The bacterial nucleoid : methods and protocols

著者

• Espeli, Olivier

書誌事項

The bacterial nucleoid : methods and protocols

edited by Olivier Espéli

（Methods in molecular biology / John M. Walker, series editor, 1624）（Springer protocols）

Humana Press, c2017

注記

Includes bibliographical references and index

内容説明・目次

内容説明

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.

目次

Preface... Table of Contents... Contributing Authors... Part I Molecular Genetic Methods to Study Bacterial Nucleoid 1. Homologous Recombineering to Generate Chromosomal Deletions in Escherichia coli Jack A. Bryant and David J. Lee 2. Measuring In Vivo Supercoil Dynamics and Transcription Elongation Rates in Bacterial Chromosomes N. Patrick Higgins 3. Revealing Sister Chromatid Interactions with the loxP/Cre Recombination Assay Elise Vickridge, Charlene Planchenault, and Olivier Espeli 4. Transposon Insertion Site Sequencing for Synthetic Lethal Screening Yoshiharu Yamaichi and Tobias Doerr Part II Study of bacterial nucleoid with whole genome analysis method 5. WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites Mickael Poidevin, Elisa Galli, Yoshiharu Yamaichi, and Francois-Xavier Barre < 6. High Resolution Chromatin Immunoprecipitation: ChIP-Sequencing Roxanne E. Diaz, Aurore Sanchez, Veronique Anton Le Berre, and Jean-Yves Bouet 7. Generation and Analysis of Chromosomal Contact Maps of Bacteria Martial Marbouty and Romain Koszul 8. Nucleoid Associated Proteins: Genome Level Occupancy and Expression Analysis Parul Singh and Aswin Sai Narain Seshasayee Part III Molecular Biology Methods to Study Nucleoid Structuring Factors 9. Isolation and Analysis of RNA Polymerase Supramolecular Complex with Associated Proteins Sanja Mehandziska, Mircea A. Petrescu, and Georgi Muskhelishvili 10. A chromosome Co-Entrapment Assay to Study Topological Protein-DNA Interactions Larissa Wilhelm and Stephan Gruber 11. Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins Ramon A. van der Valk, Niels Laurens, and Remus T. Dame 12. Biochemical Analysis of Bacterial Condensins Zoya M. Petrushenko and Valentin V. Rybenkov 13. Exploring Condensins with Magnetic Tweezers Rupa Sarkar and Valentin V. Rybenkov 14. Applications of Magnetic Tweezers to Studies of NAPs Ricksen S. Winardhi and Jie Yan 15. A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data Damien Lariviere, Rodrigo Galindo-Murillo, Eric Fourmentin, Samuel Hornus, Bruno Levy, Julie Papillon, Jean-Francois Menetret, and Valerie Lamour Part IV Imaging Bacterial Nucleoid 16. Multi-Locus Imaging of the E. coli Chromosome by Fluorescent In Situ Hybridization Bryan J. Visser, Mohan C. Joshi, and David Bates 17. Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage Gaelle Demarre, Victoria Prudent, and Olivier Espeli 18. Measuring ivo Protein Dynamics throughout the Cell Cycle using Microfluidics Roy de Leeuw, Peter Brazda, M. Charl Moolman, J.W.J. Kerssemakers, Belen Solano, and Nynke H. Dekker 19. Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy Antoine Le Gall, Diego I. Cattoni, and Marcelo Nollmann 20. 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, and Mike Heilemann 21. Procedures for Model-Guided Data Analysis of Chromosomal Loci Dynamics at Short Time Scales Marco Gherardi and Marco Cosentino Lagomarsino Part V Biophysics of the Bacterial Nucleoid 22. Isolation and Characterization of Bacterial Nucleoids in Microuidic Devices James Pelletier and Suckjoon Jun 23. Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix Thibaut Lepage and Ivan Junier 24. 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, and Andrzej Stasiak

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詳細情報

• NII書誌ID(NCID): BB24697945
• ISBN:
  • 9781493970971
• 出版国コード: us
• タイトル言語コード: eng
• 本文言語コード: eng
• 出版地: New York
• ページ数/冊数: xiv, 374 p.
• 大きさ: 27 cm
• 分類:
  • DC20 : 574.8732
• 親書誌ID:
  • BA10794673
  • BA88873632