Biology subjects

Allard, J.

Publications and source records attributed to Allard, J..

17 recordsLinked to original sources

bioRxiv2025

The impact of N-terminal dimerization on formin homology 1 (FH1) domain polymer dynamics and actin assembly

Many proteins contain intrinsically disordered regions (IDRs) that lack stable 3-dimensional structure. IDR behavior is poorly understood, leading to challenges for biochemical and computational analysis of IDR-containing proteins. Formins are a diverse set of homodimers containing an IDR -- the FH1 domain -- that facilitates polymerization of the cytoskeletal protein actin by increasing the local concentration of actin monomers at the actin assembly site. A commonly accepted model of formin-based actin polymerization involves a capture-and-deliver process: one or more binding sites (proline-rich motifs, PRMs) "capture" actin monomers and then "deliver" actin to the actin assembly site. There is evidence that formin FH1 domains are dimerized on both ends, but much research has been performed with formin constructs lacking the N-terminal dimerization site. Here, we ask: What happens when N-terminal dimerization is added to the standard model of formin-mediated actin assembly? We extend the kinetic model of FH1-mediated actin polymerization by incorporating a coarse-grain polymer model of FH1 domain dynamics, modeling the FH1 domain as a freely-jointed chain. We find that N-terminal dimerization can impact polymerization rates by modifying binding site accessibility and/or local concentration of binding sites (PRMs) at the actin assembly site (FH2 domain). Which effect dominates depends on kinetic parameters and formin properties such as FH1 domain length and binding site location. Additionally, we demonstrate that our model can be fit to experimental data and used to make predictions for the effects of N-terminal dimerization on a variety of formin family members. SignificanceIntrinsically disordered regions (IDRs) are common protein components that lack stable 3D structures and are thus difficult to study. Here, we develop a polymer-physics based computational model of the formin FH1 domain, an IDR involved in building the cells cytoskeleton. Some disease-associated mutations of formins occur in a region that is suspected to induce dimerization, forcing the FH1 domains to form a loop. Little is known about the loops prevalence, location, or impact on cytoskeletal assembly. Using simple polymer physics, we demonstrate that this dimerization can alter FH1 domain polymer dynamics and thus impact cytoskeletal assembly. These results not only highlight an important aspect of FH1-mediated cytoskeletal assembly, but also provide a framework for modeling IDRs.

biophysics↗

bioRxiv2025

Improvement in model flexibility reveals a minimal signalling pathway that explains T cell responses to pulsatile stimuli

Efforts to develop quantitative models must face a trade-off between interpretability and quantitative accuracy, which often disfavors interpretability. Here we adopt an operational definition of interpretability, specifically that a model is described by an arrow diagram wherein each arrow corresponds to a positive effect or negative effect of one component upon a process, and fewer arrows is more inter-pretable than more arrows. We then develop a method to add flexibility -- and thus accuracy in fitting data -- to mathematical models by relaxing functional form assumptions, while constrained by the same arrow diagram and thus the same interpretability. We apply this method to the T cell, where quantitative models are particularly needed, in part because of ongoing efforts to engineer T cells as therapeutics. One avenue of experiments exposes T cells to pulsatile inputs and measures their frequency response, finding several nonlinear frequency responses: high-pass, low-pass, band-pass, and band-stop. Using our modeling approach with enhanced flexibility, we show that a simple signaling model quantitatively captures the frequency response of CD69 surface expression, one of the correlates of T cells activation, with accuracy within the experimental inter-replicate standard error of the mean. Specific qualitative behaviors map to specific parts of the arrow diagram: Band-pass behavior can be explained by refractory de-sensitizing circuit (we refer to this as "first-aid icing a wound"). Band-stop behavior can be explained by removal-inhibition (we refer to this as "roommate interrupts my studying"). Apparent low-pass emerges naturally when total stimulation time is constant. We test the model on independent experimental datasets from multiple labs. Taken together, our results demonstrate the ability to achieve both quantitative prediction and interpretability in understanding cellular dynamics. Simple models may at first appear incapable of explaining complex data, but might indeed be able to by adding this modest flexibility.

systems biology↗

bioRxiv2025

Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds

A repeated pattern in cytoskeletal architecture is the aster, in which a number of F-actin filaments emerge star-shaped from a central node. Aster-based structures occur in cytoplasmic actin, the early stages of the cytokinetic ring in yeast, and in the context of biomimetic materials engineering. In this work, we use computational simulation to show that there is an optimal number of filaments per aster that maximizes rigidity, even at a fixed density of F-actin. This nonlinear dependence holds for both the shear and extensional moduli. At physiological parameters, the maximum corresponds approximately to the same filaments-per-aster observed in recent super-resolution images of cortical F-actin. Furthermore, we find that increasing filaments-per-aster leads to dramatic increases in the sample-to-sample variability in network rigidity. We explain both effects using percolation theory, wherein the probability that a given network is productively connected exhibits a sharp dependence on parameters. The dependence of network rigidity on this nanoscale architectural feature may suggest a mechanism by which cells tune the physical properties of their actin networks locally and rapidly (since no new F-actin must be assembled) and may inform efforts to create adaptive synthetic metamaterials inspired by actin networks.

biophysics↗

bioRxiv2025

The metabolic kinase LKB1 shapes the enteric nervous system bymitigating the oxidative stress and p53 activity

The enteric nervous system (ENS) comprises ganglia of neurons and glial cells derived from migratory multipotent neural crest cells. While the molecular mechanisms of ENS development are well-studied, the involvement of metabolic processes has received less attention. We previously showed that the tumor suppressor kinase LKB1 is essential for the trophic maintenance of postnatal ENS. Here we examined LKB1s role in ENS formation using a genetically engineered mouse model that conditionally inactivates Lkb1 in neural crest progenitors during gut invasion. We conducted a comprehensive phenotyping of the ENS through histology and 3D imaging of cleared tissue, combining lightsheet microscopy with adaptive optics confocal microscopy. We found that Lkb1 loss impairs early neuronal differentiation, followed by glial degeneration, leading to hypoganglionosis and compromised digestive tissue integrity. Metabolite profiling of digestive tracts revealed an increase of oxidative stress upon Lkb1 ablation. In vitro, Lkb1 knockdown induced oxidative stress in neural crest progenitors and their glial derivatives, causing DNA damage and p53 activation. Ablation of p53 rescued glial specification under these conditions. In vivo, hyperphosphorylation of p53 was also observed; however, deletion of p53 alleles in Lkb1 mutants did not restore enteric neurons number. Instead, it improved axonal fiber organization and partially rescued digestive tissue integrity. These findings establish LKB1 as a key metabolic regulator on both the development and maintenance of the ENS, suggesting that aberrant LKB1 signaling may contribute to human enteric glioneuropathies. HighlightsO_LILKB1 loss in enteric progenitors results in extensive hypoganglionosis and disrupts gut tissue homeostasis. C_LIO_LIDuring embryogenesis, LKB1 shapes enteric ganglia by sequentially regulating neuronal differentiation and preserving glial cells, partly by limiting oxidative stress and p53 activity. C_LIO_LIThese findings establish LKB1 as a critical regulator of neural crest cell formation, highlighting its multifaceted roles and potential pathological implications in digestive neuropathies. C_LI

developmental biology↗

bioRxiv2025

Scalable Inference and Identifiability of Kinetic Parameters for Transcriptional Bursting from Single Cell Data

MotivationStochastic gene expression and cell-to-cell heterogeneity have attracted increased interest in recent years, enabled by advances in single-cell measurement technologies. These studies are also increasingly complemented by quantitative biophysical modeling, often using the framework of stochastic biochemical kinetic models. However, inferring parameters for such models (that is, the kineticrates of biochemical reactions) remains a technical and computational challenge, particularly doing so in a manner that can leverage high-throughput single-cell sequencing data. ResultsIn this work, we develop a Chemical Master Equation reference library-based computational pipeline to infer kinetic parameters describing noisy mRNA distributions from single cell RNA sequencing data, using the commonly applied stochastic telegraph model. Our pipeline also serves as a tool for comprehensive analysis of parameter identifiability, in both a priori (studying model properties in the absence of data) and a posteriori (in the context of a particular dataset) use cases. The pipeline can perform both of these tasks, i.e. inference and identifiability analysis, in an efficient and scalable manner, and also serves to disentangle contributions to uncertainty in inferred parameters from experimental noise versus structural properties of the model. We found that for the telegraph model, the majority of the parameter space is not practically identifiable from single cell RNA sequencing data, and low experimental capture rates worsen the identifiability. Our methodological framework could be extended to other data types in the fitting of small biochemical network models. AvailabilityAll code relevant to this work is available at https://github.com/Read-Lab-UCI/TelegraphLikelihoodInfer.

biophysics↗

bioRxiv2025

Estimating dead fish quantities dropping out of gillnets when direct observations are impossible.

Fish that are caught in passive or fixed fishing gear and subsequently die and drop out of the gear, or that are removed by scavengers, do not show up in catch statistics and constitute unaccounted-for removals. Estimating these removals is challenging, particularly when direct observations are not possible because fishing conditions preclude the use of cameras or other devices or means to catch or observe the removals. Using a simple theoretical process model, we define two independent modelling approaches to estimate unaccounted mortalities resulting from drop-out. The first is based on a minimally refined analysis of commonly available fishery catch per unit effort data. The second, models data that can be obtained straightforwardly from field experiments and from at-sea fishery observers, specifically data on catch amounts, and catch composition according to three condition categories - live, dead-fresh and degraded. We apply these modelling approaches to data from the Gulf of St. Lawrence (Canada) Greenland halibut (Reinhardtius hippoglossoides) gillnet fishery, for which multi-day soak durations have long been suspected of generating significant unaccounted fish death while only little evidence is available. In fact, observed proportions of dead decaying and ultimately discarded catch for this fishery are small and increase only a little with increased soak duration, constituting seemingly contradictory evidence. The two modelling approaches produce similar results, estimating that total dead catches of Greenland halibut were on average 4.7 to 5.4 times the recorded landings over the period from 2000 to 2024. This result is consistent with the high mortality levels suggested by the assessment for this stock. Of broader relevance to other gillnet fisheries worldwide that may employ shorter soak duration, we found that estimated unobserved catch losses equalled retained catch after soak durations of 15 hours or less. Importantly the condition of fish in catches may belie the quantities of dead fish losses. Failing to account for fishing derived loss of the magnitude estimated here could result in important biases in stock assessments and associated sustainable harvesting frameworks, in addition to constituting an important source of waste.

ecology↗

bioRxiv2025

Preventing neuropathy and improving anti-cancer chemotherapy with a carbazole-based compound

Advances in cancer treatment have led to a steady increase in the rate of disease remission. However, while many treatment-related adverse effects gradually resolve after therapy, chemotherapy-induced peripheral neuropathy (CIPN) often persists, with no means of prevention or direct treatment available. Herein, we present Carba1, a novel bi-functional carbazole that mitigates neuropathy through two distinct mechanisms. First, by interacting with tubulin, Carba1 reduces the required dose of taxanes, widely used chemotherapy drugs notorious for their toxic side effects, including CIPN. Second, Carba1 activates nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in the NAD salvage pathway, triggering a metabolic rewiring that enhances the resilience of neurons and Schwann cells against chemotherapy-induced toxicity. We demonstrate the neuroprotective efficacy of Carba1 both in vitro, against neurotoxicity induced by paclitaxel (PTX), cisplatin, and bortezomib, and in vivo in a rat model of PTX-induced neuropathy. Importantly, we establish that Carba1 does not compromise the therapeutic efficacy of PTX nor promotes tumor growth. Comparative analyses of Carba1 derivatives further suggest the potential of designing compounds with either dual synergistic and neuroprotective activity or exclusive neuroprotective properties. Altogether, our findings position Carba1 as a promising therapeutic candidate for preventing CIPN, with the potential, if successfully translated to clinical settings, to improve both the quality of life and treatment outcome for cancer patients.

cancer biology↗

bioRxiv2024

Nucleosome placement and polymer mechanics explain genomic contacts on 100kbp scales

The 3d organization of the genome -- in particular, which two regions of DNA are in contact with each other -- plays a role in regulating gene expression. Several factors influence genome 3d organization. Nucleosomes (where [~] 100 basepairs of DNA wrap around histone proteins) bend, twist and compactify chromosomal DNA, altering its polymer mechanics. How much does the positioning of nucleosomes between gene loci influence contacts between those gene loci? And, to what extent are polymer mechanics responsible for this? To address this question, we combine a stochastic polymer mechanics model of chromosomal DNA including twists and wrapping induced by nucleosomes with two data-driven pipelines. The first estimates nucleosome positioning from ATACseq data in regions of high accessibility. Most of the genome is low-accessibility, so we combine this with a novel image analysis method that estimates the distribution of nucleosome spacing from electron microscopy data. There are no fit parameters in the biophysical model. We apply this method to IL6, IL15, CXCL9, and CXCL10, inflammatory marker genes in macrophages, before and after inflammatory stimulation, and compare the predictions with contacts measured by conformation capture experiments (4C-seq). We find that within a 500 kilo-basepairs genomic region, polymer mechanics with nucleosomes can explain 71% of close contacts. These results suggest that, while genome contacts on 100kbp-scales are multifactorial, they may be amenable to mechanistic, physical explanation. Our work also highlights the role of nucleosomes, not just at the loci of interest, but between them, and not just the total number of nucleosomes, but their specific placement. The method generalizes to other genes, and can be used to address whether a contact is under active regulation by the cell (e.g., a macrophage during inflammatory stimulation).

biophysics↗

bioRxiv2021

Zebrafish airinemes optimize their shape between ballistic and diffusive search

In addition to diffusive signals, cells in tissue also communicate via long, thin cellular protrusions, such as airinemes in zebrafish. Before establishing communication, cellular protrusions must find their target cell. Here we demonstrate that the shape of airinemes in zebrafish are consistent with a finite persistent random walk model. The probability of contacting the target cell is maximized for a balance between ballistic search (straight) and diffusive search (highly curved, random). We find that the curvature of airinemes in zebrafish, extracted from live cell microscopy, is approximately the same value as the optimum in the simple persistent random walk model. We also explore the ability of the target cell to infer direction of the airinemes source, finding that there is a theoretical trade-off between search optimality and directional information. This provides a framework to characterize the shape, and performance objectives, of non-canonical cellular protrusions in general.

systems biology↗

bioRxiv2021

Simulation of receptor triggering by kinetic segregation shows role of oligomers and close-contacts

The activation of T cells, key players of the immune system, involves local evacuation of phosphatase CD45 from a region of the T cells surface, segregating it from the T cell receptor. What drives this evacuation? In the presence of antigen, what ensures evacuation happens in the sub-second timescales necessary to initiate signaling? In the absence of antigen, what mechanisms ensure evacuation does not happen spontaneously, which could cause signaling errors? Phenomena known to influence spatial organization of CD45 or similar surface molecules include diffusive motion in the lipid bilayer, oligomerization reactions, and mechanical compression against a nearby surface, such as that of the cell presenting antigen. Computer simulations can investigate hypothesized spatiotemporal mechanisms of T cell signaling. The challenge to computational studies of evacuation is that the base process, spontaneous evacuation by simple diffusion, is in the extreme rare event limit, meaning direct stochastic simulation is unfeasible. Here we combine particle-based spatial stochastic simulation with the Weighted Ensemble method for rare events to compute the mean first-passage time for cell surface availability by surface reorganization of CD45. We confirm mathematical estimates that, at physiological concentrations, spontaneous evacuation is extremely rare, roughly 300 years. We find that dimerization decreases the time required for evacuation. A weak bi-molecular interaction (dissociation constant estimate 460 microMolar) is sufficient for an order of magnitude reduction of spontaneous evacuation times, and oligomerization to hexamers reduces times to below 1 second. This introduces a mechanism whereby CD45 oligomerization could be accessible to an engineered therapeutic. For large regions of close-contact, such as those induced by large microvilli, molecular size and compressibility imply a nonzero re-entry probability 60%, decreasing evacuation times. Simulations show that these reduced evacuation times are still unrealistically long, suggesting that a yet-to-be-described mechanism, besides compressional exclusion at a close contact, drives evacuation. Statement of SignificanceIn the immune system, T cells sensing pathogens depends on a process called T cell receptor triggering. In this process, proteins on the cell surface undergo reorganization, including local depletion of large membrane proteins from the area surrounding the T cell receptor. Computer simulations of protein dynamics provide a means to investigate phenomena in greater detail than that afforded by experiments. However, even simulations present challenges, because tracking the motion and interactions of individual molecules is computationally expensive. Combining a rare event algorithm with spatial simulations, we show that biochemical and mechanical properties drastically affect depletion timescales, and thus receptor triggering. Quantitative understanding of these timescales will constrain hypothesized mechanistic models and could suggest new strategies for T cell engineering.

biophysics↗

bioRxiv2020

Determination of the molecular reach of the protein tyrosine phosphatase SHP-1

Immune receptor signalling proceeds by the binding (or tethering) of enzymes to their cytoplasmic tails before they catalyse reactions on substrates within reach. This is the case for the enzyme SHP-1 that, upon tethering to the inhibitory receptor PD-1, dephosphorylates membrane substrates to suppress T cell activation. Precisely how tethering regulates SHP-1 activity is incompletely understood. Here, we use surface plasmon resonance to measure binding, catalysis, and molecular reach for PD-1 tethered SHP-1 reactions. We find that the reach of PD-1--SHP-1 complexes is dominated by the 13.0 nm reach of SHP-1 itself. This is longer than an estimate from the structure of the allosterically active conformation (5.3 nm), suggesting that SHP-1 explores multiple active conformations. Using modelling, we show that when uniformly distributed, PD-1--SHP-1 complexes can only reach 15% of substrates but this increases to 90% when they are co-clustered. When within reach, we show that membrane recruitment increases the activity of SHP-1 by a 1000-fold increase in local concentration. The work highlights how molecular reach regulates the activity of membrane-recruited SHP-1 with insights applicable to other membrane-tethered reactions. Significance statementImmune receptors transduce signals by recruiting (or tethering) cytoplasmic enzymes to their tails at the membrane. When tethered, these enzymes catalyse reactions on other substrates to propagate signalling. Precisely how membrane tethering regulates enzyme activity is incompletely understood. Unlike other tethered reactions, where the enzyme tethers to the substrate, the substrate in this case is a different receptor tail. Therefore, the ability of the receptor-tethered enzyme to reach a substrate can be critical in controlling reaction rates. In this work, we determine the molecular reach for the enzyme SHP-1 and the receptor PD-1 to which it can tether, and show how molecular reach controls receptor signalling.

biophysics↗

bioRxiv2020

Regulated unbinding of ZAP70 at the T cell receptor by kinetic avidity

Protein-protein binding domains are critical in signalling networks. Src homology 2 (SH2) domains are binding domains that interact with sequences containing phosphorylated tyrosines. A subset of SH2 domain-containing proteins have tandem domains, which are thought to enhance binding affinity and specificity. However, a trade-off exists between long-lived binding and the ability to rapidly reverse signalling, which is a critical requirement of noise filtering mechanisms such as kinetic proofreading. Here, we use modelling to show that the unbinding rate of tandem, but not single, SH2 domains can be accelerated by phosphatases when tandem domains bind by a kinetic, but not a static, avidity mode. We use surface plasmon resonance to show that ZAP70, a tandem SH2 domain-containing kinase, binds kinetically to biphosphorylated peptides from the T cell antigen receptor (TCR) and that the unbinding rate can be accelerated by the phosphatase CD45. An important functional prediction of regulated unbinding is that the intracellular ZAP70/TCR half-life in T cells will be correlated to the extracellular TCR/antigen half-life and we show that this is the case in both cell lines and primary T cells. The work highlights that binding by kinetic avidity breaks the trade-off between signal fidelity (requiring long half-life) and signal reversibility (requiring short half-life), which is a key requirement for T cell antigen discriminated mediated by kinetic proofreading.

immunology↗

bioRxiv2019

Molecular motor organization and mobility on cargos can overcome a tradeoff between fast binding and run length

Cellular cargos, including lipid droplets and mitochondria, are transported along microtubules using molecular motors such as kinesins. Many experimental and computational studies of cargos with rigidly attached motors, in contrast to many biological cargos that have lipid surfaces that may allow surface mobility of motors. We extend a mechanochemical 3D computational model by adding coupled-viscosity effects to compare different motor arrangements and mobilities. We show that organizational changes can optimize for different objectives: Cargos with clustered motors are transported efficiently, but are slow to bind to microtubules, whereas those with motors dispersed rigidly on their surface bind microtubules quickly, but are transported inefficiently. Finally, cargos with freely-diffusing motors have both fast binding and efficient transport, although less efficient than clustered motors. These results suggest that experimentally observed changes in motor organization may be a control point for transport.

cell biology↗

bioRxiv2018

The Influence of Molecular Reach and Diffusivity on the Efficacy of Membrane-Confined Reactions

Signalling by surface receptors often relies on tethered reactions whereby an enzyme bound to the cytoplasmic tail f a receptor catalyses reactions on substrates within reach. The overall length and stiffness of the receptor tail, the enzyme, and the substrate determine a biophysical parameter termed the molecular reach of the reaction. This parameter determines the probability that the receptor-tethered-enzyme will contact the substrate, in the volume proximal to the membrane, when separated by different distances within the membrane plane. Here, we develop particle-based stochastic reaction-diffusion models to study the interplay between molecular reach and diffusion. We find that increasing the molecular reach can increase reaction efficacy when diffusion is slow, but when diffusion is fast, increasing molecular reach reduces reaction efficacy. This switching is lost if reactions are forced to take place within the 2D plasma membrane instead of the 3D volume proximal to it, or if molecules diffuse in 3D. We show results in the context of immune receptors (PD-1 dephosphorylating CD28), a standard opposing kinase-phosphatase reaction, and a minimal two-particle model. The work highlights the 3D nature of many 2D membrane-confined interactions, illustrating a role for molecular reach in controlling biochemical reactions.

biophysics↗

bioRxiv2018

Molecular flexibility of DNA as a major determinant of RAD51 recruitment

The timely activation of homologous recombination is essential for the maintenance of genome stability, in which the RAD51 recombinase plays a central role. Biochemically, human RAD51 polymerises faster on single-stranded DNA (ssDNA) compared to double-stranded DNA (dsDNA), raising a key conceptual question: how does it discriminate between them? In this study, we tackled this problem by systematically assessing RAD51 binding kinetics on ssDNA and dsDNA differing in length and flexibility using surface plasmon resonance. By fitting detailed polymerisation models informed by our experimental datasets, we show that RAD51 is a mechano-sensor that exhibits a larger polymerisation rate constant on flexible ssDNA compared to rigid ssDNA or dsDNA. This model presents a new general framework suggesting that the flexibility of DNA, which may increase locally as a result of DNA damage, plays an important role in rapidly recruiting repair factors that multimerise at sites of DNA damage.

biochemistry↗

bioRxiv2018

Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length

In many biological settings, two or more cells come into physical contact to form a cell-cell interface. In some cases, the cell-cell contact must be transient, forming on timescales of seconds. One example is offered by the T cell, an immune cell which must attach to the surface of other cells in order to decipher information about disease. The aspect ratio of these interfaces (tens of nanometers thick and tens of micrometers in diameter) puts them into the thin-layer limit, or \"lubrication limit\", of fluid dynamics. A key question is how the receptors and ligands on opposing cells come into contact. What are the relative roles of thermal undulations of the plasma membrane and deterministic forces from active filopodia? We use a computational fluid dynamics algorithm capable of simulating 10-nanometer-scale fluid-structure interactions with thermal fluctuations up to seconds-and microns-scales. We use this to simulate two opposing membranes, variously including thermal fluctuations, active forces, and membrane permeability. In some regimes dominated by thermal fluctuations, proximity is a rare event, which we capture by computing mean first-passage times using a Weighted Ensemble rare-event computational method. Our results demonstrate that the time-to-contact increases for smaller cell-cell distances (where the thin-layer effect is strongest), leading to an optimal initial cell-cell separation for fastest receptor-ligand binding. We reproduce a previous experimental observation that fluctuation spatial scales are largely unaffected, but timescales are dramatically slowed, by the thin-layer effect. We also find that membrane permeability would need to be above physiological levels to abrogate the thin-layer effect.\n\nAuthor summaryThe elastohydrodynamics of water in and around cells is playing an increasingly recognized role in biology. In this work, we investigate the flow of extracellular fluid in between cells during the formation of a cell-cell contact, to determine whether its necessary evacuation as the cells approach is a rate-limiting step before molecules on either cell can interact. To overcome the computational challenges associated with simulating fluid in this mechanically soft, stochastic and high-aspect-ratio environment, we extend a computational framework where the cell plasma membranes are treated as immersed boundaries in the fluid, and combine this with computational methods for simulating stochastic rare events in which an ensemble of simulations are given weights according to their probability. We find that the internal dynamics of the membranes has speeds in approximately microseconds, but that as the cells approach, a new slow timescale of approximately milliseconds is introduced. Thermal undulations nor typical amounts of membrane permeability can overcome the timescale, but active forces, e.g., from the cytoskeleton, can. Our results suggest an explanation for differences in molecular interactions in live cells compared to in vitro reconstitution experiments.

biophysics↗

bioRxiv2018

Nucleo-cytoplasmic trafficking regulates nuclear surface area during nuclear organogenesis

Throughout development, nuclei must be assembled following every cell division to establish a functional organelle from compact, mitotic chromatin. During nuclear organogenesis, chromatin expands to establish a nucleus of a given size seperate from the cytoplasm. Determining how nuclear organogenesis is regulated is particularly significant in the context of certain cancers in which scaling relationships between cell and nuclear sizes are not maintained. Controlling cell size in vitro using a microfluidics approach, we determined that neither nuclear volume nor surface area scale directly with cell size. Looking to explain differential nuclear scaling relationships, we developed a simple mechano-chemical mathematical model. In simulating biological perturbations in silico, our model predicted crucial roles for nucleo-cytoplasmic trafficking in regulating nuclear expansion and in restricting the recruitment of a potential nuclear surface area factor. In mammalian tissue culture, inhibiting nuclear export increased nuclear expansion rates and reduced the amount of nuclear lamin, a candidate surface area factor, being recruited to assembling nuclei, supporting our models predictions. Targeting the principal nuclear export component in the Drosophila syncytial embryo, Embargoed, we show that nuclear expansion rates are also increased in this developmental context, consistent with our model. Using the MS2-reporter system in fly embryos, we demonstrate a role for nuclear export in regulating transcription activation timing and dynamics, suggesting that regulating nuclear assembly is crucial for downstream nuclear function. Taken together, we propose a simple model through which nuclear organogenesis is achieved and demonstrate a role for nuclear export in regulating nuclear assembly.

cell biology↗