Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session W45: Physics of Bacteria |
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Sponsoring Units: DBIO Chair: Kun Zhao, University of California, Los Angeles Room: Hilton Baltimore Holiday Ballroom 4 |
Thursday, March 21, 2013 2:30PM - 2:42PM |
W45.00001: Gene Location and DNA Density Determine Transcription Factor Distributions in \textit{E. coli} Thomas Kuhlman, Edward Cox The diffusion coefficient of the prototypical transcription factor LacI within living \textit{Escherichia coli} has been measured directly by in vivo tracking to be D~$=$~0.4 $\mu$m$^2$/s. At this rate, simple models of diffusion lead to the expectation that LacI and other proteins will rapidly homogenize throughout the cell. We have tested this expectation of spatial homogeneity by single molecule visualization of LacI molecules non-specifically bound to DNA in fixed cells. Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene. We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that \textit{E. coli} can dynamically redistribute proteins by modifying the state of its nucleoid. Finally, we show that LacI inhomogeneity increases the strength with which targets located proximally to the LacI gene are regulated. We propose a model for intranucleoid diffusion which can reconcile these results with previous measurements of LacI diffusion. [Preview Abstract] |
Thursday, March 21, 2013 2:42PM - 2:54PM |
W45.00002: A model for the condensation of the bacterial chromosome by the partitioning protein ParB Chase Broedersz, Ned Wingreen The molecular machinery responsible for faithful segregation of the chromosome in bacteria such as \textit{Caulobacter crescentus} and \textit{Bacillus} \textit{subtilis} includes the ParABS a.k.a. Spo0J/Soj partitioning system. In \textit{Caulobacter}, prior to division, hundreds of ParB proteins bind to the DNA near the origin of replication, and localize to one pole of the cell. Subsequently, the ParB-DNA complex is translocated to the far pole by the binding and retraction of the ParA spindle-like apparatus. Remarkably, the localization of ParB proteins to specific regions of the chromosome appears to be controlled by only a few centromeric \textit{parS} binding sites. Although lateral interactions between DNA-bound ParB are likely to be important for their localization, the long-range order of ParB domains on the chromosome appears to be inconsistent with a picture in which protein-protein interactions are limited to neighboring DNA-bound proteins. We developed a coarse-grained Brownian dynamics model that allows for lateral and 3D protein-protein interactions among bound ParB proteins. Our model shows how such interactions can condense and organize the DNA spatially, and can control the localization and the long-range order of the DNA-bound proteins. [Preview Abstract] |
Thursday, March 21, 2013 2:54PM - 3:06PM |
W45.00003: Effect of an Antimicrobial Compound on Different Processes within the Oscillation of Min Proteins in E. coli Bacterial Cells Maximiliano Giuliani, John Dutcher A key step in the life of a bacterium is its division into two daughter cells of equal size. This process is carefully controlled and regulated so that equal partitioning of the cellular machinery is obtained. In E. coli, this regulation is accomplished, in part, by the Min protein system. The Min proteins undergo an oscillation between the poles of rod-shaped E. coli bacteria. We use high magnification, time-resolved total internal reflection fluorescence microscopy to characterize the temporal distributions of different processes within the oscillation: the MinD-MinE interaction time, the residence time for membrane bound MinD, and the recruitment time for MinD to be observed at the opposite pole. We also characterize the change in each of these processes in the presence of the antimicrobial compound polymyxin B (PMB). We show that the times corresponding to the removal of MinD from one pole and the recruitment of MinD at the opposite pole are correlated. We explain this correlation through the existence of a concentration threshold. The effect of PMB on the concentration threshold is used to identify which process within the oscillation is most affected. [Preview Abstract] |
Thursday, March 21, 2013 3:06PM - 3:18PM |
W45.00004: Mechanism for longitudinal growth of rod-shaped bacteria Swadhin Taneja, Ben Levitan, Andrew Rutenberg The peptidoglycan (PG) cell wall along with MreB proteins are major determinants of shape in rod-shaped bacteria. However the mechanism guiding the growth of this elastic network of cross-linked PG (sacculus) that maintains the integrity and shape of the rod-shaped cell remains elusive. We propose that the known anisotropic elasticity and anisotropic loading, due to the shape and turgor pressure, of the sacculus is sufficient to direct small gaps in the sacculus to elongate around the cell, and that subsequent repair leads to longitudinal growth without radial growth. We computationally show in our anisotropically stressed anisotropic elasticity model small gaps can extend stably in the circumferential direction for the known elasticity of the sacculus. We suggest that MreB patches that normally propagate circumferentially [1], are associated with these gaps and are steered with this common mechanism. This basic picture is unchanged in Gram positive and Gram negative bacteria. We also show that small changes of elastic properties can in fact lead to bi-stable propagation of gaps, both longitudinal and circumferential, that can explain the bi-stability in patch movement observed in $\Delta mbl \Delta mreb$ mutants.\\[4pt] [1] J. Dom\'{i}nguez-Escobar {\em et al.}, Science [Preview Abstract] |
Thursday, March 21, 2013 3:18PM - 3:30PM |
W45.00005: Modeling of storage-based heterocyst commitment and patterning in cyanobacteria Aidan Brown, Andrew Rutenberg When deprived of fixed nitrogen, filamentous cyanobacteria differentiate nitrogen-fixing heterocyst cells in a regular, one-dimensional pattern. Many genes have been identified that contribute to heterocyst selection, but the selection process is still not well understood. By including fixed-nitrogen storage in a computational model of nitrogen dynamics, growth, and heterocyst differentiation with lateral inhibition along the filament we can explain the stochastic timing of heterocyst commitment. Notably, the only stochastic element of our model is growth rate randomness sufficient to achieve a natural population structure of cell lengths. Our computational model qualitatively reproduces many measurements associated with heterocyst differentiation including both initial and steady state heterocyst patterns. Our model shows that a fixed storage percentage, together with variability in cell length, can produce a strong implicit cell cycle effect on heterocyst commitment which favors the commitment of shorter cells. [Preview Abstract] |
Thursday, March 21, 2013 3:30PM - 3:42PM |
W45.00006: Low-temperature STM studies of electronic properties of microbial nanowires Kathy Walsh, Sanela Lampa-Pastirk, Joshua Veazey, Gemma Reguera, Stuart Tessmer \textit{Geobacter sulfurreducens} expresses pili that act as electrically conductive nanowires. These microbial nanowires transport metabolically generated electrons outside the cell body to electron acceptors in the organism's environment. We have performed scanning tunneling microscopy and spectroscopy on these pili in an endeavor to elucidate the mechanism of conductivity. In particular, we will discuss spectroscopy curves acquired at a temperature of 77 K. [Preview Abstract] |
Thursday, March 21, 2013 3:42PM - 3:54PM |
W45.00007: Direct observation and quantification of extracellular long-range electron flow in anaerobic bacteria Nikhil Malvankar, Sibel Yalcin, Madeline Vargas, Mark Tuominen, Derek Lovley Some anaerobic microorganisms are capable of transporting electrons outside their cell to distant electron acceptors such as metals, minerals or partner species. Previous studies have focused primarily on transport over short distances (\textless\ 1 $\mu $m) via diffusion of molecular intermediates, or alternatively via tunneling or thermally-activated hopping across biomolecules. However, we have found that \textit{Geobacter sulfurreducens} can transport electrons over long distances (\textgreater\ 10 $\mu $m) using pili filaments that show organic metal-like conductivity [1]. Pili also enable direct exchange of electrons among syntrophic \textit{Geobacter} co-cultures [2]. In order to establish the physical principles underlying this remarkable electron transport, we have employed a novel scanning probe microscopy-based method to perform quantitative measurements of electron flow at a single cell level under physiological conditions. Using this nanoscopic approach, we have directly observed the propagation and distribution of injected electrons in individual native bacterial extracellular proteins. Our direct measurements demonstrate unambiguously for the first time that the pili of \textit{G. sulfurreducens} are a novel class of electronically functional proteins that can sustain electron flow in a surprising manner that has not been observed previously in any other natural protein.\\[4pt] [1] \textit{Nature Nanotechnology}, 6, 573 (2011)\\[0pt] [2] \textit{Science}, 330, 1413 (2010) [Preview Abstract] |
Thursday, March 21, 2013 3:54PM - 4:06PM |
W45.00008: Biofilm formation and surface exploration behavior of P. aeruginosa Bernard Beckerman, Kun Zhao, Gerard Wong, Erik Luijten Despite extensive studies, the early stages of biofilm formation are not fully understood. Recent work on the opportunistic pathogen Pseudomonas aeruginosa has shown that these bacteria deposit the exopolysaccharide Psl as they move across a surface, which in turn attracts repeat visits of bacteria to the sites of deposition. Using a massively parallel cell-tracking algorithm combined with fluorescent Psl staining and computer simulations, we show that this behavior results in a surface visit distribution that can be approximated by a power law. The steepness of this Zipf's Law is a measure of the hierarchical nature of bacterial surface visits, and is (among other parameters) a function of both Psl secretion rate and sensitivity of the bacteria to Psl. We characterize the bacterial distributions using various computational techniques to quantitatively analyze the effect of Psl on microcolony organization and to identify the key stages of microcolony growth. [Preview Abstract] |
Thursday, March 21, 2013 4:06PM - 4:18PM |
W45.00009: Pel promotes symmetric, short-ranged surface attachment in P. aeruginosa B. J. Cooley, Travis Thatcher, Sara Hashmi, Guillaume L'Her, Ahmed Touhami, Daniele Provenzano, Vernita Gordon Bacterial biofilms are surface mounted, multicellular communities of interacting bacteria that are often associated with chronic infections that resist antibiotics and damage host tissue. Bacteria in a biofilm are bound in a matrix of polymeric materials that adhere the bacteria to the surface, give the system spatial structure, and cluster the bacteria near each other. The opportunistic human pathogen \emph{Pseudomonas aeruginosa} is widely studied as a model biofilm-forming organism. The polymeric matrix of \emph{P. aeruginosa} strain PAO1 biofilms is dominated by two bacteria-produced extracellular polymers, Pel and Psl. We use both optical and atomic force microscopy to examine the roles of these polymers in very early biofilm development, in the hours after initial surface attachment. In agreement with other researchers, we find that Psl mediates strong attachment to a glass surface. Unexpectedly, we find that Pel promotes symmetric attachment, in the form of the rod-shaped bacteria lying flat on the surface, independently of permanent attachment to the surface. Further, the presence of Pel makes adhesion forces more short-ranged than they are with Psl alone. We suggest that these effects may result through synergistic interactions of Pel and Psl in the polymeric matrix. [Preview Abstract] |
Thursday, March 21, 2013 4:18PM - 4:30PM |
W45.00010: Surface-attachment sequence in Vibrio Cholerae Andrew Utada, Maxsim Gibiansky, Gerard Wong Vibrio cholerae is a gram-negative bacterium that causes the human disease cholera. It is found natively in brackish costal waters in temperate climates, where it attaches to the surfaces of a variety of different aquatic life. V. cholerae has a single polar flagellum making it highly motile, as well as a number of different pili types, enabling it to attach to both biotic and abiotic surfaces. Using in-house built tracking software we track all surface-attaching bacteria from high-speed movies to examine the early-time attachment profile of v. cholerae onto a smooth glass surface. Similar to previous work,\footnote{Lauga, E., DiLuzio, W. R., Whitesides, G. M., Stone, H. A. Biophys. J. 90, 400 (2006).} we observe right-handed circular swimming trajectories near surfaces; however, in addition we see a host of distinct motility mechanisms that enable rapid exploration of the surface before forming a more permanent attachment. Using isogenic mutants we show that the motility mechanisms observed are due to a complex combination of hydrodynamics and pili-surface interactions. [Preview Abstract] |
Thursday, March 21, 2013 4:30PM - 4:42PM |
W45.00011: Large scale surface migration of \textit{P. aeruginosa }at early stages of biofilm formation Maxsim Gibiansky, Andy Utada, Kun Zhao, Wujing Xian, Gerard Wong \textit{Pseudomonas aeruginosa} is a commonly-studied bacterium which can form biofilms, surface-bound aggregates which display increased resistance to various forms of stress, including a greatly enhanced antibiotic resistance. In the early stages of biofilm formation, free-swimming planktonic cells attach to the surface and form microcolonies, expressing a variety of adhesins and transitioning from reversible to irreversible attachment. By using particle tracking algorithms, we can in principle examine the full motility and division history of all cells in a microcolony. Here, we study the effects of the \textit{pel} polysaccharides in microcolony formation by investigating how \textit{pel} impacts the initial stages of biofilm formation by the \textit{P. aeruginosa} PA14 strain. Specifically, we quantify the phenotypic effects of \textit{pel} on initial attachment, microcolony formation, and biofilm morphology. [Preview Abstract] |
Thursday, March 21, 2013 4:42PM - 4:54PM |
W45.00012: Quantifying the Dynamics of Bacterial Crowd Surfing Robert Moscaritolo, Matt Kinley, Robin White, Corey Kelly, Maximiliano Giuliani, Lori Burrows, John Dutcher Type IV pili (TFP) are thin (several nanometers in diameter) adhesive protein filaments that can be extended and retracted by certain classes of Gram-negative bacteria including \textit{P. aeruginosa} PAO1 [1]. The motion of bacteria on surfaces by TFP is referred to as twitching motility because of its jerky nature, and it leads to complex, collective motion of large numbers of cells [2]. When non-motile mutants of \textit{P. aeruginosa} cells, which do not have pili and therefore cannot twitch, are mixed with motile, wild type cells, we observed the non-motile cells being carried along (``crowd surfing'') by the moving wild type cells. Crowd surfing extends to other non-motile species as well as inert particles and can lead to unexpected transport of non-motile, pathogenic bacterial cells, with direct implications for the spread of bacterial infections. We have developed a protocol for tracking and analyzing the trajectories of moving bacterial cells. Using a custom built, temperature and humidity controlled environmental chamber, we characterize the crowd surfing phenomenon under different environmental conditions. [1] Burrows, L.L. (2005) Mol. Microbiol. 57(4): 878-888. [2] Semmler, A.B., Whitchurch, C.B., Mattick, J.S. (1999). Microbiology 145: 2863-2873. [Preview Abstract] |
Thursday, March 21, 2013 4:54PM - 5:06PM |
W45.00013: The effect of flagellar motor-rotor complexes on twitching motility in \textit{P. aeruginosa} Kun Zhao, Andrew Utada, Maxsim Gibiansky, Wujing Xian, Gerard Wong \textit{P. aeruginosa} is an opportunistic bacterium responsible for a broad range of biofilm infections. In order for biofilms to form, \textit{P. aeruginosa} uses different types of surface motility. In the current understanding, flagella are used for swarming motility and type IV pili are used for twitching motility. The flagellum also plays important roles in initial surface attachment and in shaping the architectures of mature biofilms. Here we examine how flagella and pili interact during surface motility, by using cell tracking techniques. We show that the pili driven twitching motility of \textit{P. aeruginosa} can be affected by the motor-rotor complexes of the flagellar system. [Preview Abstract] |
Thursday, March 21, 2013 5:06PM - 5:18PM |
W45.00014: Biofilm streamer formation in a microfluidic porous media mimic Aloke Kumar, Amin Valiei, Partha Mukherjee, Yang Liu, Thomas Thundat Biofilm formation in porous media is of significant importance in many environmental and industrial processes such as bioremediation, oil recovery, and wastewater treatment. Among different biological and environmental factors, hydrodynamics is considered an important determinant of the dynamics of biofilm formation. In the present study, we fabricated a microfluidic porous media mimic and investigated how fluid flow influences the formation of filamentous structures, known as streamers, between porous media structures. Streamers are viscoelastic materials composed of extracellular polymeric substances (EPS) and bacterial cells, and these filamentous structures are typically tethered at either one of both ends to surfaces. We studied evolution of streamers in different flow rates and identified a tangible link between hydrodynamic conditions and development of these filamentous structures. Our results show that hydrodynamic conditions not only determine the limit of the streamers formation, but also influence both temporal evolution and spatial organization of biofilm streamers. [Preview Abstract] |
Thursday, March 21, 2013 5:18PM - 5:30PM |
W45.00015: Observation of Spontaneous Circulation in a Confined Bacterial Suspension Hugo Wioland, Raymond Goldstein The individual swimming behavior of many microorganisms is often well described by a run-and-tumble model. However steric and fluid interactions with other cells and boundaries can strongly affect this behavior. At high concentrations, rod-like bacteria are known to exhibit self-organization reminiscent of nematic liquid crytal ordering, except with polar alignment. Depending on the experimental conditions different large scale patterns can arise such as vortices, jets, plumes and swarms. We use the model organism \textit{Bacillus subtilis} to study the effect of a quasi-2D confinement on their large scale organization. Bacteria are concentrated in flattened drops surrounded by oil. Using fluorescent microsphere tracers and particle image velocimetry, we measure the flow of the cells and of the suspending fluid inside and outside of the drop. For drop diameters ranging from 10 to 100 $\mu$m and 20 $\mu$m in height, the suspension displays spontaneous circulation in the form of a single vortex, which, for the largest drops, significantly exceeds the size of swirls in the unconfined system. Moreover we observe a striking backward flow close to the boundary. We compare these results with a theoretical analysis to gain insights into the assembly and stability of such patterns. [Preview Abstract] |
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