Seminars

Cryopreservation constrains manufacturing and clinical delivery of immune cells such as NK and T cells. DMSO protects against freezing but becomes toxic at physiological temperatures; associated infusion morbidity can require washing or divided dosing that diminishes therapeutic effectiveness. This talk presents an alternative in which reversible, cytocompatible hydrogels encapsulate cells before freezing without DMSO. The speaker examines evidence that encapsulation cushions osmotic stress, suppresses kinetic and phase transitions, and reduces injury caused by extracellular ice growth and fusion. The discussion covers recovery efficiency, function after thawing, control of biological stress responses, and the challenges of extending the approach to clinical-scale cell preservation.

Cells and microorganisms are motile, yet the stationary nature of conventional microscopes impedes comprehensive, long-term behavioral and biomechanical analysis. The limitations are twofold: a narrow focus permits high-resolution imaging but sacrifices the broader context of organism behavior, while a wider focus compromises microscopic detail. This trade-off is especially problematic when investigating rapidly motile ciliates, which often have to be confined to small volumes between coverslips affecting their natural behavior. To address this challenge, we introduce Trackoscope, an 2-axis autonomous tracking microscope designed to follow swimming organisms ranging from 10μm to 2mm across a 325 square centimeter area for extended durations—ranging from hours to days—at high resolution. Utilizing Trackoscope, we captured a diverse array of behaviors, from the air-water swimming locomotion of Amoeba to bacterial hunting dynamics in Actinosphaerium, walking gait in Tardigrada, and binary fission in motile Blepharisma. Trackoscope is a cost-effective solution well-suited for diverse settings, from high school labs to resource-constrained research environments. Its capability to capture diverse behaviors in larger, more realistic ecosystems extends our understanding of the physics of living systems. The low-cost, open architecture democratizes scientific discovery, offering a dynamic window into the lives of previously inaccessible small aquatic organisms.

The cytoskeleton has the remarkable ability to self-organize into active materials which underlie diverse cellular processes ranging from motility to cell division. Actomyosin is a canonical example of an active material, which generates cellularscale contractility in part through the forces exerted by myosin motors on actin filaments. While the molecular players underlying actomyosin contractility have been well characterized, how cellular-scale deformation in disordered actomyosin networks emerges from filament-scale interactions is not well understood. In this talk, I’ll present work done in collaboration with Sebastian Fürthauer and Nikta Fakhri addressing this question in vivo using the meiotic surface contraction wave seen in oocytes of the bat star Patiria miniata as a model system. By perturbing actin polymerization, we find that the cellular deformation rate is a nonmonotonic function of cortical actin density peaked near the wild type density. To understand this, we develop an active fluid model coarse-grained from filament-scale interactions and find quantitative agreement with the measured data. The model makes further predictions, including the surprising prediction that deformation rate decreases with increasing motor concentration. We test these predictions through protein overexpression and find quantitative agreement. Taken together, this work is an important step for bridging the molecular and cellular length scales for cytoskeletal networks in vivo.

The rising and setting of the sun is accompanied by changes in both the irradiance and the spectral distribution of the sky. Since the discovery of intrinsically photosensitive retinal ganglion cells (ipRGCs) 20 years ago, considerable progress has been made in understanding melanopsin's contributions to encoding irradiance. Much less is known about the cone inputs to ipRGCs and how they could encode changes in the color of the sky. I will summarize our recent connectomic investigation into the cone-opponent inputs to primate ipRGCs and the implications of this work on our understanding of circadian photoentrainment and the evolution of color vision.

Fly Escape Behaviors: Flexible and Modular We have identified a set of escape maneuvers performed by a fly when confronted by a looming object. These escape responses can be divided into distinct behavioral modules. Some of the modules are very stereotyped, as when the fly rapidly extends its middle legs to jump off the ground. Other modules are more complex and require the fly to combine information about both the location of the threat and its own body posture. In response to an approaching object, a fly chooses some varying subset of these behaviors to perform. We would like to understand the neural process by which a fly chooses when to perform a given escape behavior. Beyond an appealing set of behaviors, this system has two other distinct advantages for probing neural circuitry. First, the fly will perform escape behaviors even when tethered such that its head is fixed and neural activity can be imaged or monitored using electrophysiology. Second, using Drosophila as an experimental animal makes available a rich suite of genetic tools to activate, silence, or image small numbers of cells potentially involved in the behaviors. Neural Circuits for Escape Until recently, visually induced escape responses have been considered a hardwired reflex in Drosophila. White-eyed flies with deficient visual pigment will perform a stereotyped middle-leg jump in response to a light-off stimulus, and this reflexive response is known to be coordinated by the well-studied giant fiber (GF) pathway. The GFs are a pair of electrically connected, large-diameter interneurons that traverse the cervical connective. A single GF spike results in a stereotyped pattern of muscle potentials on both sides of the body that extends the fly's middle pair of legs and starts the flight motor. Recently, we have found that a fly escaping a looming object displays many more behaviors than just leg extension. Most of these behaviors could not possibly be coordinated by the known anatomy of the GF pathway. Response to a looming threat thus appears to involve activation of numerous different neural pathways, which the fly may decide if and when to employ. Our goal is to identify the descending pathways involved in coordinating these escape behaviors as well as the central brain circuits, if any, that govern their activation. Automated Single-Fly Screening We have developed a new kind of high-throughput genetic screen to automatically capture fly escape sequences and quantify individual behaviors. We use this system to perform a high-throughput genetic silencing screen to identify cell types of interest. Automation permits analysis at the level of individual fly movements, while retaining the capacity to screen through thousands of GAL4 promoter lines. Single-fly behavioral analysis is essential to detect more subtle changes in behavior during the silencing screen, and thus to identify more specific components of the contributing circuits than previously possible when screening populations of flies. Our goal is to identify candidate neurons involved in coordination and choice of escape behaviors. Measuring Neural Activity During Behavior We use whole-cell patch-clamp electrophysiology to determine the functional roles of any identified candidate neurons. Flies perform escape behaviors even when their head and thorax are immobilized for physiological recording. This allows us to link a neuron's responses directly to an action.

Networks of stiff biopolymers are an omnipresent structural motif in cells and tissues. A prominent modeling framework for describing biopolymer network mechanics is rigidity percolation theory. This theory describes model networks as nodes joined by randomly placed, springlike bonds. Increasing the amount of bonds in a network results in an abrupt, dramatic increase in elastic moduli above a certain threshold – an example of a mechanical phase transition. While homogeneous networks are well studied, many tissues are made of disparate components and exhibit spatial fluctuations in the concentrations of their constituents. In this talk, I will first discuss recent work in which we explained the structural basis of the shear mechanics of healthy and chemically degraded cartilage by coupling a rigidity percolation framework with a background gel. Our model takes into account collagen concentration, as well as the concentration of peptidoglycans in the surrounding polyelectrolyte gel, to produce a structureproperty relationship that describes the shear mechanics of both sound and diseased cartilage. I will next discuss the introduction of structural correlation in constructing networks, such that sparse and dense patches emerge. I find moderate correlation allows a network to become rigid with fewer bonds, while this benefit is partly erased by excessive correlation. We explain this phenomenon through analysis of the spatial fluctuations in strained networks’ displacement fields. Finally, I will address our work’s implications for non-invasive diagnosis of pathology, as well as rational design of prostheses and novel soft materials.

There is a recent surge of interest in the behavior of active particles that can at the same time align their direction of movement and synchronize their oscillations, known as swarmalators. While analytical and numerical models of such systems are now abundant, no real-life examples have been shown to date. I will present an experimental investigation of the collective motion of the nematode Turbatrix aceti, which self-propel by body undulation. I will show that under favorable conditions these nematodes can synchronize their body oscillations, forming striking traveling metachronal waves which, similar to the case of beating cilia, produce strong fluid flows. I will demonstrate that the location and strength of this collective state can be controlled through the shape of the confining structure; in our case the contact angle of a droplet. This opens a way for producing controlled work such as on-demand flows or displacement of objects. I will illustrate this by a practical example: showing that the force generated by the collectively moving nematodes is sufficient to change the mode of evaporation of fluid droplets, by counteracting the surface-tension force, which allow us to estimate its strength.

Tissue folding is a ubiquitous shape change event during development whereby a cell sheet bends into a curved 3D structure. This mechanical process is remarkably robust, and the correct final form is almost always achieved despite internal fluctuations and external perturbations inherent in living systems. While many genetic and molecular strategies that lead to robust development have been established, much less is known about how mechanical patterns and movements are ensured at the population level. I will describe how quantitative imaging, physical modeling and concepts from network science can uncover collective interactions that govern tissue patterning and shape change. Actin and myosin are two important cytoskeletal proteins involved in the force generation and movement of cells. Both parts of this talk will be about the spontaneous organization of actomyosin networks and their role in collective tissue dynamics. First, I will present how out-of-plane curvature can trigger the global alignment of actin fibers and a novel transition from collective to individual cell migration in culture. I will then describe how tissue-scale cytoskeletal patterns can guide tissue folding in the early fruit fly embryo. I will show that actin and myosin organize into a network that spans a domain of the embryo that will fold. Redundancy in this supracellular network encodes the tissue’s intrinsic robustness to mechanical and molecular perturbations during folding.

The motion of passive or active agents in soft materials generates long ranged deformation fields with signatures informed by hydrodynamics and the properties of the soft matter host. These signatures are even more complex when the soft matter host itself is an active material. Measurement of these fields reveals mechanics of the soft materials and hydrodynamics central to understanding self-organization. In this talk, I first introduce a new method based on correlated displacement velocimetry, and use the method to measure flow fields around particles trapped at the interface between immiscible fluids. These flow fields, decomposed into interfacial hydrodynamic multipoles, including force monopole and dipole flows, provide key insights essential to understanding the interface’s mechanical response. I then extend this method to various actomyosin systems to measure local strain fields around myosin molecular motors. I show how active stresses propagate in 2d liquid crystalline structures and in disordered networks that are formed by the actin filaments. In particular, the response functions of contractile and stable gels are characterized. Through similar analysis, I also measure the retrograde flow fields of stress fibers in single cells to understand subcellular mechanochemical systems.

Filaments (slender, microscopic elastic bodies) are prevalent in biological and industrial settings. In the biological case, the filaments are often active, in that they are driven internally by motor proteins, with the prime examples being cilia and flagella. For cilia in particular, which can appear in dense arrays, their resulting motions are coupled through the surrounding fluid, as well as through surfaces to which they are attached. In this talk, I present numerical simulations exploring the coordinated motion of active filaments and how it depends on the driving force, density of filaments, as well as the attached surface. In particular, we find that when the surface is spherical, its topology introduces local defects in coordinated motion which can then feedback and alter the global state. This is particularly true when the surface is not held fixed and is free to move in the surrounding fluid. These simulations take advantage of a computational framework we developed for fully 3D filament motion that combines unit quaternions, implicit geometric time integration, quasi-Newton methods, and fast, matrix-free methods for hydrodynamic interactions and it will also be presented.

Euglena gracilis is an interesting unicellular protist, also because it can adopt different motility strategies: swimming by flagellar propulsion, or crawling thanks to large amplitude shape changes of the whole body (a behavior known as “metaboly”, or “amoeboid motion”). Swimming trajectories are helical. The are powered by the beating of a single emerging flagellum, which spans non-planar waveforms in the shape of a twisted lasso. Finally the harmoniously coordinated shape changes that make metaboly possible, reminiscent of peristaltic waves, arise form the relative sliding of its pellicle strips, resulting in twisted helical bundles. We will report on the most recent findings on these interconnected topics, for which helical shapes provide a striking fil rouge.