Espéli The Bacterial Nucleoid

Methods and Protocols
1. Auflage 2017
ISBN: 978-1-4939-7098-8
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 1624, 374 Seiten, eBook

Reihe: Methods in Molecular Biology

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.

Zielgruppe

Professional/practitioner

Autoren/Hrsg.

Espéli, Olivier

Inhaltsverzeichnis

Homologous Recombineering to Generate Chromosomal Deletions in Escherichia coli.-  Measuring In Vivo Supercoil Dynamics and Transcription Elongation Rates in Bacterial Chromosomes.- Revealing Sister Chromatid Interactions with the loxP /Cre Recombination Assay.- Transposon Insertion Site Sequencing for Synthetic Lethal Screening.- WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites.- High Resolution Chromatin Immunoprecipitation: ChIP-Sequencing.- Generation and Analysis of Chromosomal Contact Maps of Bacteria.- Nucleoid Associated Proteins: Genome Level Occupancy and Expression Analysis.- Isolation and Analysis of RNA Polymerase Supramolecular Complex with Associated Proteins.- A chromosome Co-Entrapment Assay to Study Topological Protein-DNA Interactions.- Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins.- Biochemical Analysis of Bacterial Condensins.- Exploring Condensins with Magnetic Tweezers.- Applications of Magnetic Tweezers to Studies of NAPs.- A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data.- Multi-Locus Imaging of the E. coli Chromosome by Fluorescent In Situ Hybridization.- Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage.- Measuring In Vivo Protein Dynamics throughout the Cell Cycle using Microfluidics.- Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy.- Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells.- Procedures for Model-Guided Data Analysis of Chromosomal Loci Dynamics at Short Time Scales.- Isolation and Characterization of Bacterial Nucleoids in Microuidic Devices.- Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix.- Molecular Dynamics Simulation of Supercoiled, Knotted and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.