Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session L40: Focus Session: Noisy Dynamics as Survival Strategies and Nanopores |
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Sponsoring Units: DBP Chair: Gabor Balazsi and Gurol Suel, MD Anderson Cancer Center Room: A122/123 |
Tuesday, March 22, 2011 2:30PM - 3:06PM |
L40.00001: TBA Invited Speaker: This abstract not available. [Preview Abstract] |
Tuesday, March 22, 2011 3:06PM - 3:18PM |
L40.00002: Evolution and Biophysics of the \textit{Escherichia coli lac} Operon J. Christian Ray, Oleg Igoshin, Selwyn Quan, Russell Monds, Tim Cooper, G\'{a}bor Bal\'{a}zsi To understand, predict, and control the evolution of living organisms, we consider biophysical effects and molecular network architectures. The lactose utilization system of \textit{E. coli} is among the most well-studied molecular networks in biology, making it an ideal candidate for such studies. Simulations show how the genetic architecture of the wild-type operon attenuates large metabolic intermediate fluctuations that are predicted to occur in an equivalent system with the component genes on separate operons. Quantification of gene expression in the \textit{lac} operon evolved in growth conditions containing constant lactose, alternating with glucose, or constant glucose, shows characteristic gene expression patterns depending on conditions. We are simulating these conditions to show context-dependent biophysical sources and costs of different lac operon architectures. [Preview Abstract] |
Tuesday, March 22, 2011 3:18PM - 3:30PM |
L40.00003: The effects of nongenetic memory on population level sensitivity to stress Rhys Adams, Dmitry Nevozhay, Elizabeth Van Itallie, Matthew Bennett, Gabor Balazsi While gene expression is often thought of as a unidirectional determinant of cellular fitness, recent studies have shown how growth retardation due to protein expression can affect gene expression levels in single cells. We developed two yeast strains carrying a drug resistance protein under the control of different synthetic gene constructs, one of which was monostable, while the other was bistable. The gene expression of these cell populations was tuned using a molecular inducer so that their respective means and noises were identical, while their nongenetic memory properties were different. We tested the sensitivity of these two cell population distributions to the antibiotic zeocin. We found that the gene expression distributions of bistable cell populations were sensitive to stressful environments, while the gene expression distribution of monostable cells were nearly unchanged by stress. We conclude that cell populations with high nongenetic memory are more adaptable to their environment. [Preview Abstract] |
Tuesday, March 22, 2011 3:30PM - 4:06PM |
L40.00004: Interplay of Noisy Gene Expression and Dynamics Explains Patterns of Bacterial Operon Organization Invited Speaker: Bacterial chromosomes are organized into operons -- sets of genes co-transcribed into polycistronic messenger RNA. Hypotheses explaining the emergence and maintenance of operons include proportional co-regulation, horizontal transfer of intact ``selfish'' operons, emergence via gene duplication, and co-production of physically interacting proteins to speed their association. We hypothesized an alternative: operons can reduce or increase intrinsic gene expression noise in a manner dependent on the post-translational interactions, thereby resulting in selection for or against operons in depending on the network architecture. We devised five classes of two-gene network modules and show that the effects of operons on intrinsic noise depend on class membership. Two classes exhibit decreased noise with co-transcription, two others reveal increased noise, and the remaining one does not show a significant difference. To test our modeling predictions we employed bioinformatic analysis to determine the relationship gene expression noise and operon organization. The results confirm the overrepresentation of noise-minimizing operon architectures and provide evidence against other hypotheses. Our results thereby suggest a central role for gene expression noise in selecting for or maintaining operons in bacterial chromosomes. This demonstrates how post-translational network dynamics may provide selective pressure for organizing bacterial chromosomes, and has practical consequences for designing synthetic gene networks. [Preview Abstract] |
Tuesday, March 22, 2011 4:06PM - 4:18PM |
L40.00005: Population-level control of gene expression Dmitry Nevozhay, Rhys Adams, Elizabeth Van Itallie, Matthew Bennett, Gabor Balazsi Gene expression is the process that translates genetic information into proteins, that determine the way cells live, function and even die. It was demonstrated that cells with identical genomes exposed to the same environment can differ in their protein composition and therefore phenotypes. Protein levels can vary between cells due to the stochastic nature of intracellular biochemical events, indicating that the genotype-phenotype connection is not deterministic at the cellular level. We asked whether genomes could encode isogenic cell populations more reliably than single cells. To address this question, we built two gene circuits to control three cell population-level characteristics: gene expression mean, coefficient of variation and non-genetic memory of previous expression states. Indeed, we found that these population-level characteristics were more predictable than the gene expression of single cells in a well-controlled environment. [Preview Abstract] |
Tuesday, March 22, 2011 4:18PM - 4:30PM |
L40.00006: Functional Differentiation in EVS modeling Irina Trofimova, William Sulis Ensembles with Variable Structures (EVS) were introduced in mid-1990s as stochastic milti-agent models in which agents possessed either formal diversity (described in a multi-dimensional vector space of abstract characteristics) or resource-oriented diversity (Trofimova, 2000). The process of functional differentiation (i.e. appearance of functional roles) is modelled as constraints on the flow of resources which pass through agents of the model. These constraints are: 1) the maximum amount of resource that an individual can accept from outside, 2) the maximum amount of resource that an individual can give back to the population or other environment, 3) distribution of the exchange of the resource over time (frequency and amount of the resource per step), and 4) the maximum amount of contacts that an individual can hold with such environment (sociability). Sociability appears to have a major impact on clustering dynamics within the population and to be an order parameter in phase transition in clustering behaviour, therefore it interfered with functional differentiation. Two patterns of functional differentiation were observed, before and after the phase transition in clustering, corresponding to sociability values below and after the critical points. [Preview Abstract] |
Tuesday, March 22, 2011 4:30PM - 4:42PM |
L40.00007: Fitness in fluctuating environments Sorin Tanase Nicola, Ilya Nemenman Often environments change faster than the time needed to evolve optimal phenotypes through cycles of mutation and selection. We focus on this case, but assume that environmental oscillations are slower than an individual's lifetime. This is relevant, for example, for bacterial populations confronted with daily environmental changes. We analyze a resource-limited competition between a mutant phenotype and the ancestor. Environmental dynamics is represented by periodically varying, off-phase parameters of the corresponding Lotka-Volterra model. For the very slow dynamics (but still faster than the fixation time scale) the strength and the sign of selection are functions of the birth/death rates averaged over all of the environmental states and independent of the period of the fluctuations. For faster fluctuations, selection depends on the particular sequence of the successive environmental states. In particular, a time reversal of the environmental dynamics can change the sign of the selection. We conclude that the fittest phenotype in a changing environment can be very different from both the optimal phenotype in the average environment, and the phenotype with the largest average fitness. [Preview Abstract] |
Tuesday, March 22, 2011 4:42PM - 4:54PM |
L40.00008: Development of an electrical nanopore device towards the control of the translocation of DNA with single base resolution Hongbo Peng, Binquan Luan, Stanislav Polonsky, Stephen Rossnagel, Gustavo Stolovitzky Recently, application of nanopores to low-cost DNA sequencing has attracted great interest as there is great need to reduce the cost of sequencing a whole human genome to \$1000. A key issue in the field of nanopore DNA sequencing is to control the DNA translocation. Here we will report the development of what we call a ``DNA transistor'': a nanopore-based electrical device for controlling the translocation of DNA with single base resolution. The key part of this device is a free standing membrane, within which multiple layers of electrically addressable metal electrodes separated by dielectric layers are embedded. A 1-5 nanometer size pore is made through the membrane. We demonstrated that such a device is electrically viable for the electrode layer or the spacing dielectric layer as thin as 3 nm in 1 mM KCl solution. Induced electrical signals on the nano-electrodes by the translocating DNA, as well as the modulation of DNA translocation speed by the voltage bias applied on the nanoelectrodes are also observed. Our ongoing experiments test if the modulated electrical field can trap or translocate DNA at a single base resolution. [Preview Abstract] |
Tuesday, March 22, 2011 4:54PM - 5:06PM |
L40.00009: ABSTRACT WITHDRAWN |
Tuesday, March 22, 2011 5:06PM - 5:18PM |
L40.00010: Polymerization of nanopores for controlled surface charges Waseem Asghar, Azhar Ilyas, Richard Timmons, Samir Iqbal The solid-state nanopores have emerged as a novel candidate for DNA sequencing and protein analysis. Traditional approaches for nanopore diameter shrinking use electron microscopy induced shrinking and deposition processes. These approaches are limited due to less control on surface composition of the deposited film, slow deposition rate and initial membrane thickness dependant shrinking processes. We report a novel approach of pulsed plasma polymer deposition which addresses all of the above described issues. The surface chemical composition and geometry of solid-state nanopores are controlled by plasma deposition of highly conformal thin polymeric films. Surface energy and pore-wall surface charges are controlled using appropriate monomer during plasma deposition process. [Preview Abstract] |
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