Part I: Identification of sRNA
1. Workflow for a Computational Analysis of an sRNA Candidate in Bacteria
Patrick R. Wright and Jens Georg
2. Molecular Phylogenomics for the Identification and Characterization of trans-encoded Small Non-coding RNA Families
Antonio Lagares (Jr) and Claudio Valverde
3. Bioinformatic Approach for Prediction of CsrA/RsmA-regulating small RNAs in Bacteria
Carl T. Fakhry, Kourosh Zarringhalam, and Rahul V. Kulkarni
Part II: Function and Differential Expression of sRNA
4. Host-pathogen Transcriptomics by Dual RNA-seq
Alexander J. Westermann and Jörg Vogel
5. Identification of New Bacterial Small RNA Targets using MS2 Affinity Purification Coupled to RNA Sequencing
Marie-Claude Carrier, Guillaume Laliberté, and Eric Massé
6. Assessment of External Guide Sequences' (EGS) Efficiency as Inducers of RNase P-mediated Cleavage of mRNA Target Molecules
Saumya Jani, Alexis Jackson, Carol Davies-Sala, Kevin Chiem, Alfonso Soler-Bistué, Angeles Zorreguieta, and Marcelo E. Tolmasky
7. Evaluating the Effect of Small RNAs and Associated Chaperones on Rho-dependent Termination of Transcription in vitro
Cédric Nadiras, Annie Schwartz, Mildred Delaleau, and Marc Boudvillain
8. A Method to Map Changes in Bacterial Surface Composition Induced by Regulatory RNAs
Pierre Fechter
9. Fluorescence-based Methods for Characterizing RNA interactions in vivo
A. N. Leistra M. K. Mihailovic and L. M. Contreras
10. Mutational Analysis of sRNA-mRNA Base Pairing by Electrophoretic Mobility Shift Assay
Eva Maria Sternkopf Lillebæk and Birgitte Haahr Kallipolitis
11. An Integrated Cell-free Assay to Study Translation Regulation by Small Bacterial Non-coding RNAs
Erich Michel, Olivier Duss, and Frédéric H.-T. Allain
Part III: Quantitation and Subcellular Localisation of sRNA
12. Quantitative Super-resolution Imaging of Small RNAs in Bacterial Cells
Seongjin Park, Magda Bujnowska, Eric McLean, and Jingyi Fei
13. Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived outer Membrane Vesicles
Janine Habier, Patrick May, Anna-Heintz-Buschart, Anubrata Ghosal, Anke K. Wienecke-Baldacchino, Esther N.M. Nolte-'t Hoen, Paul Wilmes, and Joëlle V. Fritz
14. Absolute Regulatory Small Noncoding RNA Concentration and Decay Rates Measurements in Escherichia coli
Florent Busi, Véronique Arluison, and Philippe Régnier
Part IV: Cofactors of sRNA-based Regulation
15. High-resolution, High-throughput Analysis of Hfq Binding Sites using UV-crosslinking and Analysis of cDNA (CRAC)
Brandon Sy, Julia Wong, Sander Granneman, David Tollervey, David Gally, and Jai J. Tree 16. Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly
Kimberly A. Stanek and Cameron Mura
17. Single Molecule FRET Assay to Observe the Activity of Proteins Involved in RNA/RNA Annealing
Thierry Bizebard, Véronique Arluison, and Ulrich Bockelman 18. Techniques to Analyse sRNA-protein Cofactor Self-assembly in vitro
David Partouche, Antoine Malabirade, Thomas Bizien, Marisela Velez, Sylvain Trepout, Sergio Marco, Valeria Militello, Christophe Sandt, Frank Wien, and Véronique Arluison
19. Sequence-specific Affinity Chromatography of RNA-binding Proteins from Bacterial Cells
Jonathan Gans, Jonathan Osborne, Juliet Cheng, Louise Djapgne, and Amanda G. Oglesby-Sherrouse
20. Identification of Small RNA-protein Partners in Plant Symbiotic Bacteria
Marta Robledo, Ana M. Matia-González, Natalia I. García-Tomsig, and José I. Jiménez-Zurdo
Part V: Applications in Synthetic Biology
21. A Modular Genetic System for High
