Biology subjects

Freedman, S. L.

Publications and source records attributed to Freedman, S. L..

4 recordsLinked to original sources

bioRxiv2024

Growth-induced collective bending and kinetic trapping of cytoskeletal filaments

Growth and turnover of actin filaments play a crucial role in the construction and maintenance of actin networks within cells. Actin filament growth occurs within limited space and finite subunit resources in the actin cortex. To understand how filament growth shapes the emergent architecture of actin networks, we developed a minimal agent-based model coupling filament mechanics and growth in a limiting subunit pool. We find that rapid filament growth induces kinetic trapping of highly bent actin filaments. Such collective bending patterns are long-lived, organized around nematic defects, and arises from competition between filament polymerization and bending elasticity. The stability of nematic defects and the extent of kinetic trapping are amplified by an increase in the abundance of the actin pool and by crosslinking the network. These findings suggest that kinetic trapping is a robust consequence of growth in crowded environments, providing a route to program shape memory in actin networks.

biophysics↗

bioRxiv2021

Revealing cell-fate bifurcations from transcriptomic trajectories of hematopoiesis

Inspired by Waddingtons illustration of an epigenetic landscape, cell-fate transitions have been envisioned as bifurcating dynamical systems, wherein the dynamics of an exogenous signal couples to a cells enormously complex signaling and transcriptional machinery, eliciting a qualitative transition in the collective state of a cell - its fate. It remains unclear, however, whether the dynamical systems framework can go beyond a word-based caricature of the system and provide sharp quantitative insights that further our understanding of differentiation. Single-cell RNA sequencing (scRNA-seq), which measures the distributions of possible transcriptional states in large populations of differentiating cells, provides an alternate view, in which development is marked by the individual concentration variations of a myriad of genes. Here, starting from formal mathematical derivations, we challenge these transcriptomic trajectories to a rigorous statistical evaluation of whether they display signatures consistent with bifurcations. After pinpointing bifurcations along transcriptomic trajectories of the neutrophil branch of hematopoeitic differentiation we are able to further leverage the primitive features of a linear instability to identify the single-direction in gene expression space along which the bifurcation unfolds and identify possible gene contributors. This scheme identifies transcription factors long viewed to play a crucial role in the process of neutrophil differentiation in addition to identifying a host of other novel genetic players. Most broadly speaking, we provide evidence that, though very high-dimensional, a bifurcating dynamical systems formalism might be appropriate for the process of cellular differentiation and that it can be leveraged to provide insights. Ambitiously, our work attempts to take a step beyond data-analysis and towards the construction of falsifiable mathematical models that describe the dynamics of the entire transcriptome.

biophysics↗

bioRxiv2018

Mechanical and kinetic factors drive sorting of F-actin crosslinkers on bundles

In cells, actin binding proteins (ABPs) sort to different regions in order to establish F-actin networks with diverse functions, including filopodia used for cell migration, or contractile rings required for cell division. Recent experimental work uncovered a passive mechanism that may facilitate spatial localization of ABPs: binding of a short crosslinker protein to two actin filaments promotes the binding of other short crosslinkers and inhibits the binding of longer crosslinkers (and vice versa). We hypothesize this sorting arises because F-actin is semiflexible and cannot bend over short distances. We develop a mathematical theory and a kinetic Monte Carlo simulation encompassing the most important physical parameters for this process, and use simulations of a coarse-grained but molecularly explicit model to characterize and test our predictions about the interplay of mechanical and kinetic parameters. Our theory and data predict an explicit dependence of crosslinker separation on bundle polymerization rate. We perform experiments that confirm a dependence on polymerization rate, but in an unanticipated non-monotonic manner. We use simulations to show that this non-monotonic behavior can arise in situations where crosslinkers have equal bundling affinity at equilibrium, but differing microscopic binding rates to filaments. This dependence of sorting on actin polymerization rate is a non-equilibrium effect, qualitatively similar to non-equilibrium domain formation in materials growth. Thus our results reveal an avenue by which cells can organize molecular material to drive biological processes, and can also guide the choice and design of crosslinkers for engineered protein-based materials.

biophysics↗

bioRxiv2017

Filament Rigidity And Connectivity Tune The Deformation Modes Of Active Biopolymer Networks

Molecular motors embedded within collections of actin and microtubule filaments underlie the dynamic behaviors of cytoskeletal assemblies. Understanding the physics of such motor-filament materials is critical to developing a physical model of the cytoskeleton and the design of biomimetic active materials. Here, we demonstrate through experiments and simulations that the rigidity and connectivity of filaments in active biopolymer networks regulates the anisotropy and the length scale of the underlying deformations, yielding materials with varying contractility. Semi-flexible filaments that can be compressed and bent by motor stresses undergo deformations that are predominantly biaxial. By contrast, rigid filament bundles contract via actomyosin sliding deformations that are predominantly uniaxial. Networks dominated by filament buckling are robustly contractile under a wide range of connectivities, while networks dominated by actomyosin sliding can be tuned from contractile to extensile through reduced connectivity via cross-linking. These results identify physical parameters that control the forces generated within motor-filament arrays, and provide insight into the self-organization and mechanics of cytoskeletal assemblies.

biophysics↗