Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session Z45: Focus Session: From Molecules to Cells |
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Sponsoring Units: DBIO Chair: Herbert Levine, Rice University Room: Hilton Baltimore Holiday Ballroom 4 |
Friday, March 22, 2013 11:15AM - 11:51AM |
Z45.00001: Molecular Circuits that control Bacillus sporulation Invited Speaker: Gurol Suel |
Friday, March 22, 2013 11:51AM - 12:03PM |
Z45.00002: Signal processing in eukaryotic chemotaxis Igor Segota, Archana Rachakonda, Carl Franck Unlike inanimate condensed matter, living cells depend upon the detection of chemical signals for their existence. First, we experimentally determined the chemotaxis response of eukaryotic \emph{Dictyostelium} cells to static folic acid gradients and show that they can respond to gradients as shallow as 0.2\% across the cell body. Second, using Shannon's information theory, we showed that the information cells receive about the gradient exceeds the theoretically predicted information at the receptor-ligand binding step, resulting in the violation of the data processing inequality. Finally, we analyzed how eukaryotic cells can affect the gradient signals by secreting enzymes that degrade the signal. We analyzed this effect with a focus on a well described \emph{Dictyostelium} cAMP chemotaxis system where cAMP signals are affected by an extracellular cAMP phosphodiesterase (PDE) and its inhibitor (PDI). Using a reaction-diffusion model of this set of interactions in the extracellular space, we show that cells can effectively sense much steeper chemical gradients than naively expected (up to a factor of 12). We also found that the rough estimates of experimental PDE and PDI secretion rates are close to the optimal values for gradient sensing as predicted by our model. [Preview Abstract] |
Friday, March 22, 2013 12:03PM - 12:15PM |
Z45.00003: Bridging from Replication to Translation with a Thermal, Autonomous Replicator Made from Transfer RNA Dieter Braun, Friederike M. M\"oller, Hubert Krammer Central to the understanding of living systems is the interplay between DNA/RNA and proteins. Known as Eigen paradox, proteins require genetic information while proteins are needed for the replication of genes. RNA world scenarios focus on a base by base replication disconnected from translation. Here we used strategies from DNA machines to demonstrate a tight connection between a basic replication mechanism and translation [1]. A pool of hairpin molecules replicate a two-letter code. The replication is thermally driven: the energy and negative entropy to drive replication is initially stored in metastable hairpins by kinetic cooling. Both are released by a highly specific and exponential replication reaction that is solely implemented by base hybridization. The duplication time is 30s. The reaction is monitored by fluorescence and described by a detailed kinetic model. The RNA hairpins usetransfer RNA sequences and the replication is driven by the simple disequilibrium setting of a thermal gradient [2] The experiments propose a physical rather than a chemical scenario for the autonomous replication of protein encoding information.\\[4pt] [1] Physical Review Letters 108, 238104 (2012).\\[0pt] [2] Physical Review Letters 104, 188102 (2010) [Preview Abstract] |
Friday, March 22, 2013 12:15PM - 12:27PM |
Z45.00004: Symmetrical charge-charge interactions in ionic solutions and implications for cell division Eshel Faraggi As is well known in electrolyte theory, electrostatic fields are attenuated by the presence of mobile charges in the solution. This seems to limit the possibility of an electrostatic repulsion model of biological interactions such as cell division. However, for a system of two charges in an ionic solution it is found that in the context of the symmetries of the system, the electrostatic repulsion between the two parts of a dividing cell are considerably increased as compared to the electrostatic repulsion between two bare charges in a dielectric. This increase in repulsion, directly resulting from interactions between the symmetrical parts of the solute system, was found to be dependent on the magnitude of the charges and the separation between them. It was also found that this increases reaches a steady state for separation greater than a solvent determined length scale related to the Debye length. These findings strongly suggest that electrostatic interactions can play a crucial part in the physical forces that are involved in biological interactions. Most fundamentally this work presents a general physical force by which one can mechanically understand cell division. Such understanding will lead to unforetold new ways in medicine, biology, chemistry, and physics. [Preview Abstract] |
Friday, March 22, 2013 12:27PM - 1:03PM |
Z45.00005: Motorized Glasses and Crystals: Microscopic Models of Active Matter and the Cytoskeleton Invited Speaker: Peter Wolynes The interior of cells is constantly forming and reconfiguring via molecular processes that dissipate chemical energy. I will discuss simulations and analytical theories of the quasi-equilibrium phase diagram of simple models of motorized crystals and motorized network glasses. The nonequilibrium nature of molecular motors leads also to dynamical transitions to states with collective sustained flows. Analogies of these dynamical transitions seem to occur in natural and artificially reconstituted cytoskeletons. [Preview Abstract] |
Friday, March 22, 2013 1:03PM - 1:15PM |
Z45.00006: Tension-dependent dynamic microtubule model for metaphase and anaphase phenomena Edward Banigan, Michael Lampson, Andrea Liu During cell division, chromosome pairs align at the center of a bipolar microtubule (MT) spindle and oscillate as MTs attaching them to the cell poles polymerize and depolymerize. Pairs later separate as shrinking MTs pull each chromosome toward its respective cell pole. We present a minimal model for these processes. We use the measured tension-dependence of single MT kinetics [1] and extrapolate for compressed MTs. We apply these to a stochastic many MT model, which we solve numerically and with master equations. We find that tension dependence enhances the speed of chromosome pulling by retracting MTs. The force-velocity curve for the single chromosome system is bistable and hysteretic. Above some threshold load, tension fluctuations induce MTs to spontaneously switch from a pulling state into a growing, pushing state. To recover pulling from the pushing state, the load must be reduced far below the threshold. This leads to oscillations in the two-chromosome system. Unlike other models, our model also captures breathing oscillations. We also explore how various components control chromosome dynamics through MT rate constants alone. [1] Akiyoshi et al. (2010) Nature 468, 576. [Preview Abstract] |
Friday, March 22, 2013 1:15PM - 1:27PM |
Z45.00007: Cytoskeleton dynamics studied by dispersion-relation fluorescence spectroscopy Ru Wang, Lei Lei, Yingxiao Wang, Alex Levine, Gabriel Popescu Fluorescence is the most widely used microscopy technique for studying the dynamics and function in both medical and biological sciences due to its sensitivity and specificity. Inspired by the spirit of spatial fluorescence correlation spectroscopy, we propose a new method to study the transport dynamics over a broad range of spatial and temporal scales. The molecules of interest are labeled with a fluorophore whose motion gives rise to spontaneous fluorescence intensity fluctuations that can be further analyzed to quantify the governing molecular mass transport dynamics. We analyze these data by the dispersion relation in the form of a power law,$\Gamma \left( q \right)\sim q^{\alpha }$, which describe the relaxation rate of fluorescence intensity fluctuations, $\Gamma $, vs. the wavenumber, q. We used this approach to study the interplay of various cytoskeletal components in intracellular transport under the influence of protein-motor inhibitors. We found that after actin is depolymerized, the transport becomes completely random for a few minutes and then it starts to organize deterministically again. We conclude that the disrupted cytoskeletal components first diffuse in the cytoplasm, but then become attached to microtubules and get transported deterministically. [Preview Abstract] |
Friday, March 22, 2013 1:27PM - 1:39PM |
Z45.00008: Stress Generation by Actin-Myosin Networks and Bundles Anders Carlsson, Nilushi Dasanayake Forces and stresses generated by the action of myosin minifilaments are calculated in idealized computer-generated actin networks and bundles. The networks are generated as random collections of actin filaments in two dimensions, and bundles are obtained by constraining the filament orientations. The actin filaments are crosslinked and attached to two fixed walls. Myosin minifilaments are placed on actin filament pairs and allowed to move and deform the network so that it exerts forces on the walls. The vast majority of simulation runs end with contractile minifilament stress, because minifilaments rotate into energetically stable contractile configurations. This process is aided by the bending of actin filaments, which accomodates minifilament rotation. Stresses for bundles are greater than those for isotropic networks, and antiparallel filaments generate more tension than parallel filaments. The forces transmitted by the actin network to the walls of the simulation cell often exceed the tension in the minifilament itself. [Preview Abstract] |
Friday, March 22, 2013 1:39PM - 1:51PM |
Z45.00009: Cytoplasmic streaming emerges naturally from hydrodynamic self-organisation of a microfilament suspension Francis Woodhouse, Raymond Goldstein Cytoplasmic streaming is the ubiquitous phenomenon of deliberate, active circulation of the entire liquid contents of a plant or animal cell by the walking of motor proteins on polymer filament tracks. Its manifestation in the plant kingdom is particularly striking, where many cells exhibit highly organised patterns of flow. How these regimented flow templates develop is biologically unclear, but there is growing experimental evidence to support hydrodynamically-mediated self-organisation of the underlying microfilament tracks. Using the spirally-streaming giant internodal cells of the characean algae Chara and Nitella as our prototype, we model the developing sub-cortical streaming cytoplasm as a continuum microfilament suspension subject to hydrodynamic and geometric forcing. We show that our model successfully reproduces emergent streaming behaviour by evolving from a totally disordered initial state into a steady characean ``conveyor belt'' configuration as a consequence of the cell geometry, and discuss applicability to other classes of steadily streaming plant cells. [Preview Abstract] |
Friday, March 22, 2013 1:51PM - 2:03PM |
Z45.00010: Coordinated Switching of Bacterial Flagellar Motors in a Single E. Coli Bo Hu, Yuhai Tu The swimming of Escherichia coli is propelled by its multiple flagellar motors. Each motor spins either clockwise or counterclockwise, under the control of an intracellular regulator, CheY-P. A long standing question is whether these motors work independently or not. There can be two mechanisms (extrinsic and intrinsic) to coordinate the switching of bacterial motors. The extrinsic one arises from the fact that different motors in the same cell sense a common biochemical signal (CheY-P) which fluctuates near the motors' response threshold. An alternative, intrinsic mechanism is direct motor-motor coupling which makes synchronized switching energetically favorable. Here, we develop simple models for both mechanisms and uncover their different hallmarks. A quantitative comparison to the recent experiments suggest that the direct coupling mechanism may be accountable for the observed sharp correlation between motors in a single E. coli. Possible origins of this coupling are discussed. [Preview Abstract] |
Friday, March 22, 2013 2:03PM - 2:15PM |
Z45.00011: High-Content Movement Analysis as a Diagnostic Tool in \textit{C. elegans} Peter Winter, Andrea Lancichinetti, Leah Krevitt, Luis Amaral, Rick Morimoto Many neurodegenerative diseases manifest themselves through a loss of motor control and give us information about the underlying disease. This loss of coordination is observed in humans and in the model organisms used to study neurodegeneration. In \textit{Caenorhabditis elegans}, there is an extensive genetic library of strains that lack functional neuronal signaling pathways and expressing proteins associated with neurodegenerative diseases. While most of these strains have decrease motility or cause paralysis, relatively few have been screened to look for more subtle changes in motor control such as stiffness, twitching, or other changes in behavior. we use high-resolution position and posture data to automatically analyze the movement of worms from different genetic backgrounds and characterize 14 movement characteristics. By creating a quantitative mapping between the movement characterization and an online database of gene annotation, gene expression, and anatomy, we aim to predict a likely set of cellular and molecular disruptions. This work provides a proof of concept for the use of detailed movement analysis to uncover novel disruptions in certain motor control processes. Knowledge of the molecular origin of these disruptions provided by our understanding of \textit{C. elegans} genetics and physiology could lead to new diagnostic and therapeutic targets for neurodegenerative disease. [Preview Abstract] |
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