Chromosome Architecture: Methods and Protocols

ISBN-13: 9781071622209 / Angielski / Twarda / 2022

Leake, Mark C.

Opis

This detailed new edition collects cutting-edge laboratory protocols, techniques, and applications in use by some of the leading international experts in the broad field of chromosome architecture. The book emphasizes the increasing physiological relevance of chromosome architecture investigation, manifest both through application of more complex bottom-up assays in vitro as well as through maintaining the native physiological context through the investigation of living, functional cells. In addition, the chapters reflect the dramatic improvement in the length scale of precision by utilizing single-molecule approaches, both for imaging the DNA content of chromosome and proteins that bind to DNA as well as using methods that can controllably manipulate single DNA molecules, and the use of advanced computational methods and mathematical analysis is also featured. Written for the highly successful Methods in Molecular Biology series, 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. 

Authoritative and up-to-date, Chromosome Architecture: Methods and Protocols, Second Edition is an ideal guide for researchers working in this dynamic area of study.

Spis treści

1. A Next Generation of Advances in Chromosome Architecture

            Mark C. Leake

 

2. Single Molecule Narrowfield Microscopy of Protein-DNA Binding Dynamics in Glucose Signal Transduction of Live Yeast Cells

            Adam J.M. Wollman and Mark C. Leake

 

3. Convolutional Neural Networks for Classifying Chromatin Morphology in Live Cell Imaging

            Kristina Ulicna, Laure T.L. Ho, Christopher J. Soelistyo, Nathan J. Day, and Alan R. Lowe

 

4. Fluorescence Recovery After Photobleaching (FRAP) to Study Dynamics of the Structural Maintenance of Chromosome (SMC) Complex in Live Escherichia coli Bacteria

            Anjana Badrinarayanan and Mark C. Leake

 

5. Atomic Force Microscopy of DNA and DNA-Protein Interactions

            Philip J. Haynes, Kavit H.S. Main, and Alice L.B. Pyne

 

6. Live-Cell Visualization of DNA Transfer and Pilus Dynamics during Bacterial Conjugation

            Kelly Goldlust, Agathe Couturier, Laurent Terradot, and Christian Lesterlin

 

7. Transverse Magnetic Tweezers Allowing Coincident Epi-Fluorescence Microscopy on Horizontally Extended DNA

            Stephen J. Cross, Claire E. Brown, and Christoph G. Baumann

 

8. Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments

            George Watson, Victor Velasco-Berrelleza, and Agnes Noy

 

9. Replication Labeling Methods for Super-Resolution Imaging of Chromosome Territories and Chromatin Domains

            Ezequiel Miron, Joseph Windo, Fena Ochs, and Lothar Schermelleh

 

10. DNA-Protein Interactions Studied Directly Using iSCAT Imaging of GNP-Tagged Proteins

            Robert J. Charman and Neil M. Kad

 

11. Escherichia coli Chromosome Copy Number Measurement Using Flow Cytometry Analysis

            Michelle Hawkins, John Atkinson, and Peter McGlynn

 

12. Dynamics of Bacterial Chromosomes by Locus Tracking in Fluorescence Microscopy

            Leonardo Mancini, Estelle Crozat, Avelino Javer, Marco Cosentino Lagomarsino, and Pietro Cicuta

 

13. Measuring Nuclear Mechanics with Atomic Force Microscopy

            Ália dos Santos, Florian Rehfeldt, and Christopher P. Toseland

 

14. Copy Number Analysis of the Yeast Histone Deacetylase Complex Component Cti6 Directly in Living Cells

            Sviatlana Shashkova, Thomas Nyström, and Mark C. Leake

 

15. Super-Resolution Microscopy and Tracking of DNA-Binding Proteins in Bacterial Cells

            Chloé J. Cassaro and Stephan Uphoff

 

16. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy

            Maike Steindel, Igor de Almeida, Stanley Strawbridge, Valentyna Chernova, David Holcman, Aleks Ponjavic, and Srinjan Basu

 

17. The End Restraint Method for Mechanically Perturbing Nucleic Acids In Silico

            Jack W. Shepherd and Mark C. Leake

 

18. Visualizing the Replisome, Chromosome Breaks, and Replication Restart in Bacillus subtilis

            Hannah Gaimster, Charles Winterhalter, Alan Koh, and Heath Murray

 

19. High-Throughput Imaging of Bacillus subtilis

            Paula Montero Llopis, Ryan Stephansky, and Xindan Wang

 

20. Measuring Nuclear Organization of Proteins with STORM Imaging and Cluster Analysis

            Ália dos Santos, Rosemarie E. Gough, Lin Wang, and Christopher P. Toseland

 

21. Single-Molecular Quantification of Flowering Control Proteins within Nuclear Condensates in Live Whole Arabidopsis Root

            Alex L. Payne-Dwyer and Mark C. Leake