Seminars
September 17, 2024: (4PM) – Baruch Barzel, Bar-Ilan University
Network GPS – Navigating Network Dynamics.
Host: Merav Stern
In the past two decades we made significant advances in mapping the structure of social, biological and technological networks. The challenge that remains is to translate everything we know about network structure into its actual observed dynamics. In essence, whether it’s communicable diseases, genetic regulation, or the spread of failures in an infrastructure network, these dynamics boil down to the patterns of information spread in the network. It all begins with a local perturbation, such as a sudden disease outbreak or a local power failure, which then propagates to impact all other nodes. The challenge is that the resulting spatio-temporal propagation patterns are diverse and unpredictable – indeed, a zoo of spreading patterns – that seem to be only loosely connected to the network structure. We show that we can tame this zoo by exposing a systematic translation of network structural elements into their dynamic outcome, allowing us to navigate networks, and, most importantly, to expose a deep universality behind their seemingly diverse dynamics. Along the way, we predict how long it takes for viruses to spread between countries, which metabolites contribute most to the system’s information flow, and how to resuscitate a collapsed microbial network back into functionality.
October 15, 2024: (4PM) – Bertrand Ottino-Loffler, Rockefeller University
On Possible Indicators Of Negative Selection In Germinal Centers.
Host: Merav Stern
A central feature of vertebrate immune response is affinity maturation, wherein antibody-producing B cells undergo evolutionary selection in microanatomical structures called germinal centers, which form in secondary lymphoid organs upon antigen exposure. While it has been shown that the median B cell affinity dependably increases over the course of maturation, the exact logic behind this evolution remains vague. Three potential selection methods include encouraging the reproduction of high affinity cells (“birth/positive selection”), encouraging cell death in low affinity cells (“death/negative selection”), and adjusting the mutation rate based on cell affinity (“mutational selection”). While all three forms of selection would lead to a net increase in affinity, different selection methods may lead to distinct statistical dynamics. We present a tractable model of selection and analyze proposed signatures of negative selection. Given the simplicity of the model, such signatures should be stronger here than in real systems. However, we find a number of intuitively appealing metrics — such as preferential ancestry ratios, terminal node counts, and mutation count skewness — require nuance to properly interpret.
October 22, 2024: (4PM) – Karen E. Kasza, Columbia University
Stress Management: Dissecting How Epithelial Tissues Flow And Fold Inside Developing Embryos.
Host: Eric Siggia
During embryonic development, groups of cells reorganize into functional tissues with complex form and structure. Tissue reorganization can be rapid and dramatic, often occurring through striking embryo-scale flows or folds that are mediated by the coordinated actions of hundreds or thousands of cells. These types of tissue movements can be driven by internal forces generated by the cells themselves or by external forces. While much is known about the molecules involved in these cell and tissue movements, it is not yet clear how these molecules work together to coordinate cell behaviors, give rise to emergent tissue mechanics, and generate coherent tissue movements at the embryo scale. To gain mechanistic insight into this problem, my lab develops and uses optogenetic technologies for manipulating mechanical activities of cells in the developing Drosophila embryo. First, I will discuss how mechanical forces are regulated in space and time to drive tissue flows that rapidly and symmetrically elongate the head-to-tail body axis of the embryo. Second, I will discuss some of our recent findings on the biological and physical mechanisms underlying distinct modes of generating curvature and folds in epithelial tissue sheets.
October 29, 2024: (4PM) – Francis Corson, Ecole Normale Superieure
Spatial And Temporal Order In The Developing Drosophila Eye.
Host: Eric Siggia
There are many instances in development where a regular arrangement of cell fates self-organizes through cell-cell interactions, yet the dynamics by which these patterns arise, and the underlying logic, often remain elusive. In the developing Drosophila eye, regular rows of light-receiving units emerge in the wake of a traveling differentiation front to form a crystal-like array. The propagation of this pattern is thought to proceed by templating, with inhibitory signaling from each row providing a negative template for the next, but its dynamics had not been directly observed. Live imaging reveals unanticipated oscillations of the proneural factor Atonal, associated with pulses of Notch signaling activity. Our observations inform a new relay model for eye patterning, in which dynamic signaling from row n triggers differentiation at row n+2, conveying both spatial and temporal information to propagate crystal-like order.
November 12, 2024: (4PM) – Wilten Nicola, University of Calgary
Learning And Memory In Stress Circuits.
Host: Merav Stern
The hypothalamic stress response is kicked off by the corticotropin releasing hormone (CRH) neurons of the paraventricular nucleus (PVN-CRH). As these neurons act as the final neural controller for the stress response, they are uniquely suited to adapting their neural responses to novel information in potentially stressful environments. Here, with both computational modelling and in vivo one-photon/miniscope recordings of PVN-CRH neurons, we show that these neurons change their tuning properties to novel environments with simple supervised learning rules in the absence or presence of threats or rewards. These changes persist across days and can be induced with only a single exposure to an environment paired with either an aversive stimulus (foot shock) or reward (Nutella). This work was performed in collaboration with the lab of Jaideep Bains[1]. References[1] Füzesi, T., Rasiah, N.P., Rosenegger, D.G., Rojas-Carvajal, M., Chomiak, T., Daviu, N., Molina, L.A., Simone, K., Sterley, T.L., Nicola, W. and Bains, J.S., 2023. Hypothalamic CRH neurons represent physiological memory of positive and negative experience. Nature Communications, 14(1), p.8522.
December 10, 2024: (4PM) – Anne Churchland, University of California, Los Angeles
Movements And Engagement During Perceptual Decision-Making.
Host: Merav Stern
Switching between cognitive states is a natural tendency, even for trained experts. To test how cognitive state impacts the relationship between neural activity and behavior, we measured cortex-wide neural activity during decision-making in mice. Task variables and instructed movements elicited similar neural responses regardless of state, but the neural activity associated with spontaneous, uninstructed movements became highly variable during disengagement. Surprisingly, this heightened variability was not due to an increase in movements: behavioral videos showed equally frequent movements in both cognitive states. But while the movement frequency remained similar, movement timing changed: as animals slipped into disengagement, their movements became erratically timed. These idiosyncratic movements were a strong predictor of task performance and drove the increased variance that we observed in the neural activity. Taken together, our results argue that the temporal structure of movement patterns constitutes an embodied signature of cognitive state with profound impacts on neural activity.
December 17, 2024: (4PM) – Giancarlo La Camera, Stony Brook University
Neural Mechanisms of Strategy-dependent Decision-making in the Prefrontal Cortex.
Host: Merav Stern
The ability to make decisions according to context is a hallmark of intelligent behavior. The prefrontal cortex (PFC) is known for processing contextual information, but many questions remain open. This is especially the case for “strategic” behavior where the context follows from abstract rules rather than dedicated input cues. In this work, we investigate the neural basis of two strategies called `repeat-stay’ and `change-shift’ strategy, respectively. These strategies have been observed in monkeys performing certain types of context-dependent tasks; in the task studied here, one of three targets are chosen based on an instruction stimulus and the outcome of previous trials. The same stimulus may instruct different decisions and the same decision may result from different stimuli, requiring the ability to develop strategic rules that span multiple trials. We found that PFC activity makes sharp transitions across latent neural states encoding task variables such as strategy, decision, action, reward, and previous-trial decisions. We compared two models able to perform the same task: a recurrent neural network (RNN) trained via backpropagation through time, and a multi-modular spiking network (MMSN) containing realistic ingredients of real cortical networks. Both models successfully attain levels of performance comparable to the monkeys’; however, the RNN seems to learn specific combinations of task conditions while the MMSN adopts the abstract strategies. The MMSN also reproduces the sequence of sharp transients observed in the PFC data, and explains some behavioral errors as the consequence of temporally misplaced transitions. In summary, the spiking network’s modular architecture suggests possible mechanisms for storing information across trials and subserve strategic behavior in complex tasks.
January 14, 2025: (4PM)- Ned Wingreen, Princeton University
Capillary Attraction Underlies Bacterial Collective Dynamics. “Water Is The Driving Force Of All Nature.” — Leonardo da Vinci.
Host: Eric Siggia
Collective motion of active matter occurs in many living systems, such as bacterial communities, epithelial cell populations, bird flocks, and fish schools. A remarkable example can be found in the soil-dwelling bacterium Myxococcus xanthus. Key to the life cycle of M. xanthus cells is the formation of collective groups: they feed on prey in swarms and aggregate upon starvation. However, the physical mechanisms that keep M. xanthus cells together remains unclear. I’ll present a computational model to explore the role that capillary forces play in bacterial collective dynamics. The modeling results, combined with experiments, show that water menisci forming around bacteria mediate strong capillary attraction between cells. The model accounts for a variety of previously observed phases of collective dynamics as the result of a competition between cell-cell capillary attraction and cell motility. Finally, I’ll discuss the large-scale self-organization of bacterial populations and highlight the importance of capillary force in this process. Together, these results suggest that cell-cell capillary attraction provides a generic mechanism underpinning bacterial collective dynamics.
January 21, 2025: (4PM)
To Be Announced.
Host: TBD
To come.
January 28, 2025: (4PM)- Jason Kim, Cornell University
To Be Announced.
Host: Eric Siggia
To come.
February 4, 2025: (4PM)- Hava Siegelman, University of Massachusetts, Amherst
To Be Announced.
Host: Marcelo Magnasco
To come.
February 11, 2025: (4PM)
To Be Announced.
Host: TBD
To come.
February 18, 2025: (4PM)- Gautum Reddy, Princeton University
To Be Announced.
Host: Eric Siggia
To come.
February 25, 2025: (4PM)- Marcella Noorman, Howard Hughes Medical Institute (Janelia)
To Be Announced.
Host: Nikolas Schonsheck
To come.
March 4, 2025: (4PM)
To Be Announced.
Host: TBD
To come.
March 11, 2025: (4PM)
To Be Announced.
Host: TBD
To come.
March 18, 2025: (4PM)
To Be Announced.
Host: TBD
To come.
March 25, 2025: (4PM)- Nathan Lord, University of Pittsburgh
To Be Announced.
Host: Amy Shyer/Alan Rodrigues
To come.
April 1, 2025: (4PM)- Carina Curto, Brown University
To Be Announced.
Host: Nikolas Schonsheck
To come.
April 8, 2025: (4PM)- Edouard Hannezo, Institute of Science and Technology Austria
To Be Announced.
Host: Amy Shyer/Alan Rodrigues
To come.
April 15, 2025: (4PM)- Brent Doiron, University of Chicago
To Be Announced.
Host: Nikolas Schonsheck
To come.
April 22, 2025: (4PM)- Max Wilson, University of California, Santa Barbara
To Be Announced.
Host: Amy Shyer/Alan Rodrigues
To come.
April 29, 2025: (4PM)- Elias Barriga, Technical University Dresden
To Be Announced.
Host: Amy Shyer/Alan Rodrigues
To come.
May 6, 2025: (4PM)
To Be Announced.
Host: TBD
To come.