopher S. Sullivan                               

 

10. Detection of viral microRNA with S1 Nuclease Protection assay      

Matthias John and Sébastien Pfeffer                         

 

11. Characterization of RISC associated adenoviral small RNAs           

Ning Xu and Göran Akusjärvi                                   

                       

                       

Part III: RNAi-based antiviral defense

                                               

12. Identification of Viral Suppressors of RNAi by a Reporter Assay in Drosophila S2 Cell Culture

Koen W.R. van Cleef, Joël T van Mierlo, Marius van den Beek, and Ronald P. van Rij                             

13. Dicer assay in Drosophila S2 cell extract         

Baojun Yang and Hongwei Li           

                       

14. Slicer activity in Drosophila melanogaster S2 extract 

Arabinda Nayak and Raul Andino                

           

15. Gel Mobility Shift Assays for RNA-binding viral RNAi suppressors           

Tibor Csorba and József Burgyán      

                       

16. dsRNA uptake in adult Drosophila      

Benjamin Obadia and Maria-Carla Saleh                               

 

                                               

Part IV: Antiviral RNAi therapy

                                               

17. Design of small interfering RNAs for antiviral applications  

Diana Rothe, Erik J. Wade, and Jens Kurreck                       

           

18. RNAi inducing lentiviral vectors for anti-HIV-1 gene therapy          

Ying Poi Liu, Jan-Tinus Westerink, Olivier ter Brake, and Ben Berkhout    

                       

19. Production of multicopy shRNA lentiviral vectors for antiviral therapy     

Scot D. Henry, Quiwei Pan, and Luc J.W. van der Laan      

                       

20. Intranasal delivery of antiviral siRNA 

Sailen Barik                            

 

21. Antibody mediated delivery of siRNAs for anti-HIV therapy           

Sang-Soo Kim, Sandesh Subramanya, Dan Peer, Motomu Shimaoka, and Premlata Shankar         

                       

22. Aptamer-targeted RNAi for HIV-1 therapy   

Jiehua Zhou and John J. Rossi                                   

                                                           

 

 

Part V: RNAi screens to study virus-host interactions

                                               

23. RNAi screening for host factors involved in viral infection using Drosophila cells 

Sara Cherry                            

 

24. Genome-wide RNAi Screen for Viral Replication in Mammalian Cell Culture      

Bhupesh K. Prusty, Alexander Karlas, Thomas F. Meyer, and Thomas Rudel         

                       

25. RNAi screening in mammalian cells to identify novel host cell molecules involved in the regulation of viral infections       

Carolyn B. Coyne and Sara Cherry

Blurb

Viruses and RNAi share an intricate relationship at many levels. RNAi is an important antiviral defense mechanism in plants and invertebrates, microRNAs – of viral or cellular origin – affect many aspects of virus biology, and replication of many, if not all, mammalian viruses can be suppressed by RNAi. Antiviral RNAi: Concepts, Methods, and Applications provides a collection of protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as for the development and optimization of RNAi-based antiviral drugs. As RNAi is a central regulatory mechanism in the cell, the methods in this volume can also be applied out of the context of a virus infection. Divided into five convenient parts, this detailed volume reviews important basic concepts in the field of antiviral RNAi, provides experimental and bio-informatic tools for the analysis of small silencing RNAs, covers methods to biochemically dissect RNAi-based antiviral defense and viral counter-defense mechanisms, describes methods for the design, expression, and delivery of therapeutic antiviral siRNAs, and finally presents genome-wide RNAi approaches for the identification of factors involved in virus replication. Written in the highly successful Methods in Molecular Biology™ series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and accessible, Antiviral RNAi: Concepts, Methods, and Applications serves as an ideal guide for both novice and experienced researchers alike striving to dissect the role of RNAi in the viral life cycle or to further boost the development of novel therapeutics and experimental tools based on RNAi technology.