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