Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session W34: Biological Physics and Bacterial Behaviors |
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Sponsoring Units: DBP Chair: Robert Austin, Princeton University Room: Colorado Convention Center 404 |
Thursday, March 8, 2007 2:30PM - 2:42PM |
W34.00001: Near-Perfect Adaptation in the {\it E. coli} Chemotaxis Signal Transduction Network Yang Yang, Sima Setayeshgar Biochemical reaction networks constitute the computing language of the cell, from converting external stimuli into appropriate intracellular signals to regulating gene expression. Precise adaptation is an important property of many signaling networks, allowing compensation for continued stimulation without saturation. Furthermore, a common feature of intracellular reaction networks is the ability to operate in a noisy environment where concentrations of key components, such as signaling molecules and enzymes controlling reaction rates are typically small and therefore fluctuations in their numbers are significant. In the context of the well- characterized {\it E. coli} chemotaxis signal transduction network, we present a new computational scheme that explores surfaces in the space of total protein concentrations and reaction rates on which (near-)perfect adaptation holds. The resulting dependencies between parameters provide conditions for (near-)perfect adaptation as well as ranges of numerical values for parameters not reliably known from experiments. We generalize the applicability of this scheme to other signaling networks. [Preview Abstract] |
Thursday, March 8, 2007 2:42PM - 2:54PM |
W34.00002: Adaptation, Bacteria and Maxwell's Demons Peter Galajda, Juan E. Keymer, Robert H. Austin We propose a method to study the adaptation of bacterial populations with an asymmetric wall of Maxwell Demon openings. A Maxwell Demon opening is a funnel which is easier to enter than to leave. The interaction of swimming cells with such a Maxwell Demon Wall results in a population density separation, in apparent (but not real) violation of the Second Law of Thermodynamics, as we will show. Bacteria can be exposed to spatial challenges in order to move to e. g. higher food levels. The question we address in these experiments is: do the bacteria adapt and overcome the Maxwell Demon Wall? [Preview Abstract] |
Thursday, March 8, 2007 2:54PM - 3:06PM |
W34.00003: Effects of Noise on Ecological Invasion Processes: Bacteriophage-mediated Competition in Bacteria Jaewook Joo, Harvill Eric, Reka Albert Pathogen-mediated competition, through which an invasive species carrying and transmitting a pathogen can be a superior competitor to a more vulnerable resident species, is one of the principle driving forces influencing biodiversity in nature. Using an experimental system of bacteriophage-mediated competition in bacterial populations and a deterministic model, we have shown in [Joo et al 2005] that the competitive advantage conferred by the phage depends only on the relative phage pathology and is independent of the initial phage concentration and other phage and host parameters such as the infection-causing contact rate, the spontaneous and infection-induced lysis rates, and the phage burst size. Here we investigate the effects of stochastic fluctuations on bacterial invasion facilitated by bacteriophage, and examine the validity of the deterministic approach. We use both numerical and analytical methods of stochastic processes to identify the source of noise and assess its magnitude. We show that the conclusions obtained from the deterministic model are robust against stochastic fluctuations, yet deviations become prominently large when the phage are more pathological to the invading bacterial strain. [Preview Abstract] |
Thursday, March 8, 2007 3:06PM - 3:18PM |
W34.00004: Synchronized Cycles: An allosteric model of the cyanobacterial circadian oscillator David Lubensky, J.S. van Zon, P. Altena, P.R. ten Wolde In a remarkable experiment, Nakajima et al. [Science, 2005] showed that the 3 cyanobacterial clock proteins KaiA, KaiB, and KaiC are sufficient to generate circadian phosphorylation of KaiC \textit{in vitro}. This system is thus a rare example of a functioning biochemical circuit that can be reconstituted in the test tube. Theoretically, it presents the further challenge that the only reactions driven out of equilibrium are those associated with KaiC phosphorylation and dephosphorylation. Here, we present a model of the Kai system. At its heart is the assumption, motivated by classical models of allostery, that each KaiC hexamer to tends to be phosphorylated in a cyclic manner. For macroscopic oscillations to be possible, however, the cycles of the different hexamers must be synchronized. We propose a novel synchronisation mechanism that allows us to reproduce a wide range of published data, including temperature compensation of the oscillation period, and to make nontrivial predictions about the effects of varying the concentrations of the Kai proteins. [Preview Abstract] |
Thursday, March 8, 2007 3:18PM - 3:30PM |
W34.00005: ABSTRACT WITHDRAWN |
Thursday, March 8, 2007 3:30PM - 3:42PM |
W34.00006: The \textit{E. Coli} Response To A Phage Perturbation Emily Chapman-McQuiston, Xiao-Lun Wu Bacteria have evolved a variety of defenses against extreme environmental pressure. While a majority of the population dies during times of stress, a portion of the population continues to survive due to the cell's phenotypic state. We study the response of the bacterial system to attack by a particular virus called lambda phage. During times of phage attack bacteria continue to create and lose receptors making the bacteria more or less sensitive to the applied phage concentration. We use experiment and modeling to study how the creation and loss of receptors affects the response and recovery of the bacterial population due to an applied phage pressure. [Preview Abstract] |
Thursday, March 8, 2007 3:42PM - 3:54PM |
W34.00007: Spatio-Temporal Analysis of Cell-Cell Signaling in a Living Cell Microarray Utkur Mirsaidov, Winston Timp, Kaethe Timp, Paul Matsudaira, Greg Timp Cell-cell signaling plays a central role in biology, enabling individual cells to coordinate their activities. For example, bacteria show evidence of intercellular signaling through \textit{quorum sensing}, a regulatory mechanism that launches a coordinated response, depending on the population density. To explore the spatio-temporal development of cell-to-cell signaling, we have created regular, heterotypic microarrays of living cells in hydrogel using time-multiplexed optical traps for submicron positional control of the cell orientation and location without loss of viability. We studied the \textit{Lux} system for quorum sensing; splitting it into sender and receiver plasmids, which were subsequently introduced into \textit{E. Coli}. Induced by IPTG, the sender cells express a fluorescent reporter (mRFP1) and the \textit{LuxI} enzyme that catalyzes the synthesis of a molecular signal AHL that diffuses through the cell membrane and the extra-cellular scaffold. The receiver cells collect the AHL signal that binds to the \textit{LuxR} regulator and reports it through GFP production. We have measured the time-delay between the onset of mRFP1 and GFP dependence on intercellular spacing in the array. [Preview Abstract] |
Thursday, March 8, 2007 3:54PM - 4:06PM |
W34.00008: \textit{in silico} simulation and analysis of microbial metabolism. Sheng Hui, Shenghua Liang, Lei-Han Tang Through evolution living organisms have developed an elaborate network of enzyme-facilitated reactions and transport to process and cycle biochemical compounds for cell growth. A majority of these reactions are uni-directional, yet the network allows an organism to live on a variety of carbon sources and synthesize a diverse set of compounds in varying amounts. We found that biosynthesis of the end products can proceed independently. In the three genome-wide \textit{in silico} models examined, the optimal yield for simultaneous synthesis of two compounds is only about 3{\%} higher than what is achievable under separate production of individual compounds. In most cases, the residual correlation can be attributed to the requirement of energy, redox potential, or charge balance. These observations quantify, in the context of cellular metabolism, the bow-tie analogy which has been argued to provide a ubiquitous architecture for multi-input/multi-output networks. [Preview Abstract] |
Thursday, March 8, 2007 4:06PM - 4:18PM |
W34.00009: Study of Signal Detection, Integration, and Propagation in Quorum Sensing at the Single Cell Level Tao Long, Bonnie Bassler, Ned Wingreen Bacteria respond to their environment and to each other and accordingly adjust their gene-expression levels. Accurate signal detection, appropriate signal integration, and faithful signal propagation are essential for a cell to make correct adjustments in response to various extracellular cues. To better understand this information processing by living cells, we studied a model system -- the quorum-sensing circuit in \textit{Vibrio harveyi}. Quorum sensing is a process in which bacteria communicate with each other by diffusible chemical molecules, termed ``autoinducers'', to commit to coordinated developmental decisions. Three types of autoinducers are detected coincidently by three parallel receptors. The signals are then integrated into the same signaling pathway and propagated by phosphorylation or dephosphorylation of the pathway components. To quantitatively measure the intracellular response, we applied a fluorescent protein reporter, whose production is regulated by a phosphorylated protein in the pathway. By single-cell microscopy, we can explore features of this information-processing circuit such as coincidence detection, signal integration, noise reduction or filtering, and especially the fidelity in signal processing achieved in the presence of inevitable fluctuations. [Preview Abstract] |
Thursday, March 8, 2007 4:18PM - 4:30PM |
W34.00010: Evolution of Mutation Rate in Asexual Populations Scott Wylie, Herbert Levine, David Kessler Several evolution experiments with \textit{E. coli} document the spontaneous emergence and eventual fixation of so called ``mutator'' alleles that increase the genomic mutation rate by the order of 100-fold. Variations in mutation rates are due to polymorphisms in the molecular machinery that copies and checks the genome for errors. These polymorphisms are coded in the genome and thus heritable. Like any heritable trait, elevated mutation rates are subject to natural selection and evolution. However, unlike other traits, mutation rate does not directly affect the rate at which an organism reproduces, i.e. its fitness. Rather, it affects the statistical distribution of the offspring's fitness. This fitness distribution, in turn, leads via ``hitchhiking'' to a change in the frequency of the mutator allele, i.e. evolution of the mutation rate itself. In our work we simulate a birth-death process that approximates simple asexual populations and we measure the fixation probability of rare mutators. We then develop an approximate analytic model of the population dynamics, the results of which agree reasonably well with simulation. In particular, we are able to analytically predict the ``effective fitness'' of mutators and the conditions under which they are expected to emerge. [Preview Abstract] |
Thursday, March 8, 2007 4:30PM - 4:42PM |
W34.00011: Control of growth and adaptation to nutritional shifts for bacteria exposed to amino acid-limiting environments Eduard M. Mateescu, Terence Hwa In order to grow at the highest rate sustainable by the environment, bacteria turn on different metabolic pathways and utilize a myriad of adaptive strategies. The macromolecular composition (RNA, DNA, protein) and overall cell size (mass) can be very different in different environments. Surprisingly however, these differences appear to depend only on the growth rate and not on the growth medium itself. As the nutritional environment changes in time, the cells quickly adapt their composition to the one corresponding to the new conditions. Here, we propose a phenomenological model of growth and adaptation control for the bacterial cell, based on a simplified formulation of the central dogma and a simplified implementation of the stringent response. The core model contains no free parameters and provides a simple intuitive understanding of cell growth control. The results generated by the model, physiological state of the cell as well as the characteristics of the transition between optimized states of growth, are in qualitative and semi-quantitative agreement (i.e. within a factor of 2) with the experimental observations. [Preview Abstract] |
Thursday, March 8, 2007 4:42PM - 4:54PM |
W34.00012: Phase Transitions in Bacterial Cultures Hanna Salman, Anton Zilman, Albert Libchaber We study how the concentration of bacteria affects their response to temperature changes. The bacteria are grown in a batch mode culture, which affects their physiological state due to nutrient depletion. For bacteria at a constant physiological state, we observe a critical transition in behavior in a one-dimensional temperature gradient as their initial concentration in the sample increases. Above a concentration of 10$^{8}$cells/cm$^{3}$, an early accumulation near their favored temperature, caused by thermotaxis, develops into a sharp pulse moving at a fast velocity ($\sim $3$.$5 \textit{$\mu $}m$/$sec). This mode is the result of a positive feedback mechanism provided by inter-bacterial communication. A theoretical model describing this interaction shows good agreement with the experimental results. For different physiological states, we observe a critical transition in the bacterial response to localized heating by infrared laser. When the bacteria are grown to concentrations below 2x10$^{8}$cells/cm$^{3}$ they swim towards the heated region; when they are grown beyond this concentration they escape from the heated region. This effect is reversible. Also, mixing populations from different physiological states does not affect the response of either population. A genetic switch controlled by the nutrients' availability seems to be responsible for this behavior. [Preview Abstract] |
Thursday, March 8, 2007 4:54PM - 5:06PM |
W34.00013: Positioning of receptor clusters along the bacterial cell wall Ranjan Mukhopadhyay, Hui Wang, Yigal Meir, Ned Wingreen Chemotaxis receptors in {\it E. coli} form clusters that are located at the cell poles and also laterally along the cell body, and clustering plays an important role in signal transduction. Recently, experiments using fluorescence imaging, have studied cluster dynamics during cell growth and found that lateral clusters transiently localize at positions approximately periodically spaced along the cell body. We have studied a lattice model of the dynamics of receptor clustering in the presence of cell growth. In this talk we will present results from our model and explore whether lateral cluster positioning could arise spontaneously from receptor clustering dynamics or whether the experimental results indicate the existence of periodically positioned markers along the cell wall that are targeted by the receptors. [Preview Abstract] |
Thursday, March 8, 2007 5:06PM - 5:18PM |
W34.00014: Genome-scale reconstruction of the metabolic network in {\it Yersinia pestis} CO92 Ali Navid, Eivind Almaas The gram-negative bacterium {\it Yersinia pestis} is the causative agent of bubonic plague. Using publicly available genomic, biochemical and physiological data, we have developed a constraint-based flux balance model of metabolism in the CO92 strain (biovar {\it Orientalis}) of this organism. The metabolic reactions were appropriately compartmentalized, and the model accounts for the exchange of metabolites, as well as the import of nutrients and export of waste products. We have characterized the metabolic capabilities and phenotypes of this organism, after comparing the model predictions with available experimental observations to evaluate accuracy and completeness. We have also begun preliminary studies into how cellular metabolism affects virulence. [Preview Abstract] |
Thursday, March 8, 2007 5:18PM - 5:30PM |
W34.00015: Modeling of the Effect of Dynamical Changes of Cell Geometry on MinCDE Oscillations During Cell Division in \textit{E. coli}. Jason Ellis, Diane Stroup, Michael Lee {In the process of cell division in \textit{E. coli}, spatio-temporal oscillations of the MinCDE proteins act to determine the specific site of FtsZ-ring formation which initiates the process of cell separation. The reaction diffusion processes which drive the biochemical oscillations of the MinCDE system have been studied and we have developed a model which incorporates the dynamics of these oscillations while cell division is accomplished through the formation of the peptidoglycan wall at the location of the FtsZ-ring. This model investigates the mechanisms that cause observed protein segregation in the daughter cells as well as the changes in oscillation characteristics observed between early and late stages of cell growth. Simulations of this model are carried out in space and time based on the reaction diffusion dynamics of individual proteins. The model allows the investigation of effects of cell geometry for both the normal cylindrical rod geometry; as well other hypothetical geometries not easily accessible in laboratory cultures.} [Preview Abstract] |
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