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Gerst, Jeffrey E. (Herausgeber)

RNA Detection and Visualization Methods and Protocols (Gebundene Ausgabe)

Humana Press, Humana Press Inc., April 2011

2011 - 512 S. - Sprache: Englisch - 263x189x33 mm Book

ISBN: 1617790044 EAN: 9781617790041

With its complex and extensively regulated metabolism, the study of the RNA lifecycle demands tools that allow for the localization of RNAs to be observed either in an in situ setting or, preferably, under in vivo conditions.  In RNA Detection and Visualization: Methods and Protocols, the best and brightest investigators provide an up-to-date and in-depth description of basic methods and protocols used for detecting and visualizing mRNAs in both fixed and live cells, from bacteria to mammals.  For novices and experts alike, this mix of classic in situ hybridization and advanced live imaging techniques, cell fractionation and affinity purification procedures, and bioinformatics tools gives researchers the most complete and extensive array of research aids possible. As a volume written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls.  Authoritative and cutting-edge, RNA Detection and Visualization: Methods and Protocols offers well-honed techniques in order to inspire researchers around the world to further our knowledge of the vital biological significance of RNA.

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-Features methods and protocols relevant for both fixed and live cells from everything from bacteria to mammalian models-Provides detailed techniques from established and up-and-coming experts in the field-Includes vital notes on troubleshooting and avoiding known pitfalls for easier implementation of the methods


Part I: Visualizing mRNAs In situ 1. Single Molecule Imaging of RNA In situ            Mona Batish, Arjun Raj and Sanjay Tyagi 2. FISH and Immunofluorescence Staining in Chlamydomonas            James Uniacke, Daniel Colón-Ramos, and William Zerges 3. High Resolution Fluorescent In situ Hybridization in Drosophila            Eric Lécuyer 4. Localization and Anchorage of Maternal mRNAs to Cortical Structures of Ascidian Eggs and Embryos Using High Resolution In situ Hybridization            Alexandre Paix, Janet Chenevert, and Christian Sardet 5. Visualization of mRNA Localization in Xenopus Oocytes            James A. Gagnon and Kimberly L. Mowry 6. Visualization of mRNA Expression in the Zebrafish Embryo            Yossy Machluf and Gil Levkowitz 7. High-Resolution Fluorescence In situ Hybridization to Detect mRNAs in Neuronal Compartments In vitro and In vivo            Sharon A. Swanger, Gary J. Bassell, and Christina Gross 8. Localization of mRNA in Vertebrate Axons Using In situ Hybridization            José Roberto Sotelo-Silveira, Aldo Calliari, Alejandra Kun, Victoria Elizondo, Lucía Canclini, and José Roberto Sotelo Part II: Visualizing mRNAs In vivo Using Molecular Probes or Reconstituted Fluorescent Proteins 9. Tiny Molecular Beacons for In vivo mRNA Detection            Diana P. Bratu, Irina E. Catrina, and Salvatore A.E. Marras 10. Delivery of Molecular Beacons for Live-Cell Imaging and Analysis of RNA            Antony K. Chen, Won Jong Rhee, Gang Bao, and Andrew Tsourkas 11. Genetically-Encoded Fluorescent Probes for Imaging Endogenous mRNA in Living Cells            Takeaki Ozawa and Yoshio Umezawa 12. Visualization of Induced RNA in Single Bacterial Cells            Azra Borogovac and Natalia E. Broude Part III: Visualizing mRNAs In vivo Using Aptamers and Intact Fluorescent Proteins 13. Visualizing mRNAs in Fixed and Living Yeast Cells            Franck Gallardo and Pascal Chartrand 14. In vivo Visualization of RNA Using the U1A-Based Tagged RNA System            Sunglan Chung and Peter A. Takizawa 15. Visualizing Endogenous mRNAs in Living Yeast Using m-TAG, a PCR-Based RNA Aptamer Integration Method, and Fluorescence Microscopy            Liora Haim-Vilmovsky and Jeffrey. E. Gerst 16. Imaging mRNAs in Living Mammalian Cells            Sharon Yunger and Yaron Shav-Tal 17. Using the mRNA-MS2/MS2CP-FP System to Study mRNA Transport during Drosophila Oogenesis            Katsiaryna Belaya and Daniel St. Johnston Part IV: Use of Cell Fractionation to Demonstrate the Sub-Cellular Localization of RNA 18. Genome-Wide Analysis of RNA Extracted from Isolated Mitochondria            Erez Eliyahu, Daniel Melamed, and Yoav Arava 19. Analyzing mRNA Localization to the Endoplasmic Reticulum via Cell Fractionation            Sujatha Jagannathan, Christine Nwosu, and Christopher V. Nicchitta 20. Isolation of mRNAs Encoding Peroxisomal Proteins from Yeast Using a Combined Cell Fractionation and Affinity Purification Procedure            Gadi Zipor, Cecile Brocard, and Jeffrey. E. Gerst 21. Profiling Axonal mRNA Transport            Dianna E. Willis and Jeffery L. Twiss 22. RNA Purification from Tumor Cell Protrusions Using Porous Polycarbonate Filters            Jay Shankar and Ivan R. Nabi Part V: Affinity Purification of mRNAs and the Identification of Trans-Acting Factors 23. RNA-Binding Protein Immunopurification-Microarray (RIP-Chip) Analysis to Profile Localized RNAs            Alessia Galgano and André P. Gerber 24. RaPID: An Aptamer-Based mRNA Affinity Purification Technique for the Identification of RNA and Protein Factors Present in Ribonucleoprotein Complexes            Boris Slobodin and Jeffrey E. Gerst 25. RIP: An mRNA Localization Technique            Sabarinath Jayaseelan, Francis Doyle, Salvatore Currenti, and Scott Tenenbaum 26. The Dual Use of RNA Aptamer Sequences for Affinity Purification and Localization Studies of RNAs and RNA-Protein Complexes            Scott C. Walker, Paul D. Good, Theresa A. Gipson, and David R. Engelke Part VI: Use of Bioinformatics to Identify Cis-Acting Motifs and Structures in RNAs 27. Identifying and Searching for Conserved RNA Localization Signals            Russell S. Hamilton and Ilan Davis 28. Computational Prediction of RNA Structural Motifs Involved in Post Transcriptional Regulatory Processes            Michal Rabani, Michael Kertesz, and Eran Segal

ISBN 1-617790-04-4, ISBN 1-61-779004-4, ISBN 1-61779-004-4, ISBN 1-617-79004-4, ISBN 1-6177-9004-4

ISBN 978-1-617790-04-1, ISBN 978-1-61-779004-1, ISBN 978-1-61779-004-1, ISBN 978-1-617-79004-1, ISBN 978-1-6177-9004-1

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