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BioPhysics Journal Club

Old Schedules

Date

Speaker

Paper

Oct. 6, 2010

Vickie

Reaction -Diffusion Model as a Framework for Understanding Biological Pattern Formation

Shigeru Kondo and Takashi Miura

Science 24 September 2010: 1616-1620.

http://www.sciencemag.org/cgi/content/full/329/5999/1616

Oct. 13, 2010

Chiharu

Video imaging of walking myosin V by high-speed atomic force microscopy
Kodera et al., Nature, Oct. 2010 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09450.html

Oct. 20, 2010

Michelle

Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows

Mayer et al Nature 467 30 September 2010: 617–621

http://www.nature.com/nature/journal/v467/n7315/full/nature09376.html#/main

Oct. 27, 2010

Maire

Elicitation of structure-specific antibodies by epitope scaffolds
Kwong et al PNAS, 107, 42: 17880-17887 - October 19, 2010

http://www.pnas.org/content/early/2010/09/21/1004728107.abstract

Nov. 10

Andrew

Phosphatidic Acid Is a pH Biosensor That Links Membrane Biogenesis to Metabolism
Barry et al. Science 27 August 2010: Vol. 329. no. 5995, pp. 1085 - 1088
http://www.sciencemag.org/cgi/content/full/329/5995/1085/DC1

Nov. 17

Marina

RESEARCH ARTICLES
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, and Willy Wriggers (15 October 2010)
Science 330 (6002), 341. [DOI: 10.1126/science.1187409]
http://www.sciencemag.org/cgi/content/full/sci;330/6002/341
http://www.sciencemag.org/cgi/content/full/330/6002/308-a

Dec. 1

Raghu

Biomechanical analysis of gait adaptation in the nematode Caenorhabditis elegans

PNAS      November 23, 2010      vol. 107 no. 47 20323-20328
http://www.pnas.org/content/107/47/20323.abstract

Schedule (Spring 2010):

  • April 7 - Raghu. -- "Bipedal locomotion in crawling cells" -- Biophys. J. 98: 933-942 (2010 Mar 17).Link
  • April 14 - Andrew Loftus -- "Lethal protein produced in response to competition between sibling bacterial colonies" PNAS April 6, 2010 vol. 107 no. 14 6258-6263, Link
  • April 21 - Jay McCarty: "Nonspecifically bound proteins spin while diffusing along DNA", Nature Structural and Molecular Biology, Dec. 09.
  • April 28 - Michelle Lu: C Lou and colleagues' article in Molecular Systems Biology titled, "Synthesizing a novel geneti sequential logic circuit: a push-on push-off switch."
  • May 5 - (Streisinger Lectures Tues and Wednesday)
  • May 12 - Chiharu: "Steric confinement of proteins on lipid membranes can drive curvature and tubulation, PNAS Link .
  • May 19 - Mike Taormina: "Coupling a sensory hair-cell bundle to cyber clones enhances nonlinear amplification," PNAS vol. 107 (2010).
  • May 26 - Maire: "Dynamics of Bacterial Swarming," Nicholas C. Darnton, Linda Turner, Svetlana Rojevsky and Howard C. Berg. Biophysical Journal Volume 98, May 2010, 2082–2090 Link
  • June 2- Vickie: "Production of Extracellular Traps against Aspergillus fumigatus In Vitro and in Infected Lung Tissue Is Dependent on Invading Neutrophils and Influenced by Hydrophobin RodA," Sandra Bruns1 et al., PLOS Pathogens, April 2010 Link

Fall 2009 and Winter 2010:

  • October 7 - Maire, "Coupling of Pressure-Induced Structural Shifts to Spectral Changes in a Yellow Fluorescent Protein." Biophysical Journal . 2009, 97: 1719-1727. Link
  • October 14 -- Raghu. -- Tam, B. K., Shin, J. H., Pfeiffer, E., Matsudaira, P., and Mahadevan, L. "Calcium regulation of an actin spring." Biophys J 97, 1125-1129 (2009) Link
  • Oct. 21 – Mike : Tanner et al, "Coherent Movement of Cell Layers during Wound Healing by Image Correlation Spectroscopy ," Biophys. J. 97 (7), 2098-2106 (2009). Link
  • Oct. 28 – Chiharu: "Kinesin-8 Motors Act Cooperatively to Mediate Length-Dependent Microtubule Depolymerization" Link
  • Nov. 4 – Morgan : Solon, J., Kaya-Copur, A., Colombelli, J., and Brunner, D. "Pulsed forces timed by a ratchet-like mechanism drive directed tissue movement during dorsal closure." Cell 137, 1331-1342 (June 2009). Link
  • Nov. 11 – James: "Modeling proteasome dynamics in Parkinson's disease", Sneppen, et. al., Physical Biology, 2009, vol 6. Link
  • Nov. 18 – Andrew: "Single-cell response to stiffness exhibits muscle-like behavior," Mitrossilis, D. et al., PNAS October 27, 2009 vol. 106 no. 43 18243-18248 Link
  • Nov. 25 (skip, Thanksgiving week)
  • Dec. 2 – Jim Remington: "some recent theoretical and experimental results on
    bacterial chemotaxis". (See email for two background papers.)
  • A week or two in which I forgot to update the web page -- Raghu
  • Jan. 27; James McCarty: "Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells" Cell 136, (2009) p 337. Link
  • Feb. 3; Jim Remington: "Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy" Link
  • Feb. 10; Chris Harland: "Cytoskeleton-based forecasting of stem cell lineage fates" from Matthew Treiser and company (PNAS) . Quick blurb = human stem cells + pictures + computers + hip slang for the old word "variables" Link
  • Feb. 17; Michelle Lu: A PLoS Biology paper on the biophysics of a Type Four Pilus. Link
  • Feb. 24; No journal club (Biophysical Society Meeting)
  • Mar. 3; Highlights from the Biophysical Society Meeting

Spring 2009:

  • April 1 - Eric Senning. ...a paper looking at actin filament depletion zones, "Filament rigidity causes F-actin depletion from nonbinding surfaces." Proc. Natl. Acad. Sci. USA . 2009 Jan 6; 106 (1):133-8. Link
  • April 8 -- Michelle Lu -- Quantitative 3D Video Microscopy of HIV Transfer Across T Cell Virological Synapses, Wolfgang Hübner et al., Science 323: 1743-1747 (2009) Link
  • April 15 -- **NOTE this will be in KLA214** -- Raghu Parthasarathy -- Ramamurthi, K. S., Lecuyer, S., Stone, H. A., and Losick, R. Geometric cue for protein localization in a bacterium. Science 323, 1354-1357 (2009). Link
  • April 22 -- Morgan Goulding
  • April 29 -- [postponed]
  • May 6 -- [postponed]
  • May 13 -- Greg Gemmen -- "Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence," A.C. Ferreon, et al. (2009) PNAS 106(14): 5645-5650. Link
  • May 20 -- Jay McCarty -- "Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules"
    Jan Philipp Junker, Fabian Ziegler, Matthias Rief, Link
  • May 27 -- [OPEN] **NOTE this will be in KLA214** [OPEN]
  • June 3 -- Nate Kuwada and Chris Harland -- Super-resolution microscopies (various papers)

Winter 2009:

  • Jan. 21 - Ryan **NOTE this will be in KLA214** Paper: Crowded, cell-like environment induces shape changes in aspherical protein, PNAS 105, 11754-11759 (2008) Link
  • Jan. 28 - Vickie. Paper: Cell-Cell Mechanical Communication through Compliant Substrates, Cynthia A. Reinhart-King et al. Biophysical Journal, Volume 95, Issue 12, 6044-6051, 15 December 2008.
  • Feb. 4 - Michelle. Paper: Functional Implications of Plasma Membrane Condensation for T Cell Activation, C. Rentero et al. PLOS One, 3, 2008, e2262 Link
  • Feb. 11 - Greg
  • Feb. 18 - Raghu. Paper: Characterization of Protein Dynamics in Asymmetric Cell Division by Scanning Fluorescence Correlation Spectroscopy, Zdenek Petrášek, Carsten Hoege, Alireza Mashaghi, Thomas Ohrt, Anthony A. Hyman, Petra Schwille. Biophys. J. 95: 5476 (2008) Link
  • Feb. 25 - Chris. Paper: 'Structural Basis of Membrane Invagination by F-BAR Domains" Frost et al. Cell (2008) 132, 807
  • Mar. 4 - Chiharu
  • Mar. 11 - Eric

Fall 2008:

  • December 3, 2008: Brandi Dickinson. Paper: "DNA-programmable nanoparticle crystallization ," Park et al, 2008, Nature 451, 553-556-15754( 2008) . Link.

  • November 19, 2008: Heiner Linke. Paper: "Accuracy of direct gradient sensing by single cells ," R.G. Endres and N.S. Wingreen, PNAS 105, 15749-15754( 2008) . Link.

  • November 12, 2008: Michelle Lu. Paper: "Dynamic restacking of Escherichia Coli P-pili," Lugmaier RA et al, Eur Biophys J 37, 111-120 ( 2008) . Link.

  • November 5, 2008: Eric Senning. Paper: "Mechanism of shape determination in motile cells." Keren K, Pincus Z, Allen GM, Barnhart EL, Marriott G, Mogilner A, Theriot JA, Nature 453, 475-480 (22 May 2008) . Link. News & Views Link.

  • October 22, 2008: Marina Guenza. Paper 1: Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling . Paolo De Los Rios, Anat Ben-Zvi, Olga Slutsky, Abdussalam Azem, and Pierre Goloubinoff, PNAS 103 April 18, 2006. Link. Paper 2: Volume-Exclusion Effects in Tethered-Particle Experiments: Bead Size Matters. Darren E. Segall, Philip C. Nelson, and Rob Phillips , Phys. Rev. Lett. 96 088306 , 2006. Link.

  • October 15, 2008: Vickie DeRose. Paper: Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Pramodh Vallurupalli, D. Flemming Hansen, and Lewis E. Kay, PNAS 105 (33), 11766, August 2008. Link.

  • October 8, 2008: Raghu Parthasarathy. Paper Dynamics of Chromatin Decondensation Reveals the Structural Integrity of a Mechanically Prestressed Nucleus. A. Mazumder et al. Biophys. J. 95 , 3028-3035 (2008). Link.

 

© 2009 University of Oregon.

Unauthorized duplication of images is strictly prohibited.

Maintained by Raghuveer Parthasarathy

Contact:  raghu [at] uoregon.edu

Last updated: April 5, 2010