Biology subjects

Wingreen, N. S.

Publications and source records attributed to Wingreen, N. S..

At least 19 recordsLinked to original sources

bioRxiv2026

A minimal kinase-phosphatase system and its lipid substrates self-organize into dynamic patterns

Competing lipid kinases and phosphatases are critical for organizing cellular membranes, but whether a minimal system can autonomously organize proteins and lipids into dynamic spatiotemporal patterns is unknown. Here, we report the in vitro reconstitution of the Legionella phosphatidylinositol (PI) 3-kinase MavQ and PI 3-phosphatase SidP. Together with their lipid substrates, PI and PI 3-phosphate (PI3P), these enzymes form a minimal self-organizing system that generates ATP-dependent spatiotemporal patterns, including traveling waves, on model membranes. These behaviors arise from MavQs cooperative membrane binding, SidPs phosphatase activity, and the continual interconversion and redistribution of PI and PI3P within a conserved membrane pool. A reaction-diffusion model reproduces the observed dynamics and predicts that lipid conservation prevents patterns from propagating across membrane discontinuities, which we verify experimentally. Together, these findings establish enzymatic modification of membrane lipids as a distinct molecular strategy for biological pattern formation.

biophysics↗

bioRxiv2026

Emergence of large-scale polar microtubule swarms for dense molecular transport

Microtubules (MTs) and their motor proteins collectively harness chemical energy to generate mechanical work, driving some of the most coordinated self-organized dynamics in living cells. The unique properties of these molecules also make them versatile building blocks of cytoskeletal active matter and biomimetic nanomachines that recapitulate cellular motility, emergent pattern formation, and motor-driven transport. However, these canonical systems use MTs of fixed length and do not incorporate the natural ability of MTs to grow and regenerate. Here, we go beyond these limits by using dynamic self-amplifying branched MT networks. Driven by kinesin-1 and cytoplasmic dynein activity, surface-gliding branched MT bundles undergo swarming that yields large-scale collective MT architectures with several sought-after features. They are polar and orientationally aligned, dense, span millimeter scales, and persist over hours. We then show that these features enable molecular transport along the swarm at unprecedented capacities, with up to six million motor complexes walking in parallel across millimeter-scale distances over hours. Our results introduce a new regime in cytoskeletal active matter in which the interplay between motor-driven activity and filament generation via branching leads to emergent polar order in proliferating swarms. Such emergent polarity makes these swarms suitable for engineering scalable transport nanotechnologies and programmable soft materials.

biophysics↗

bioRxiv2026

Do plasmid-dependent phages enable the survival of costly plasmids?

Plasmids benefit bacterial communities by storing auxiliary genes that address environmental challenges such as antibiotics. Subsequent plasmid loss can also be advantageous if plasmid benefits are temporary but costs are permanent. However, unless positive selection is sustained, plasmid loss can proceed to extinction, with access to plasmid-derived benefits permanently lost. In principle, horizontal transmission can maintain a plasmid in a population, but if the plasmid cost is too high, the host can become uncompetitive. We examine how survival of costly but occasionally beneficial plasmids is possible in a bacterial population. Using population models, we demonstrate that plasmid-dependent phages can, counterintuitively, solve this plasmid survival problem for their bacterial hosts. Phage predation pins the plasmid at low but nonzero abundance, such that the plasmid cost is effectively neutralized at the population level, dramatically lengthening the persistence time of the plasmid. When conditions change and the costly plasmid becomes beneficial, it spreads across the host population and switches to a vertical-transmission lifestyle until benefits again subside.

microbiology↗

bioRxiv2026

Counting to two: how phages decide between lysis and lysogeny

Upon infecting a bacterium, temperate phages must decide between killing the cell to reproduce (lysis) and entering a symbiotic lifestyle (lysogeny). This choice is often informed by the cells state and by the number of infecting phage particles, or multiplicity of infection (MOI). Because the copy numbers of all phage genes scale identically with MOI, an MOI-dependent decision requires a rapidly established asymmetry between the lytic and lysogenic pathways. We introduce a minimal model showing how a simple coupling to host machinery (e.g. a protease) can generate such an asymmetry. Our analytical model yields scaling laws that predict how the lysislysogeny decision responds to perturbations of the host. It also quantitatively predicts stochastic features of infection outcomes, such as lysogeny probabilities, consistent with experimental data. By reducing complex regulatory networks to their essential components, our framework reveals the organizing principles of lysislysogeny decisions across phage species.

biophysics↗

bioRxiv2026

Virus-like antigen display delivers a stand-alone danger signal through the BCR that circumvents tolerance

How B cells discriminate self from foreign antigens remains a central question, given inherent autoreactivity of the mature B cell receptor (BCR) repertoire. Soluble antigen (sAg) induces tolerance, whereas patterned antigen display on virus-like particles (pAg) triggers robust B cell responses that can proceed without T cell help. Here, we show how this divergence arises early in BCR signaling. Unlike sAg, pAg can bypass a Lyn-dependent negative feedback loop to trigger digital signaling, such that ultra-low concentrations of pAg produce strong and sustained Ca2+ responses. Surprisingly, pAg drives maximal nuclear NF-{kappa}B but limited NFAT, whereas sAg does the opposite, reflecting differential production of diacylglycerol. Consequently, sAg induced an NFAT-dependent anergy program, whereas pAg evaded this state and instead engaged a cMyc-driven program that partially resembles a TLR-dependent danger response. Our findings reveal how proximal signaling directs distinct transcriptional fate to enable immunogenic B cell responses to virus-like antigen display.

immunology↗

bioRxiv2026

Pseudomonas aeruginosa deploys competitor-specific antagonistic strategies

1Microbial competition shapes polymicrobial communities, yet it remains unclear whether bacteria deploy fixed or specific antagonistic strategies against different rivals. Here we show that Pseudomonas aeruginosa deploys distinct strategies to outcompete two clinically relevant species, Burkholderia cenocepacia and Staphylococcus aureus. Under matched conditions, competition with B. cenocepacia is mediated by contact-dependent Type VI secretion, whereas competition with S. aureus follows a staged diffusible program of alkyl quinolone-mediated growth inhibition followed by LasA-dependent lysis. Transcriptomic analysis supports a "Swiss Army knife" model of antagonism in which different competitive context triggers distinct subsets of P. aeruginosas arsenal. Minimal dynamical models verify that contact-dependent killing is effective against slower-growing competitors, whereas a staged strategy of growth inhibition followed by killing via diffusible factors is preferable against faster-growing rivals. Together, these results show that the competitive success of P. aeruginosa depends on competitor-specific antagonistic strategies.

microbiology↗

bioRxiv2026

Death & Chemotaxis: Bacterial chemotaxis enables collective escape from phage predation

Bacteriophages ("phage") are viruses that prey on bacteria in diverse environments, from biological tissues to soils. In many of these environments, bacterial hosts are constantly migrating, yet how bacterial migration is influenced by phage predation remains poorly understood. Using transparent granular hydrogels that mimic natural habitats, we directly visualize populations of motile Escherichia coli encountering lytic T4 phage. Unexpectedly, we find that even in phage-rich environments, bacteria successfully form chemotactic fronts that enable them to migrate over large distances without needing to develop phage resistance. Higher phage concentrations delay front formation but not steady-state front speed or shape. By combining our experiments with biophysical modeling, we demonstrate that this phenomenon arises from the ability of cells to collectively outrun trailing phage bursts--as quantified by a dimensionless "escape parameter" comparing chemotactic and predation rates. This work thus reveals and provides mechanistic insight into the role of cell motility in shaping phage-bacteria interactions in spatially-extended environments.

microbiology↗

bioRxiv2026

Antigen tethering proteins on follicular dendritic cells influence the affinity and diversity of germinal-center B cells

To optimally protect a host, the adaptive immune system must generate antibodies (Abs) that bind the pathogen with high affinity, yet are diverse enough to protect against potential escape mutations. How the immune system can steer between affinity and diversity remains an open question. During the immune response, B cells inside germinal centers (GCs) compete for survival based on their ability to extract antigen from the surface of specialized presenting cells called follicular dendritic cells (FDCs). Curiously, FDCs tether antigen via not one, but two qualitatively distinct routes: direct tethering, in which the linking protein is covalently bound to the Ag, and indirect, Ab-mediated tethering, in which the linking protein is an Ab itself. Using agent-based simulations motivated by the biophysics of Ag extraction, we suggest that the dual-tethering system can improve the robustness of affinity maturation, and may provide a mechanism to steer the balance between affinity and diversity of the GC B cell population. Our model is consistent with experimental observations reporting low-affinity but high-diversity GCs in the absence of Fc{gamma}R, a key Ab-tethering receptor on FDCs.

immunology↗

bioRxiv2026

Cell-body curvature modulates stall frequency to enhance Vibrio cholerae swimming and chemotaxis through hydrogels

The swimming motility of Vibrio cholerae is a virulence factor that aids in breaching the mucus layer of the small intestine. V. cholerae cells have a curved cell shape and previous work demonstrated that loss of curvature decreases infectivity. Here we investigate the mechanism by which V. choleraes curvature affects single-cell motility within mucus-mimicking environments. Using a multiscale chemotaxis assay, we compared the chemotactic performance of wild-type curved cells (O1 El Tor C6706) and straight mutants under linear chemical gradients in liquid solutions, viscous solutions, and soft agar hydrogels. Our findings reveal that curved and straight V. cholerae exhibit similar swimming properties in liquid and purely viscous solutions but significantly differ in hydrogels, with curved cells demonstrating an 86% increase in average chemotactic drift compared to straight mutants in the same chemical gradients. Trajectory analysis indicates that swimming speeds are comparable, but straight mutants experience more frequent stalls, reducing the total time spent swimming. We also found that stalls further reduce chemotactic performances by imposing an average reorientation of bacteria down the chemical gradient, regardless of cell shape. In-silico coarse-grained molecular dynamics simulations corroborate these results and extend them over the wide range of intestinal mucus hydrogel stiffnesses. This model also identifies an optimal curvature for enhanced movement through hydrogel-like meshes that is close to the real median curvature of the pathogen. Our findings thus highlight the mechanisms underpinning cell shapes role in V. choleraes pathogenicity and underscore the necessity of studying bacterial behaviors under conditions that simulate host environments.

microbiology↗

bioRxiv2025

Modeling the Synergetic Dynamics of B cells and TFH cells in Germinal Center Reactions

B cells producing high-affinity antibodies arise through affinity maturation within germinal centers (GCs), where selection is driven by T follicular helper (TFH) cells. Recent studies have shown that, like GC B cells, TFH cells also undergo antigen-dependent selection, with competition among TFH clones dictated by their ability to recognize and stimulate B cells. This sensitivity-dependent selection process leads to dynamic remodeling of the TFH repertoire over time. Despite the essential role of TFH cells in B cell selection, the functional consequences of the time evolution of the TFH cell population remains poorly understood. To address this gap, we developed a population dynamics model that explicitly incorporates key TFH cell properties and dynamics. Our analysis predicts that dynamic feedback between B and TFH cell populations provides robust homeostatic regulation of their numbers in the GC, yielding a stable lymphocyte ratio that we verify experimentally. Moreover, our model predicts that TFH clone sensitivity dictates distinct evolutionary strategies during affinity maturation, with low-sensitivity TFH cells accelerating affinity gain at the expense of B cell diversity, while high-sensitivity TFH cells slow affinity maturation but preserve a broader B cell repertoire. These findings highlight the importance of co-regulation between TFH and B cells and suggest that reciprocal stimulation allows the immune system to tune the tradeoff between the speed of affinity gain and the breadth of B cell diversity--a principle that may extend to other adaptive systems. Significance StatementEffector B cells that secrete high-affinity antibodies and form immunological memory are essential for humoral immunity and arise from germinal center (GC) reactions. Within GCs, B cells undergo an accelerated version of Darwinian evolution to enhance antibody affinity. This process is orchestrated by T follicular helper (TFH) cells which provide stimulatory signals to selected B cells and undergo their own antigen-driven selection. To investigate this co-evolutionary process, we developed a tractable population-level model of the GC reaction. Our analysis reveals that the reciprocal stimulation of B and TFH cells provides a robust mechanism for regulating the B:TFH ratio and tuning the tradeoff between the speed of affinity maturation and the diversity of the antibody response.

immunology↗

bioRxiv2025

Temporal Dynamics of Antigen-Specific T Cell Expansion in Primary SARS-CoV-2 Infection

Quantifying T cell response during primary infection in humans is crucial for understanding adaptive immunity. Leveraging a controlled human challenge to SARS-CoV-2, we characterized antigen-specific T cell response within and across individuals. Notably, individual clones reached similar maximum frequencies despite differences in the timing of their peak expansion. Mathematical modeling showed that this observation is consistent with precursor frequency, but not TCR signal strength, as the source of inter-clonal variability. Single-cell profiling revealed distinct temporal programs for CD4+ and CD8+ T cells, with CD4+ cells expanding earlier but contracting to a lower frequency. Clones with similar receptors, likely recognizing the same antigen, expanded at similar times. Together, these findings highlight how clone-intrinsic properties such as precursor frequency and lineage shape T cell clonal kinetics. These insights provide a quantitative framework for understanding T cell response in humans, with implications for vaccine design.

biophysics↗

bioRxiv2025

Phenotypic heterogeneity in lag reflects an evolutionarily stable bet-hedging strategy

Single-cell experiments in yeast reveal two distinct heritable phenotypes-- arresters and recoverers--when a clonal population experiences a negative shift in its growth environment. Recoverers exhibit a variable yet finite lag before resuming growth in the new environment, whereas arresters remain in a non-growing, arrested state until more favorable conditions return. Although the diversification of individual cells into arresters and recoverers is a robust phenomenon, it remains unclear whether this coexistence constitutes an evolutionarily stable strategy. Here, we demonstrate that a heterogeneous strategy composed of both arrester and recoverer phenotypes maximizes long-term population fitness across a broad spectrum of growth-lag trade-offs. Our analysis employs a dynamic programming framework to identify the fitness-maximizing distribution of phenotypes for populations that stochastically switch between preferred and non-preferred environments. We propose a minimal model incorporating metabolism, growth, and enzyme allocation to explain the physiological origin of a power-law growth-lag trade-off that favors phenotypic heterogeneity. The theory predicts a nontrivial relationship between the fraction of recoverers and their lag time, which aligns with existing data from wild yeast strains, evolved isolates, and variations in pre-shift growth conditions. This relationship suggests an evolutionary rheostat-like mechanism that enables populations to rapidly adapt to changing environmental conditions.

systems biology↗

bioRxiv2025

Competitive catabolism in systemic mammalian metabolic homeostasis

Systemic metabolic homeostasis maintains circulating nutrient concentrations within physiological ranges. Insulin is central to this process, lowering circulating levels of glucose, free fatty acids, and ketones. Yet, how simultaneous homeostasis of these nutrients is achieved remains unclear. Here we develop a differential equation model of fasting metabolic homeostasis. Grounded in mass action kinetics, this multi-nutrient model reveals how a fixed energy demand naturally leads to competition between major circulating nutrients for oxidation ( competitive catabolism). Perturbative nutrient infusions confirm this emergent behavior. The multi-nutrient model predicts that insulin promotes fasting glucose homeostasis primarily indirectly by slowing lipolysis. It further identifies a physiological circuit by which obesity causes diabetes: Increased fat mass promotes lipolysis, releasing fatty acids into circulation that compete with glucose for oxidation, elevating glucose. Resulting hyperinsulinemia restores proper lipid catabolic flux but not euglycemia. Thus, quantitative modeling reveals a physiological homeostatic circuit through which obesity causes type 2 diabetes.

physiology↗

bioRxiv2025

Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions

Biomolecular condensates spatially organize cellular functions, but the regulation of their size, number, dissolution, and re-condensation is poorly understood. The pyrenoid, an algal biomolecular condensate that mediates one-third of global CO2 fixation, typically exists as one large condensate per chloroplast, but during cell division it transiently dissolves and reconfigures into multiple smaller condensates. Here, we identify a kinase, KEY1, in the model alga Chlamydomonas reinhardtii that regulates pyrenoid condensate size and number dynamics throughout the cell cycle and is necessary for normal pyrenoid function and growth. Unlike wild type, key1 mutant cells have multiple smaller condensates throughout the cell cycle that fail to dissolve during cell division. We show that KEY1 localizes to the condensates and promotes their dissolution by disrupting interactions between their core constituents, the CO2-fixing enzyme Rubisco and its linker protein EPYC1, through EPYC1 phosphorylation. We develop a biophysical model that recapitulates KEY1-mediated condensate size and number regulation and suggests a mechanism for controlling condensate position. These data provide a foundation for the mechanistic understanding of the regulation of size, number, position, and dissolution in pyrenoids and other biomolecular condensates.

cell biology↗

bioRxiv2025

When is microbial cross-feeding evolutionarily stable?

Cross-feeding, a phenomenon in which organisms share metabolites, is frequently observed in microbial communities across the natural world. One of the most common forms is waste-product cross-feeding, a unidirectional interaction in which the waste products of one microbe support the growth of another. Despite its ubiquity, it is not well-understood why waste-product cross-feeding persists when a single organism could in principle perform both the producer and consumer role. To address this question, we first analyze cross-feeding evolution in a minimal model of microbial metabolism. The model describes multi-step extraction of energy from a substrate in a simple but thermodynamically correct formulation. Surprisingly, we find that cross-feeding is never evolutionarily stable in this model. By analyzing models with more complex growth functions, we identify a novel mechanism for the evolutionary stability of waste-product cross-feeding, namely, generalized intracellular metabolite toxicity. Such toxicity arises because, in excess, the same intracellular metabolites that cells require for metabolism can be detrimental to growth (e.g., due to osmotic stress). We show that some but not all forms of such toxicity can lead to evolutionarily stable consortia of microbes that cross-feed waste products. This stability results from the potential of such consortia to divide the burden of toxic metabolites among a larger population, allowing them to perform their collective metabolism more efficiently than non-cross-feeders. More generally, we predict that growth penalties that scale nonlinearly with intracellular metabolite levels promote cross-feeding. We find that this mechanism for cross-feeding evolutionary stability implies nontrivial population dynamics, such as a discontinuity in population biomass at the onset of cross-feeding. Significance statementThe chemical reactions performed by microbes have large impacts on our world: from nitrification within the nitrogen cycle to the breakdown of fiber in animal digestive tracts. A striking commonality in many of these processes is that the chemical reactions are a collective effort, with the complete reaction subdivided between many microbes. This phenomenon is known as cross-feeding, and its origins are poorly understood. Understanding the eco-evolutionary forces promoting cross-feeding have the potential to not only enhance our understanding of natural ecosystems, but also improve our ability to engineer such distributed reactions in biotechnology. Here, we develop mathematical theory for the evolution of a common type of cross-feeding and provide predictions for what metabolic and environmental conditions promote this behavior.

microbiology↗

bioRxiv2024

Membrane wetting by biomolecular condensates is facilitated by mobile tethers

Biomolecular condensates frequently rely on membrane interactions for recruitment, localization, and biochemical substrates. Many of these interactions are mediated by membrane-anchored molecules such as proteins or specific lipids, which we refer to as "mobile tethers" since they can typically diffuse within the membrane while still interacting with the condensate. The presence of mobile tethers creates a surface with dynamic and spatially inhomogeneous wetting properties that are typically overlooked by traditional wetting theories. Here, we propose a general theoretical framework to study how mobile tethers impact both equilibrium and dynamic properties of condensate wetting. We show that a favorable tether-condensate interaction leads to tether enrichment at the condensate-membrane interface, which modifies the equilibrium surface tension and contact angle. Increasing tether abundance on the membrane can drive transitions between wetting regimes, with only a modest tether density and binding energy required for biologically relevant scenarios. Furthermore, tethers modulate how condensates react to complex membrane geometries. By helping condensates coat membranes, mobile tethers can facilitate condensate localization to junctions of membrane structures, such as the reticulated membranes inside the algal pyrenoid. Both tether abundance and mobility affect how droplets interact with complex membrane geometries, such as droplet migration along membrane tubules of varying radii. These results provide a framework to study the implications of tether-mediated condensate-membrane interactions for cellular organization and function.

biophysics↗

bioRxiv2024

Sticky enzymes: increased metabolic efficiency via substrate-dependent enzyme clustering

Coclustering of subsequent enzymes in a pathway can accelerate the processing of metabolic intermediates, with benefits including increased pathway fluxes, reduced toxicity, and sensitive branch-point regulation. While the optimal organization of such clusters has been explored theoretically, little is known about how to achieve such organization inside cells. Here we propose that phase-separating enzymes can self-organize into nearly-optimally sized and spaced clusters, provided that their "stickiness" is regulated by local substrate availability. In a nutshell, enzyme clusters only form when and where they are needed to process substrate. We study a mathematical model that implements this scheme for simple metabolic pathways, including all thermodynamic constraints. We find that pathway fluxes can be increased by 50 to 1000-fold and toxic metabolites can be decreased by 10 to 100-fold, at realistic enzyme densities. Finally, we discuss how enzyme "stickiness" could be allosterically regulated. This study presents a self-organization strategy that goes beyond current paradigms for natural and engineered enzyme clusters, and thus represents a motivating challenge to the fields of synthetic biology and metabolic engineering.

biophysics↗

bioRxiv2024

DNA/polysome phase separation and cell width confinement couple nucleoid segregation to cell growth in Escherichia coli

Chromosome segregation is essential for cellular proliferation. Unlike eukaryotes, bacteria lack cytoskeleton-based machinery to segregate their chromosomal DNA (nucleoid). The bacterial ParABS system segregates the duplicated chromosomal regions near the origin of replication. However, this function does not explain how bacterial cells partition the rest (bulk) of the chromosomal material. Furthermore, some bacteria, including Escherichia coli, lack a ParABS system. Yet, E. coli faithfully segregates nucleoids across various growth rates. Here, we provide theoretical and experimental evidence that polysome production during chromosomal gene expression helps compact, split, segregate, and position nucleoids in E. coli through out-of-equilibrium dynamics and polysome exclusion from the DNA meshwork, inherently coupling these processes to biomass growth across nutritional conditions. Halting chromosomal gene expression and thus polysome production immediately stops sister nucleoid migration while ensuing polysome depletion gradually reverses nucleoid segregation. Redirecting gene expression away from the chromosome and toward plasmids causes ectopic polysome accumulations that are sufficient to drive aberrant nucleoid dynamics. Cell width enlargement suggest that the proximity of the DNA to the membrane along the radial axis is important to limit the exchange of polysomes across DNA-free regions, ensuring nucleoid segregation along the cell length. Our findings suggest a self-organizing mechanism for coupling nucleoid segregation to cell growth.

microbiology↗