The Nucleus (Methods in Molecular Biology) by Ronald Hancock [Hardback]

Description: This volume presents detailed, recently-developed protocols ranging from isolation of nuclei to purification of chromatin regions containing single genes, with a particular focus on some less well-explored aspects of the nucleus. The methods described include new strategies for isolation of nuclei, for purification of cell type-specific nuclei from a mixture, and for rapid isolation and fractionation of nucleoli. For gene delivery into and expression in nuclei, a novel gentle approach using gold nanowires is presented. As the concentration and localization of water and ions are crucial for macromolecular interactions in the nucleus, a new approach to measure these parameters by correlative optical and cryo-electron microscopy is described. The Nucleus, Second Edition presents methods and software for high-throughput quantitative analysis of 3D fluorescence microscopy images, for quantification of the formation of amyloid fibrils in the nucleus, and for quantitative analysis of chromosome territory localization. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, The Nucleus, Second Edition seeks to serve both professionals and novices with its well-honed methods for the study of the nucleus. Part I. Isolation of Nuclei 1. Cell Type-Specific Affinity Purification of Nuclei for Chromatin Profiling in Whole Animals Florian A. Steiner and Steven Henikoff 2. Lysis Gradient Centrifugation - A Flexible Method for the Isolation of Nuclei from Primary Cells Karl Katholnig, Marko Poglitsch, Markus Hengstschläger, and Thomas Weichhart 3. Isolation of Nuclei in Media Containing an Inert Polymer to Mimic the Crowded Cytoplasm Ronald Hancock and Yasmina Hadj-Sahraoui Part II. Nucleoli 4. A New Rapid Method for Isolating Nucleoli Zhou Fang Li, Yun Wah Lam 5. Sequential Recovery of Macromolecular Components of the Nucleolus Baoyan Bai and Marikki Laiho Part III. Genes and Chromatin 6. Au Nanoinjectors for Electrotriggered Gene Delivery into the Cell Nucleus Mijeong Kang and Bongsoo Kim 7. Improving Chromatin Immunoprecipitation (ChIP) by Suppression of Method-Induced DNA-Damage Signaling Sascha Beneke 8. Purification of Specific Chromatin Loci for Proteomic Analysis Stephanie D. Byrum, Sean D. Taverna, and Alan J. Tackett 9. Chromatin Structure Analysis of Single Gene Molecules by Psoralen Crosslinking and Electron Microscopy Chris Brown, Julian Eskin, Stephan Hamperl, Joachim Griesenbeck, Melissa Jurica, Hinrich Boeger 10. Purification of Proteins on Newly Synthesized DNA Using iPOND Huzefa Dungrawala and David Cortez 11. Applying the Ribopuromycylation Method to Detect Nuclear Translation Alexandre David and Jonathan W. Yewdell Part IV. The Intranuclear Milieu 12. Targeted Nano Analysis of Water and Ions in the Nucleus Using Cryo-Correlative Microscopy Frédérique Nolin, Dominique Ploton, Laurence Wortham, Pavel Tchelidze, Hélène Bobichon, Vincent Banchet, Nathalie Lalun, Christine Terryn, and Jean Michel 13. A Redox-Sensitive Yellow Fluorescent Protein Sensor for Monitoring Nuclear Glutathione Redox Dynamics Agata Banach-Latapy, Michèle Dardalhon, and Meng-Er Huang Part V. Imaging Nuclear Structures 14. Determination of the Dissociation Constant of the NFkB p50/p65 Heterodimer in Living Cells Using Fluorescence Cross-Correlation Spectroscopy Manisha Tiwari and Masataka Kinjo 15. Imaging and Quantification of Amyloid Fibrillation in the Cell Nucleus Florian Arnhold, Andrea Scharf, and Anna von Mikecz 16. Analysis of Nuclear Organization with TANGO, Software for High-Throughput Quantitative Analysis of 3D Fluorescence Microscopy Images Jean Ollion, Julien Cochennec. François Loll, Christophe Escudé, and Thomas Boudier 17. Quantitative Analysis of Chromosome Localization in the Nucleus Sandeep Chakraborty, Ishita Mehta, Mugdha Kulashreshtha, and B. J. Rao

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