Daniel J. Needleman
Department of Applied Physics
Research Interests:Physics of Macromolecular Assemblies and Subcellular Organization
My research combines soft condensed matter physics, biophysics, and cell biology by using quantitative experimental techniques to examine how cooperative interactions between macromolecules result in biological structures and behaviors. These collective effects are not only directly relevant to subcellular organization, they also raise a number of fascinating physics questions concerning the forces between molecules and their resulting phase behavior, the mechanics and fluctuations of macromolecular assemblies, and the statistical physics of non-equilibrium systems. This work involves studying cells, cell extracts, and purified components with a range of biophysical techniques including small-angle x-ray scattering, single molecule imaging, quantitative fluorescent and polarized light microscopy, fluorescence correlation spectroscopy, and electron microscopy.
My long term goal is to establish a framework to understand how the collective behaviors of molecules give rise to the structures and dynamics of self-organizing subcellular structures and to use the resulting knowledge of these properties to quantitatively predict biological behaviors. I will carry out this ambitious research program using three complimentary approaches: 1) I will make quantitative measurements of the structure and dynamics of self-organizing systems in cells and cell extracts. 2) I will develop new experimental techniques to carry out this work, as existing tools are insufficient to measure much of the relevant structures, dynamics, and forces. 3) I will study self-organization in simple model systems reconstituted from purified components.
My laboratory will initially focus on studying the spindle, the self-organizing molecular machine that segregates chromosomes during cell division. The spindle is a dynamic steady-state structure composed of a plethora of molecules, most notably DNA, which is compacted into chromosomes, and the protein tubulin, which forms long fibers, called microtubules, which are oriented into a bipolar array that constitutes the bulk of the spindle. Even though the overall structure of the spindle can remain unchanged for hours, the molecules that make up the spindle undergo rapid turnover with a half-life of tens of seconds or less, and if the spindle is damaged, or even totally destroyed, it can repair itself. While many of the individual components of the spindle have been studied in detail, it is still unclear how these molecular constituents self-organize into this structure and how this leads to the internal balance of forces that are harnessed to divide the chromosomes. A major goal of my research on the spindle will be to develop experimental and theoretical tools to combine data from static and dynamic measurements and to bridge multiple length scales. For example, my group will develop novel image processing techniques for cellular electron tomography and, in collaboration with Eileen O’Toole and Dick McIntosh at the Boulder Lab for 3D Electron Microscopy, will work to obtain the first complete reconstruction of metaphase spindles from human tissue culture cells (which are approximately fifteen microns long, composed of thousands of microtubules, and have a volume hundreds of times greater than the largest spindles reconstructed so far). This high resolution structural data on microtubule lengths, locations, and confirmations in spindles will be integrated with measurements of the dynamics of proteins in these spindles using single molecule tracking and other quantitative techniques developed and performed in my lab. Ultimately, we will attempt to create models which quantitatively reconcile the data on spindle architecture and dynamics, with the aim of understanding how microtubules self-organize into this structure.
Aaron C. Groen, Daniel J. Needleman, Clifford Brangwynne, Christian Gradinaru, Brandon Fowler, Ralph Mazitschek, Timothy J. Mitchison (2008). A Novel Small-Molecule Inhibitor Reveals a Possible Role of Kinesin-5 in Anastral Spindle-Pole Assembly. Journal of Cell Science 121(14): 2293-300.
Daniel J. Needleman (2008). Plasmid Segregation: Is a Total Understanding within Reach? Current Biology 18: R212-R214.
Wühr M, Chen Y, Dumont S, Groen AC, Needleman DJ, Salic A, Mitchison TJ. (2008). Evidence for an Upper Limit to Mitotic Spindle Length. Current Biology 18(16): 1256-61.
Uri Raviv, Daniel J, Needleman, Kai Ewert, Cyrus R. Safinya (2007). Hierarchical Bionanotubes Formed by the Self Assembly of Microtubules with Cationic Membranes or Polypeptides. Journal of Applied Crystallography 40: s83-s87.
Uri Raviv, Toan Nguyen, Rouzbeh Ghafouri, Daniel J, Needleman, Youli Li, Herbert P. Miller, Leslie Wilson, Robijn F. Bruinsma, Cyrus R. Safinya (2007). Microtubule Protofilament Number is Modulated in a Step-Wise Fashion by the Charge Density of an Enveloping Layer. Biophysical Journal 92: 278-287.
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