Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session B23: Cellular Biophysics: structure, mechanics, and dynamics |
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Sponsoring Units: DBIO DSOFT Chair: Mary Elting, North Carolina State University Room: 304 |
Monday, March 2, 2020 11:15AM - 11:27AM |
B23.00001: “Cellular Stokesian Dynamics”: a computational model for biological cells Roseanna Zia, Drew Endy, Akshay Maheshwari, Emma del Carmen Gonzalez Gonzalez, Alp M Sunol The frontier in operational mastery of biological cells arguably resides at the interface between biology and colloid physics: cellular processes that operate over colloidal length scales, where continuum fluid mechanics and Brownian motion underlie whole-cell scale behavior. It is at this scale that much of cell machinery operates and is where reconstitution and manipulation of cells is most challenging. This operational regime is centered between the two well-studied limits of structural and systems biology: the former focuses on atomistic-scale spatial resolution with little time evolution, and the latter on kinetic models that abstract space away. Colloidal hydrodynamics modeling bridges this divide by unifying the disparate length and time-scales of solvent-molecule and colloidal dynamics, and may hold a key to numerous open questions in biological cell function. I will discuss our physics-based computational model of a biological cell, where biomolecules and their interactions are physically represented, individually and explicitly. With it, we study a model process: translation elongation. We find that Brownian self-diffusion alone is insufficient to recover experimentally measured elongation rates but accounting for other colloidal forces improves agreement. |
Monday, March 2, 2020 11:27AM - 11:39AM |
B23.00002: The roles of patchy attractions and Brownian motion in fundamental biological processes in a model cell Jennifer Hofmann, Roseanna Zia Microscopic forces and physical phenomena at the colloidal scale are involved with fundamental processes inside living cells [Maheshwari et al., Phys. Rev. Fluids, 2019]. Examples of such phenomena include Brownian motion, confinement within the boundary of a cell membrane or wall, and hydrodynamic & electrostatic interactions between constituents of the cellular milieu (e.g. proteins). In the case of electrostatic interactions, isotropic inter-particle potentials are often insufficient to reproduce experimental results due to anisotropic charge distributions on protein surfaces [Bucciarelli et al., Sci. Rep., 2018]. To connect these microscopic forces to whole-cell functions, we examine the interplay between these colloidal-scale phenomena in dynamic simulations. Specifically, we use coarse-grained, patchy simulations to study the biological process of translation elongation in a model prokaryotic cell. Here, we present our results investigating the structure and dynamics of these coarse-grained systems, probing the inseparable connection between colloidal-scale transport and biological function. |
Monday, March 2, 2020 11:39AM - 11:51AM |
B23.00003: The structure of tubular organelle networks can accelerate diffusive transport and kinetics Aidan Brown, Elena Koslover Diffusion is an important, and often dominant, mode of transport for molecules inside cells. Many cell processes occur within specialized organelles with a variety of internal geometries, notably the tubular networks of the endoplasmic reticulum and mitochondria, which form a complex meshwork of loops spanning much of the cell. We describe how the structure of these tubular network organelles controls diffusive search times and kinetic rates, using both analytical calculation and computational simulation of diffusive first-passage times on organelle structures extracted from yeast and mammalian cells. We find that total network length alone is not a good predictor of search time. However, total length combined with the number of loops robustly determines search times. Strikingly, increasing the number of loops substantially accelerates diffusive search and reaction kinetics. Mitochondrial mutant networks deficient in fusion and fission have many fewer loops than wild-type networks. By comparing these two network types we show wild-type networks can nearly double diffusive reaction rates for sparse reactants, compared to mutant networks. Overall, we find that the looped structure of organelle networks can function to accelerate diffusive processes. |
Monday, March 2, 2020 11:51AM - 12:03PM |
B23.00004: Elucidating mechanics of vascular regression in Botryllus schlosseri using image analysis Roopa Madhu, Delany Rodriguez, Claudia Guzik, Shambhavi Singh, Anthony Tomaso, Megan Valentine, Dinah Loerke Epithelial tubules form critical structures in various body tissues; however, due to experimental inaccessibility, their architecture and dynamics are not well understood. We examined epithelial tube remodeling in vivo using a novel model system: Botryllus schlosseri vasculature. |
Monday, March 2, 2020 12:03PM - 12:15PM |
B23.00005: Vesicle formation processes on the Golgi significantly altered by overexpression - Duel FRAP investigation Garrett C Sager, Elizabeth S. Sztul, Ryoichi Kawai Overexpression of a target protein is commonly used in fluorescence-based experiments, such as fluorescence-recovery-after-photobleaching (FRAP), to boost the fluorescence intensity. Since the order of magnitude of protein concentration is artificially altered, the biochemical processes under investigation might be altered as well. We have studied how overexpression could affect the way we understand vesicle formation using FRAP experiments and kinetic Monte Carlo simulation based on continuous-time random walk. Specifically, we are investigating two proteins that are vital during initial vesicle formation on the Golgi (GBF1 and Arf1). Traditionally, either GBF1 or Arf1 would be overexpressed during FRAP, but we also performed dual FRAP where both proteins are overexpressed and measured simultaneously. Comparing the single versus dual FRAP measurements with the computer simulation and a simple mathematical model, we show a significant difference between the two cases. More importantly, the difference would affect the way vesicle formation is understood in cell biology. This shows overexpression can affect biochemical dynamics enough to alter our conclusion(s) from the data. |
Monday, March 2, 2020 12:15PM - 12:27PM |
B23.00006: Probing force balance in the S. pombe mitotic spindle by laser ablation Parsa Zareiesfandabadi, Mary Elting A microtubule-based machine called the mitotic spindle segregates chromosomes when eukaryotic cells divide. In the fission yeast S. pombe, which undergoes closed mitosis, the spindle forms a single bundle of microtubules inside the nucleus. During elongation, the spindle extends via antiparallel microtubule sliding by molecular motors. These extensile forces from the spindle resist compressive forces from inside the nucleus. We probe the source of this force balance via laser ablation of spindles at various stages of mitosis. We find that spindle pole bodies collapse toward each other following ablation, but that spindle geometry is often rescued, allowing spindles to resume elongation. While this basic behavior has been previously observed [1,2], many questions remain as to the timing, mechanics, and molecular requirements of these phenomena. Here, we quantify the time scales of both the relaxation and rescue responses and probe their molecular requirements. We test the possible mechanical roles of nuclear envelope-, centrosome- and microtubule-based forces. |
Monday, March 2, 2020 12:27PM - 12:39PM |
B23.00007: Theoretical framework for the description of transmembrane receptor cluster coalescence in cells Kathrin Spendier, Vasudev M Kenkre Moving boundary problems that appear in many fields of science are notoriously difficult to formulate and solve. Due to their complexity, approximation methods play an important role and are widely used to analyze such systems. We present an approximation method for moving boundaries or traps in reaction-diffusion processes that is applied to investigate coalescence of receptor clusters in mast cells. To handle the complexity, which stems from boundary growth due to particle melding, the study is divided into three parts. The first is about stationary trapping problems investigated by the standard defect technique, and the second is about a validity study of an adiabatic approximation for moving boundaries. In the last part, a coalescence theory is developed, which is based on a completely self-consistent approach. Finally, the developed theoretical framework is applied to study the kinetics of immunoglobulin E receptors (FcεRI) cluster coalescence in rat basophilic leukemia cells. |
Monday, March 2, 2020 12:39PM - 12:51PM |
B23.00008: Modeling cells as pressurized elastic shells Behzad Golshaei, Samaneh Rezvani, Octavio Albarran, Christoph F. Schmidt Animal cells and bacteria are enveloped and sealed by lipid membranes and mechanically protected by cortical polymer networks. Cells typically actively maintain a small (eukaryotic cells) or large (prokaryotic cells) positive osmotic pressure against their environment. Volume and shape regulation impact the mechanical properties of cells. The mechanical properties of cells can be probed by exerting external force and measuring cell response. To interpret micro-mechanical optical trapping experiments with suspended rounded eukaryotic cells, we developed finite element simulations and modeled cells as pressurized elastic shells. During deformation, competition between osmotic pressure resulting from compression of the cytosol and the elastic stretching of the actin cortex determines the cell response. The finite element simulations suggest that (eukaryotic) cell deformations are essentially isovolumetric. |
Monday, March 2, 2020 12:51PM - 1:03PM |
B23.00009: Probing the mechanical integrity of the mammalian k-fiber in live cells by laser ablation and speckle microscopy Marcus Begley, Elizabeth Mae Davis, Ryoma Ohi, Mary Elting When cells divide, a microtubule-based machine called the mitotic spindle delivers chromosomes to two new daughter cells. Microtubule bundles called kinetochore-fibers (k-fibers) attach chromosomes to the spindle, and forces transmitted through k-fibers ultimately segregate chromosomes. Thus, the mechanical integrity of the k-fiber is critical to accurate chromosome segregation, which in turn is essential for cell and organismal health. Yet, the k-fiber itself as a mechanical object is not well understood. We do not fully understand how or where k-fiber microtubules attach to each other along their lengths, nor what molecules mediate these connections. To address these questions, we are probing the mechanics of the k-fiber by severing it via laser ablation, and by using single-molecule speckle microscopy to analyze intra-k-fiber microtubule movements. Speckle microscopy suggests that k-fiber microtubules move poleward together as a single mechanical unit. However, splaying of the k-fiber in response to laser ablation demonstrates that these intra-k-fiber connections can be disrupted. Furthermore, initial evidence suggests more splaying after perturbation of the molecular motor kinesin Kif15, supporting its role as an inter-k-fiber crosslinker. |
Monday, March 2, 2020 1:03PM - 1:15PM |
B23.00010: 3D particle diffusion in Escherichia coli cells. Diana Valverde Mendez, Benjamin P Bratton, Joseph P Sheehan, Zemer Gitai, Joshua Shaevitz 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 diffusion of objects ranging in size from 20 to 50 nm, similar in scale to ribosomes and other macromolecular complexes in the cell. We also vary the total charge of the fluorescent proteins from -17 e to +48 e and investigate the effect on diffusion. Using specific small molecule drug treatment, we show progress towards understanding the effects of the nucleoid and cell metabolic state on the 3D diffusion of particles inside bacterial cells. |
Monday, March 2, 2020 1:15PM - 1:27PM |
B23.00011: Opto-genetic control of gene regulation in living fly embryos Anand Singh, Ping Wu, Eric Wieschaus, Jared Toettcher, Thomas Gregor Gene regulation is a hallmark of most processes in biology, in particular for cell fate decisions and patterning during early development of an organism. Precise and highly coordinated dynamic gene activity dictates the functional output in the context of complex genetic networks. In order to construct causal relationships in the programs underlying gene regulatory networks and transcription, we developed a light-inducible system to directly interfere with these programs and to quantitatively measure the cellular response in living fly embryos. Our approach allows us to precisely control transcription factor (TF) levels and their immediate response in gene expression. We show how nuclear concentration and TF residence times affect the kinetic rates and expression levels of downstream gene targets, and we test the limits of natural expression patterns by altering the shapes and strengths of the input patterns and measuring their genetic responses. The following questions will be asked: How cells utilize the differential levels of TF to make cell fate decisions? How do downstream genes respond to spatially and temporally modulated doses of TF input concentration? |
Monday, March 2, 2020 1:27PM - 1:39PM |
B23.00012: NMR and small-angle neutron scattering examination of dynamics and structure in a polymer-colloid model system directed at understanding macromolecular crowding in cells SWOMITRA PALIT, Lilin He, William A Hamilton, Arun Yethiraj, Anand Yethiraj The inside of a living cell is crowded (30 - 40% volume fraction) with many macromolecular components, so that each individual macromolecule is not necessarily highly concentrated. This unique system calls for a colloidal perspective to tease out the competing roles of size, shape, flexibility, charge, hydrodynamic interactions, and chemical specificity. |
Monday, March 2, 2020 1:39PM - 1:51PM |
B23.00013: Analysis and simulations of Bcl10 self-assembly and degradation in activated T cells Leonard Campanello, Maria Traver, Brian Schaefer, Wolfgang Losert The adaptive immune system serves as a potent and highly specific defense mechanism against pathogens. A component of this system, the effector T cell, provides rapid pathogen-clearing responses upon detecting pathogen-associated signals. Stimulation of the T cell receptor leads to a signaling cascade resulting in pathogen eradication. Bcl10, a key regulatory protein in this cascade, rapidly assembles into filaments that form the core of the signal transduction machinery; simultaneously, Bcl10 is targeted for slow degradation to ensure tight control of immune activation. Despite the importance of Bcl10 for an effective immune response, the mechanisms and timescales of its assembly and degradation are poorly understood. Here, we will provide insights into Bcl10 filament formation and degradation via image analysis and Monte Carlo simulations. Using image-based bootstrapping, we show that Bcl10 preferentially colocalizes with autophagosomes and that the spatial organization of this complex is significant for immune function. Using stochastic Monte Carlo simulations, we shed light on key Bcl10 filament dynamics, including nucleation, growth, and degradation. Together, these data provide key insights into important mechanism that regulate adaptive immunity. |
Monday, March 2, 2020 1:51PM - 2:03PM |
B23.00014: Investigating the eukaryotic CO2-fixing phase-separated organelle, the pyrenoid Guanhua He, Shan He, Martin Jonikas, Ned Wingreen In most eukaryotic algae, an organelle called the pyrenoid helps concentrate CO2 to enhance carbon fixation by the enzyme Rubisco. We recently found that in Chlamydomonas reinhardtii, the pyrenoid has liquid-like behavior including rapid condensation and dissolution during cell division. Our data suggests that the matrix is primarily composed of Rubisco and a linker protein, EPYC1. Rubisco and EPYC1 each have multiple binding sites for the other, allowing the two proteins to form a multivalent phase separation system. We showed that Rubisco and EPYC1 are sufficient to phase separate in an in vitro reconstitution experiment. Here, we measure the phase boundary in terms of concentration of both proteins, which is in the uM range. We use microscale thermophoresis (MST) to determine the dissociation constant (Kd) of EPYC1-Rubisco binding. And we use fluorescence correlation spectrometer (FCS) to determine the protein particle sizes. Combined together, our results suggest the existence of small oligomer complexes composed of EPYC1 and Rubisco in the dilute phase. Our work reveals that the stoichiometry of oligomer complexes is a key factor that regulates phase separation, which might be a general principle in multivalent phase separation system in biology. |
Monday, March 2, 2020 2:03PM - 2:15PM |
B23.00015: Dynamics of Self-Organized Organelle Transport in a Developing Macroscopic Single-Celled Organism Eldad Afik, Elliot M. Meyerowitz Caulerpa is a marine green alga exhibiting differentiated organs resembling leaves, stems and roots; while individuals can exceed a meter in size, each one is comprised of a single multinucleated giant cell. Thus, according to current understanding, the distinction between the cellular and organismal levels in Caulerpa does not exist. In turn, this challenges our intuition that morphogenesis on large scales necessitates division into cells. |
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