Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session L13: Microbiological PhysicsLive
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Sponsoring Units: DBIO Chair: Raghuveer Parthasarathy, University of Oregon; Sujit Datta, Princeton University |
Wednesday, March 17, 2021 8:00AM - 8:12AM Live |
L13.00001: Quantifying the flexural rigidity of cyanobacteria using a microfluidic flow cell Mixon Faluweki, Lucas Goehring Mechanical properties of biofilms and biomats define their structure and contribute to their adaption to a variety of ecological niches. In filamentous cyanobacteria, self-driven multicellular filaments assemble into a complex structure with macroscopic properties such as bundles and vortices. One of the most important parameters relating to the motion of filamentous cyanobacteria is their flexural rigidity or bending modulus, which characterises how flexible the filaments are. We directly measure the flexural rigidity of three species of filamentous cyanobacteria via bending tests in a microfluidic flow device where single cyanobacteria filaments are introduced into flow channel and then deflected by fluid flow. Our measurements are consistent with direct measurements of the Young’s modulus of cell walls made on the same strains using atomic force microscopy and from available data on cell wall thickness of these species. The flexural rigidity of filamentous cyanobacteria will control how individual filaments bend under flow or their own activity allowing us to estimate the free energy and the force exerted on nearby objects. The flexural rigidity alongside filament length and the driving force influence filament motion through crowded environments such as porous media. |
Wednesday, March 17, 2021 8:12AM - 8:24AM Live |
L13.00002: Altering competition outcomes of a pair of gut bacterial species via manipulation of spatial and temporal structure Deepika Sundarraman, Jarrod Smith, Jade Kast, Karen Guillemin, Raghuveer Parthasarathy The gut microbiome contains hundreds of interacting species that shape host health and disease. To clarify the still poorly understood forces that shape community composition, especially general consequences of spatial and temporal structure, we have made use of larval zebrafish with controlled combinations of intestinal microbes. In earlier work, we discovered a pair of commensal species that exhibits strong competitive interactions. Here, we explore factors that can alter this outcome in favor of either species. A mutant of one of the species, revealed by live in vivo imaging to be less aggregated than the wild type, tunes the competition outcome further in favor of this species. Conversely, the outcome can be shifted in favor of the other species by allowing it to colonize the gut before its competitor. In addition to bacterial dynamics, we observe species-dependent activity of the host immune system, assessed with Tuning two-species competition outcomes could be relevant to manipulating the outcomes of competition in more complex gut bacterial communities. |
Wednesday, March 17, 2021 8:24AM - 8:36AM Live |
L13.00003: Dynamics of commensal gut bacterial colonization in larval zebrafish populations Vivek Ramakrishna, Raghuveer Parthasarathy There is a constant flux of microorganisms between the guts of animals and the environment they live in. The ability of a microbe to colonize a host is influenced by microbial density, duration of exposure, movement both autonomous (motility) and externally driven (flow, diffusion), and direct and indirect transfer between host individuals. The relative importance of these transmission mechanisms is underexplored and poorly quantified, especially for commensal microbes of the intestinal microbiome. The larval zebrafish is an established model vertebrate system that allows for the controlled study of gut-associated microorganisms using optical microscopy. Here, we present an imaging-based assay to study the dynamics of colonization of larval zebrafish hosts by multiple species of fluorescently labelled bacteria. By assessing bacterial colonization in a large number of hosts, we extract statistical parameters such as colonization rate, and their dependence on temporal and spatial factors. We also show that there develop phenotypic variations between bacteria that have previously been inside zebrafish guts and those that have not, indicative of a bacterial ‘memory’. |
Wednesday, March 17, 2021 8:36AM - 8:48AM Live |
L13.00004: Bacterial species abundance covariance structure in C. elegans shows signatures of bacteria-bacteria and host-bacteria interactions K. Michael Martini, Megan Taylor, Ilya M Nemenman, Nicole Vega The internal dynamics and assembly of microbial communities in the guts of organisms is poorly understood. We analyze a simplified microbiome in the gut of Caenorhabditis elegans, a roundworm. Germ-free adult C. elegans are placed in an environment with equal concentrations of eight bacterial species from the native worm microbiome. After four days, we determine abundances of these bacterial species within individual worm gut communities and calculate their covariance structure. We find statistically significant off diagonal covariances. We demonstrate that a simple model only considering migration, birth, death, and competition for space among the bacteria can capture the mean values of bacterial abundances and their variances. However, it is incapable of explaining the off-diagonal covariances. We also show that the positive off diagonal covariances can be partially explained by variation of the death rate and other bacterial parameters among the worm hosts. However, to explain the off diagonal negative covariances observed in the experiment requires interactions between bacteria beyond competition for space. We thus show that the structure of the microbiome is affected by both bacteria-bacteria and bacteria-host interactions. |
Wednesday, March 17, 2021 8:48AM - 9:00AM Live |
L13.00005: Investigating structural stability of SARS-CoV-2 virus like particles. Abhimanyu Sharma, Benjamin Preece, Heather Swann, Xyu Fan, Richard J McKenney, Kassandra Ori-McKenney, Saveez Saffarian, Michael Vershinin A better understanding of the SARS-CoV-2, a novel coronavirus which has caused the Covid-19 pandemic, is urgently needed. I will present our recent work concerning the structural stability of SARS-CoV-2 Virus-Like Particles (VLPs). SARS-CoV-2 virions exit the infected host as bioaerosol, i.e., embedded within airborne liquid droplets. Although there is compelling evidence that direct exposure to bioaerosol can lead to virus transmission, droplet deposition on surfaces could be a crucial intermediary for COVID-19 spread. Studies show that virus particles can remain infectious on surfaces for long durations of time. I will present our Atomic Force Microscopy (AFM) imaging of SARS-CoV-2 VLPs, the effect of nanoscale forces on the structure of these particles, and the effect of temperature variation on the stability of VLP in liquid and dry conditions. I’ll also discuss how our results support a substantial seasonal variation of COVID-19 disease spread. |
Wednesday, March 17, 2021 9:00AM - 9:12AM Live |
L13.00006: Utilizing massively parallel CRISPRi assays to investigate persistence during antibiotic exposure Keiran Stevenson, Guillaume Lambert Bacterial persisters are characterised by a subgroup of cells within a population that have significant tolerance to antibiotics. This tolerance is primarily achieved due to the reduction of cell growth and metabolic activity which allows the bacteria to wait out the stress that would otherwise kill the cell and enabling the population to regrow once the stress is removed. The process has previously been attributed, at least in part, to toxin-antitoxin systems that allow the cell to inactivate itself in a probabilistic manner, however it is still unclear as to the global mechanisms that cause this. |
Wednesday, March 17, 2021 9:12AM - 9:24AM Live |
L13.00007: Vimentin binds to SARS-2 spike protein and antibodies targeting extracellular vimentin block uptake of SARS-2 virus-like particles Maxx Swoger, Sarthak Gupta, Robert Bucki, Paul Janmey, J. M. Schwarz, Alison Patteson The infection of human cells by pathogens, including SARS-CoV-2, typically proceeds by cell surface binding to a crucial receptor. In the case of SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2) has been identified as a necessary but not solely sufficient receptor, suggesting other extracellular factors are involved in host cell invasion by SARS-CoV-2. Vimentin is an intermediate filament protein that is increasingly recognized as being present on the extracellular surface of cells, where it can bind to and facilitate pathogens’ cellular uptake. Here, we present evidence that extracellular vimentin might acts as a critical component of the SARS-CoV-2 spike protein-ACE2 complex in mediating SARS-2 cell entry. We demonstrate direct binding between vimentin and pseudovirions bearing the SARS-2 spike protein and show that antibodies against vimentin block infection by these viral particles. Our results suggest new therapeutic strategies for preventing and slowing SARS-CoV-2 infection, focusing on targeting cell host surface vimentin. |
Wednesday, March 17, 2021 9:24AM - 9:36AM Live |
L13.00008: Chemotaxis in run-reversing bacterial species Jyot D Antani, Anita Sumali, Tanmay Lele, Pushkar Lele Motile bacteria that localize all their flagella at one pole (polar-flagellates) engage in runs and reversals. This pattern of motility differs from the standard run and tumble model of E. coli. I will discuss how this subtle difference in cell movements makes it challenging to extend the canonical chemotaxis framework to explain biased migration in polar-flagellates. I will present our novel approach to characterize the chemotaxis signaling output in one such polar-flagellate, Helicobacter pylori. I will explain how the hydrodynamic coupling of motile H. pylori with underlying glass substrates makes it possible to quantify flagellar functions. Our results conclusively establish that H. pylori modulate flagellar functions similar to E. coli. I will discuss the implications of these findings for current understanding of chemotaxis in polar flagellates. Our discoveries hint at a novel regulatory module in the network. Broadly, these studies are biomedically significant as H. pylori cause certain types of stomach cancers and chemotaxis promotes their ability to target niches in the host. |
Wednesday, March 17, 2021 9:36AM - 9:48AM Live |
L13.00009: Growth Curves Reveal How Multicellularity Enhances Drug Resistance Oleksandra Romanyshyn, Gabor Balazsi Drug resistance is a major cause of failure in treating many infectious diseases. Today’s demands for accurate drug design and effective treatment strategies require precise drug response quantitation and modeling, coupled with fast experimental testing. In this work we chose the multicellular clump-forming budding yeast (Saccharomyces cerevisiae) Sigma 1278b, or TBR1 strain as the potential model of multicellular drug-resistant yeast. By deleting the AMN1 gene responsible for clumping, we obtained a unicellular strain with otherwise identical genetic background. Drug-specific responses of multicellular versus unicellular yeast revealed by quantitative growth curve analysis indicate that multicellularity promotes resistance, producing altered drug response profiles. Finally, detailed modeling of the growth curves suggests parameters associated with molecular processes underlying multicellular drug resistance in yeast and possibly other microbes. |
Wednesday, March 17, 2021 9:48AM - 10:00AM Live |
L13.00010: Particle size dependence of 3D diffusion in live Escherichia coli cells Diana Valverde Mendez, Benjamin P Bratton, Joseph P Sheehan, Liam J Holt, Zemer Gitai, Joshua Shaevitz The bacterial cytoplasm is an extremely crowded and polydisperse environment and this leads to unexpected anomalous diffusion. We use Genetically Encoded Multimeric nanoparticles (GEMs) to probe the microrheology of the Escherichia coli cytoplasm. We reconstruct three-dimensional trajectories from optical microscopy images obtained with a custom-built biplane microscope. The use of different sized GEM particles enables us to explore the diffusion of objects ranging in size from 20 to 50 nm, similar in scale to ribosomes and other macromolecular complexes in the cell. We observe that for larger particles, the motion is confined to cylindrical shells around the nucleoid, with several diffusion regimes. We also vary the total charge of the fluorescent proteins from -18 e to +22 e and investigate the effect on diffusion. Using small molecule drug treatments, we show progress towards understanding the effects of the nucleoid and cell metabolic state on the 3D diffusion of particles inside bacterial cells. |
Wednesday, March 17, 2021 10:00AM - 10:12AM Live |
L13.00011: Extended Keller-Segel model of chemotactic migration in heterogeneous porous media Daniel Amchin, Jenna Ott, Tapomoy Bhattacharjee, Felix Sebastian Kratz, Sujit Datta How bacteria move in heterogeneous porous media like tissues and soil underlies processes like infection and bioremediation. However, existing models of bacteria transport fail to describe collective migration in porous media. To address this gap in knowledge, we use direct observation of bacteria populations inside transparent porous media that form traveling fronts following self-generated nutrient gradients. Unlike similar population scale behavior in liquid media, the front speed and shape are also strongly regulated by the structure of the porous medium itself. We show that the classic Keller-Segel model of chemotaxis can describe this behavior, but only when two revisions to the motility parameters are incorporated: (i) they are reduced in a confinement-dependent manner, and (ii) they are corrected to incorporate cell-cell collisions that are promoted by confinement. Using this revised model, we elucidate how nutrient consumption, cellular growth, and confinement-dependent motility together shape the dynamics and morphology of these traveling fronts. Taken together, our work provides a quantitative description of chemotactic migration of bacteria, and active matter in general, in heterogeneous environments. |
Wednesday, March 17, 2021 10:12AM - 10:24AM Live |
L13.00012: How to Search Space using Active Filaments Deepak Krishnamurthy, Eliott Flaum, Manu Prakash Searching space is key for organisms to find food, mates and suitable ecological niches. But how does one search when one is very small and stuck in place? The ciliate Lacrymaria olor presents a striking example of such a "search" behavior wherein a single-cell rapidly extends a neck-like protrusion to several times its body size to dynamically and efficiently hunt for prey in its surrounding space. Inspired by this remarkable behavior, here we present a framework for how cells search by combining experiments using the ciliate Lacrymaria olor, and a physical model based on deformable active filaments: i.e. filaments capable of exerting active hydrodynamic stresses on the surrounding fluid. Using our model we show that the "self-deforming activity" of these filaments can lead to complex filament dynamics even with simple patterns of underlying activity. Exploring how this dynamics depends on filament parameters such as length, stiffness and activity time-scales allows us to identify distinct regimes where effective "search" behaviors can emerge. Our model and results serve as the starting framework for understanding how the behavior of biological and man-made systems at the microscale can be programmed through the interplay of motility and morphodynamics. |
Wednesday, March 17, 2021 10:24AM - 10:36AM On Demand |
L13.00013: Top-down analysis of the complexity of environmental and human-associated microbial ecosystems Yogev Yonatan, Guy Amit, Amir Bashan According to May's half-century-old theory, ecological systems can be stable up to a critical level of complexity, which is a product of the number of resident species and their interactions. |
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