The bacterial nucleoid : methods and protocols

Description

This volume presents state-of-the-art protocols for key experiments that have revolutionized our understanding of the bacterial nucleoid. This book is divided into five parts: Part I introduces molecular genetic methods to study bacterial nucleoids; Part II highlights the study of bacterial nucleoid with whole genome analysis method; Part III discusses molecular biology methods to study nucleoid structuring factors; Part IV looks at imaging bacterial nucleoid; and Part V explores biophysics of the bacterial nucleoid. 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 tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, The Bacterial Nucleoid: Methods and Protocols is a valuable resource that provides a wealth of new information about this chromosome. Read more... Abstract: This volume presents state-of-the-art protocols for key experiments that have revolutionized our understanding of the bacterial nucleoid. Read more... Front Matter ....Pages i-xiv Front Matter ....Pages 1-1 Homologous Recombineering to Generate Chromosomal Deletions in Escherichia coli (Jack A. Bryant, David J. Lee)....Pages 3-16 Measuring In Vivo Supercoil Dynamics and Transcription Elongation Rates in Bacterial Chromosomes (N. Patrick Higgins)....Pages 17-27 Revealing Sister Chromatid Interactions with the loxP/Cre Recombination Assay (Elise Vickridge, Charlène Planchenault, Olivier Espéli)....Pages 29-37 Transposon Insertion Site Sequencing for Synthetic Lethal Screening (Yoshiharu Yamaichi, Tobias Dörr)....Pages 39-49 Front Matter ....Pages 51-51 WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites (Mickaël Poidevin, Elisa Galli, Yoshiharu Yamaichi, François-Xavier Barre)....Pages 53-60 High-Resolution Chromatin Immunoprecipitation: ChIP-Sequencing (Roxanne E. Diaz, Aurore Sanchez, Véronique Anton Le Berre, Jean-Yves Bouet)....Pages 61-73 Generation and Analysis of Chromosomal Contact Maps of Bacteria (Martial Marbouty, Romain Koszul)....Pages 75-84 Nucleoid-Associated Proteins: Genome Level Occupancy and Expression Analysis (Parul Singh, Aswin Sai Narain Seshasayee)....Pages 85-97 Front Matter ....Pages 99-99 Isolation and Analysis of RNA Polymerase Supramolecular Complex with Associated Proteins (Sanja Mehandziska, Alexander M. Petrescu, Georgi Muskhelishvili)....Pages 101-116 A Chromosome Co-Entrapment Assay to Study Topological Protein–DNA Interactions (Larissa Wilhelm, Stephan Gruber)....Pages 117-126 Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins (Ramon A. van der Valk, Niels Laurens, Remus T. Dame)....Pages 127-143 Biochemical Analysis of Bacterial Condensins (Zoya M. Petrushenko, Valentin V. Rybenkov)....Pages 145-159 Exploring Condensins with Magnetic Tweezers (Rupa Sarkar, Valentin V. Rybenkov)....Pages 161-171 Applications of Magnetic Tweezers to Studies of NAPs (Ricksen S. Winardhi, Jie Yan)....Pages 173-191 A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data (Damien Larivière, Rodrigo Galindo-Murillo, Eric Fourmentin, Samuel Hornus, Bruno Lévy, Julie Papillon et al.)....Pages 193-210 Front Matter ....Pages 211-211 Multilocus Imaging of the E. coli Chromosome by Fluorescent In Situ Hybridization (Bryan J. Visser, Mohan C. Joshi, David Bates)....Pages 213-226 Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage (Gaëlle Demarre, Victoria Prudent, Olivier Espéli)....Pages 227-236 Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics (Roy de Leeuw, Peter Brazda, M. Charl Moolman, J. W. J. Kerssemakers, Belen Solano, Nynke H. Dekker)....Pages 237-252 Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy (Antoine Le Gall, Diego I. Cattoni, Marcelo Nollmann)....Pages 253-268 Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells (Christoph Spahn, Mathilda Glaesmann, Yunfeng Gao, Yong Hwee Foo, Marko Lampe, Linda J. Kenney et al.)....Pages 269-289 Procedures for Model-Guided Data Analysis of Chromosomal Loci Dynamics at Short Time Scales (Marco Gherardi, Marco Cosentino Lagomarsino)....Pages 291-307 Front Matter ....Pages 309-309 Isolation and Characterization of Bacterial Nucleoids in Microfluidic Devices (James Pelletier, Suckjoon Jun)....Pages 311-322 Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix (Thibaut Lepage, Ivan Junier)....Pages 323-337 Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase (Dusan Racko, Fabrizio Benedetti, Julien Dorier, Yannis Burnier, Andrzej Stasiak)....Pages 339-372 Erratum to: Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells (Christoph Spahn, Mathilda Glaesmann, Yunfeng Gao, Yong Hwee Foo, Marko Lampe, Linda J. Kenney et al.)....Pages E1-E1 Back Matter ....Pages 373-374