The Nucleus: Volume 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging

ISBN-13: 9781603274609 / Angielski / Twarda / 2008 / 444 str.

Ronald Hancock

Opis

Although our understanding of the structure and activities of the cell nucleus and of the nanomachines which it contains is increasing rapidly, much remains to be learned. The application and continuing development of the new, powerful biochemical and biophysical methodologies described here are essential in this quest. In The Nucleus, researchers from more than forty leading international laboratories describe state-of-the-art methods for isolating nuclei and their components and for studying their structure and activities, including some pathology-associated features. Volume 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging presents biophysical approaches to study the mechanical properties of nuclei, together with a comprehensive range of imaging methods. These include FISH, FRAP, FRET, molecular beacons, fluorescence correlation spectroscopy, single molecule tracking, and combing DNA for optical microscopy, recognition imaging for atomic force microscopy, and hybridisation, tomography, and spectroscopic imaging for electron microscopy. Written in the highly successful Methods in Molecular BiologyT series format, chapters contain lists of necessary materials and reagents, readily reproducible protocols, and tips for troubleshooting and avoiding known pitfalls. The Nucleus, Volume 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging provides a comprehensive collection of the cutting-edge methods making a major contribution to understanding the nucleus and its nanostructure today. Written for: Nucleic acid chemists, cellular biologists, biochemists, protein scientists, imaging specialists

Spis treści

I. PHYSICAL AND MECHANICAL PROPERTIES 1. Physical properties of the nucleus studied by micropipette aspiration. Amy C. Rowat 2. Mechanical properties of interphase nuclei probed by cellular strain application. Jan Lammerding and Richard T. Lee II. CHROMATIN AND TRANSCRIPTION 3. Gene expression in polytene nuclei. Petra Björk and Lars Wieslander 4. Electron microscope visualization of RNA transcription and processing in Saccharomyces cerevisiae by Miller chromatin spreading. Yvonne N. Osheim, Sarah L. French, Martha L. Sikes and Ann L. Beyer 5. Combing Genomic DNA for Structural and Functional Studies. Catherine Schurra and Aaron Bensimon 6. Using molecular beacons to study dispersal of mRNPs from the gene locus. Patrick T. C. van den Bogaard and Sanjay Tyagi 7. Mapping cis- and trans- chromatin interaction networks using Chromosome Conformation Capture (3C). Adriana Miele and Job Dekker 8. Recognition Imaging of Chromatin and Chromatin-Remodeling Complexes in the Atomic Force Microscope. D. Lohr, H. Wang, R. Bash and S.M. Lindsay 9. Using cells encapsulated in agarose microbeads to analyse nuclear structure and functions. Dean Jackson III. THE NUCLEAR ENVELOPE 10. Investigation of nuclear envelope structure and passive permeability. Victor Shahin, Yvonne Ludwig and Hans Oberleithner. 11. Reconstitution of nuclear import in permeabilized cells. Aurelia Cassany and Larry Gerace 12. Nuclear Envelope Formation In Vitro: A Sea Urchin Egg Cell-Free System. Richard D. Byrne, Vanessa Zhendre, Banafshé Larijani and Dominic L. Poccia IV: MODIFICATIONS OF NUCLEAR PROTEINS 13. Detection and Analysis of (O-linked ß-N-acetyl-glucosamine)-modified proteins. Natasha E. Zachara 14. Detection of Sumoylated Proteins. Ok-Kyong Park-Sarge and Kevin D. Sarge 15. Detection of the nuclear poly(ADP-ribose)-metabolizing enzymes and activities in response to DNA damage. Jean-Christophe Amé, Antoinette Hakmé, Delphine Quenet, Elise Fouquerel, Françoise Dantzer and Valérie Schreiber 16. Purification and Analysis of Variant and Modified Histones Using 2D PAGE. G.R. Green and D.P. Do 17. Quantification of redox conditions in the nucleus. Young-Mi Go, Jan Pohl and Dean P. Jones V. PROTEIN DYNAMICS IN THE NUCLEUS 18. Fluorescence Correlation Spectroscopy to assess the Mobility of Nuclear Proteins. Stefanie Weidtkamp-Peters, Klaus Weisshart, Lars Schmiedeberg and Peter Hemmerich 19. Single Molecule Tracking for Studying Nucleo-cytoplasmic Transport and Intranuclear Dynamics. Jan Peter Siebrasse and Ulrich Kubitscheck 20. FRAP (Fluorescence Recovery After Photobleaching) to Study Nuclear Protein Dynamics in Living Cells. Martin E. van Royen, Pascal Farla, Karin A. Mattern, Bart Geverts, Jan Trapman and Adriaan B. Houtsmuller VI: IMAGING METHODS 21. Nanosizing by Spatially Modulated Illumination (SMI) Microscopy and Applications to the Nucleus. Udo J. Birk, David Baddeley and Christoph Cremer 22. Visualisation of RNA by Electron Microscopic in situ Hybridization. Jacques Rouquette, Karl-Henning Kalland and Stanislav Fakan 23. Electron Spectroscopic Imaging of the Nuclear Landscape. Kashif Ahmed, Ren Li and David P. Bazett-Jones 24. Cryoelectron microscopy of vitreous sections: a step further towards the native state. Cedric Bouchet-Marquis and Stanislav Fakan

Blurb

Although our understanding of the structure and activities of the cell nucleus and of the nanomachines which it contains is increasing rapidly, much remains to be learned. The application and continuing development of the new, powerful biochemical and biophysical methodologies described here are essential in this quest. In The Nucleus, researchers from more than forty leading international laboratories describe state-of-the-art methods for isolating nuclei and their components and for studying their structure and activities, including some pathology-associated features. Volume 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging presents biophysical approaches to study the mechanical properties of nuclei, together with a comprehensive range of imaging methods. These include FISH, FRAP, FRET, molecular beacons, fluorescence correlation spectroscopy, single molecule tracking, and combing DNA for optical microscopy, recognition imaging for atomic force microscopy, and hybridisation, tomography, and spectroscopic imaging for electron microscopy.  Written in the highly successful Methods in Molecular Biology™ series format, chapters contain lists of necessary materials and reagents, readily reproducible protocols, and tips for troubleshooting and avoiding known pitfalls.

The Nucleus, Volume 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging provides a comprehensive collection of the cutting-edge methods making a major contribution to understanding the nucleus and its nanostructure today.