Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session T43: Physics of Bacteria |
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Sponsoring Units: DBP Chair: Rob Phillips, California Institute of Technology Room: A306/307 |
Wednesday, March 23, 2011 2:30PM - 2:42PM |
T43.00001: Guided Motion of Individual and Collective Swimmers in Funnel Arrays Cynthia Olson Reichhardt, Thuc Mai, Charles Reichhardt We generalize a model of swimming bacteria in asymmetric arrays of obstacles [1] to include different rules of motion, including various rules for collective behvaiors. For individual noninteracting swimmers, we observe guided motion and rectification by the asymmetric barriers when the particles align with the walls they contact, but we find no rectification if the particles are reflected by the walls or bounce off the walls. For collectively interacting swimmers, it is possible for the particles to form large swimming clumps that can move against the normal rectification direction of the asymmetric barrier array. In general, the rectification by the barriers is lost when the length scale of the swarms of collectively moving particles is significantly larger than the length scale of the funnel shaped barriers. A particle swarm can become trapped inside a funnel; however, individual strings of particles that follow each other can escape from the trap and move against the funnel direction. \\[4pt] [1] M.B. Wan, C.J. Olson Reichhardt, Z. Nussinov, and C. Reichhardt, Phys. Rev. Lett. 101, 018102 (2008). [Preview Abstract] |
Wednesday, March 23, 2011 2:42PM - 2:54PM |
T43.00002: Surface motility of Myxococcus Xanthus Maxsim Gibiansky, William Hu, Fan Jin, Kun Zhao, Wenyuan Shi, Gerard Wong We examine the surface motility of Myxococcus Xanthus, a bacterium species found in soil that exhibits a broad range of self-organizing behavior, including predatory ``swarms'' and survival-enhancing ``fruiting bodies.'' To quantify the effects of exopolysaccharides (EPS) on surface adhesion and motility, we use modified versions of particle tracking algorithms from colloid physics to analyze bacterial trajectories, and compare the wild type (WT) strain to EPS knockout and EPS overproducer strains. We find that EPS deficiency leads to an increase in the number of ``standing'' bacteria oriented normal to the surface, attached by one end with minimal motility. EPS overproduction, by contrast, suppresses this phenotype. A detailed investigation of the influence of EPS on Myxococcus social motility will be presented. [Preview Abstract] |
Wednesday, March 23, 2011 2:54PM - 3:06PM |
T43.00003: Dynamics of microorganisms with autochemotactic interactions Johannes Taktikos, Vasily Zaburdaev, Holger Stark Our work aims at the description of the early stage of bacterial biofilm formation. In light of this, we model bacteria as self-propelled particles that move on a surface with constant speed and whose directions of motion diffuse on the unit circle. Individual cells communicate by autochemotaxis, so they follow the gradient of a chemical which is produced by the microorganisms themselves. We investigate how the autochemotactic coupling influences the mean squared displacement of a single particle and show that the long-time dynamics is diffusive. We present theoretical predictions for the diffusion coefficient and compare them to numerical results. To incorporate the size of bacteria, we model them as disks that experience a harmonic repulsion force when they start to overlap. Our repulsion mechanism for particles in contact assumes a linear relationship between force and velocity. For such a soft model microorganism, we present numerical results on two-particle collisions and study the cluster formation in a multi-particle system. [Preview Abstract] |
Wednesday, March 23, 2011 3:06PM - 3:18PM |
T43.00004: Shear flow influences the twitching motility of \textit{Pseudomonas Aeruginosa} Yi Shen, Sigolene Lecuyer, Albert Siryaporn, Zemer Gitai, Howard Stone Twitching motility is one of the mechanisms by which bacteria can spread on surfaces and is important in the process of biofilm formation. Flow is often involved in biofilm formation, for instance when bacteria contaminate medical devices or water systems. We have studied the twitching mobility of \textit{Pseudomonas aeruginosa }in straight microfluidic channels under laminar shear flow at low Reynolds number. We tracked all the bacteria adhering and moving on the immersed glass surface. We observed that upon applying a flow, a significant fraction of bacteria started to twitch, and that many twitched upstream, opposite to the flow direction. By measuring the displacement and residence time of the bacteria staying on the surface, we found that the flow not only tuned the direction of twitching by orienting bacteria, but also that the shear rate significantly influenced the fraction of bacteria moving upstream, with an optimal shear rate about 500s$^{-1}$. [Preview Abstract] |
Wednesday, March 23, 2011 3:18PM - 3:30PM |
T43.00005: Biofilm growth: a lattice Monte Carlo model Yuguo Tao, Gary Slater Biofilms are complex colonies of bacteria that grow in contact with a wall, often in the presence of a flow. In the current work, biofilm growth is investigated using a new two-dimensional lattice Monte Carlo algorithm based on the Bond-Fluctuation Algorithm (BFA). One of the distinguishing characteristics of biofilms, the synthesis and physical properties of the extracellular polymeric substance (EPS) in which the cells are embedded, is explicitly taken into account. Cells are modelled as autonomous closed loops with well-defined mechanical and thermodynamic properties, while the EPS is modelled as flexible polymeric chains. This BFA model allows us to add biologically relevant features such as: the uptake of nutrients; cell growth, division and death; the production of EPS; cell maintenance and hibernation; the generation of waste and the impact of toxic molecules; cell mutation and evolution; cell motility. By tuning the structural, interactional and morphologic parameters of the model, the cell shapes as well as the growth and maturation of various types of biofilm colonies can be controlled. [Preview Abstract] |
Wednesday, March 23, 2011 3:30PM - 3:42PM |
T43.00006: Transitions in biofilm formation Vernita Gordon, Travis Thatcher, Benjamin Cooley Biofilms are multicellular, dynamic communities formed by interacting unicellular organisms bound to a surface. Forming a biofilm is a developmental process, characterized by sequential changes in gene expression and behavior as bacteria and yeast progress from discrete, free-swimming cells though stages that arrive at a mature biofilm. We are developing automated metrics to identify key transitions in early biofilm formation as cells attach to a surface, populate that surface, and adhere to each other to form early microcolonies. Our metrics use high-throughput tracking and analysis of microscopy movies to localize these transitions in space and time. Each of these transitions is associated with a loss of entropy in the bacterial system and, therefore, with biological activity that drives this loss of entropy. Better understanding of these transitions will allow automated determination of the strength and turn-on of attractive cell-surface and cell-cell interactions as biofilm development progresses. [Preview Abstract] |
Wednesday, March 23, 2011 3:42PM - 3:54PM |
T43.00007: Changes in the Mechanical Properties of Pseudomonas aeruginosa Bacterial Cells Induced by Antimicrobial Peptides Shun Lu, John Dutcher In our research group, we have developed an atomic force microscopy nano-creep technique [1] to study the mechanical properties of individual Pseudomonas aeruginosa bacterial cells in a liquid environment. In the present study, we have used this technique to measure changes to the mechanical properties of the cells produced by exposing the cells to well-studied antimicrobial peptides: polymyxin B (PMB) and its derivative polymyxin B nonapeptide (PMBN). We find that the creep response of cells under a fixed applied load is very different after exposure of the cells to PMB and PMBN, which is possibly due to the disruption of its outer membrane. To describe the viscoelastic properties of the cells exposed to PMB and PMBN, we found that it was necessary to use a four element spring and dashpot model, instead of the three element standard linear solid model that describes the viscoelastic properties of cells in Millipore water [1]. We also found that PMB and PMBN have qualitatively different effects on the stiffness of the cell membrane. These measurements provide a first step towards understanding the different mechanisms of action of PMB and PMBN on bacterial cells. \\[4pt] [1] V. Vadillo-Rodriguez, T. J. Beveridge, and J. R. Dutcher, J. Bacteriol., 190, 4225-4232, 2008. [Preview Abstract] |
Wednesday, March 23, 2011 3:54PM - 4:06PM |
T43.00008: Nanofabrication and Detection of Molecular Shuttles powered by Kinesin Motor Proteins Daniel Oliveira, Kim Domyoung, Mitsuo Umetsu, Tadafumi Adschiri, Winfried Teizer The intracellular cargo delivery performed by kinesin motor proteins can be biomimetically employed to engineer tailor-made artificial nanotransport systems. Kinesin (expressed on an \textit{Escherichia coli} system) and microtubules (obtained from the polymerization of tubulin proteins) were prepared and characterized. We report recent results and explore the aim of the construction of Nanoelectromechanical Systems and their potential applications, e.g. as drug delivery systems. This work was supported by the WPI Program. [Preview Abstract] |
Wednesday, March 23, 2011 4:06PM - 4:18PM |
T43.00009: Electrodynamics of Nanosystems Samina Masood We use Electrodynamics to study the nanosystems. Quantum nature of electrodynamics has been used to describe the physics of nanosystems including carbon nanotubes as well as the cellular growth. We use bacterial cell as an example and test a part of our theory on the bacterial growth experimentally. Preliminary results of these experiments are also mentioned here. [Preview Abstract] |
Wednesday, March 23, 2011 4:18PM - 4:30PM |
T43.00010: Long range electronic transport in microbial nanowires bridging an electrode and scanned probe Joshua Veazey, Sanela Lampa-Pastirk, Kathy Walsh, Jiebing Sun, Pengpeng Zhang, Gemma Reguera, Stuart Tessmer The filament-like appendages known as pili, expressed by the bacterium \textit{Geobacter sulfurreducens}, are believed to act as electrically conductive nanowires [1]. Previously, we used scanning tunneling microscopy to study the local density of states at different positions along the wire. However, the long range electron transfer believed to occur in this protein has not been directly observed. Here we discuss a system for verifying long range transport using a scanning probe technique. Transport at distances of more than a few nanometers would require a novel biological electron transfer process. \\[4pt] [1] G. Reguera, K.D. McCarthy, T. Mehta, J.S. Nicoll, M.T. Tuominen, and D.R. Lovley, Nature 435, 1098 (2005) [Preview Abstract] |
Wednesday, March 23, 2011 4:30PM - 4:42PM |
T43.00011: Heterogeneous diversity of spacers within CRISPR Michael Deem, Jiankui He Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face. 1) J. He and M. W. Deem, Phys. Rev. Lett. 105 (2010) 128102 [Preview Abstract] |
Wednesday, March 23, 2011 4:42PM - 4:54PM |
T43.00012: Filament depolymerization can pull a chromosome during bacterial mitosis Edward Banigan, Michael Gelbart, Zemer Gitai, Andrea Liu, Ned Wingreen Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. {\it Caulobacter crescentus} utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole and binds to a ParB-decorated chromosome, and then retracts via disassembly, thus pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that is disassembling it. We perform Brownian dynamics simulations with a simple and physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is ``self-diffusiophoretic'': by disassembling ParA, ParB generates a ParA concentration gradient so that the concentration of ParA is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is controlled by the product of an effective relaxation time for the chromosome and the rate of ParA disassembly. Our results provide a physical explanation of the mechanism of depolymerization-driven translocation and suggest physical explanations for recent experimental observations. [Preview Abstract] |
Wednesday, March 23, 2011 4:54PM - 5:06PM |
T43.00013: Polymerization and oscillation stuttering in a filamentous model of the subcellular Min oscillation Andrew Rutenberg, Supratim Sengupta, Anirban Sain, Julien Derr We present a computational model of the {\em E. coli} Min oscillation that involves polymerization of MinD filaments followed by depolymerization stimulated by filament-end zones of MinE. Our stochastic model is fully three-dimensional, and tracks the diffusion and interactions of every MinD and MinE molecule. We recover self-organized Min oscillations. We investigate the experimental phenomenon of oscillation stuttering, which we relate to the disruption of MinE tip-binding at the filament scale. [Preview Abstract] |
Wednesday, March 23, 2011 5:06PM - 5:18PM |
T43.00014: Effect of Antimicrobial Agents on MinD Protein Oscillations in E. coli Bacterial Cells Corey Kelly, Megan Murphy, Maximiliano Giuliani, John Dutcher The pole-to-pole oscillation of the MinD proteins in E. coli determines the location of the division septum, and is integral to healthy cell division. It has been shown previously that the MinD oscillation period is approximately 40 s for healthy cells [1] but is strongly dependant on environmental factors such as temperature, which may place stress on the cell [2,3]. We use a strain of E. coli in which the MinD proteins are tagged with green fluorescent protein (GFP), allowing fluorescence visualization of the MinD oscillation. We use high resolution total internal reflection fluorescence (TIRF) microscopy to observe the effect of exposure to antimicrobial agents on the MinD oscillation period and, more generally, to analyze the time variation of the spatial distribution of the MinD proteins within the cells. These measurements provide insight into the mechanism of antimicrobial action. \\[4pt] [1] Raskin, D.M.; de Boer, P. (1999) Proc Natl. Acad. Sci. 96: 4971-4976.\\[0pt] [2] Colville, K.; Tompkins, N.; Rutenberg, A. D.; Jericho, M. H. (2010) Langmuir 2010:26.\\[0pt] [3] Downing, B.; Rutenberg, A.; Touhami, A.; Jericho, M. (2009) PLoS ONE 4: e7285. [Preview Abstract] |
Wednesday, March 23, 2011 5:18PM - 5:30PM |
T43.00015: Pattern Transitions in Bacterial Oscillating System under Nanofluidic Confinement Jie-Pan Shen, Chia-Fu Chou Successful binary fission in E. coli relies on remarkable oscillatory behavior of the MinCDE protein system to determine the exact division site. The most favorable models to explain this fascinating spatiotemporal regulation on dynamic MinDE pattern formation in cells are based on reaction-diffusion scenario. Although not fully understood, geometric factors caused by bacterial morphology play a crucial role in MinDE dynamics. In the present study, bacteria were cultured, confined and reshaped in various micro/nanofluidic devices, to mimic either curvature changes of cell peripherals. Fluorescence imaging was utilized to detail the mode transitions in multiple MinDE patterns. The understanding of the physics in multiple pattern formations is further complemented via in silico modeling. The study synergizes the join merits of in vivo, in vitro and in silico approaches, to grasp the insight of stochastic dynamics inherited from the noisy mesoscopic biophysics. [Preview Abstract] |
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