Bacterial Regulatory RNA: Methods and Protocols by Kenneth C. KeilerBacterial Regulatory RNA: Methods and Protocols by Kenneth C. Keiler

Bacterial Regulatory RNA: Methods and Protocols

EditorKenneth C. Keiler

Hardcover | June 28, 2012

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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 BiologyT 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.
Title:Bacterial Regulatory RNA: Methods and ProtocolsFormat:HardcoverDimensions:344 pagesPublished:June 28, 2012Publisher:Humana PressLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:1617799483

ISBN - 13:9781617799488

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Table of Contents

Part I- Identification of Regulatory RNAs   1. Bioinformatic Discovery of Bacterial Regulatory RNAs using SIPH Jonathan Livny   2. How to Identify CRISPRs in Sequencing Data Christine Drevet and Christine Pourcel   3. A Strategy for Identifying Non-coding RNAs using Whole-genome Tiling Arrays Stephen G. Landt and Eduardo Abeliuk   4. Genetic Screens to Identify Bacterial sRNA Regulators Pierre Mandin     Part II - Function and Expression of Regulatory RNAs   5. Competition Assays Using Barcoded Deletion Strains to Gain Insight Into Small RNA Function Errett C. Hobbs and Gisela Storz   6. Use of Semi-quantitative Northern Blot Analysis to Determine Relative Quantities of Bacterial CRISPR Transcripts Ksenia Pougach and Konstantin Severinov   7. RNA Visualization in Bacteria by Fluorescence in Situ Hybridization Jay H. Russell and Kenneth C. Keiler     Part III - RNA Structure and Biophysical Measurements  8. RNA Structure Prediction: An Overview of MethodsMatthew G. Seetin and David H. Mathews   9. Crystallization of RNA-Protein Complexes: From Synthesis and Purification of Individual Components to Crystals Anna Perederina and Andrey S. Krasilnikov   10. Analysis of RNA Folding and Ligand Binding by Conventional and High-Throughput Calorimetry Joshua E. Sokoloski and Philip C. Bevilacqua   Part IV - RNA-Protein Interactions 11. 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 12. Gel Mobility Shift Assays to Detect Protein-RNA Interactions Alexander V. Yakhnin, Helen Yakhnin and Paul Babitzke   13. RNase Footprinting of Protein Binding Sites on an mRNA Target of Small RNAs Peng Yi, Soper, Toby J., and Woodson Sarah A   Part V - RNA-RNA Interactions 14.Computational Identification of sRNA Targets Brian Tjaden  15. Detection of sRNA-mRNA Interactions by Electrophoretic Mobility Shift AssayTeppei Morita , Kimika Maki, and Hiroji Aiba   16. Activity of Small RNAs on the Stability of Targeted mRNAs in vivo Guillaume Desnoyers and Eric Massé   Part VI -Interactions of Regulatory RNA with RNA Polymerase and the Ribosome 17. Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA Karen M. Wassarman   18. Ribosome Purification Approaches for Studying Interactions of Regulatory Proteins and RNAs with the Ribosome Preeti Mehta, Perry Woo, Krithika Venkataraman, and A. Wali Karzai   19. Analysis of Aminoacyl- and Peptidyl-tRNAs by Gel Electrophoresis Brian D. Jansse, Elie J. Diner, and Christopher S. Hayes   20. In vitro trans-translation Assays Daisuke Kurit, Akira Muto, and Hyouta Himeno