Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session Y65: Biological Navigation and OrientationFocus Undergraduate
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Sponsoring Units: DBIO Chair: Adam Fine, Yale Univ Room: BCEC 260 |
Friday, March 8, 2019 11:15AM - 11:27AM |
Y65.00001: ABSTRACT WITHDRAWN
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Friday, March 8, 2019 11:27AM - 11:39AM |
Y65.00002: Measured effect of boundary distance on flagellar motor torque Bruce Rodenborn, Mackenzie Conkling, Cesar Romero, Philip Lockett Darnton et al. (2007) used resistive force theory to derive experimental measurements of the torque generated by bacterial motors in free swimming Escherichia coli. Recent reports have found similar torque values using both boundary element methods and slender body theory to model flagella swimming near a boundary (Das et al. 2018). Such numerical methods have also been used to model constrained bacteria swimming near a boundary, where their flagella act as micropumps (Dauparas et al., 2018). We use scaled macroscopic experiments to directly measure the torque on constrained, pumping flagella as a function of boundary distance. The helical flagella have a diameter ≈12 mm and are immersed in a fluid with viscosity 105 times that of water to ensure the Reynolds number in the experiments is much less than unity, just as in the bacterial experiments. We compare our nondimensionalized values to the numerical data and find good agreement, particularly in the dependence of motor torque on boundary distance. We also report a similar functional dependence of propulsive force measurements as a function of boundary distance. |
Friday, March 8, 2019 11:39AM - 11:51AM |
Y65.00003: Bacteria push the limits of sensory precision to navigate dynamic chemical gradients Douglas Brumley, Francesco Carrara, Andrew Hein, Yutaka Yawata, Simon Levin, Roman Stocker The limited precision of sensory organs places fundamental constraints on organismal performance. An open question, however, is whether organisms are routinely pushed to these limits, and how limits might influence interactions between populations of organisms and their environment. By combining a method to generate dynamic, replicable resource landscapes, high-speed tracking of freely moving bacteria, a new mathematical theory, and agent-based simulations, we show that sensory noise ultimately limits when and where bacteria can detect and climb chemical gradients. Our results suggest the typical chemical landscapes bacteria inhabit are dominated by noise that masks shallow gradients, and that the spatiotemporal dynamics of bacterial aggregations can be predicted by mapping the region where gradient signal rises above noise. |
Friday, March 8, 2019 11:51AM - 12:03PM |
Y65.00004: A theory of searching for a target with partial information Gautam Reddy, Massimo Vergassola Animals often need to find and navigate to distant targets, such as food, mates or prey, using partial information about their location. Search algorithms that deal with such scenarios have been proposed, but there is no theoretical framework that offers a standard baseline to compare the search efficiency of different algorithms. In this work, we propose a general theoretical framework to describe the task of a decision-making agent searching for a distant target emitting noisy cues. Within this framework, we define a notion of an `asymptotically optimal' search algorithm and show how its performance produces a lower bound to the expected cost of any other algorithm. We demonstrate how the optimal decision boundaries and the corresponding PDFs of search times can be computed in a simplified one-dimensional search task, and compare them to those of a previously proposed `Infotaxis' algorithm. Generic features of searching in higher dimensions are discussed. |
Friday, March 8, 2019 12:03PM - 12:15PM |
Y65.00005: Cell decision making at a microfluidic fork Vamsi Spandan, Chon U. Chan, L Mahadevan Many cell types, such as white blood cells, undergo directed migration during wound healing, development and immune response. A simple paradigm for this is related to the aphorism attributed to Yogi Berra "When you come to a fork, take it” - so that one can ask what happens when an active cell comes to a junction in a vasculature? Since the paths may have different mechanical resistance and/or chemokine concentrations, how does the cell respond by integrating multiple signals across different spatial-temporal scales and reject transient noise? We use a combination of numerical simulations and microfluidic experiments to understand the mechanochemistry of cellular decision-making at a confined bifurcation junction. The cell is modelled as a deformable, active acto-myosin cortex surrounding a fluid volume, with active stresses which are a function of the local hydrodynamic and chemical cues. We show how the system shows a range of phenomena reminiscent of critical slowing down, and noise-induced tipping, and compare the results with experiments on single cells moving through a confined microfluidic fork. |
Friday, March 8, 2019 12:15PM - 12:27PM |
Y65.00006: Variance Adaptation in Navigational Decision Making Jason Wolk, Ruben Gepner, Digvijay S Wadekar, Sophie Dvali, Marc H Gershow Sensory systems relay information about the world to the brain, which enacts behaviors through motor outputs. To maximize information transmission, sensory systems discard redundant information through adaptation to the statistics of the environment. The behavioral consequences of sensory adaptation to environmental variance have been largely unexplored. We study how larval Drosophila adapt sensory-motor computations underlying navigation to changes in the variance of visual and olfactory inputs. We show that variance adaptation can be characterized by rescaling of the sensory input and that for both visual and olfactory inputs, the temporal dynamics of adaptation are consistent with optimal variance estimation. In multisensory contexts, larvae adapt independently to variance in each sense, and portions of the navigational pathway encoding mixed odor and light signals are also capable of variance adaptation. Our results suggest multiplication as a mechanism for odor-light integration. |
Friday, March 8, 2019 12:27PM - 12:39PM |
Y65.00007: Individual and Automatic Training and Assay of Learned Navigational Behaviors in Drosophila larva Amanda Lesar, Javan MF Tahir, Marc H Gershow Previous studies of olfactory learning in Drosophila larva show larva can learn through classical conditioning. While behavioral responses of trained larva have been studied, neural responses of freely moving, trained larva are unexplored. Previous training experiments present larva population with an odor and reinforcer in a small number of training trials, then allow larvae to make a decision in the presence of odor without reinforcer once. We develop a chamber which involves rigorous training and testing. The Y maze training chamber allows larva to make a decision, turn around, and go back to Y intersection to quickly make another decision, allowing us to study large number of decisions in short times in individual larva. We will study neural responses of trained versus untrained larva, while larva is making decisions, which can help us to connect stimulus, behavioral responses, and neural activity. We will present initial results for olfactory training of individual larva. |
Friday, March 8, 2019 12:39PM - 12:51PM |
Y65.00008: Internal bias vs. external sensory cues: the role of "handedness" in navigation decisions of invertebrate model systems Mason Klein, Anggie Ferrer, Rowanne Ali, Joshua Forer, Joseph Shomar, Kyobi Skutt-Kakaria, Zachary Werkoven, Benjamin de Bivort How do the internal properties of individual animals combine with external environmental stimuli to produce a physical output? Answering this is important for understanding how the brain functions, and we examine the question using simple invertebrate animals, the Drosophila larva and C. elegans. Both animals have well-mapped brain circuits and limited behavioral repertoires, and exhibit exploratory behavior as they search for food, while at the same time responding to external stimuli. We focus on one specific internal property, the tendency of an animal to turn leftward or rightward (“handedness”). We find statistically significant bias in individual turning and drifting directions, but that turn and drift handedness are uncorrelated. This lack of correlation explains why even strongly left- or right-turning crawlers on average have similar diffusion rates as unbiased turners. Both handedness types are also weakly persistent, with frequent shifts to new biases. |
Friday, March 8, 2019 12:51PM - 1:03PM |
Y65.00009: Development of an automated system for long-term observation of navigational behavior in D. melanogaster larvae. James Yu, Maria Paz, Dave Zucker, Mason Klein, Vivek Venkatachalam Navigational behavior in an animal can be modified due to learning, and can exhibit variations between individuals to create behavioral phenotypes. To achieve high precision and reliability for either of these phenomena, observations of individual animals must be over long timescales (10-100% of a lifetime). This can be difficult to carry out manually, so we implement and demonstrate an automated approach to achieve new orders of magnitude in precision and experimental duration with both free and biased roaming Drosophila melangaster larvae. We modify a 3D printer system to automatically maintain exploratory behavior while confining the animals within the experiment area via a “pick-and-place” mechanism. Here, we demonstrate the ability of this system to quantify and observe significant changes in larval run speed, turn rate, and turn handedness over experimental durations of several hours, indicative of some previously unexamined behavioral adaptations and mechanisms in learning and memory. We will continue to further exploit its high customizability to explore other creative applications for the robotic system, such as adapting the system for experiments with C. elegans and other model organisms. |
Friday, March 8, 2019 1:03PM - 1:15PM |
Y65.00010: Mechanisms of Cell Migration through Size-Limiting Environments Pei-En Chou, Taeyoon Kim Cells can migrate through a basement membrane (BM) which is a highly dense network with very small pores. It has been hypothesized that such migration occurs via either protease degradation or force-induced deformation of BM. A recent experiment demonstrated that breast cancer cells without the ability of protease degradation can invade into a very dense network, implying the important role of the mechanical deformation of BM. In this study, using an agent-based computational model, we investigated how a cell can invade into a dense network. We evaluated the extent of invasion with various properties of the cell and the BM. We found that the cell exhibits quite different invasive behaviors depending on conditions. If the BM has high stiffness, the cell deforms the BM slightly and maintains a relatively round cell shape. By contrast, if the BM also has viscoplastic properties, the cell can invade much deeper by forming a narrow space to migrate, resulting in a highly elongated cell shape. These results are similar to recent experimental observations and provide insights into understanding how a cell migrates through size-limiting environments during physiological processes. |
Friday, March 8, 2019 1:15PM - 1:27PM |
Y65.00011: Chemotaxis of Spatially Patterned T cell Populations near 3D Printed Tumors Cameron Morley, Ginger Moore, Catherine Flores, Duane Mitchell, Thomas Angelini Priming T cells with tumor RNA triggers an immune response that drives them toward the corresponding tumors. The efficacy of these treatments have been promising in the mouse model, however the fundamental driving mechanisms behind the T cells’ targeting tumors is still being investigated. To study the spatiotemporal relationships between T cell populations and nearby tumors, we employ a method of 3D bioprinting into a bed of jammed microgels. With this capability, we can systematically study chemotactic responses of the T cells to the tumor by printing radially symmetric Saturn-like structures of which the center is made of mouse glioma and the rings are made of T cells. Data on the temporal evolution of T cells targeting the tumor will be shown, in which biased motion toward the tumor correlates with a diffusion time for cytokines to leave the tumor and trigger T cell targeting. This spatiotemporal relationship allows the determination of the cytokine diffusion coefficient. |
Friday, March 8, 2019 1:27PM - 1:39PM |
Y65.00012: Motility Characteristics of Maze Navigating Fibroblasts N. G. Hallfors, Z. Husain, J. Teo, G. Alhusein, D. Ruta, A. F. Isakovic Micropatterned substrates, in the form of mazes, are utilized to study cell migration. Highly motile cells such as fibroblasts rely on complex combination of forces exerted by the surrounding environment and neighboring cells to achieve motion. Substrate stiffness and topology of the patterned maze, together with the cell-cell neighbor interaction are shown to enhance or inhibit cells’ self-propulsive behavior. Fluorescence imaging was used to quantify kinematics of the contractile motion of fibroblasts. It is shown that the density of cell population is a critical variable, and that, for sufficiently high densities, cells appear to self-organize into groups that move around (that is “solve the maze”) in qualitatively different manner we termed “rule following” and “cheating”. The motility analysis shows that Hurst exponent of cell dynamics shows a spread of values, indicating that only a fraction of cells follows near-diffusive dynamics, with other, non-diffusive modes of motion being clearly present as well. Similarly, the motility index and chemotactic index analysis show qualitatively more than one mode of cells. |
Friday, March 8, 2019 1:39PM - 1:51PM |
Y65.00013: Development of flow-less linear gradient microfluidic devices Dragos Amarie, Arturo Ruben Diaz, Ileene Ashley Diaz, Dwayne G. Stupack Our previous work showed that by splitting and recombining the input flows through a combination of bifurcated and trifurcated channels one can generate a linear chemical gradient across a microfluidics chamber. However, when such devices are meant to study cell migration one must consider that physical factors of the microenvironment have influences in regulating cell fate. Such biomechanical cues have gained significant attention in recent years for their roles in defining fundamental cell properties, including motility, chemotaxis and migration. One such factor is the mechanical stress introduced by the flow in the gradient chamber that induces shear stress thus impacting the migration patterns. In this work we present a microfluidics device that generates highly linear chemical gradients into a cell culture chamber that is separated, flow-wise, from the gradient chamber and any investigated live cells will not experience any confounding fluid flows. The slope and the offset of the gradient can be manipulated with respect to experimental needs to enhance migration. |
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