Bulletin of the American Physical Society
76th Annual Meeting of the Southeastern Section of APS
Volume 54, Number 16
Wednesday–Saturday, November 11–14, 2009; Atlanta, Georgia
Session CC: Experimental Biophysics I |
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Chair: Gennady Cymbalyuk, Georgia State University Room: Paris |
Thursday, November 12, 2009 10:45AM - 10:57AM |
CC.00001: Is the brain's inertia for motor movement different for acceleration and deceleration? Bhim Adhikari, Kristen Quinn, Mukeshwar Dhamala The brain's ability to synchronize movement with external cues is used daily, yet neuroscience is far from a full understanding of the processes that allow these simple sequential performances. This experimental design was implemented to determine differences in brain activity when finger tapping at increasing and decreasing rhythms. Eight subjects tapped their right index finger on a response box following visual cues projected on a screen during an fMRI session. Isolating continuous and discrete finger tapping (sinusoidal variation of rate and step-like variation) decelerations versus accelerations revealed much greater activity in the left and right primary motor cortices when completing the sinusoidal rhythm task. Decelerating rates recruited distributed regions of the brain in contrast to brain stimulation during accelerating rates. These results suggest that the brain's inertia for movement is different for acceleration and deceleration. [Preview Abstract] |
Thursday, November 12, 2009 10:57AM - 11:09AM |
CC.00002: Flagellar force production during regeneration in \textit{Chlamydomonas reinhardtii} John N. Yukich, Catherine Clodfelter, Karen K. Bernd Several respiratory, digestive, and reproductive disorders originate with motional dysfunction of cilia and flagella. The usefulness of cilia and flagella is understood, but the internal mechanism for creating their breast stroke-like motion is not. This study reports on standardization of calibration, trapping and cell movement recording methods. Our techniques permit us to measure the flagellar swimming force of \textit{Chlamydomonas} during flagella regeneration. We find that as flagella length increases, the flagellar force is maximized after 50{\%} of full length is achieved \textit{except} for a significant dip at 75{\%} of full length. These results raise many questions regarding the flagella infrastructure. [Preview Abstract] |
Thursday, November 12, 2009 11:09AM - 11:21AM |
CC.00003: Legged locomotion on sand Chen Li, Paul Umbanhowar, Haldun Komsuoglu, Daniel Koditschek, Daniel Goldman To understand how and why animals modulate foot kinematics to achieve effective locomotion on granular media, we study the speed of a six-legged robot with c-shaped legs, SandBot, moving on granular media for varying volume fraction, $\phi$, limb frequency, $f$, and gait timing parameters.\footnote{Li et. al, PNAS, {\bf 106}, 3029, 2009} Speed is determined by step length which in turn depends on limb penetration. At low $f$ and high $\phi$ penetration is small, step length is large, and SandBot advances with a rotary walking gait in which c-legs rotate about their centers by slipping relative to stationary grains. In the opposite extreme, grains cannot support the robot; its underside always contacts the ground and it advances slowly via thrust generated as the c-legs translate through the grains. For varied gait parameters, high speeds are only observed in a small area of parameter space. A yield stress based model predicts the speed and reveals that performance is maximized when gait parameters minimize limb acceleration and interference, and limbs utilize the solidification properties of the media. [Preview Abstract] |
Thursday, November 12, 2009 11:21AM - 11:33AM |
CC.00004: ABSTRACT HAS BEEN MOVED TO LA.00037 |
Thursday, November 12, 2009 11:33AM - 11:45AM |
CC.00005: Dynamic investigation of DNA bending and wrapping by type II topoisomerases Qing Shao, Laura Finzi, David Dunlap Type II topoisomerases catalyze DNA decatenation and unwinding which is crucial for cell division, and therefore type II topoisomerases are some of the main targets of anti-cancer drugs. A recent crystal structure shows that, during the catalytic cycle, a yeast type II topoimerase can bend a 10 base pair DNA segment by up to 150 degrees. Bacterial gyrase, another type II topoisomerase, can wrap DNA into a tight 180 degree turn. Bending a stiff polymer like DNA requires considerable energy and could represent the rate limiting step in the catalytic (topological) cycle. Using modified deoxyribonucleotides in PCR reactions, stiffer DNA fragments have been produced and used as substrates for topoisomerase II-mediated relaxation of plectonemes introduced in single molecules using magnetic tweezers. The wrapping ability of gyrase decreases for diamino-purine-substituted DNA in which every base pair has three hydrogen-bonds. The overall rate of relaxation of plectonemes by recombinant human topoisomerase II alpha also decreases. These results reveal the dynamic properties of DNA bending and wrapping by type II topisomerases and suggest that A:T base pair melting is a rate determining step for bending and wrapping. [Preview Abstract] |
Thursday, November 12, 2009 11:45AM - 11:57AM |
CC.00006: Nano-scale Topographical Studies on the Growth Cones of Nerve Cells using AFM Goksel Durkaya, Lei Zhong, Vincent Rehder, Nikolaus Dietz Nerve cells are the fundamental units which are responsible for intercommunication within the nervous system. The neurites, fibrous cable-like extensions for information delivery, of nerve cells are tipped by highly motile sensory structures known as the growth cones which execute important functions; neural construction, decision making and navigation during development and regeneration of the nervous system. The highly dynamic subcomponents of the growth cones are important in neural activity. Atomic Force Microscopy (AFM) is the most powerful microscopy technique which is capable of imaging without conductivity constraint and in liquid media. AFM providing nano-scale topographical information on biological structures is also informative on the physical properties such as: elasticity, adhesion, and softness. This contribution focuses on AFM analysis of the growth cones of the nerve cells removed from the buccal ganglion of Helisoma trivolvis. The results of nano-scale topography and softness analysis on growth cone central domain, filopodia and overlying lamellopodium (veil) are presented. The subcomponents of the growth cones of different nerve cells are compared to each other. The results of the analysis are linked to the mechanical properties and internal molecular density distribution of the growth cones. [Preview Abstract] |
Thursday, November 12, 2009 11:57AM - 12:09PM |
CC.00007: Phyical and molecular characterization of a genetic switch Laura Finzi, Chiara Zurla, Carlo Manzo, Haowei Wang, David Dunlap The lambda bacteriophage epigenetic switch determines the growth lifestyle of the virus after infection of its host (\textit{E. coli}). It is now clear that the switch consists of a $\sim $2.3 kbp-long DNA loop mediated by the lambda repressor protein. Using tethered particle microscopy (TPM), magnetic tweezers and AFM, our laboratory has novel, direct evidence of loop formation and breakdown by the repressor, the first characterization of the thermodynamics and kinetics of the looping reaction and its dependence on repressor non-specific binding and DNA supercoiling. These \textit{in vitro} data provide insight into the different possible nucleoprotein complexes and into the lambda repressor-mediated looping mechanism which leads to predictions for that \textit{in vivo}. The significance of this work consists not only of the new insight into the physical parameters at the basis of a paradigmatic epigenetic switch that governs lysogeny vs. lysis, but also the detailed mechanics of regulatory DNA loops mediated by proteins bound to multipartite operators and capable of different levels of oligomerization. [Preview Abstract] |
Thursday, November 12, 2009 12:09PM - 12:21PM |
CC.00008: Coliphage 186 genetic switch: a single molecule study Haowei Wang, Ian B. Dodd, Keith Shearwin, David Dunlap, Laura Finzi It is increasingly clear that in most cases genes are regulated by wrapping or looping of DNA on large, cooperatively assembled protein complexes. In most eukaryotic organisms, 150 bp of DNA are wrapped twice around histone octamers (nucleosomes). Furthermore, interaction between proteins bound at distant sites on the DNA may cause looping out of the intervening DNA with regulatory significance. The mechanism by which these DNA- protein nanostructures are formed is not clear. It is tantalizing how little information is available about the energetics, kinetics and equilibrium between DNA wrapping and looping given the crucial role they play on gene regulation and DNA physiology. The interaction between the bacteriophage repressor 186CI and its DNA is an ideal model system to study DNA wrapping and looping and to reveal fundamental principles of long-range interactions and regulation by nucleoprotein complexes. Here we report on AFM work aimed at elucidating the 186CI-DNA interaction. [Preview Abstract] |
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