Filter
Associated Lab
- Ahrens Lab (2) Apply Ahrens Lab filter
- Betzig Lab (1) Apply Betzig Lab filter
- Card Lab (1) Apply Card Lab filter
- Cardona Lab (1) Apply Cardona Lab filter
- Dudman Lab (1) Apply Dudman Lab filter
- Egnor Lab (2) Apply Egnor Lab filter
- Gonen Lab (1) Apply Gonen Lab filter
- Heberlein Lab (2) Apply Heberlein Lab filter
- Hess Lab (1) Apply Hess Lab filter
- Jayaraman Lab (1) Apply Jayaraman Lab filter
- Keller Lab (2) Apply Keller Lab filter
- Lavis Lab (2) Apply Lavis Lab filter
- Lee (Albert) Lab (1) Apply Lee (Albert) Lab filter
- Liu (Zhe) Lab (3) Apply Liu (Zhe) Lab filter
- Magee Lab (5) Apply Magee Lab filter
- Murphy Lab (1) Apply Murphy Lab filter
- Pastalkova Lab (1) Apply Pastalkova Lab filter
- Riddiford Lab (3) Apply Riddiford Lab filter
- Romani Lab (1) Apply Romani Lab filter
- Rubin Lab (1) Apply Rubin Lab filter
- Schreiter Lab (2) Apply Schreiter Lab filter
- Spruston Lab (2) Apply Spruston Lab filter
- Stern Lab (6) Apply Stern Lab filter
- Tjian Lab (6) Apply Tjian Lab filter
- Truman Lab (3) Apply Truman Lab filter
- Turaga Lab (1) Apply Turaga Lab filter
- Zuker Lab (3) Apply Zuker Lab filter
Publication Date
- December 2006 (4) Apply December 2006 filter
- November 2006 (10) Apply November 2006 filter
- October 2006 (7) Apply October 2006 filter
- September 2006 (7) Apply September 2006 filter
- August 2006 (14) Apply August 2006 filter
- July 2006 (4) Apply July 2006 filter
- June 2006 (7) Apply June 2006 filter
- May 2006 (9) Apply May 2006 filter
- April 2006 (4) Apply April 2006 filter
- March 2006 (12) Apply March 2006 filter
- February 2006 (6) Apply February 2006 filter
- January 2006 (8) Apply January 2006 filter
- Remove 2006 filter 2006
Type of Publication
92 Publications
Showing 91-92 of 92 resultsChromatin structure and nucleosome positioning play a crucial role in gene expression regulation. Nucleosome positioning is often inferred by the protection of underlying DNA to nucleases. Because nucleases are excluded by plasma membranes, chromatin mapping requires isolating nuclei from cells and digesting the chromatin in situ with nucleases. The quality of this data is highly dependent on the nuclei preparation. Here we describe a method to isolate nuclei from the budding yeast Saccharomyces cerevisiae and the use of micrococcal nuclease to map the chromatin structure at the RNR3 gene. Nuclei isolated by this procedure are competent for many of the common chromatin mapping and detection procedures.
Our understanding of the input-output function of single cells has been substantially advanced by biophysically accurate multi-compartmental models. The large number of parameters needing hand tuning in these models has, however, somewhat hampered their applicability and interpretability. Here we propose a simple and well-founded method for automatic estimation of many of these key parameters: 1) the spatial distribution of channel densities on the cell’s membrane; 2) the spatiotemporal pattern of synaptic input; 3) the channels’ reversal potentials; 4) the intercompartmental conductances; and 5) the noise level in each compartment. We assume experimental access to: a) the spatiotemporal voltage signal in the dendrite (or some contiguous subpart thereof, e.g. via voltage sensitive imaging techniques), b) an approximate kinetic description of the channels and synapses present in each compartment, and c) the morphology of the part of the neuron under investigation. The key observation is that, given data a)-c), all of the parameters 1)-4) may be simultaneously inferred by a version of constrained linear regression; this regression, in turn, is efficiently solved using standard algorithms, without any “local minima” problems despite the large number of parameters and complex dynamics. The noise level 5) may also be estimated by standard techniques. We demonstrate the method’s accuracy on several model datasets, and describe techniques for quantifying the uncertainty in our estimates.