# Schedule for: 21w5154 - Mathematics of the Cell: Integrating Signaling, Transport and Mechanics

Beginning on Sunday, October 17 and ending Friday October 22, 2021

All times in Banff, Alberta time, MDT (UTC-6).

Sunday, October 17
16:00 - 17:30 Check-in begins at 16:00 on Sunday and is open 24 hours (Front Desk - Professional Development Centre)
17:30 - 19:30 Dinner
A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
20:00 - 22:00 Informal Gathering
In-person participants are welcome to gather in the TCPL foyer on arrival day. No BIRS staff present.
(TCPL Foyer)
Monday, October 18
07:00 - 08:45 Breakfast
Breakfast is served daily between 7 and 9am in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
08:45 - 09:00 Introduction and Welcome by BIRS Staff
A brief introduction to BIRS with important logistical information, technology instruction, and opportunity for participants to ask questions.
(TCPL 201)
09:00 - 09:40 Bill Bement: A versatile cytokinetic circuit based on Rho, F-actin, Ect2 and RGA34
Cytokinesis in animal cells is dependent on the concentration of active Rho (Rho-GTP or Rho-T) at the equatorial cell cortex, where it directs formation of the F-actin (filamentous actin) and myosin-2-rich cytokinetic apparatus. Immediately prior to and during cytokinesis, the cortex behaves as an excitable medium, generating propagating waves of Rho activity and F-actin assembly which become concentrated and amplified at the equatorial cortex by the action of the mitotic spindle. Excitable dynamics implies the existence of a circuit based on positive feedback coupled to delayed negative feedback. Previous work indicated that positive feedback during cytokinesis is based on Rho-T and Ect2 (a Rho activator), while negative feedback is somehow dependent on F-actin. Here we show that the delayed feedback is based on the GAP (Rho inactivator) RGA34: RGA34 localizes to waves that are concentrated and amplified at the equatorial cortex; RGA34 waves "chase" (follow) Rho-T waves; RGA34 colocalizes with F-actin; experimental disruption or modulation of cortical F-actin results in corresponding disruption or modulation of RGA34 distribution; and, most compellingly, coexpression of RGA34 and Ect2 in cells that are not normally excitable is sufficient to induce high amplitude waves of Rho-T and F-actin that pervade the entire cortex. Variation of the ratio of RGA34 to Ect2 produces quantitative and qualitative changes in cortical dynamics, with low ratios producing pulsed contractions and high ratios producing overtly psychedelic waves. We conclude that Rho, F-actin, Ect2 and RGA34 form the core of a versatile cortical excitability circuit that regulates diverse cortical behaviors.
(TCPL 201)
09:40 - 10:20 Andreas Buttenschoen: Spatio-temporal heterogeneities in a mechano-chemical model of collective cell migration
Abstract: Small GTPases, such as Rac and Rho, are well known central regulators of cell morphology and motility, whose dynamics also play a role in coordinating collective cell migration. Experiments have shown GTPase dynamics to be affected by both chemical and mechanical cues, but also to be spatially and temporally heterogeneous. This heterogeneity is found both within a single cell, and between cells in a tissue. For example, sometimes the leader and follower cells display an inverted GTPase configuration. While progress on understanding GTPase dynamics in single cells has been made, a major remaining challenge is to understand the role of GTPase heterogeneity in collective cell migration. Motivated by recent one-dimensional experiments (e.g. micro-channels) we introduce a one-dimensional modelling framework allowing us to integrate cell bio-mechanics, changes in cell size, and detailed intra-cellular signalling circuits (reaction-diffusion equations). Using this framework, we build cell migration models of both loose (mesenchymal) and cohering (epithelial) tissues. We use numerical simulations, and analysis tools, such as bifurcation analysis, to provide insights into the regulatory mechanisms coordinating collective cell migration. We show how local perturbations to GTPase signalling due to cell-cell interactions or tension lead to a variety of dynamics, resembling the behavior of small cell groups.
(TCPL 201)
10:20 - 10:40 Coffee Break (TCPL Foyer)
10:40 - 11:20 Garegin Papoian: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks
TBA
(Online)
11:20 - 12:00 Ajay Gopinathan: From geometric incompatibility to function: Curvature sensing with twisted filaments
Filamentous biopolymers are involved in a variety of critical cellular processes including facilitating intracellular transport, segregating genetic material and force production during motility and cell division. In this talk, I will discuss how geometrical incompatibility, such as size or curvature mismatches, between the biopolymer structure and its environment can be translated into function. As a particular example, I will describe how the frustrated interplay between the helicity of protein filaments, their elasticity and their interactions with curved surfaces can lead to novel conformational states with functional implications. Our work shows that biopolymers are inherently very sensitive to this coupling, allowing twisted filaments to sense curvature at length scales much larger than themselves. Such a coupling could be exploited for the regulation of a variety of processes such as the targeted exertion of forces, signaling, and self-assembly in response to geometric cues including the local mean and Gaussian curvatures. I will discuss recent in vivo experiments to validate our predictions and conclude with some of our latest work extending our formalism as well as future prospects.
(Online)
11:30 - 13:00 Lunch
Lunch is served daily between 11:30am and 1:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
13:00 - 14:00 Guided Tour of The Banff Centre
Meet in the Corbett Hall Lounge for a guided tour of The Banff Centre campus.
(TCPL Foyer)
14:00 - 14:20 Group Photo
Meet in foyer of TCPL to participate in the BIRS group photo. The photograph will be taken outdoors, so dress appropriately for the weather. Please don't be late, or you might not be in the official group photo!
(TCPL Foyer)
14:20 - 15:00 Ed Munro: Structural memory of filament alignment during contractile ring assembly in C. elegans embryos
During cytokinesis in animal cells, signals from the mitotic apparatus position an equatorial zone of RhoA activity which drives local assembly of actin filaments and bipolar myosin II minifilaments. These in turn reorganize to form a circumferentially array of filaments that constricts to drive cell division. But how cells rapidly build and maintain this alignment in the face of continuous turnover of filaments and motors has remained somewhat mysterious. I will describe our recent efforts to resolve this mystery through a combination of high speed TIRF microscopy, single molecule imaging, particle tracking analysis and computational modeling. We have found that locally compressive flows, driven by myosin II, reorient filaments to build alignment. However, single filaments turn over far too fast for reorientation of single filaments to do this job. Instead, we find that long filaments assembled by formins use existing filaments as templates to orient their growth. We refer to this process as filament guided filament assembly (FGFA). We show that FGFA endows small filament bundles within the cortex with a structural memory of filament orientation; by tuning the strength of FGFA, the duration of this memory can be made arbitrarily long relative to the lifetimes of individual filaments. In particular, we show that FGFA is sufficiently strong to explain the rapid emergence and stable persistence of orientation in the C. elegans contractile ring. I will also discuss the implications of these findings for the maintenance of cortical actin network architecture and the microscopic origins of self-organized contractility.
(Online)
15:00 - 15:40 Orion Weiner: Self-organization of actin regulators guides cell morphogenesis
To control their shape and movement, cells leverage nucleation promoting factors (NPFs) to regulate when and where they polymerize actin. Despite having similar upstream activators and downstream effectors, different NPFs organize dramatically different membrane deformations ranging from finger-like filopodia to sheet-like lamellipodia to endocytic membrane invaginations. We seek to understand the local rules that underlie these disparate morphological programs. We have uncovered different patterns of protein oligomerization and geometry-sensing that regulate two important regulators of cell movement. The WAVE complex oligomerizes into a saddle-sensing linear template that could explain expanding self-straightening lamellipodia. In contrast, the homologous NPF WASP repurposes an arrested endocytic-like program to connect substrate topology to cell polarity. Our work suggests how feedback between cell shape and actin regulators instructs cell morphogenesis.
(Online)
15:40 - 16:00 Coffee Break (TCPL Foyer)
16:00 - 16:40 Adriana Dawes: Dynein localization and pronuclear movement in the early C. elegans embryo
Asymmetric cell division, where daughter cells inherit unequal amounts of specific factors, is critical for development and cell fate specification. In polarized cells, where specific factors are segregated to opposite ends of the cell, asymmetric cell division occurs as a result of dynein-mediated centrosome positioning along the polarity axis. Early embryos of the nematode worm C. elegans polarize in response to fertilization, and rely on proper centrosome positioning for cell fate specification and development. Depletion of certain proteins results in defective movement of centrosomes and the associated pronuclear complex in the early embryo. We developed a novel measure to characterize the oscillatory nature of these movement defects, and demonstrated that dynein localization is not impaired in the presence of wobble. Stochastic and continuum modeling of the centrosome and pronuclear complex movement is being used to identify possible mechanisms responsible for the impaired movement.
(TCPL 201)
16:40 - 17:20 Stéphanie Portet: Transport of intermediate filaments in cells
Together with actin and microtubules, intermediate filaments (IFs) are essential components of the cytoskeleton. IF proteins self-assemble into long elastic filaments organized in networks. Intracellular transport of IFs is essential for the dynamic rearrangements of the network and is regulated by intracellular signals. Network dynamics and organization regulate IF cellular functions. In collaboration with experimentalists, we have been working on deciphering the features of the intracellular transport of IFs that results from the interplay between actin-dependent retrograde flow, and anterograde and retrograde microtubule-dependent transports driven by processive motors kinesin-1 and dynein. I will present an overview of models and data we have been developing for a few years.
(TCPL 201)
17:30 - 19:30 Dinner
A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Kinnear Center 105)
Tuesday, October 19
07:00 - 09:00 Breakfast (Vistas Dining Room)
09:00 - 09:40 William Holmes: Modeling intra-cellular insulin transport dynamics in pancreatic Beta cells
In this talk, I will discuss the role of cytoskeletal-mediated transport (by microtubules) in regulating insulin dynamics in pancreatic cells. Due to the increasing prevalence of diabetes and related disorders, understanding how individual cells regulate insulin availability and secretion in response to glucose stimulation is of utmost importance. While it has been known for decades that dysregulated microtubule dynamics alter insulin secretion, their role in insulin regulation has been murky. Here I use computational modeling to demonstrate a new mechanism by which apparently random trafficking of insulin on a random network of microtubules regulates the intra-cellular localization and availability of insulin. These results demonstrate that microtubule mediated trafficking negatively regulates insulin secretion. Accompanying experiments confirm this hypothesis and demonstrate the potential for targeting of microtubule dynamics to provide a new avenue to manipulate insulin secretion.
(TCPL 201)
09:40 - 10:20 Thomas Fai: Coarse-grained stochastic model of myosin-driven vesicles into dendritic spines
We model vesicle transport into dendritic spines, which are micron-sized structures located at the postsynapses of neurons characterized by their thin necks and bulbous heads. Recent high-resolution 3D images show that spine morphologies are highly diverse. To study the influence of geometry on transport, our model reduces the fluid dynamics of vesicle motion to two essential parameters representing the system geometry and elasticity. Upon including competing molecular motor species that push and pull on vesicles, the model exhibits multiple steady states that neurons could exploit in order to control the strength of synapses. Moreover, the small numbers of motors lead to random switching between these steady states. We describe a method that incorporates stochasticity into the model to predict the probability and mean time of translocation as a function of spine geometry.
(TCPL 201)
10:20 - 10:40 Coffee Break (TCPL Foyer)
10:40 - 11:20 Paul Bressloff: Biological pattern formation: beyond classical diffusion-based morphogenesis
A fundamental question in modern cell biology is how cellular and subcellular structures are formed and maintained given their particular molecular components. How are the different shapes, sizes, and functions of cellular organelles determined, and why are specific structures formed at particular locations and stages of the life cycle of a cell? In order to address these questions, it is necessary to consider the theory of self-organizing non-equilibrium systems. We are particularly interested in identifying and analyzing novel mechanisms for pattern formation that go beyond the standard Turing mechanism and diffusion-based mechanisms of protein gradient formation. In this talk we present three examples of non-classical biological pattern formation: (i) Transport models of cytoneme-based morphogenesis. (ii) Space-dependent switching diffusivities and cytoplasmic protein gradients in the C. elegans zygote (iii) Hybrid Turing mechanism for the homeostatic control of synaptogenesis in C. elegans.
(Online)
11:20 - 12:00 Alexandria Volkening: Modeling and topological data analysis of zebrafish patterns
Wild-type zebrafish are small fish named for their dark and light stripes, but mutant zebrafish feature variable skin patterns, including spots and labyrinth curves. All of these patterns form as the fish grow due to the interactions of tens of thousands of pigment cells in the skin. This leads to the question: how do cell interactions change to create mutant patterns? The longterm motivation for my work is to help shed light on this question and better link genes, cell behavior, and visible animal characteristics. Toward this goal, I develop agent-based and continuum models to describe cell behavior in growing 2D domains. However, my agent-based models are stochastic and have many parameters, and comparing simulated patterns and fish images is often a qualitative process. In this talk, I will overview our models and discuss how methods from topological data analysis can be used to quantitatively describe cell-based patterns and compare in vivo and in silico images.
(Online)
12:00 - 12:05 Virtual Group Photo (Online)
12:05 - 13:30 Lunch (Kinnear Center 105)
13:30 - 14:10 Padmini Rangamani: Elucidating the role of membrane tension in cellular processes using continuum modeling
Membrane tension plays a critical role in many cellular processes. Experiments using both cellular and reconstituted systems have shown that tension plays a critical role in membrane-protein interactions for curvature generation. Cellular membranes can be thought of as elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors and scaffolding proteins. These proteins are known to diffuse and aggregate in the plane of the membrane and to influence the bending of the membrane. Experiments have shown that lipid flow in the plane of the membrane is closely coupled with the diffusion and aggregation of proteins. Thus, there is a need for a comprehensive framework that accounts for the interplay between these processes. In this talk, I will discuss some recent theoretical and computational developments from my group using continuum modeling that allows for better comparison of membrane deformations with experiments. Our primary focus will be membrane trafficking, particularly endocytosis but the theoretical developments are broadly applicable to many membrane curvature generating processes. We formulate the free energy of the membrane with a Helfrich-like curvature elastic energy density function modified to account for the chemical potential energy of the proteins. We derive the conservation laws and equations of motion for this system. Finally, we present results from dimensional analysis and numerical simulations and demonstrate the effect of coupled transport processes in governing the dynamics of membrane bending, protein aggregation, and diffusion. We find that feedback between curvature and aggregation results in domains that result in membrane microdomains. This work is in collaboration with David Saintillan (UCSD, MAE).
(Online)
14:10 - 14:50 Wouter-Jan Rappel: Combining experiments and modeling to better understand chemotaxis
Many motile eukaryotic cells can respond to external chemical gradients, resulting in direct motion. During this motion, cells can use and switch between different modes of migration. To better understand these different modes, we combine experiments, that use traction force and fluorescent microscopy, and modeling. Specifically, we quantitatively determine the distribution of of actin and myosin and correlate these with traction force patterns in eukaryotic cells that move and switch between keratocyte-like fan-shaped, oscillatory, and amoeboid modes. We find that the wave dynamics of the cytoskeletal components critically determine the traction force pattern, cell morphology, and migration mode. Furthermore, we find that fan-shaped cells can exhibit two different propulsion mechanisms, each with a distinct traction force pattern. Finally, we show that the traction force patterns can be recapitulated using the computational model, which uses the experimentally determined spatio-temporal distributions of actin and myosin forces and a viscous cytoskeletal network. Our results suggest that cell motion can be generated by friction between flow of this network and the substrate. Authors: Elisabeth Ghabache, Yuansheng Cao, Yuchuan Miao*, Alex Groisman, Peter N. Devreotes*, Wouter-Jan Rappel Department of Physics, University of California, San Diego, La Jolla, California 92093, USA *Department of Cell Biology, Johns Hopkins University, Baltimore, MD, USA
(Online)
14:50 - 15:30 Ruth Baker: Quantifying the impact of electric fields on single-cell motility
TBA
(Online)
15:30 - 16:00 Coffee Break (TCPL Foyer)
16:00 - 16:40 David Odde: Cellular sensing of material stiffness and negative durotaxis
The ability of cells to sense the mechanical stiffness of their environment is critical to their function, and allows cells to migrate in a stiffness-dependent manner. In my talk I will describe how we have developed a computational motor-clutch model for the biophysics of cell migration and applied it to glioma cell migration. Whereas an extensive literature across a wide range of cell types demonstrates the phenomenon of durotaxis – the tendency of cells to migrate toward mechanically stiffer environments – we demonstrate that our motor-clutch cell migration model (Bangasser et al., Nat Comm, 2017) predicts “negative durotaxis” – biased migration toward softer environments – which we confirm experimentally for the first time. Also, we used the model to mechanically phenotype genetically induced glioma mouse models. The biophysical modeling and experiments help point us toward potentially new therapeutic strategies.
(TCPL 201)
16:40 - 17:20 Daniel Coombs: A hierarchy of hidden Markov methods for single particle tracking
Hidden Markov models (HMM) provide a powerful tool for analysis of particle mobility. Briefly, labelled objects are assumed to exist in discrete states, where each state has a distinct mode of mobility - commonly, Brownian diffusion with a state-dependent diffusivity. In this talk, I will describe a set of HMM, beginning with simplest, two-state model, developing to many states, and discussing how we can allow for experimental positional uncertainties. I’ll show results using simulated data, as well as using experimental data for motion of membrane receptors on the surfaces of lymphocytes. The methods shown in this talk were developed jointly with Raibatak Das, Jennifer Morrison, Suzanne ten Hage and especially Rebeca Cardim Falcao.
(TCPL 201)
17:30 - 19:30 Dinner (Vistas Dining Room)
Wednesday, October 20
07:00 - 09:00 Breakfast (Vistas Dining Room)
09:00 - 09:40 Melissa Rolls: Mechanisms and modeling of neuronal microtubule dynamics and polarity
The polarity and stability of the microtubule cytoskeleton are critical in supporting long-range directed transport of cellular cargo and long-term survival of neurons. However, microtubules also need to be dynamic and reorganize in response to injury events. Using live imaging and genetics, multiple mechanisms that contribute to the primarily minus-end-out filament organization in Drosophila dendrites have been identified. These include local microtubule nucleation, quality control of new microtubules and microtubule steering. Our objective is to understand how these complex mechanisms ensure both healthy function over long time periods and dramatic rearrangement in response to injury. To this end, we propose a spatially-explicit mathematical model of the dendritic microtubule system in Drosophila neurons. The stochastic modeling framework includes microtubule turnover dynamics and a spatial multiscale model that captures microtubule organization in branched dendrites. The model predicts the maintenance of polarity in simulated microtubule populations. Paired with biological experiments, this modeling framework has the potential to provide insight into the impact of turnover parameters as well as of individual polarity control mechanisms, such as steering and nucleation, on polarity and dynamics in Drosophila dendrites. Joint talk with Veronica Ciocanel.
(Online)
09:40 - 10:20 Peter Kramer: Spatial Parameterization of Attachment Processes in Molecular Motor-Cargo Systems
Intracellular transport is conducted largely by molecular motor proteins which process along cytoskeletal filaments, from which they can attach or detach. We describe an analytical framework to characterize motor attachment or reattachment rates to microtubules as a function of the physical and geometric properties of the motor, the cargo to which it is attached, and possibly a second motor attached to the same cargo and a microtubule. The biophysical model is coarse-grained at the level of the macromolecular motors and formulated in terms of stochastic differential equations, allowing for rotation of the cargo and nonlinear force laws for the motor-cargo tether. Various asymptotic approximations based on small target'' first passage time calculations are possible depending on the relationship of the motor-cargo tether length, the distance between microtubules, whether the cargo has a rigid or lipid membrane surface, and the initial configuration of the motor and cargo relative to the microtubules. The same methodology also allows the computation of the probability distribution for which nearby microtubule a motor will attach next. These results have potential application for modeling motor attachment in engineered systems where, for example, the cargo is introduced in a geometrically controlled way by optical trap or flow.
(Online)
10:20 - 10:40 Coffee Break (TCPL Foyer)
10:40 - 11:20 Christine Payne: Intracellular transport of lysosomes decreases in the perinuclear region: Insights from changepoint analysis
Lysosomes are membrane-bound organelles responsible for processing endocytic molecules, particles, and viruses, phagocytic destruction of pathogens, and the cellular housekeeping of autophagy. These cellular functions require intracellular transport. A collaborative team led by Prof. Christine Payne in the Department of Mechanical Engineering and Materials Science at Duke University and Prof. Scott McKinley in the Department of Mathematics at Tulane University, enabled by the NSF-Simons Foundation Southeast Center for Mathematics and Biology (SCMB), has investigated the intracellular transport of these organelles. We use fluorescence microscopy to characterize the motion of lysosomes as a function of intracellular region, perinuclear or periphery, and lysosome diameter. Single particle tracking data is complemented by changepoint identification and analysis of a mathematical model for state-switching. We classify motion as motile or stationary and then study how lysosome location and diameter affects the proportion of time spent in each state and the speed during motile periods. We find that the proportion of time spent stationary is strongly region-dependent with significantly decreased motility in the perinuclear region. Increased diameter only slightly decreases speed. These results show that intracellular region, rather than lysosome diameter, is a major factor in the motion of lysosomes. Overall, these results demonstrate the importance of decomposing particle trajectories into qualitatively different behaviors before conducting population-wide statistical analysis. This approach shows that intracellular region, which is not regularly included as a factor in studies of intracellular transport, is a major factor.
(Online)
11:20 - 12:00 Scott McKinley: On the use and misuse of Bayesian methods for uncertainty quantification
An intrinsic challenge in studying intracellular transport is that the time scale of experimental observation is far shorter than the time scales associated with many biological events of interest. This is why mathematical modeling is so important -- making good predictions is impossible without good models -- but it can be difficult to associate predictions with credible quantifications of uncertainty. In this talk, in which I will review a Bayesian approach to communicating predictions with uncertainty, visiting some successes and failures I’ve experienced along the way. One issue that arises is that a “fully principled” UQ approach can be computationally prohibitive, and can even introduce biophysically unrealistic results. Some compromises must be made, but where and how are open for debate. My hope is to open a conversation within the workshop about how others view the communication of uncertainty, and whether and how we should teach these methods in our graduate programs.
(Online)
11:30 - 13:30 Lunch (Vistas Dining Room)
12:00 - 12:30 Lightning talks
Short 2-minute presentations from workshop participants
(Online)
13:30 - 14:30 Gather Town social/Poster session (Online)
14:30 - 17:30 Free Afternoon (Banff National Park)
17:30 - 19:30 Dinner (Vistas Dining Room)
19:30 - 20:10 Ruth Baker: Test lecture - ignore
Testing automated video system
(Online)
Thursday, October 21
07:00 - 09:00 Breakfast (Vistas Dining Room)
09:00 - 09:40 Alex Mogilner: Rapid and accurate assembly of mitotic spindle
Mitotic spindle is a remarkable molecular machine segregating chromosomes and positioning cytokinetic ring prior to cell division. The spindle self-assembles from centrosomes, microtubules and chromosomes very rapidly and accurately. For decades, the so-called search-and-capture model of this self-assembly was dominant. This model posited that the microtubules randomly probe the cell space until, by chance, all chromosomes are connected to the spindle. Recent data puts this model in doubt. I will show that both current data and stochastic computational model argue that a much more deterministic process of polarity sorting in a complex microtubule-motor system accounts for the rapid and accurate assembly of the spindle. Notably, both centripetal chromosome transport, and chromosome connection mechanics are the key to speed and accuracy.
(Online)
09:40 - 10:20 Samuel Isaacson: Stochastic Reaction-Drift-Diffusion Methods for Studying Cell Signaling
Particle-based stochastic reaction-diffusion (PBSRD) models are one approach to study biological systems in which both the noisy diffusion of individual molecules, and stochastic reactions between pairs of molecules, may influence system behavior. They provide a more microscopic model than deterministic reaction-diffusion PDEs or stochastic reaction-diffusion SPDEs, which treat molecular populations as continuous fields. The reaction-diffusion master equation (RDME) and convergent RDME (CRDME) are lattice PBSRD models, with the latter providing a convergent approximation to the spatially-continuous volume-reactivity PBSRD model as the lattice spacing is taken to zero. In this talk I will present several generalizations of the RDME and CRDME to support spatial transport mechanisms needed for resolving spatially-distributed cellular signaling processes in general geometries, including drift due to background potentials, interaction potentials between molecules, and continuous-time random walks to approximate molecular transport on surfaces.
(Online)
10:20 - 10:40 Coffee Break (TCPL Foyer)
10:40 - 11:20 Fred Chang: Role of osmotic forces in determining the size of the nucleus
The size of the nucleus scales with cell size so that the nuclear-to-cell volume ratio (NC Ratio) is maintained during cell growth. The mechanism responsible for this scaling is still mysterious. Nuclear volume is not determined merely by DNA amount, but is influenced by factors such and nuclear transport and nuclear envelope mechanics. Here, we develop a quantitative model for nuclear size control and scaling based upon colloid osmotic pressure that is determined by numbers of macromolecules in the nucleoplasm and cytoplasm. Osmotic shift experiments show that in the fission yeast, the nucleus behaves as an ideal osmometer. Perturbations that disrupt the relative numbers of macromolecules in each compartment lead to predictable changes in the NC ratio. Further this model provides an explanation for NC ratio homeostasis behavior. These studies highlight the primary role of osmotic forces that determine the size of the nucleus and possibly other organelles.
(Online)
11:20 - 12:00 Maitreyi Das: Spatiotemporal regulation of Cdc42 activity organizes cytokinetic events
Cell polarization is a fundamental process by which proteins asymmetrically localize to their functional site in response to a signal thus determining cell shape. One of the major regulators of polarization is the highly conserved small GTPase Cdc42. Cdc42 is activated at the sites of cell growth in a dynamic manner. In fission yeast, active Cdc42 displays an anti-correlated oscillatory pattern that determines cell polarity and dimension. This oscillatory behavior of Cdc42 activation is an outcome of self-organizing positive and time-delayed negative feedback loops. Cdc42 is also activated at the division site during cytokinesis, but here it does not display a similar oscillatory pattern. Using the fission yeast model system, we have shown that Cdc42 at the division site promotes polarization during cytokinesis. We find that once the actomyosin ring is assembled, membrane trafficking at specific sites and times enables different steps in cytokinesis. Membrane trafficking events allow delivery of membrane and enzymes necessary for furrow formation and septum/cell wall synthesis, respectively. Later, trafficking is also required for the delivery of glucanases that promote cell separation. It is not clear how the cell spatiotemporally organizes these precise membrane trafficking events during cytokinesis. We find that the Cdc42 activation pattern at the division site matches that of these trafficking events. This Cdc42 activity pattern spatiotemporally regulates membrane trafficking during cytokinesis. Our data indicate that this pattern arises as a result of the interplay between the positive and negative regulators of Cdc42 which in turn enables spatiotemporal organization of cytokinetic events. Understanding how the same regulators give rise to distinct activation patterns at the cell ends compared to the division site will help to understand how cells spatiotemporally organize complex multi-step events such as cytokinesis and polarized growth.
(Online)
11:30 - 13:30 Lunch (Vistas Dining Room)
13:30 - 14:10 Timothy Elston: Modeling polarity establishment
TBA
(Online)
14:10 - 14:50 Dimitrios Vavylonis: Cytoskeletal and membrane flows for cell polarization and motility
The ability of cells to polarize, move by crawling, or divide, requires coordinated interactions of the cytoskeleton with membranes as well as with signaling systems organizing on membranes. Predictive models of these mechanisms of subcellular organization requires accounting of how interactions at the molecular level lead to collective behavior involving patterns, flows and forces over cellular scales. I will describe two recent examples of how mathematical and computational modeling by our group was combined with experiments by collaborators to make progress on understanding membrane and cytoskeletal flow and turnover at regions of cell extension. In the first example, we showed that polarized exocytosis causes lateral membrane flows away from regions of membrane insertion. In rod-shaped fission yeast cells, this causes membrane-bound inhibitors of Cdc42 with sufficiently low diffusion and/or detachment rates to deplete, thus patterning the growing cell tip in way that establishes its rod shape. In the second example, we looked at actin cytoskeleton retrograde flows in regions of cell protrusion. Using filament-level kinetic and mechanical models we provided an explanation of how distributed turnover through severing and annealing generates structural changes of Arp2/3-complex dendritic networks. We also provide a filament-level implementation of the clutch mechanism and force transmission through the whole lamellipodial actin network flowing over focal adhesions.
(Online)
14:50 - 15:30 Grace McLaughlin: Modeling Asynchronous Nuclear Division
Multinucleate cells are common in biology, with examples including muscle cells, placenta, and fungi. Despite this, many aspects of their cell biology are not well understood. Dividing nuclei residing in a common cytosol would be expected to synchronize, as the oscillating levels of cell cycle regulators from each nucleus should in theory entrain neighbors. However, in the multinucleate fungus Ashbya Gossypii, spatially neighboring nuclei have been observed to divide out of sync. Here we mathematically model Ashbya nuclei as a dynamically growing system of coupled phase oscillators to determine possible mechanisms that could lead to asynchronous division. Nuclear movement in space is modeled to capture core features of Ashbya nuclear dynamics, including both repulsion of and rearrangement with neighbors. We study the effects of mobility, cytosolic compartmentalization, inhibitory signals, and noise on transient phase dynamics. To compare the model with experimental results, we develop a nuclear tracking pipeline with the aim of tracking nuclei during bypassing events, identifying nuclear division, and linking nuclei into hyphae. Initial results suggest a combination of locally and globally acting mechanisms might be at play leading to the observed dynamics in Ashbya.
(Online)
15:30 - 16:00 Coffee Break (TCPL Foyer)
16:00 - 16:40 Jian Liu: Spatial control over near-critical-point operation ensures fidelity of ParABS-mediated DNA partition
In bacteria, most low-copy-number plasmid and chromosomally encoded partition systems belong to the tripartite ParABS partition machinery. Despite the importance in genetic inheritance, the mechanisms of ParABS-mediated genome partition are not well understood. Combining theory and experiment, we provided evidence that the ParABS system – DNA partitioning in vivo via the ParA gradient-based Brownian ratcheting – operates near a transition point in parameter space (i.e., a critical point), across which the system displays qualitatively different motile behaviors. This near-critical-point operation adapts the segregation distance of replicated plasmids to the half-length of the elongating nucleoid, ensuring both cell halves to inherit one copy of the plasmids. Further, we demonstrated that the plasmid localizes the cytoplasmic ParA to buffer the partition fidelity against the large cell-to-cell fluctuations in ParA level. The spatial control over the near-critical-point operation not only ensures both sensitive adaption and robust execution of partitioning, but also sheds light on the fundamental question in cell biology: How do cells faithfully measure cellular-scale distance by only using molecular-scale interactions?
(Online)
16:40 - 17:20 Will Hancock: The role of the fluid lipid bilayer in kinesin-driven vesicle transport
Most cargo carried by kinesin motors are membrane bound, which has implications for motor-based transport. We are investigating the role of membrane fluidity in kinesin-based transport using two geometries – a supported lipid bilayer and free vesicles. From attaching motors to a supported lipid bilayer, we can estimate the effect of the membrane on motor on- and off-rates. By taking these values, we can interpret our vesicle experiments where we find that run length increases with increasing motor numbers. Notably, clustering motors enhances the motor run length, showing that the geometry of motor attachment to lipid bilayers may be a regulator of bidirectional transport.
(Online)
17:30 - 19:30 Dinner (Vistas Dining Room)
Friday, October 22
07:00 - 09:00 Breakfast (Vistas Dining Room)
09:00 - 09:40 Khanh Dao Duc: Impact of ribosomes on translation across scales and new metrics for biological shape analysis
TBA
(TCPL 201)
09:40 - 10:20 Jay Newby: Resolving spatial heterogeneity of the cytoplasm in living cells
Despite being one of the fundamental cell structures, we know surprisingly little about the cytosol. Its physical properties are difficult to measure due to technical challenges: the means of spatially resolving viscosity, elasticity, flow, crowding, and confinement within cells that fluctuate and grow. Changes in macromolecular crowding can directly influence protein diffusion, reaction rates, and phase separation. I will discuss new particle tracking tools and how we use them to quantitatively measure the physical state of the cytosol by studying the three-dimensional stochastic motion of genetically expressed fluorescent nanoparticles (GEMs). Using these particle probes, we find that the physical properties of the cytosol vary significantly within and between cells, indicating that the fundamental state of the cytosol is a key source of heterogeneity within genetically identical cells.
(TCPL 201)
10:20 - 10:40 Coffee Break (TCPL Foyer)
10:40 - 11:20 Tom Chou: Biophysics of X-inactivation and integration site T cell populations in HIV-infected individuals
TBA
(Online)
11:20 - 12:00 Carlos Floyd: Dissipation and large mechanical energy fluctuations during cytoskeletal self-organization
The actin-based cytoskeleton is a polymer network that plays an essential role in cell biology. It is also an example of biological active matter, consuming chemical energy at a local scale to produce directed motion and do mechanical work. While cytoskeletal energy transduction has long been known to occur, it has been a significant challenge to say anything quantitative about this far-from-equilibrium process due to the difficulty of making the necessary experimental measurements. To address this, we developed a high-resolution computational method to quantify chemical and mechanical energy changes during simulated cytoskeletal self-organization using the software package MEDYAN. We will discuss applications of this tool to measure the thermodynamic efficiency of mechanical stress generation, as well as the time-dependent dissipation rates. We will also discuss the recent experimentally discovered phenomenon of large earthquake-like cytoskeletal motions, called “cytoquakes.” Our in silico investigation of this phenomenon explores the connection between anomalous energy fluctuations and mechanical stability in cytoskeletal networks, and we propose that these large fluctuations imply that the cell is highly attuned to respond to a changing local environment.
(Online)
11:30 - 12:00 Checkout by 11AM
5-day workshop participants are welcome to use BIRS facilities (BIRS Coffee Lounge, TCPL and Reading Room) until 3 pm on Friday, although participants are still required to checkout of the guest rooms by 11AM.
(Front Desk - Professional Development Centre)
12:00 - 13:30 Lunch from 11:30 to 13:30 (Vistas Dining Room)