Bacterial regulatory RNA : methods and protocols / edited by Kenneth C. Keiler.

Contributor(s): Keiler, Kenneth C [edt]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 905.; Springer protocols (Series): Publisher: New York, N.Y. : Humana Press, 2012Description: 1 online resource (xi, 333 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781617799495; 1617799491Subject(s): Bacterial genetics | RNA | RNA | Gene Expression Regulation, Bacterial -- physiology | Bacterial genetics | RNA | biomedische wetenschappen | biomedicine | microorganisms | genomica | genomics | humane genetica | human genetics | Medicine (General) | Geneeskunde (algemeen)Genre/Form: Laboratory Manual. | Electronic books. Additional physical formats: Print version:: Bacterial regulatory RNA.DDC classification: 579/.135 LOC classification: QH434 | .B338 2012Online resources: Click here to access online
Contents:
Bioinformatic discovery of bacterial regulatory RNAs using SIPHT / Jonathan Livny -- How to identify CRISPRs in sequencing data / Christine Drevet and Christine Pourcel -- Strategy for identifying noncoding RNAs using whole-genome tiling arrays / Stephen G. Landt and Eduardo Abeliuk -- Genetic screens to identify bacterial sRNA regulators / Pierre Mandin -- Competition assays using barcoded deletion strains to gain insight into small RNA function / Errett C. Hobbs and Gisela Storz -- Use of semi-quantitative northern blot analysis to determine relative quantities of bacterial CRISPR transcripts / Ksenia Pougach and Konstantin Severinov -- RNA visualization in bacteria by fluorescence in situ hybridization / Jay H. Russell and Kenneth C. Keiler -- RNA structure prediction : an overview of methods / Matthew G. Seetin and David H. Mathews -- Crystallization of RNA-protein complexes : from synthesis and purification of individual components to crystals / Anna Perederina and Andrey S. Krasilnikov -- Analysis of RNA folding and ligand binding by conventional and high-throughput calorimetry / Joshua E. Sokoloski and Philip C. Bevilacqua -- Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs / Colin P. Corcoran, Renate Rieder, Dimitri Podkaminski, Benjamin Hofmann, and Jörg Vogel -- Gel mobility shift assays to detect protein-RNA interactions / Alexander V. Yakhnin, Helen Yakhnin, and Paul Babitzke -- RNase footprinting of protein binding sites on an mRNA target of small RNAs / Yi Peng, Toby J. Soper, and Sarah A. Woodson -- Computational identification of sRNA targets / Brian Tjaden -- Detection of sRNA-mRNA interactions by electrophoretic mobility shift assay / Teppei Morita, Kimika Maki, and Hiroji Aiba -- Activity of small RNAs on the stability of targeted mRNAs in vivo / Guillaume Desnoyers and Eric Massé -- Native gel electrophoresis to study the binding and release of RNA polymerase by 6S RNA / Karen M. Wassarman -- Ribosome purification approaches for studying interactions of regulatory proteins and RNAs with the ribosome / Preeti Mehta, Perry Woo, Krithika Venkataraman, and A. Wali Karzai -- Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis / Brian D. Janssen, Elie J. Diner, and Christopher S. Hayes -- In vitro trans-translation assays / Daisuke Kurita, Akira Muto, and Hyouta Himeno.
Summary: The discovery of wide-spread RNA-based regulation in bacteria has led to new evaluations of the importance of bacterial regulatory RNA in every aspect of bacterial physiology. In Bacteria Regulatory RNA: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study bacterial regulatory RNA. These include methods and techniques to identify regulatory RNAs, characterizing the function and expression of regulatory RNAs in bacterial cells, RNA structure prediction, and interactions between regulatory RNAs and proteins. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Bacteria Regulatory RNA: Methods and Protocols seeks to aid scientists in the further study of bacterial regulatory RNA.
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Bioinformatic discovery of bacterial regulatory RNAs using SIPHT / Jonathan Livny -- How to identify CRISPRs in sequencing data / Christine Drevet and Christine Pourcel -- Strategy for identifying noncoding RNAs using whole-genome tiling arrays / Stephen G. Landt and Eduardo Abeliuk -- Genetic screens to identify bacterial sRNA regulators / Pierre Mandin -- Competition assays using barcoded deletion strains to gain insight into small RNA function / Errett C. Hobbs and Gisela Storz -- Use of semi-quantitative northern blot analysis to determine relative quantities of bacterial CRISPR transcripts / Ksenia Pougach and Konstantin Severinov -- RNA visualization in bacteria by fluorescence in situ hybridization / Jay H. Russell and Kenneth C. Keiler -- RNA structure prediction : an overview of methods / Matthew G. Seetin and David H. Mathews -- Crystallization of RNA-protein complexes : from synthesis and purification of individual components to crystals / Anna Perederina and Andrey S. Krasilnikov -- Analysis of RNA folding and ligand binding by conventional and high-throughput calorimetry / Joshua E. Sokoloski and Philip C. Bevilacqua -- Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs / Colin P. Corcoran, Renate Rieder, Dimitri Podkaminski, Benjamin Hofmann, and Jörg Vogel -- Gel mobility shift assays to detect protein-RNA interactions / Alexander V. Yakhnin, Helen Yakhnin, and Paul Babitzke -- RNase footprinting of protein binding sites on an mRNA target of small RNAs / Yi Peng, Toby J. Soper, and Sarah A. Woodson -- Computational identification of sRNA targets / Brian Tjaden -- Detection of sRNA-mRNA interactions by electrophoretic mobility shift assay / Teppei Morita, Kimika Maki, and Hiroji Aiba -- Activity of small RNAs on the stability of targeted mRNAs in vivo / Guillaume Desnoyers and Eric Massé -- Native gel electrophoresis to study the binding and release of RNA polymerase by 6S RNA / Karen M. Wassarman -- Ribosome purification approaches for studying interactions of regulatory proteins and RNAs with the ribosome / Preeti Mehta, Perry Woo, Krithika Venkataraman, and A. Wali Karzai -- Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis / Brian D. Janssen, Elie J. Diner, and Christopher S. Hayes -- In vitro trans-translation assays / Daisuke Kurita, Akira Muto, and Hyouta Himeno.

Includes bibliographical references and index.

Online resource; title from PDF title page (Springer, viewed Jun. 27, 2012).

The discovery of wide-spread RNA-based regulation in bacteria has led to new evaluations of the importance of bacterial regulatory RNA in every aspect of bacterial physiology. In Bacteria Regulatory RNA: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study bacterial regulatory RNA. These include methods and techniques to identify regulatory RNAs, characterizing the function and expression of regulatory RNAs in bacterial cells, RNA structure prediction, and interactions between regulatory RNAs and proteins. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Bacteria Regulatory RNA: Methods and Protocols seeks to aid scientists in the further study of bacterial regulatory RNA.

English.

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