Hancock R. (Ed.) The Nucleus Volume 2: Chromatin, Transcription, Envelope, Proteins, Dynamics, and Imaging

Humana Press, 2008. — 444 p. — (Methods in Molecular Biology 464). — ISBN: 978-1-60327-461-6 (eBook), 978-1-61737-898-0 (Softcover), 978-1-60327-460-9 (Hardcover).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 hereare 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 Imagingpresentsbiophysical 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.Physical and Mechanical Properties
Physical Properties of the Nucleus Studied by Micropipette Aspiration
Mechanical Properties of Interphase Nuclei Probed by Cellular Strain Application
Chromatin and Transcription
Gene Expression in Polytene Nuclei
Electron Microscope Visualization of RNA Transcription and Processing in Saccharomyces cerevisiae by Miller Chromatin Spreading
Combing Genomic DNA for Structural and Functional Studies
Using Molecular Beacons to Study Dispersal of mRNPs from the Gene Locus
Mapping Cis- and Trans- Chromatin Interaction Networks Using Chromosome Conformation Capture (3C)
Recognition Imaging of Chromatin and Chromatin-Remodeling Complexes in the Atomic Force Microscope
Using Cells Encapsulated in Agarose Microbeads to Analyse Nuclear Structure and Functions
The Nuclear Envelope
Investigation of Nuclear Envelope Structure and Passive Permeability
Reconstitution of Nuclear Import in Permeabilized Cells
Nuclear Envelope Formation In Vitro: A Sea Urchin Egg Cell-Free System
Modifications of Nuclear Proteins
Detection and Analysis of (O-linked β-N-Acetylglucosamine)-Modified Proteins
Detection of Sumoylated Proteins
Detection of the Nuclear Poly(ADP-ribose)-Metabolizing Enzymes and Activities in Response to DNA Damage
Purification and Analysis of Variant and Modified Histones Using 2D PAGE
Quantification of Redox Conditions in the Nucleus
Protein Dynamics in the Nucleus
Fluorescence Correlation Spectroscopy to Assess the Mobility of Nuclear Proteins
Single Molecule Tracking for Studying Nucleocytoplasmic Transport and Intranuclear Dynamics
Fluorescence Recovery After Photobleaching (FRAP) to Study Nuclear Protein Dynamics in Living Cells
Imaging Methods
Nanosizing by Spatially Modulated Illumination (SMI) Microscopy and Applications to the Nucleus
Visualisation of RNA by Electron Microscopic In Situ Hybridisation
Electron Spectroscopic Imaging of the Nuclear Landscape
Cryoelectron Microscopy of Vitreous Sections: A Step Further Towards the Native State