Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session Q47: Physics of Bacteria and Viruses |
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Sponsoring Units: DBIO Chair: Guannan Liu, Princeton University Room: 217B |
Wednesday, March 4, 2015 2:30PM - 2:42PM |
Q47.00001: Using Fitness Landscapes for Rational Hepatitis C Immunogen Design Gregory Hart, Andrew Ferguson Hepatitis C virus afflicts 170 million people worldwide, 2-3{\%} of the global population. Prophylactic vaccination offers the most realistic and cost effective hope of controlling this epidemic, particularly in the developing world where expensive drug therapies are unavailable. Despite 20 years of research, the high mutability of the virus, and lack of knowledge of what constitutes effective immune responses, have impeded development of an effective vaccine. Coupling data mining of sequence databases with the Potts model, we have developed a computational approach to systematically identify viral vulnerabilities and perform rational design of vaccine immunogens. We applied our approach to the nonstructural proteins NS3, NSA, NSA, and NSB which are crucial for viral replication.The predictions of our model are in good accord with experimental measurements and clinical observations, and we have used our model to design immunogen candidates to elicit T-cell responses against vulnerable regions of theseviral proteins. [Preview Abstract] |
Wednesday, March 4, 2015 2:42PM - 2:54PM |
Q47.00002: Impact of cell regeneration in human respiratory tract on simultaneous viral infections Lubna Jahan Rashid Pinky, Hana Dobrovolny Studies have found that $\sim$ 40{\%} of patients hospitalized with influenza-like illness are infected with at least two different viruses. In these longer infections, we need to consider the role of cell regeneration. Several mathematical models have been used to describe cell regeneration in infection models, though the effect of model choice on the predicted time course of simultaneous viral infections is not clear. We investigate a series of mathematical models of cell regeneration during simultaneous respiratory virus infections to determine the effect of cell regeneration on infection dynamics. We perform a nonlinear stability analysis for each model. The analysis suggests that coexistence of two viral species is not possible for any form of regeneration. We find that chronic illness is possible, but with only one viral species. [Preview Abstract] |
Wednesday, March 4, 2015 2:54PM - 3:06PM |
Q47.00003: Basic Reproduction Number of a Gamma-Distributed Within-Host Infection Model Irma Rodriguez, Hana Dobrovolny In epidemiology, the basic reproduction number (R0) is used to measure the spread potential of a disease. It is defined as the number of secondary infections produced by a first infection in a homogeneous susceptible population. Traditional ordinary differential equation infection models assume exponential transitions between different stages of cell infection. This assumption is not biologically realistic, so non-exponential models are now being investigated. The basic reproduction number of non-exponential models has yet to be calculated. Here we present an analysis of a gamma-distributed model that has allowed us to calculate R0 for this model. [Preview Abstract] |
Wednesday, March 4, 2015 3:06PM - 3:18PM |
Q47.00004: Observations of Bacterial Behavior during Infection Using the ARGOS Method A.J. Charest, S. Algarni, G.S. Iannacchione This research employed the Area Recorded Generalized Optical Scattering (ARGOS) approach which allowed for the observation of bacterial changes in terms of individual particles and population dynamics in real time. This new approach allows for an aqueous environment to be manipulated while conducting time-specific measurements over an indefinite amount of time. This current study provides a more time-specific method in which the bacteria remained within the initial conditions and allows for more time precision than provided by analyzing concentrations of plaque-forming units (PFU). This study involved the bacteria (F-amp) during infection by bacteriophage (MS2). The relative total intensity allows for detailed measurements of the bacteria population over time. The bacteria characteristics were also evaluated such as the root mean square image difference (at specific wavevectors), fractal dimension and effective radius. The growth rate of the infected bacteria occurred at a rate higher than the uninfected bacteria similarly, the death rates were also higher for the infected bacteria than the uninfected bacteria. The present study indicates that bacteria may react to infection by increasing the rate of population growth. [Preview Abstract] |
Wednesday, March 4, 2015 3:18PM - 3:30PM |
Q47.00005: Flagellation of \textit{Pseudomonas aeruginosa} in newly divided cells kun zhao, Calvin Lee, Jaime Anda, Gerard Wong For monotrichous bacteria, \textit{Pseudomonas aeruginosa}, after cell division, one daughter cell inherits the old flagellum from its mother cell, and the other grows a new flagellum during or after cell division. It had been shown that the new flagellum grows at the distal pole of the dividing cell when the two daughter cells haven't completely separated. However, for those daughter cells who grow new flagella after division, it still remains unknown at which pole the new flagellum will grow. Here, by combining our newly developed bacteria family tree tracking techniques with genetic manipulation method, we showed that for the daughter cell who did not inherit the old flagellum, a new flagellum has about 90{\%} chances to grow at the newly formed pole. We proposed a model for flagellation of \textit{P. aeruginosa}. [Preview Abstract] |
Wednesday, March 4, 2015 3:30PM - 3:42PM |
Q47.00006: Seeing is believing: Direct imaging of charge flow along pili proteins reveals new mechanism for bacterial electron transfer Nikhil Malvankar, Sibel Ebru Yalcin, Ramesh Adhikari, Mark Tuominen, Derek Lovley Visualization of charge flow on the nanoscale in proteins is crucial for a fundamental understanding of several life processes. Here, we report direct visualization of charge propagation along native pili of \textit{Geobacter sulfurreducens} at nanometer resolution using electrostatic force microscopy [1]. Surprisingly, charges injected at a single point into individual, untreated pili, still attached to cells, propagate over the entire filament. The charges propagate despite a lack of cytochromes on the pili, in contrast to the dominant biochemical model that proteins are electronically insulating and must incorporate redox-active cofactors in order to achieve electron transport functionality. The mobile charge density in pili is comparable to synthetic organic conductors, increasing with proton doping, and with temperature-dependence consistent with previously discovered metallic-like transport mechanism [2]. Conductive pili enable syntrophic bacteria to share energy by directly exchanging electrons among each other [3]. Measurements along individual pilus using nanoelectrodes showed ohmic behavior strongly dependent on the amino acid composition of pili. Electron transfer rate measurement revealed that the pili conductivity is the decisive factor in controlling the bacterial respiration rate. \\[4pt] [1] \textit{Nature Nano}, AOP (2014)\\[0pt] [2] \textit{Nature Nano}, 6, 573 (2011)\\[0pt] [3] \textit{Science}, 330, 1413 (2010) [Preview Abstract] |
Wednesday, March 4, 2015 3:42PM - 3:54PM |
Q47.00007: Phase separation like dynamics during \textit{Myxococcus xanthus} fruiting body formation Guannan Liu, Shashi Thutupalli, Manon Wigbers, Joshua Shaevitz Collective motion exists in many living organisms as an advantageous strategy to help the entire group with predation, forage, and survival. However, the principles of self-organization underlying such collective motions remain unclear. During various developmental stages of the soil-dwelling bacterium, \textit{Myxococcus xanthus}, different types of collective motions are observed. In particular, when starved, \textit{M. xanthus} cells eventually aggregate together to form 3-dimensional structures (fruiting bodies), inside which cells sporulate in response to the stress. We study the fruiting body formation process as an out of equilibrium phase separation process. As local cell density increases, the dynamics of the aggregation \textit{M. xanthus} cells switch from a spatio-temporally random process, resembling nucleation and growth, to an emergent pattern formation process similar to a spinodal decomposition. By employing high-resolution microscopy and a video analysis system, we are able to track the motion of single cells within motile collective groups, while separately tuning local cell density, cell velocity and reversal frequency, probing the multi-dimensional phase space of \textit{M. xanthus} development. [Preview Abstract] |
Wednesday, March 4, 2015 3:54PM - 4:06PM |
Q47.00008: Cell size control and homeostasis in bacteria Serena Bradde, Sattar Taheri, John Sauls, Nobert Hill, Petra Levine, Johan Paulsson, Massimo Vergassola, Suckjoon Jun How cells control their size is a fundamental question in biology. The mechanisms for sensing size, time, or a combination of the two are not supported by experimental evidence. By analysing distributions of size at division at birth and generation time of hundreds of thousands of Gram-negative E. coli and Gram-positive B. subtilis cells under a wide range of tightly controlled steady-state growth conditions, we are now in the position to validate different theoretical models. In this talk I will present all possible models in details and present a general mechanism that quantitatively explains all measurable aspects of growth and cell division at both population and single-cell levels. [Preview Abstract] |
Wednesday, March 4, 2015 4:06PM - 4:18PM |
Q47.00009: Population Dynamics of the Stationary Phase Utilizing the ARGOS Method S. Algarni, A.J. Charest, G.S. Iannacchione The Area Recorded Generalized Optical Scattering (ARGOS) approach to light scattering employs large image capture array allowing for a well-defined geometry in which images may be manipulated to extract structure with intensity at a specific scattering wave vector (I(q)) and dynamics with intensity at a specific scattering wave vector over time (I (q,t)). The ARGOS method provides morphological dynamics noninvasively over a long time period and allows for a variety of aqueous conditions. This is important because traditional growth models do not provide for conditions similar to the natural environment. The present study found that the population dynamics of bacteria do not follow a traditional growth model and that the ARGOS method allowed for the observation of bacterial changes in terms of individual particles and population dynamics in real time. The observations of relative total intensity suggest that there is no stationary phase and that the bacterial population demonstrates sinusoidal type patterns consistently subsequent to the log phase growth. These observation were compared to shape changes by modeling fractal dimension and size changes by modeling effective radius. [Preview Abstract] |
Wednesday, March 4, 2015 4:18PM - 4:30PM |
Q47.00010: Nanomechanical Response of Bacterial Cells to Antimicrobial Peptides Richard Parg, John Dutcher The effectiveness of antimicrobial compounds can be easily screened, however their mechanism of action is much more difficult to determine. Many compounds act by compromising the mechanical integrity of the bacterial cell envelope, and we have developed an atomic force microscopy (AFM)-based creep deformation technique to evaluate changes in the time-dependent mechanical properties of bacterial cells upon exposure to antimicrobial peptides [1]. Measurements performed before and after exposure, as well as time-resolved measurements and those performed at different antimicrobial concentrations, revealed large changes to the viscoelastic parameters including a distinctive signature for the loss of integrity of the bacterial cell envelope. Our previous experiments have focused on \textit{Pseudomonas aeruginosa }PAO1 bacterial cells in Milli-Q water, for which the cells can withstand the large osmotic pressure. In the present study we have focused on performing the measurements in buffer to obtain more biologically relevant results. The AFM creep deformation measurement provides new, unique insight into the kinetics and mechanism of action of antimicrobial peptides on bacteria. [1]~S. Lu, G. Walters, R. Parg and J.R. Dutcher,~\textit{Soft Matter}~\textbf{10}, 1806-1815 (2014). [Preview Abstract] |
Wednesday, March 4, 2015 4:30PM - 4:42PM |
Q47.00011: Quantifying Spatiotemporal Patterns in the Expansion of Twitching Bacterial Colonies Erin Shelton, Maximiliano Giuliani, Lori Burrows, John Dutcher Type IV pili (T4P) are very thin (5-8 nm in diameter) protein filaments that can be extended and retracted by certain classes of Gram-negative bacteria including \textit{P. aeruginosa }[1]. These bacteria use T4P to move across viscous interfaces, referred to twitching motility. Twitching can occur for isolated cells or in a collective manner [2]. We have developed experimental and data analysis techniques to quantify the expansion of \textit{P. aeruginosa} PAO1 bacterial colonies at the glass-agar interface under well-controlled environmental conditions. By using particle image velocimetry (PIV) and Fourier analysis techniques, we have characterized the evolution of the advancing front of expanding colonies for a range of agar concentrations. This has allowed us to observe a transition in the collective motion of the bacterial cells as the agar concentration is increased. [1] Burrows, L.L. (2012) Annu. Rev. Microbiol. 66: 493--520; [2] Semmler, A.B., Whitchurch, C.B., Mattick, J.S. (1999) Microbiology 145: 2863-2873. [Preview Abstract] |
Wednesday, March 4, 2015 4:42PM - 4:54PM |
Q47.00012: Characterization of MreB polymers in E. coli and their correlations to cell shape Jeffrey Nguyen, Nikolay Ouzonov, Zemer Gitai, Joshua Shaevitz Shape influences all facets of how bacteria interact with their environment. The size of E. coli is determined by the peptidoglycan cell wall and internal turgor pressure. The cell wall is patterned by MreB, an actin homolog that forms short polymers on the cytoplasmic membrane. MreB coordinates the breaking of old material and the insertion of new material for growth, but it is currently unknown what mechanism sets the absolute diameter of the cell. Using new techniques in fluorescence microscopy and image processing, we are able to quantify cell shape in 3- dimensions and access previously unattainable data on the conformation of MreB polymers. To study how MreB affects the diameter of bacteria, we analyzed the shapes and polymers of cells that have had MreB perturbed by one of two methods. We first treated cells with the MreB polymerization-inhibiting drug A22. Secondly, we created point mutants in MreB that change MreB polymer conformation and the cell shape. By analyzing the correlations between different shape and polymer metrics, we find that under both treatments, the average helical pitch angle of the polymers correlates strongly with the cell diameter. This observation links the micron scale shape of the cell to the nanometer scale MreB cytoskeleton. [Preview Abstract] |
Wednesday, March 4, 2015 4:54PM - 5:06PM |
Q47.00013: Mechanism of cell alignment in groups of Myxococcus xanthus bacteria Rajesh Balgam, Oleg Igoshin \textit{Myxococcus xanthus} is a model for studying self-organization in bacteria. These flexible cylindrical bacteria move along. In groups, \textit{M. xanthus} cells align themselves into dynamic cell clusters but the mechanism underlying their formation is unknown. It has been shown that steric interactions can cause alignment in self-propelled hard rods [1] but it is not clear how flexibility and reversals affect the alignment and cluster formation. We have investigated cell alignment process using our biophysical model of \textit{M. xanthus} cell [2] in an agent-based simulation framework under realistic cell flexibility values. We observed that flexible model cells can form aligned cell clusters when reversals are suppressed but these clusters disappeared when reversals frequency becomes similar to the observed value. However, \textit{M. xanthus} cells follow slime (polysaccharide gel like material) trails left by other cells and we show that implementing this into our model rescues cell clustering for reversing cells. Our results show that slime following along with periodic cell reversals act as positive feedback to reinforce existing slime trails and recruit more cells. Furthermore, we have observed that mechanical cell alignment combined with slime following is sufficient to explain the distinct clustering patterns of reversing and non-reversing cells as observed in recent experiments [3]. \textbf{References} 1. Peruani, F., et al., Phys. Rev. E, 2006. 2. Balagam, R., et al., PLoS Comput Biol, 2014. 3. Thutupalli, S., et al., 2014. http://arxiv.org/pdf/1410.7230.pdf [Preview Abstract] |
Wednesday, March 4, 2015 5:06PM - 5:18PM |
Q47.00014: Magnetically-Actuated \textit{Escherichia coli} System for Micro Lithography S. Lauback, E. Brown, L. P\'erez- Guzman, C. Peace, C. Pierce, B.H. Lower, S.K. Lower, R. Sooryakumar Technologies that control matter at the nano- and micro-scale are crucial for developing new engineered materials and devices. While the more traditional approaches for such manipulations often depend on lithographic fabrication, they can be expanded upon by taking advantage of the biological systems within a living cell which also operate on the nano- and micro- scale. In this study, a system is being developed to functionalize a targeted location on the surface of a chip with the protein AmCyan from transformed Escherichia coli cells. Using established methods in molecular biology where a plasmid with the amcyan gene sequence is inserted into the cell, E. coli are engineered to express the AmCyan protein on their outer surface. In order to transport the cells to the targeted location, the transformed E. coli are labeled with superparamagnetic micro-beads which exert directed forces on the cells in an external field. Preliminary results of the protein expression on E. coli, the transport of the cell through weak magnetic fields to targeted locations and the potential to transfer protein from the cell to the chip surface will be presented. [Preview Abstract] |
Wednesday, March 4, 2015 5:18PM - 5:30PM |
Q47.00015: Bactericidal Effects of Charged Silver Nanoparticles in Methicillin-resistant \textit{Staphylococcus aureus} Dulce Romero-Urbina, J. Jesus Velazquez-Salazar, Humberto H. Lara, Josefina Arellano-Jimenez, Eduardo Larios, Tony T. Yuan, Yoon Hwang, Mauris N. DeSilva, Miguel Jose-Yacaman The increased number of infections due to antibiotic-resistant bacteria is a major concern to society. The objective of this work is to determine the effect of positively charged AgNPs on methicillin-sensitive \textit{Staphylococcus aureus} (MSSA) and methicillin-resistant \textit{Staphylococcus aureus}(MRSA) cell wall using advanced electron microscopy techniques. Positively charged AgNPs suspensions were synthesized via a microwave heating technique. The suspensions were then characterized by Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM) showing AgNPs size range from 5 to 30 nm. MSSA and MRSA were treated with positively charged AgNPs concentrations ranging from 0.06 mM to 31 mM. The MIC$_{50}$ studies showed that viability of MSSA and MRSA could be reduced by 50{\%} at a positively charged AgNPs concentration of 0.12 mM supported by Scanning-TEM (STEM) images demonstrating bacteria cell wall disruption leading to lysis after treatment with AgNPs. The results provide insights into one mechanism in which positively charged AgNPs are able to reduce the viability of MSSA and MRSA. [Preview Abstract] |
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