Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session W27: Microbiological Physics |
Hide Abstracts |
Sponsoring Units: DBIO Chair: Seth Coleman, Rice Univ Room: 404 |
Friday, March 6, 2020 8:00AM - 8:12AM |
W27.00001: Temperature-dependent Motility in H. pylori Jyot Antani, Pushkar Lele Helicobacter pylori employ a run-reversal strategy in contrast to the run-tumble strategy employed by E. coli during navigation. As a result, their migration patterns are anticipated to be different from those in E. coli. We have quantitatively determined the effect of medium temperatures on the two modes of H. pylori motility – a pusher mode in which the flagella lag behind the body and a puller mode in which the flagella precede the body. Our data show that the cells swam faster in one mode relative to another as a function of temperature. The mean durations of the runs in either mode also depended on the temperature, as did the fraction of the time that the flagellar filaments rotated counterclockwise. We analyzed the mean squared displacements of the cell populations and determined that the bacterial spread was the highest at temperatures close to physiological temperatures. We will present a quantitative model that accounts for the anisotropic random walk to predict the temperature dependence of the bacterial diffusion. The fundamental insights from this work are likely to provide a handle for determining the motile responses of H. pylori to various types of environmental stressors. |
Friday, March 6, 2020 8:12AM - 8:24AM |
W27.00002: Developing Methods for Two-Way Communication to Explore the Dynamic Sense of Touch in Bacteria Zhou Xu, Wuqi Niu, Sylvia Rivera, Sloan Siegrist, Mark Thomas Tuominen, Maria Santore Living organisms usually utilize chemical or biomolecular signals that travel relatively slowly. However, bacterial cells can respond very quickly, yielding interesting opportunities for interfacing with bacteria. In this work, we study the bacterial sense of touch to establish the new research area of sensory-based bacterial communication. The focus is on fast two-way transmission of mechanical and electrical signals between bacteria and man-made devices. Bacterial touch acts through mechanical and electrical stimuli at timescales much less than chemical- and nutrient-based bacterial interactions. Employing high resolution microscopy with a flow cell system, we investigate the adsorption rate and growth of E. coli on different surfaces such as poly-l-lysine coated surface and hydrophobic. We use indium tin oxide coated glass as electrodes to apply electric stimulus on bacterial and measure the response. Using biomolecular engineering, we investigate the response to stimuli based on their gene expression. |
Friday, March 6, 2020 8:24AM - 8:36AM |
W27.00003: Comparative study of bacterial growth on different surfaces and the effect of weak magnetic field on the growth rates Samina Masood We investigate the growth of bacteria on different sufaces. The presence of nanoripple structure on glass is known to affect the growth rate. The growth of bacteria in the weak field is also affected by the type of the applied field, if all other conditions remains unchanged. Affect of weak magnetic field sustains for more than one generation. Moreover, the growth rate of bacteria and the structure of bacteria is also affected if it is grown over different materials including gold and silver surfaces. |
Friday, March 6, 2020 8:36AM - 8:48AM |
W27.00004: Rigid Body Dynamics of Motile Bacteria Near Surfaces Orrin Shindell, Keaton Holt, Quan Hoang, Nam Dung Hoang, Frank Healy, Hoa Nguyen Motile bacteria in their natural environment commonly interact with surfaces. Using total internal reflection fluorescence microscopy, we record the trajectories of Escherichia coli cells swimming near surfaces. By fitting ellipsoids to the fluorescent intensity profiles of the bacteria via a novel method, we extract their translational and rotational dynamics. We present results from our analysis for experiments with both wild-type and smooth-swimming E. coli strains. |
Friday, March 6, 2020 8:48AM - 9:00AM |
W27.00005: Fast Modulation of Phenotypic Diversity in Bacterial Chemotaxis Keita Kamino, Johannes M Keegstra, Junjiajia Long, Thierry Emonet, Thomas S Shimizu A central question in cell biology is how cell populations deal with ever-changing environments. It has been shown that gene regulatory networks can modulate in an environment-dependent manner not only the average phenotype, but also its diversity within isogenic populations. Here, we demonstrate that cells can also tune the level of phenotypic diversity much more rapidly than is possible by gene expression, using covalent modification of signaling proteins. In the E.coli chemotaxis pathway, we find that the diversity of a key sensory parameter, the response sensitivity, is modulated depending on the presence or absence of ambient chemoattractant molecules. We show how this diversity tuning originates from an environment-dependent mapping between the sensitivity phenotype and the standing cell-to-cell variation in the number of allosterically-coupled receptors. This diversity tuning enhances the population’s readiness for uncertain future signals in the absence of any signal, but allows the population to rapidly switch to tracking the signal once it is perceived. |
Friday, March 6, 2020 9:00AM - 9:12AM |
W27.00006: Flow-induced symmetry breaking in growing bacterial biofilms Philip Pearce, Boya Song, Dominic Skinner, Rachel V Mok, Raimo Hartmann, Praveen Singh, Hannah Jeckel, Jeffrey S Oishi, Knut Drescher, Jörn Dunkel Bacterial biofilms represent a major form of microbial life on Earth and serve as a model active nematic system, in which activity results from growth of the rod-shaped bacterial cells. In their natural environments, ranging from human organs to industrial pipelines, biofilms have evolved to grow robustly under significant fluid shear. Despite intense practical and theoretical interest, it is unclear how strong fluid flow alters the local and global architectures of biofilms. Here, we combine highly time-resolved single-cell live imaging with 3D multi-scale modeling to investigate the mechanisms by which flow affects the dynamics of all individual cells in growing biofilms. Our experiments and cell-based simulations reveal three quantitatively different growth phases in strong external flow, and the transitions between them. In the initial stages of biofilm development, flow induces a downstream gradient in cell orientation, causing asymmetrical droplet-like biofilm shapes. In the later developmental stages, when the majority of cells are sheltered from the flow by the surrounding extracellular matrix, buckling-induced cell verticalization in the biofilm core restores radially symmetric biofilm growth, in agreement with predictions of a 3D continuum model. |
Friday, March 6, 2020 9:12AM - 9:24AM |
W27.00007: Resource allocation model for bacterial shape control under growth perturbations Diana Serbanescu, Nikola Ojkic, Shiladitya Banerjee Single bacterial cells adapt their growth rates and morphologies to changes in environmental conditions in order to optimize their fitness for proliferation. Control of cell size demands making tradeoffs between cellular resources allocated towards growth and division. Understanding the nature of these tradeoffs remains an outstanding challenge. Here we propose a coarse-grained theory for how bacteria allocate their molecular resources to regulate their cell shapes and growth rates in varying nutrient environments and antibiotic induced perturbations. We propose that a balanced tradeoff between ribosomal resources allocated towards growth and division determines the control of bacterial cell volume and surface area. The results from our model are in excellent quantitative agreement with available experimental data on single-cell growth and shape under nutrient and translational perturbations. By calibrating our model with experimental data, we further predict that a combination of antibiotics that induce cell filamentation and inhibit translation may be more efficient in bacterial killing. |
Friday, March 6, 2020 9:24AM - 9:36AM |
W27.00008: Multi-scale dynamical description Gram-negative bacterial responses to antibiotics towards drug resistance Pedro Manrique, Kumkum Ganguly, S Gnanakaran Contemporary medicine struggles with bacterial infections on a daily basis. The ongoing challenge is to describe how these organisms adapt and protect at different levels when attacked by drugs. In the presence of these agents, colonies of bacteria carry out myriad processes at the molecular, genetic, and cellular scales that grant resistant against intruders threatening its survival. Even though mechanisms of specific processes in different scales have been characterized, a framework that integrates the processes at different scales remains absent. Here we propose a dynamical model that integrates these scales in the context of bacterial survival and efficacy of drugs. Using experimental inputs, our approach produces testable outputs that are in agreement with empirical data. In general, this framework provides a mathematical tool to test stress response strategies in organisms that can potentially guide experiments in natural and synthetic cellular systems. |
Friday, March 6, 2020 9:36AM - 9:48AM |
W27.00009: A Facile Accelerated Specific Therapeutic (FAST) Platform that Reverses Carbapenem Resistance in Multi-Drug Resistant E. coli Thomas Aunins, Keesha Erickson, Anushree Chatterjee
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Friday, March 6, 2020 9:48AM - 10:00AM |
W27.00010: A Comparative Analysis of Various Cas Proteins in CRISPRi Gene Circuits Lior Kreindler, Guillaume Lambert Cas proteins with deactivated cutting domains can be used as programmable components in genetic circuits in E. Coli. While dSpCas9 and dFnCas12a have proven functional in gene circuits, there exist Cas proteins from other species of bacteria that have yet to be explored and fully understood. A particularly new and mysterious Cas protein is CasX, which is completely distinct from both Cas9 and Cas12a. CasX is much smaller than both Cas9 and Cas12a; it could potentially be preferable for use in gene circuits. Cas9 and Cas12a proteins from varying species of bacteria recognize unique PAM sequences, and thus function slightly differently. To explore these differences, six versions of a CRISPRi inverter circuit that previously worked with FnCas12a in E. Coli were developed, each using the deactivated version of a different Cas protein (SaCas9, St1Cas9, TdCas9, NmCas9, AsCas12a, and CasX) programmed to target a cassette of tetA (tetracycline resistance) and sacB (sucrose sensitivity). The circuits are transformed into E. Coli, which are then selected for growth in tetracycline and sucrose. Additionally, another version of each circuit targeting GFP is tested, to confirm the results of the multiplexed tetA-sacB selection serially and to compare the effects of targeting different genes. |
Friday, March 6, 2020 10:00AM - 10:12AM |
W27.00011: Tuning programmable CRISPR-based toggle switches with buffer sites in Escherichia coli Yasu Xu, Guillaume Lambert Recent developments and advances in CRISPR-Cas systems have ushered a new generation of powerful genetic engineering tools in synthetic biology. In particular, a catalytically ‘dead’ version of Cas proteins that lack nuclease activity can essentially function as a logic NOT gate by selectively binding to a promoter and preventing transcription initiation. In this work, we first create programmable genetic toggle switches(TSs) using pairs of mutually repressible orthogonal CRISPR-based NOT gates and measure the strength of these TSs using massive parallel CRISPRi assay called “Xseq”. Specifically, hundred pairs of CRISPR nodes with different barcoded targets are simultaneously cloned into a plasmid that contains a TetA-SacB cassette as a reporter, then transformed into E. coli. Each cell has a single TS construct. By selecting cell survival under sucrose and tetracycline conditions, we are able to sort out matched CRISPR TSs among numerous randomized promoter-target pairs and quantify relative strength of each NOT gate in all possible combination at the same time. Later, adding a second plasmid that shares the same target as the TS and competes with TS for dCas pool, we can tune the efficiency of each NOT gate via manipulating the number of buffers, and thus the performance of TS. |
Friday, March 6, 2020 10:12AM - 10:24AM |
W27.00012: Development of non-linear gradient microfluidic devices Dragos Amarie, Ileene Harden, Arturo Diaz, Elijah Waters, Dwayne G. Stupack Mechanical stress introduced by the flow in microfluidic chambers induces shear stress thus impacting the live cells migration patterns. Our last-year work showed that constructing a flowless linear gradient requires two mirrored gradient chambers. In this work we present microfluidic devices that generates non-linear chemical gradients. By splitting and recombining the input flows through a combination of bifurcated (mixers and splitters) and trifurcated (splitters) channels one can generate a chemical gradient across a microfluidics chamber. As the input chemicals flowing downstream mix, a linear gradient can only achieve relative lateral gradients either from 0% to 50% or from 50% to 100%. However, we demonstrate that these mirrored gradient can be non-linear in order to accommodate a steeper flowless gradient. By introducing bias when recombining the flows in the mixers one can generate non-linear gradients. Different bias between mixers input channels can accommodate steeper lateral gradients from 100% to: (a) 37% for a 2:1 bias, (b) 30% for a 3:1 bias, (c) 27% for a 4:1 bias and (d) 24% for a 5:1 bias. This type of separated, flowless gradient offers new opportunities to study the migration of live cells free of physical flow. |
Friday, March 6, 2020 10:24AM - 10:36AM |
W27.00013: Acoustic Micromotors for Cellular Manipulation Jeffrey McNeill, Austin Maaddi, Sambeeta Das Cell manipulation is an important aspect of many studies such as single cell analysis, tissue engineering, and mechanobiology. Despite the recent surge of activity in this area, there still does not exist a system that contains most of the practical components for carrying out high-throughput cellular manipulation. The small size of cells and lack of bio-compatibility are critical challenges in cell manipulation, especially for mammalian cells. Here, we demonstrate the use of acoustically powered micromotors steered by an applied magnetic field for mammalian cell rotation and manipulation. The acoustic propulsion mechanism provides a variety of highly desirable features, such as high speed, precision, short-range attractive forces utilized as an end effector, and orthogonality in any aqueous medium. The potential power of this approach is also highlighted by cargo pickup and delivery to individual cells. |
Friday, March 6, 2020 10:36AM - 10:48AM |
W27.00014: The biophysics of cellular counting — uncovering how viral copy number drives cell-fate decision Seth Coleman, Tianyou Yao, Thu Vu Phuc Nguyen, Oleg A Igoshin, Ido Golding After infecting an E. coli cell, the virus lambda either kills the host cell (lysis) or enters a stable, dormant state (lysogeny). Such cell-fate decisions are ubiquitous in biology, but few are well understood mechanistically. The lambda decision is an attractive model system, as it is comparatively simple, well-studied, and shares multiple features with more complex systems. A key factor affecting the decision is the multiplicity of infection (MOI), i.e. the number of co-infecting viruses. Increasing MOI raises the likelihood of a lysogenic outcome, but the mechanisms by which viral copy number drives the decision are unclear. To determine these mechanisms, we combine single-cell resolution experiments with coarse-grained modeling of infection over a range of MOI. We find that the expression of essential genes in the decision network exhibits power-law scaling with MOI. Notably, the expression of cro, a key lytic gene, scales sublinearly, whereas the expression of cI, the gene responsible for establishing the lysogenic state, scales superlinearly. This nonlinear, gene-specific response to MOI is a consequence of negative and positive feedback loops in the regulatory network. This feedback causes increasing MOI to drive expression of cI, pushing the decision towards lysogeny. |
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