Antiviral RNAi : concepts, methods, and applications / edited by Ronald P. van Rij.

Contributor(s): Rij, Ronald P. van
Material type: TextTextSeries: Springer protocols (Series): ; Methods in molecular biology (Clifton, N.J.): v. 721.Publisher: New York, N.Y. : Humana Press, ©2011Description: 1 online resource (xi, 411 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781617790379; 1617790370Subject(s): RNA | Antiviral agents | Gene silencing | RNA Interference | RNA, Small Interfering | MicroRNAs | Antiviral Agents | Genetic Therapy | Virus Diseases -- therapy | Antiviral agents | Gene silencing | RNA | virologie | virology | biomedische wetenschappen | biomedicine | humane genetica | human genetics | Medicine (General) | Geneeskunde (algemeen)Genre/Form: Electronic books. Additional physical formats: Print version:: Antiviral RNAi.DDC classification: 615/.7924 LOC classification: RM411Online resources: Click here to access online
Contents:
Defense and counterdefense in the RNAi-based antiviral / Joel T. van Mierlo, Koen W.R. van Cleef, and Ronald P. van Rij -- RNAi and cellular miRNAs in infections by mammalian viruses / Joost Haasnoot and Ben Berkhout -- Viral miRNAs / Karlie Plaisance-Bonstaff and Rolf Renne -- Progress in RNAi-based antiviral therapeutics / Jiehua Zhou and John J. Rossi -- Chemical modification of small interfering RNA / Jesper B. Bramsen and Jørgen Kjems -- Viral small RNA cloning and sequencing / Valerie Gausson and Maria-Carla Saleh -- Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets / Christophe Antoniewski -- Computational prediction of viral miRNAs / Adam Grundhoff -- Detection of viral microRNAs by northern blot analysis / Lydia V. McClure, Yao-Tang Lin, and Christopher S. Sullivan -- Detection of viral microRNA with S1 nuclease protection assay / Matthias John and Sebastien Pfeffer -- Characterization of RISC-associated adenoviral small RNAs / Ning Xu and Goran Akusjarvi -- Identification of viral suppressors of RNAi by a reporter assay in Drosophila S2 cell culture / Koen W.R. van Cleef [and others] -- Dicer assay in Drosophila S2 cell extract / Baojun Yang and Hongwei Li -- Slicer activity in Drosophila melanogaster S2 extract / Arabinda Nayak and Raul Andino -- Gel mobility shift assays for RNA binding viral RNAi suppressors / Tibor Csorba and Jozsef Burgyan -- dsRNA uptake in adult Drosophila / Benjamin Obadia and Maria-Carla Saleh -- Design of small interfering RNAs for antiviral applications / Diana Rothe, Erik J. Wade, and Jens Kurreck -- RNAi-inducing lentiviral vectors for anti-HIV-1 gene therapy / Ying Poi Liu [and others] -- Production of multicopy shRNA lentiviral vectors for antiviral therapy / Scot D. Henry, Quiwei Pan, and Luc J.W. van der Laan -- Intranasal delivery of antiviral siRNA / Sailen Barik -- Antibody-mediated delivery of siRNAs for anti-HIV therapy / Sang-Soo Kim [and others] -- Aptamer-targeted RNAi for HIV-1 therapy / Jiehua Zhou and John J. Rossi -- RNAi screening for host factors involved in viral infection using Drosophila cells / Sara Cherry -- Genome-wide RNAi screen for viral replication in mammalian cell culture / Bhupesh K. Prusty [and others] -- RNAi screening in mammalian cells to identify novel host cell molecules involved in the regulation of viral infections / Carolyn B. Coyne and Sara Cherry.
Summary: 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.
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Includes bibliographical references and index.

Defense and counterdefense in the RNAi-based antiviral / Joel T. van Mierlo, Koen W.R. van Cleef, and Ronald P. van Rij -- RNAi and cellular miRNAs in infections by mammalian viruses / Joost Haasnoot and Ben Berkhout -- Viral miRNAs / Karlie Plaisance-Bonstaff and Rolf Renne -- Progress in RNAi-based antiviral therapeutics / Jiehua Zhou and John J. Rossi -- Chemical modification of small interfering RNA / Jesper B. Bramsen and Jørgen Kjems -- Viral small RNA cloning and sequencing / Valerie Gausson and Maria-Carla Saleh -- Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets / Christophe Antoniewski -- Computational prediction of viral miRNAs / Adam Grundhoff -- Detection of viral microRNAs by northern blot analysis / Lydia V. McClure, Yao-Tang Lin, and Christopher S. Sullivan -- Detection of viral microRNA with S1 nuclease protection assay / Matthias John and Sebastien Pfeffer -- Characterization of RISC-associated adenoviral small RNAs / Ning Xu and Goran Akusjarvi -- Identification of viral suppressors of RNAi by a reporter assay in Drosophila S2 cell culture / Koen W.R. van Cleef [and others] -- Dicer assay in Drosophila S2 cell extract / Baojun Yang and Hongwei Li -- Slicer activity in Drosophila melanogaster S2 extract / Arabinda Nayak and Raul Andino -- Gel mobility shift assays for RNA binding viral RNAi suppressors / Tibor Csorba and Jozsef Burgyan -- dsRNA uptake in adult Drosophila / Benjamin Obadia and Maria-Carla Saleh -- Design of small interfering RNAs for antiviral applications / Diana Rothe, Erik J. Wade, and Jens Kurreck -- RNAi-inducing lentiviral vectors for anti-HIV-1 gene therapy / Ying Poi Liu [and others] -- Production of multicopy shRNA lentiviral vectors for antiviral therapy / Scot D. Henry, Quiwei Pan, and Luc J.W. van der Laan -- Intranasal delivery of antiviral siRNA / Sailen Barik -- Antibody-mediated delivery of siRNAs for anti-HIV therapy / Sang-Soo Kim [and others] -- Aptamer-targeted RNAi for HIV-1 therapy / Jiehua Zhou and John J. Rossi -- RNAi screening for host factors involved in viral infection using Drosophila cells / Sara Cherry -- Genome-wide RNAi screen for viral replication in mammalian cell culture / Bhupesh K. Prusty [and others] -- RNAi screening in mammalian cells to identify novel host cell molecules involved in the regulation of viral infections / Carolyn B. Coyne and Sara Cherry.

Print version record.

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.

English.

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