Biology subjects

Goychuk, A.

Publications and source records attributed to Goychuk, A..

10 recordsLinked to original sources

bioRxiv2026

Biophysical properties of IgD determine thresholds for self-tolerance and selection into germinal centers

Immunoglobulin D (IgD) is among the most conserved antibody isotypes, found in virtually all jawed vertebrates1. Unlike other isotypes, IgD contains an unusually long hinge region of up to 160 amino acids that connects the constant and variable regions. Its expression pattern is also conserved; IgD is co-expressed with IgM on transitional and mature naive B cells. However, the function of IgD has remained enigmatic since its discovery in 19652,3. Here we present and test a biophysical model positing that IgD increases the entropic cost of bivalent antigen binding. Single-molecule measurements revealed that the antigen-binding arms of IgD are substantially more dynamic than those of IgM, suggesting that cell surface IgD would be energetically penalized in bivalent antigen binding. Consistent with the model and biophysical data, we find that the long hinge compromises antigen capture by IgD B cell receptors (BCRs) compared to IgM BCRs. To determine how the difference in antigen binding impacts immunity, we produced mice that express only IgM and IgD, exclusively IgM or IgD, or IgD with a truncated hinge region. The data indicate that the increased entropic cost of antigen binding imposed by the IgD hinge attenuates negative selection by self-antigen while increasing the affinity-based threshold for positive selection into the germinal center (GC). Together the results indicate that IgD functions physiologically to desensitize B cells to antigen, thereby expanding the B cell repertoire while optimizing affinity-based selection into the GC.

immunology↗

bioRxiv2026

Interplay between the immune response and the adaptation of metabolic pathways upon infection

Glucose is the principal metabolic fuel for the energy needs of most cell types. Upon infection, cytokines secreted by the immune system regulate redistribution of glucose to meet new metabolic needs associated with clearing the pathogen. We develop a mathematical model to describe the dynamics of such adaptation of metabolic pathways mediated by the immune response and its impact on the ability to clear pathogen and restore health. We find that cytokine-regulated redistribution of glucose resources in different tissues is critical for an effective immune response to pathogen as strictly clamping plasma glucose levels to homeostatic levels results in an ineffective immune response. By studying the effects of various parameters in our model, we describe how aberrant regulation of adaptation mechanisms affect outcomes of infection. Too high a glucose consumption rate by innate immune cells to mediate functions results in failure to clear pathogen. Pathogens with a very high replication rate can be controlled to low levels, but at a very high metabolic cost. Too low a pathogen replication rate allows the pathogen to hide from the immune system and rebound to high levels at later times. Finally, the strength of the innate immune response must be regulated to not be too high, not only to limit immunopathogenesis, but also for mediating an effective adaptive immune response.

immunology↗

bioRxiv2024

RNA gradients can guide condensates toward promoters: implications for enhancer-promoter contacts and condensate-promoter kissing

We study how protein condensates respond to a site of active RNA transcription (i.e., a gene promoter) due to electrostatic protein-RNA interactions. Our results indicate that condensates can show directed motion towards the promoter, driven by gradients in the RNA concentration. Analytical theory, consistent with simulations, predicts that the droplet velocity has a non-monotonic dependence on the distance to the promoter. We explore the consequences of this gradient-sensing mechanism for enhancer-promoter (E-P) communication using polymer simulations of the intervening chromatin chain. Directed motion of enhancer-bound condensates can, together with loop extrusion by cohesin, collaboratively increase the enhancer-promoter contact probability. Finally, we investigate under which conditions condensates can exhibit oscillations in their morphology and in the distance to the promoter. Oscillatory dynamics are caused by a delayed response of transcription to condensate-promoter contact and negative feedback from the accumulation of RNA at the promoter, which results in charge repulsion.

biophysics↗

bioRxiv2024

Active RNA synthesis patterns nuclear condensates

Biomolecular condensates are membraneless compartments that organize biochemical processes in cells. In contrast to well-understood mechanisms describing how condensates form and dissolve, the principles underlying condensate patterning - including their size, number and spacing in the cell - remain largely unknown. We hypothesized that RNA, a key regulator of condensate formation and dissolution, influences condensate patterning. Using nucleolar fibrillar centers (FCs) as a model condensate, we found that inhibiting ribosomal RNA synthesis significantly alters the patterning of FCs. Physical theory and experimental observations support a model whereby active RNA synthesis generates a non-equilibrium state that arrests condensate coarsening and thus contributes to condensate patterning. Altering FC condensate patterning by expression of the FC component TCOF1 impairs ribosomal RNA processing, linking condensate patterning to biological function. These results reveal how non-equilibrium states driven by active chemical processes regulate condensate patterning, which is important for cellular biochemistry and function.

biophysics↗

bioRxiv2022

Polymer folding through active processes recreates features of genome organization

From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate (ATP). Moreover, chromatin motion varies with genomic coordinate, pointing towards a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers non-equilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward disentangling active and passive mechanisms of folding, we discuss a data-driven approach to discern if and how active processes affect genome organization.

biophysics↗

bioRxiv2021

Tissue flow through pores: a computational study

AO_SCPLOWBSTRACTC_SCPLOWCell migration is of major importance for the understanding of phenomena such as morphogenesis, cancer metastasis, or wound healing. In many of these situations cells are under external confinement. In this work we show by means of computer simulations with a Cellular Potts Model (CPM) that the presence of a bottleneck in an otherwise straight channel has a major influence on the internal organisation of an invading cellular monolayer and the motion of individual cells therein. Comparable to a glass or viscoelastic material, the cell sheet is found to exhibit features of both classical solids and classical fluids. The local ordering on average corresponds to a regular hexagonal lattice, while the relative motion of cells is unbounded. Compared to an unconstricted channel, we observe that a bottleneck perturbs the formation of regular hexagonal arrangements in the epithelial sheet and leads to pile-ups and backflow of cells near the entrance to the constriction, which also affects the overall invasion speed. The scale of these various phenomena depends on the dimensions of the different channel parts, as well as the shape of the funnel domain that connects wider to narrower regions.

biophysics↗

bioRxiv2020

ATP driven diffusiophoresis: active cargo transport without motor proteins

Morphogenesis and homeostasis of biological systems are intricately linked to gradient formation through energy dissipation. Such spatial organization may be achieved via reaction-diffusion or directional cargo transport, as prominently executed by motor proteins. In contrast to these processes that rely on specific protein interactions, active transport based on a non-specific, purely physical mechanism remains poorly explored. Here, by a joint experimental and theoretical approach, we describe a hidden function of the MinDE protein system from E. coli: Besides forming dynamic patterns, this system accomplishes the active transport of large, functionally unrelated cargo on membranes in vitro. Remarkably, this mechanism allows to sort diffusive objects according to their effective size, as evidenced using modular DNA origami-streptavidin nanostructures. We show that the diffusive fluxes of MinDE and cargo couple via density-dependent friction. This non-specific process constitutes a Maxwell-Stefan diffusiophoresis, so far undescribed in a biologically relevant setting. Such nonlinear coupling between diffusive fluxes could represent a generic physical mechanism for the intracellular organization of biomolecules.

biophysics↗

bioRxiv2019

Cell based strain stiffening of a non-fibrous matrix as organizing principle for morphogenesis

Endothelial tube formation on a reconstituted extracellular matrix (Matrigel) is a well-established in vitro model for studying the processes of angiogenesis and vasculogenesis. However, to date, the organizing principles that underlie the morphogenesis of this network, and that shape the initial process of cell-cell finding remain elusive. Furthermore, it is unclear how in vitro results extrapolate to in vivo morphogenesis. Here, we identify a mechanism that allows cells to form networks by mechanically reorganizing and stiffening their extracellular matrix, independent of chemical guidance cues. Interestingly, we find that this cellular self-organization strongly depends on the connectivity and topology of the surrounding matrix, as well as on cell contractility and cell density. Cells rearrange the matrix, and form bridges of matrix material that are stiffer than their surroundings, thus creating a durotactic track for the initiation of cell-cell contacts. This contractility-based communication via strain stiffening and matrix rearrangement might be a general organizing principle during tissue development or regeneration.\n\nSignificance StatementIn addition to chemotactic gradients, biomechanical cues are important for guiding biological pattern formation. Self-assembly of cells has often been ascribed to reorganization of collagen fibres in the extracellular matrix. However, the basement membrane surrounding vascular cells, is per se non-fibrous. Here, we find that this difference in matrix topology can crucially influence cell behaviour and pattern formation. In a homogeneously elastic environment like the basement membrane, endothelial cells rearrange extracellular matrix proteins by contractile force, forming stiff intercellular bridges as tracks for cell-cell contacts. Our findings shine some light why there is a lot of merit in having multiple approaches to matrix elasticity (like continuum theories or dilated network approaches). Our observations might help to understand why vascular nets look different in different tissues and after rearrangement of the extracellular matrix during disease.

cell biology↗

bioRxiv2019

Quasi-periodic migration of single cells on short microlanes

Cell migration on microlanes represents a suitable and simple platform for the exploration of the molecular mechanisms underlying cell cytoskeleton dynamics. Here, we report on the quasi-periodic movement of cells confined in stripe-shaped microlanes. We observe persistent polarized cell shapes and directed pole-to-pole motion within the microlanes. Cells depolarize at one end of a given microlane, followed by delayed repolarization towards the opposite end. We analyze cell motility via the spatial velocity distribution, the velocity frequency spectrum and the reversal time as a measure for depolarization and spontaneous repolarization of cells at the microlane ends. The frequent encounters of a boundary in the stripe geometry provides a robust framework for quantitative investigations of the cytoskeleton protrusion and repolarization dynamics. In a first advance to rigorously test physical models of cell migration, we find that the statistics of the cell migration is recapitulated by a Cellular Potts model with a minimal description of cytoskeleton dynamics. Using LifeAct-GFP transfected cells and microlanes with differently shaped ends, we show that the local deformation of the leading cell edge in response to the tip geometry can locally either amplify or quench actin polymerization, while leaving the average reversal times unaffected.

biophysics↗

bioRxiv2019

Bridging the gap between single cell migration and collective dynamics

A wealth of experimental data relating to the emergence of collective cell migration as one proceeds from the behavioral dynamics of small cohorts of cells to the coordinated migratory response of cells in extended tissues is now available. Integrating these findings into a mechanistic picture of cell migration that is applicable across such a broad range of system sizes constitutes a crucial step towards a better understanding of the basic factors that determine the emergence of collective cell motion. Here we present a cellular-automaton-based modeling framework, which focuses on the integration of high-level cell functions and their concerted effect on cellular migration patterns. In particular, we adopt a top-down approach to incorporate a coarse-grained description of cell polarity and its response to mechanical cues, and address the impact of cell adhesion on collective migration in cell groups. We demonstrate that the model faithfully reproduces typical cell shapes and movements down to the level of single cells, yet is computationally efficient enough to allow for the simulation of (currently) up to [O](104) cells. To develop a mechanistic picture that illuminates the relationship between cell functions and collective migration, we present a detailed study of small groups of cells in confined circular geometries, and discuss the emerging patterns of collective motion in terms of specific cellular properties. Finally, we apply our computational model at the level of extended tissues, and investigate stress and velocity distributions, as well as front morphologies, in expanding cellular sheets.

biophysics↗