Biophysics seminars

Individual bacteria transported in viscous flows, show complex interactions with flows and bounding surfaces resulting from their complex shape as well as their activity. Understanding these transport dynamics is crucial, as they impact soil contamination, transport in biological conducts or catheters, and constitute thus a serious health threat. Here we investigate the trajectories of individual E-coli bacteria in confined geometries under flow, using microfluidic model systems in bulk flows as well as close to surfaces using a novel Langrangian 3D tracking method. Combining experimental observations and modelling we elucidate the origin of upstream swimming, lateral drift or persistent transport along corners. [1] Junot et al, EPL, 126 (2019) 44003 [2] Mathijssen et al. 10:3 (2019) Nature Comm. [3] Figueroa-Morales et al., Soft Matter, 2015,11, 6284-6293 [4] Darnige et al. Review of Scientific Instruments 88, 055106 (2017) [5] Jing et al, Science Advances, 2020; 6 : eabb2012 [6] Figueroa-Morales et al, Sci. Adv. 2020; 6 : eaay0155, 2020, 10.1126/sciadv.aay0155

While the motion and collective behavior of cells are well-studied on flat surfaces or in unconfined liquid media, in most natural settings, cells thrive in complex 3D environments. Bioprinting processes are capable of structuring cells in 3D and conventional bioprinting approaches address this challenge by embedding cells in bio-degradable polymer networks. However, heterogeneity in network structure and biodegradation often preclude quantitative studies of cell behavior in specified 3D architectures. Here, I will present a new approach to 3D bioprinting of cellular communities that utilizes jammed, granular polyelectrolyte microgels as a support medium. The self-healing nature of this medium allows the creation of highly precise cellular communities and tissue-like structures by direct injection of cells inside the 3D medium. Further, the transparent nature of this medium enables precise characterization of cellular behavior. I will describe two examples of my work using this platform to study the behavior of two different classes of cells in 3D. First, I will describe how we interrogate the growth, viability, and migration of mammalian cells—ranging from epithelial cells, cancer cells, and T cells—in the 3D pore space. Second, I will describe how we interrogate the migration of E. coli bacteria through the 3D pore space. Direct visualization enables us to reveal a new mode of motility exhibited by individual cells, in stark contrast to the paradigm of run-and-tumble motility, in which cells are intermittently and transiently trapped as they navigate the pore space; further, analysis of these dynamics enables prediction of single-cell transport over large length and time scales. Moreover, we show that concentrated populations of E. coli can collectively migrate through a porous medium—despite being strongly confined—by chemotactically “surfing” a self-generated nutrient gradient. Together, these studies highlight how the jammed microgel medium provides a powerful platform to design and interrogate complex cellular communities in 3D—with implications for tissue engineering, microtissue mechanics, studies of cellular interactions, and biophysical studies of active matter.

There is little consensus on the level of spatial complexity at which dendrites operate. On the one hand, emergent evidence indicates that synapses cluster at micrometer spatial scales. On the other hand, most modelling and network studies ignore dendrites altogether. This dichotomy raises an urgent question: what is the smallest relevant spatial scale for understanding dendritic computation? We have developed a method to construct compartmental models at any level of spatial complexity. Through carefully chosen parameter fits, solvable in the least-squares sense, we obtain accurate reduced compartmental models. Thus, we are able to systematically construct passive as well as active dendrite models at varying degrees of spatial complexity. We evaluate which elements of the dendritic computational repertoire are captured by these models. We show that many canonical elements of the dendritic computational repertoire can be reproduced with few compartments. For instance, for a model to behave as a two-layer network, it is sufficient to fit a reduced model at the soma and at locations at the dendritic tips. In the basal dendrites of an L2/3 pyramidal model, we reproduce the backpropagation of somatic action potentials (APs) with a single dendritic compartment at the tip. Further, we obtain the well-known Ca-spike coincidence detection mechanism in L5 Pyramidal cells with as few as eleven compartments, the requirement being that their spacing along the apical trunk supports AP backpropagation. We also investigate whether afferent spatial connectivity motifs admit simplification by ablating targeted branches and grouping affected synapses onto the next proximal dendrite. We find that voltage in the remaining branches is reproduced if temporal conductance fluctuations stay below a limit that depends on the average difference in input resistance between the ablated branches and the next proximal dendrite. Consequently, when the average conductance load on distal synapses is constant, the dendritic tree can be simplified while appropriately decreasing synaptic weights. When the conductance level fluctuates strongly, for instance through a-priori unpredictable fluctuations in NMDA activation, a constant weight rescale factor cannot be found, and the dendrite cannot be simplified. We have created an open source Python toolbox (NEAT - https://neatdend.readthedocs.io/en/latest/) that automatises the simplification process. A NEST implementation of the reduced models, currently under construction, will enable the simulation of few-compartment models in large-scale networks, thus bridging the gap between cellular and network level neuroscience.

Studying the pathophysiology of late stage Parkinson’s disease (PD) – after the patients have experienced severe neuronal loss – has helped develop various symptomatic treatments for PD (e.g., deep brain stimulation). However, it has been of limited use in developing neuroprotective disease-modifying therapies (DMTs), because DMTs require interventions at much earlier stages of PD when vulnerable neurons are still intact. Because PD patients exhibit various non-motor prodromal symptoms (ie, symptoms that predate diagnosis), understanding the pathophysiology underlying these symptom could lead to earlier diagnosis and intervention. In my talk, I will present a recently elucidated example of how PD pathologies alter the channel biophysics of intact vagal motoneurons (known to be selectively vulnerable in PD) to drive dysautonomia that is reminiscent of prodromal PD. I will discuss how elucidating the pathophysiology of prodromal symptoms can lead to earlier diagnosis through the development of physiological biomarkers for PD.

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.

The spontaneous collective motion of self-propelled agents is ubiquitous in the natural world, and it often occurs in complex environments, be it bacteria and cells migrating through polymeric extracellular matrix or animal herds and human crowds navigating structured terrains. Much is known about flocking dynamics in pristine backgrounds, but how do spatio-temporal heterogeneities in the environment impact such collective self-organization? I will present two model systems, a colloidal active fluid negotiating disordered obstacles and a confined dense bacterial suspension in a viscoelastic medium, as controllable platforms to explore this question and highlight general mechanisms for active self-organization in complex environments. By combining theory and experiment, I will show how flocks on disordered substrates organize into a novel dynamic vortex glass phase, akin to vortex glasses in dirty superconductors, while the presence of viscoelasticity can calm the otherwise turbulent swarming of bacteria, allowing the emergence of a large scale coherent and even oscillatory vortex when confined on the millimetre scale.

Active matter systems are composed of constituents, each one in nonequilibrium, that consume energy in order to move [1]. A characteristic feature of active matter is collective motion leading to nonequilibrium phase transitions or large scale directed motion [2]. A number of recent works have featured active particles interacting with obstacles, either moving or fixed [3,4,5]. When an active particle encounters an asymmetric obstacle, different behaviours are detected depending on the nature of its active motion. On the one side, rectification effects arise in a suspension of run-and-tumble particles interacting with a wall of funnelled-shaped openings, caused by particles persistence length [6]. The same trapping mechanism could be responsible for the intake of microorganisms in the underground leaves [7] of Carnivorous plants [8]. On the other side, for aligning particles [9] interacting with a wall of funnelled-shaped openings, trapping happens on the (opposite) wider opening side of the funnels [10,11]. Interestingly, when funnels are located on a circular array, trapping is more localised and depends on the nature of the Vicsek model. Active particles can be synthetic (such as synthetic active colloids) or alive (such as living bacteria). A prototypical model to study living microswimmers is P. fluorescens, a rod shaped and biofilm forming bacterium. Biofilms are microbial communities self-assembled onto external interfaces. Biofilms can be described within the Soft Matter physics framework [12] as a viscoelastic material consisting of colloids (bacterial cells) embedded in a cross-linked polymer gel (polysaccharides cross-linked via proteins/multivalent cations), whose water content vary depending on the environmental conditions. Bacteria embedded in the polymeric matrix control biofilm structure and mechanical properties by regulating its matrix composition. We have recently monitored structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress [13,14]. We have demonstrated that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions. REFERENCES [1] C. Bechinger et al. Rev. Mod. Phys. 88, 045006 (2016); [2] T. Vicsek, A. Zafeiris Phys. Rep. 517, 71 (2012); [3] C. Bechinger, R. Di Leonardo, H. Lowen, C. Reichhardt, G. Volpe, and G. Volpe, Reviews of Modern Physics 88, 045006 (2016); [4] R Martinez, F Alarcon, DR Rodriguez, JL Aragones, C Valeriani The European Physical Journal E 41, 1 (2018); [5] DR Rodriguez, F Alarcon, R Martinez, J Ramírez, C Valeriani, Soft matter 16 (5), 1162 (2020); [6] C. O. Reichhardt and C. Reichhardt, Annual Review of Condensed Matter Physics 8, 51 (2017); [7] W Barthlott, S Porembski, E Fischer, B Gemmel Nature 392, 447 (1998); [8] C B. Giuliano, R Zhang, R.Martinez Fernandez, C.Valeriani and L.Wilson (in preparation, 2021); [9] R Martinez, F Alarcon, JL Aragones, C Valeriani Soft matter 16 (20), 4739 (2020); [10] P. Galajada, J. Keymer, P. Chaikin and R.Austin, Journal of bacteriology, 189, 8704 (2007); [11] M. Wan, C.O. Reichhardt, Z. Nussinov, and C. Reichhardt, Physical Review Letters 101, 018102 (2008); [12] J N. Wilking , T E. Angelini , A Seminara , M P. Brenner , and D A. Weitz MRS Bulletin 36, 385 (2011); [13]J Jara, F Alarcón, A K Monnappa, J Ignacio Santos, V Bianco, P Nie, M Pica Ciamarra, A Canales, L Dinis, I López-Montero, C Valeriani, B Orgaz, Frontiers in microbiology 11, 3460 (2021); [14] P Nie, F Alarcon, I López-Montero, B Orgaz, C Valeriani, M Pica Ciamarra

Three complementary lectures explain the development and applications of optogenetics. Gero Miesenböck traces optical control of neuronal activity from early experiments to studies of sleep, including neurons that respond to accumulated sleep need and molecular mechanisms governing sleep pressure. Peter Hegemann connects microbial photobiology to channelrhodopsins that control neuronal membrane voltage. He discusses their use in studying development and learning, and prospects for extending optical control to enzymes, transcription and translation. Georg Nagel follows the discovery and expression of microbial rhodopsins with light-sensitive transport and enzymatic functions. His examples include Channelrhodopsin-2 and its H134R variant, halorhodopsin, the more light-sensitive ChR2/XXL, the rhodopsin guanylyl cyclase Cyclop, and anion-channelrhodopsins in tobacco plants. Together, the talks connect molecular mechanisms with experimental control of neural and plant systems.

The processing of temporal sound features is fundamental to hearing, and the auditory system displays a plethora of specializations, at many levels, to enable such processing. Octopus neurons are the most extreme temporally-specialized cells in the auditory (and perhaps entire) brain, which make them intriguing but also difficult to study. Notwithstanding the scant physiological data, these neurons have been a favorite cell type of modeling studies which have proposed that octopus cells have critical roles in pitch and speech perception. We used a range of in vivo recording and labeling methods to examine the hypothesis that tonotopic ordering of cochlear afferents combines with dendritic delays to compensate for cochlear delay - which would explain the highly entrained responses of octopus cells to sound transients. Unexpectedly, the experiments revealed that these neurons have marked selectivity to the direction of fast frequency glides, which is tied in a surprising way to intrinsic membrane properties and subthreshold events. The data suggest that octopus cells have a role in temporal comparisons across frequency and may play a role in auditory scene analysis.

In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (the minimal chromatin model) explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data is presented. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. This model was generalized by utilizing a neural network to infer these chromatin types using epigenetic marks present at a locus, as assayed by ChIP-Seq. The ensemble of structures resulting from these simulations completely agree with HI-C data and exhibits unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories. Although this theoretical methodology was trained in one cell line, the human GM12878 lymphoblastoid cells, it has successfully predicted the structural ensembles of multiple human cell lines. Finally, going beyond Hi-C, our predicted structures are also consistent with microscopy measurements. Analysis of both structures from simulation and microscopy reveals that short segments of chromatin make two-state transitions between closed conformations and open dumbbell conformations. For gene active segments, the vast majority of genes appear clustered in the linker region of the chromatin segment, allowing us to speculate possible mechanisms by which chromatin structure and dynamics may be involved in controlling gene expression. * Supported by the NSF

Many microorganisms and cells function in complex (non-Newtonian) fluids, which are mixtures of different materials and exhibit both viscous and elastic stresses. For example, mammalian sperm swim through cervical mucus on their journey through the female reproductive tract, and they must penetrate the viscoelastic gel outside the ovum to fertilize. In micro-scale swimming the dynamics emerge from the coupled interactions between the complex rheology of the surrounding media and the passive and active body dynamics of the swimmer. We use computational models of swimmers in viscoelastic fluids to investigate and provide mechanistic explanations for emergent swimming behaviors. I will discuss how flexible filaments (such as flagella) can store energy from a viscoelastic fluid to gain stroke boosts due to fluid elasticity. I will also describe 3D simulations of model organisms such as C. Reinhardtii and mammalian sperm, where we use experimentally measured stroke data to separate naturally coupled stroke and fluid effects. We explore why strokes that are adapted to Newtonian fluid environments might not do well in viscoelastic environments.

The journey of development begins with sperm swimming through the female reproductive tract en-route to the egg. In order to successfully complete this journey sperm must beat a single flagellum, propelling themselves through a wide range of fluids, from liquified semen to viscous cervical mucus. It is well-known that the beating tail is driven by an array of 9 microtubule doublets surrounding a central pair, with interconnecting dynein motors generating shear forces and driving elastic wave propagation. Despite this knowledge, the exact mechanism by which coordination of these motors drives oscillating waves along the flagellum remains unknown; hypothesised mechanisms include curvature control, sliding control, and geometric clutch. In this talk we will discuss the mechanisms of flagellar bending, and present a simple model of active curvature that is able to produce many of the various sperm waveforms that are seen experimentally, including those in low and high viscosity fluids and after a cell has ‘hyperactivated’ (a chemical process thought to be key for fertilization). We will show comparisons between these simulated waveforms and sperm that have been experimentally tracked, and discuss methods for fitting simulated mechanistic parameters to these real cells.

Living cells contain millions of enzymes and proteins, which carry out multiple reactions simultaneously. To optimize these processes, cells compartmentalize reactions in membraneless liquid condensates. Certain features of cellular condensates can be explained by principles of liquid-liquid phase separation studied in material science. However, biological condensates exist in the inherently out of equilibrium environment of a living cell, being driven by force-generating microscopic processes. These cellular conditions are fundamentally different than the equilibrium conditions of liquid-liquid phase separation studied in materials science and physics. How condensates function in the active riotous environment of a cell is essential for understanding of cellular functions, as well as to the onset of neurodegenerative diseases. Currently, we lack model systems that enable rigorous studies of these processes. Living cells are too complex for quantitative analysis, while reconstituted equilibrium condensates fail to capture the non-equilibrium environment of biological cells. To bridge this gap, we reconstituted a DNA based membraneless condensates in an active environment that mimics the conditions of a living cell. We combine condensates with a reconstituted network of cytoskeletal filaments and molecular motors, and study how the mechanical interactions change the phase behavior and dynamics of membraneless structures. Studying these composite materials elucidates the fundamental physics rules that govern the behavior of liquid-liquid phase separation away from equilibrium while providing insight into the mechanism of condensate phase separation in cellular environments.

Cells and microorganisms produce and consume all sorts of chemicals, from nutrients to signalling molecules. The same happens at the nanoscale inside cells themselves, where enzymes catalyse the production and consumption of the chemicals needed for life. In this work, we have found a generic mechanism by which such chemically-active particles, be it cells or enzymes or engineered synthetic colloids, can "sense" each other and ultimately self- organize in a multitude of ways. A peculiarity of these chemical-mediated interactions is that they break action-reaction symmetry : for example, one particle may be repelled from a second particle, which is in turn attracted to the first one, so that it ends up "chasing" it. Such chasing interactions allow for the formation of large clusters of particles that "swim" autonomously. Regarding enzymes, we find that they can spontaneously aggregate into clusters with precisely the right composition, so that the product of one enzyme is passed on, without lack or excess, to the next enzyme in the metabolic cascade.

Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables at criticality. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context.

What are the things that draw us to a particular field of science and what is it that keeps us there? For Dr. Bahia, there was a particular attraction to sensory nerves; the monitors of the worlds inside and outside of our bodies. In this talk, Dr. Bahia will outline her career path as a neuroscientist resulting in the title of Research Associate. She will also talk about the longest project she has participated in, 'exploring the role of ion channels in sensory nerves' (rupress.org/jgp/article/147/6/451/43495/The-exceptionally-high-reactivity-of-Cys-621-is)

A key question for basic biology and regenerative medicine concerns the way in which evolution exploits physics toward adaptive form and function. While genomes specify the molecular hardware of cells, what algorithms enable cellular collectives to reliably build specific, complex, target morphologies? Our lab studies the way in which all cells, not just neurons, communicate as electrical networks that enable scaling of single-cell properties into collective intelligences that solve problems in anatomical feature space. By learning to read, interpret, and write bioelectrical information in vivo, we have identified some novel controls of growth and form that enable incredible plasticity and robustness in anatomical homeostasis. In this talk, I will describe the fundamental knowledge gaps with respect to anatomical plasticity and pattern control beyond emergence, and discuss our efforts to understand large-scale morphological control circuits. I will show examples in embryogenesis, regeneration, cancer, and synthetic living machines. I will also discuss the implications of this work for not only regenerative medicine, but also for fundamental understanding of the origin of bodyplans and the relationship between genomes and functional anatomy.

Biologists have recently come to appreciate that eukaryotic cells are home to a multiplicity of non-membrane bound compartments, many of which form and dissolve as needed for the cell to function. These dynamical “condensates” enable many central cellular functions – from ribosome assembly, to RNA regulation and storage, to signaling and metabolism. While it is clear that these compartments represent a type of separated phase, what controls their formation, how specific biological components are included or excluded, and how these structures influence physiological and biochemical processes remain largely mysterious. I will discuss recent experiments on phase separated condensates both in vitro and in vivo, and will present theoretical results that highlight a novel “magic number” effect relevant to the formation and control of two-component phase separated condensates.

Bacteria exhibit a bewildering diversity of morphologies, but despite their impact on nearly all aspects of life, they are frequently classified into a few general categories, usually just “spheres” and “rods.” Curved-rod bacteria are one simple variation observed in many environments, particularly the ocean. However, why so many species have evolved this shape is unknown. We used a regularized Stokeslet Boundary Element Method to model the motility of flagellated, curved bacteria. We show that curvature can increase swimming efficiency, revealing a widely applicable selective advantage. Furthermore, we show that the distribution of cell lengths and curvatures observed across bacteria in nature is predicted by evolutionary trade-offs between three tasks influenced by shape: efficient swimming, the ability to detect chemical gradients, and reduced cost of cell construction. We therefore reveal shape as an important component of microbial fitness.

Understanding the properties of active matter is a challenge which is currently driving a rapid growth in soft- and bio-physics. Some of the most important examples of active matter are at the microscale, and include active colloids and suspensions of microorganisms, both as a simple active fluid (single species) and as mixed suspensions of active and passive elements. In this last class of systems, recent experimental and theoretical work has started to provide a window into new phenomena including activity-induced depletion interactions, phase separation, and the possibility to extract net work from active suspensions. Here I will present our work on a paradigmatic example of mixed active-passive system, where the activity is provided by swimming microalgae. Macro- and micro-scopic experiments reveal that microorganism-colloid interactions are dominated by rare close encounters leading to large displacements through direct entrainment. Simulations and theoretical modelling show that the ensuing particle dynamics can be understood in terms of a simple jump-diffusion process, combining standard diffusion with Poisson-distributed jumps. Entrainment length can be understood within the framework of Taylor dispersion as a competition between advection by the no-slip surface of the cell body and microparticle diffusion. Building on these results, we then ask how external control of the dynamics of the active component (e.g. induced microswimmer anisotropy/inhomogeneity) can be used to alter the transport of passive cargo. As a first step in this direction, we study the behaviour of mixed active-passive systems in confinement. The resulting spatial inhomogeneity in swimmers’ distribution and orientation has a dramatic effect on the spatial distribution of passive particles, with the colloids accumulating either towards the boundaries or towards the bulk of the sample depending on the size of the container. We show that this can be used to induce the system to de-mix spontaneously.