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Zaburdaev, V.

Publications and source records attributed to Zaburdaev, V..

At least 19 recordsLinked to original sources

In silico model of neuronal pathfinding during spinal cord regeneration in zebrafish larvae

Functional spinal cord repair in zebrafish is governed by regeneration-favorable biochemical and mechanical cues within the lesion microenvironment. Alterations in extracellular matrix composition and stiffness are closely associated with axon regeneration. However, experimentally dissecting the interplay between mechanical signals and axonal regrowth in vivo remains technically challenging. Here, we present an agent-based modeling framework to simulate stiffness-mediated axonal growth trajectories across the lesion. We use this model to explore potential mechanisms underlying the characteristic growth patterns observed during zebrafish spinal cord regeneration. Computational predictions were qualitatively compared with confocal imaging data obtained from larval zebrafish. These phenomenological comparisons revealed a close agreement between simulated and experimentally observed axon growth, indicating that experimentally observed patterns could be governed by transient changes in the stiffness profile of the spinal cord and lesion microenvironment. Hence, our computational framework provides an in silico platform for investigating the role of mechanical cues in axon regeneration in the injured spinal cord.

biophysics↗

In silico neuritogenesis model underpins mechanical interactionswith extracellular matrix as determinants of persistent axonal growthin stiffer microenvironments

It has been broadly recognized that the crosstalk between cells and their extracellular matrix (ECM) is crucial for the proper function of biological tissues. Relatively recently the role of ECM came in focus in the context of neuronal development and regeneration, where the effects of the ECM mechanics on the migration of neurons and neurite growth are still incompletely understood. Here we present an in silico twin framework for neurite growth focusing on its biophysical interactions with the ECM. This coarsegrained model accounts for viscoelastic liquid- and solid-like ECMs and neurite growth by ECM-mediated traction forces. Resulting growth trajectories can be rationalized based on the theory of random walks and polymer physics. To critically assess models predictive power, we performed experiments on neurites of hippocampal rat neurons growing in 3D collagen gels and observed a more persistent axon outgrowth in denser matricies. The model fully recapitulated the effect, thereby underpinning the central role of mechanical interactions with ECM as guiding principle of axonal growth. We argue that a combination our model with optical microscopy may provide an is silico twin helping to disentangle the contributions of "passive" physics from more complex effects of chemical queues or an apparent mechanosensing.

neuroscience↗

A bacterial extracellular matrix protein forms a supramolecular metallogel

The microbial extracellular matrix (ECM) is a complex network of self-secreted biopolymers uniting the cells in biofilms, providing them with structural integrity, and contributing to their elevated resistance to antibiotic treatments. Recently, there is a growing realization that a regulated, bidirectional cross-talk of bacteria and ECM confers biofilms with tissue-like traits, however, the mechanisms of spatio-temporal self-organisation of ECM and its regulation are still poorly understood. In the model organism for biofilm formation Bacillus subtilis, TasA is the major protein component of the extracellular matrix. We recently showed that TasA, isolated in the form of stable and structured globules, assembles into elongated and ordered fibers via a donor-strand complementation mechanism. In this study, we discovered that in the presence of zinc metal ions, TasA is able to form hydrogels with > 97% water content. Electron- and atomic force-microscopies as well as small angle X-ray scattering measurements show that cross-linking with zinc ions induces a transition in TasA morphology from one-dimensional fibers to two-dimensional sheets. Electron paramagnetic resonance measurements then show that such a significant morphological shift is associated with molecular changes in the coordination environment of zinc ions, which lead to structural changes at the protein level. When assembling into macroscopic networks, TasA-Zn metallogels exhibit viscoelastic properties and a fast recovery following an excessive strain. These metallogels represent a novel class of bacterially-derived ECMs that form easily at room temperature without covalent crosslinking, and may be used as a natural matrix-mimics in biofilm models for infection studies.

biochemistry↗

Quantifying distribution shifts in single-cell data with scXMatch

A basic task that frequently arises when analyzing single-cell data is to assess if there is a global distribution shift between the data profiles of cells from two different conditions. Widely used approaches to address this task such as visual inspection of two-dimensional representations or clustering-based workflows lack a solid statistical underpinning and are notoriously unstable and prone to confirmation bias. To promote more rigorous analysis, we here present the scverse-compatible Python tool scXMatch. scXMatch is based on a non-parametric graph-based test to quantify distribution shifts in arbitrary data spaces for which a suitable distance measure is available. We evaluated scXMatch on single-cell gene expression, chromatin accessibility, and imaging-derived cell morphology data, showing that it can robustly detect distribution shifts for different types of single-cell data. scXMatch thus aims to set a new standard in the single-cell biology field, replacing easy-to-manipulate semi-manual distribution shift quantification workflows by principled statistical testing.

bioinformatics↗

Hierarchical Heterogeneities in Spatio-Temporal Dynamics of the Cytoplasm

The physical properties of the cytoplasm fundamentally constrain the dynamics and fidelity of cellular processes. Endogenous fluctuations carry signatures of these properties, yet how their collective dynamics across mesoscopic spatiotemporal scales relate to cytoplasmic heterogeneity and organization remains poorly understood. Here, we use differential dynamic microscopy (DDM) to quantify these fluctuations in eukaryotic cytoplasms. In Xenopus laevis egg extracts, we identify signatures of subdiffusive fractional Brownian motion (fBm) and non-Gaussian displacement distributions, consistent with a crowded, heterogeneous environment. We introduce an empirical model combining fBm with an inverse Gaussian diffusivity distribution, enabling robust estimation of fractional diffusivities and scaling exponents across conditions. Denser cytoplasm exhibits lower fractional diffusivity and scaling exponent, while energy addition induces non-stationary dynamics. Stabilization of microtubule networks introduces a secondary timescale, rationalized by a two-state fBm model separating cytosolic and network-associated contributions. In HeLa cells, the framework reveals comparable scaling exponents but lower diffusivities than in egg extract. Upon microtubule depolymerization, the dynamics become slower yet more Brownian-like. This highlights dual roles of the cytoskeleton as confinement but also as fluidizer of the cytoplasm. These results establish label-free DDM as an interpretable, collective, multiscale readout of how composition, activity, and cytoskeletal organization shape hierarchical cytoplasmic dynamics.

biophysics↗

Aberrant formation of long-range projections across different neurodevelopmental disorders converges on molecular and cellular nexuses

Establishing long-range connections during human brain development is an intricate multi-step process disturbed in many neurodevelopmental disorders (NDDs). The aberrant formation of these connections is caused by mutations in a plethora of different genes with distinct molecular functions, triggering the question of whether there are common key downstream mediators at which different pathologies are converging. We employed brain organoids to model early human brain developmental aspects of Coffin-Siris-like 9, Opitz BBB/G, and Pitt-Hopkins syndromes. These NDDs are caused by mutations in SOX11, MID1, and TCF4 respectively, and are characterized by a multitude of distinct symptoms yet share alterations in long-range projections as a common feature. Here, we uncover that mutations in all three genes phenotypically converge, showing impaired neurite extension with increased tortuosity and decreased growth speed resulting in shorter beelines. Moreover, the mutant neurites exhibit a decrease in growth persistence providing a conceptual framework explaining why long- but not short-range connections are affected. Correlating with the converging cellular phenotype, molecular characterization revealed a striking convergence on signaling pathways implicated in the interaction of neurites with their extracellular environment. In-silico modeling and perturbation of neurite outgrowth suggest that altered neurite-extracellular environment interactions are sufficient to recapitulate the mutant phenotypes but also facilitate the prediction of specific parameters causing disturbed neurite growth in mutant neurons.

developmental biology↗

Spatiotemporal Dynamics of the Dihydrolipoyl Dehydrogenase LpdA Determine the Intrinsic Autofluorescence in Filamentous Actinobacteria

The hyphal nature of filamentous streptomycetes poses unique challenges to their multicellular lifestyle, since it requires organizing cellular functions at the scale of hundreds of micrometers length. Streptomycetes exhibit a strong and patchy autofluorescence of so far unknown origin in their hyphae that - as we demonstrate - is a natural property of filamentous actinobacteria. The foci are dynamic and evenly distributed throughout the hyphae, including the hyphal tips, where they are cell membrane-associated. Here, we resolved the high spatiotemporal dynamics of these foci during spore germination and vegetative growth in Streptomyces venezuelae. We isolated a fluorescent protein band and identified the responsible protein as dihydrolipoyl dehydrogenase LpdA. An lpdA deletion mutant lacked these fluorescent foci and showed minor deficiencies in growth and development. Heterologous LpdA production in E. coli and characterization of the enzyme verified that a flavin cofactor is responsible for the green autofluorescence. LpdA is highly conserved in actinomycetes as a part of multienzyme complexes involved in central metabolism. Such delocalized metabolic centers provide a potential solution to mycelial multicellular lifestyle, where diffusion becomes a major challenge.

microbiology↗

Cell State-Specific Cytoplasmic Material Properties Control Spindle Architecture and Scaling

Mitotic spindles are dynamically intertwined with the cytoplasm they assemble in. How the physicochemical properties of the cytoplasm affect spindle architecture and size remains largely unknown. Using quantitative biochemistry in combination with adaptive feedback microscopy, we investigated mitotic cell and spindle morphology during neural differentiation of embryonic stem cells. While tubulin biochemistry and microtubule dynamics remained unchanged, spindles changed their scaling behaviour: in differentiating cells, spindles were significantly smaller than those in equally-sized undifferentiated stem cells. Integrating quantitative phase imaging, biophysical perturbations and theory, we found that as cells differentiated, their cytoplasm became more dilute. The concomitant decrease in free tubulin activated CPAP (centrosomal P4.1-associated protein) to enhance the centrosomal nucleation capacity. As a consequence, in differentiating cells, microtubule mass shifted towards spindle poles at the expense of the spindle bulk, explaining the differentiation-associated switch in spindle architecture. This study shows that cell state-specific cytoplasmic density tunes mitotic spindle architecture. Thus, we reveal physical properties of the cytoplasm as a major determinant in organelle size control.

cell biology↗

Cell morphology as a quantifier for functional states of resident tissue macrophages

Resident tissue macrophages (RTMs) are essential for tissue homeostasis. Their diverse functions, from monitoring interstitial fluids to clearing cellular debris, are accompanied by characteristic morphological changes that reflect their functional status. While current knowledge of macrophage behaviour comes primarily from in vitro studies, their dynamic behavior in vivo is fundamentally different, necessitating a more physiologically relevant approach to their understanding. In this study, we employed intravital imaging to generate dynamic data from peritoneal RTMs in mice under various conditions and developed a comprehensive image processing pipeline to quantify RTM morphodynamics over time, defining human-interpretable cell size and shape features. These features allowed for the quantitative and qualitative differentiation of cell populations in various functional states, including pro- and anti-inflammatory activation and endosomal dysfunction. The study revealed that under steady-state conditions, RTMs exhibit a wide range of morphodynamical phenotypes, constituting a naive morphospace of behavioral motifs. Upon challenge, morphodynamic patterns changed uniformly at the population level but predominantly within the constraints of this naive morphospace. Notably, aged animals displayed a markedly shifted naive morphospace, indicating drastically different behavioral patterns compared to their young counterparts. The developed method also proved valuable in optimizing explanted tissue setups, bringing RTM behavior closer to the physiological native state. Our versatile approach thus provides novel insights into the dynamic behavior of bona fide macrophages in vivo, enabling the distinction between physiological and pathological cell states and the assessment of functional tissue age on a population level. Author summaryIn this study, we combine state-of-the-art in vivo imaging with advanced computational analysis to reveal the dynamic behavior of peritoneal resident tissue macrophages (RTMs) in their natural environment. These sentinel cells, which are crucial for tissue homeostasis, constantly monitor their environment and, in the process, undergo dynamic morphological changes that have remained largely uninvestigated due to technical limitations. Using two-photon microscopy, we captured time-lapse images of RTMs in the peritoneal serosa under various experimental conditions. Our customized image processing pipeline allowed a comprehensive assessment of cell morphology and dynamics and provided unprecedented insights into the behavior of RTMs in vivo, enabling us to distinguish cell populations in different physiological and pathological states. Our work opens up new avenues for the dynamic in situ phenotyping of macrophage functionality in disease contexts without their extraction from tissues and provides a novel perspective on the behavior of RTMs in their natural microenvironment. This versatile tool promises to advance our understanding of tissue homeostasis and macrophage function in health and disease, with potential applications in both basic research and clinical settings.

immunology↗

Estimation of the mass density of biological matter from refractive index measurements

The quantification of physical properties of biological matter gives rise to novel ways of understanding functional mechanisms by utilizing models that explicitly depend on physical observables. One of the basic biophysical properties is the mass density (MD), which determines the degree of crowdedness. It impacts the dynamics in sub-cellular compartments and further plays a major role in defining the opto-acoustical properties of cells and tissues. As such, the MD can be connected to the refractive index (RI) via the well known Lorentz-Lorenz relation, which takes into account the polarizability of matter. However, computing the MD based on RI measurements poses a challenge as it requires detailed knowledge of the biochemical composition of the sample. Here we propose a methodology on how to account for a priori and a posteriori assumptions about the biochemical composition of the sample as well as respective RI measurements. To that aim, we employ the Biot mixing rule of RIs alongside the assumption of volume additivity to find an approximate relation of MD and RI. We use Monte-Carlo simulations as well as Gaussian propagation of uncertainty to obtain approximate analytical solutions for the respective uncertainties of MD and RI. We validate this approach by applying it to a set of well characterized complex mixtures given by bovine milk and intralipid emulsion. Further, we employ it to estimate the mass density of trunk tissue of living zebrafish (Danio rerio) larvae. Our results enable quantifying changes of mass density estimates based on variations in the a priori assumptions. This illustrates the importance of implementing this methodology not only for MD estimations but for many other related biophysical problems, such as mechanical measurements using Brillouin microscopy and transient optical coherence elastography.

biophysics↗

Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes

The packing and confinement of macromolecules in the cytoplasm and nucleoplasm has profound implications for cellular biochemistry. How intracellular density distributions vary and affect cellular physiology remains largely unknown. Here, we show that the nucleus is less dense than the cytoplasm and that living systems establish and maintain a constant density ratio between these compartments. Using label-free biophotonics and theory, we show that nuclear density is set by a pressure balance across the nuclear envelope in vitro, in vivo and during early development. Nuclear transport establishes a specific nuclear proteome that exerts a colloid osmotic pressure, which, assisted by entropic chromatin pressure, draws water into the nucleus. Using C. elegans, we show that while nuclear-to-cytoplasmic (N/C) volume ratios change during early development, the N/C density ratio is robustly maintained. We propose that the maintenance of a constant N/C density ratio is the biophysical driver of one of the oldest tenets of cell biology: the N/C volume ratio. In summary, this study reveals a previously unidentified homeostatic coupling of macromolecular densities that drives cellular organization with implications for pathophysiologies such as senescence and cancer.

biophysics↗

Transcriptional clusters follow a conserved condensation-dispersal sequence during stem cell differentiation

Spatiotemporal organization of transcription is essential for organism development. Most eukaryotic genes are transcribed by RNA polymerase II (Pol II). In stem cells, Pol II forms prominent clusters, which gradually disappear during differentiation, such that only smaller clusters remain. Here, we ask whether the formation and loss of large Pol II clusters is a stereotypical process explicable by changes in the Pol II transcriptional state during differentiation. We assess clusters by super-resolution microscopy in differentiating mouse embryonic stem cells, sperm precursor formation in fruit flies, and germ layer induction in zebrafish. In all cases, Pol II clusters first become larger and rounder, then unfold, and finally disperse into small clusters. These shape changes are accompanied by initial increase in recruited Pol II, subsequent transition into transcript elongation, and finally reduction of active enhancers. We reproduce these observations using a biophysical surface condensation model, where enhancers support Pol II cluster formation, and transcriptional activity unfolds clusters. Our work indicates that changes in enhancer marks and transcriptional activity during differentiation define a stereotyped trajectory through a generally applicable space of cluster shapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/547621v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1fb769borg.highwire.dtl.DTLVardef@27f6a0org.highwire.dtl.DTLVardef@1b0ab7corg.highwire.dtl.DTLVardef@1ca932d_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

Amphiphiles formed from synthetic DNA-nanomotifs mimic the dispersal of transcriptional clusters in the cell nucleus

Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Low amphiphile concentrations induce rounding of droplets, followed by splitting and, ultimately, full dispersal at higher concentrations. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of the complex organization of transcription in biological cells using relatively simple, DNA sequence-programmable nanostructures, opening novel ways to control mesoscopic organization of synthetic nanomaterials. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/525851v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1a8cc4borg.highwire.dtl.DTLVardef@fc6651org.highwire.dtl.DTLVardef@a17c74org.highwire.dtl.DTLVardef@1f1cf14_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

A DNA segregation module for synthetic cells

The bottom-up construction of an artificial cell requires the realization of synthetic cell division. Significant progress has been made towards reliable compartment division, yet mechanisms to segregate the DNA-encoded informational content are still in their infancy. Herein, droplets of DNA Y-motifs are formed by liquid-liquid phase separation (LLPS). Entropy-driven DNA droplet segregation is obtained by cleaving the linking component between two populations of DNA Y-motifs. In addition to enzymatic cleavage, photolabile sites are introduced for spatio-temporally controlled DNA segregation in bulk as well as in cell-sized water-in-oil droplets and giant unilamellar lipid vesicles (GUVs). Notably, the segregation process is slower in confinement than in bulk. The ionic strength of the solution and the nucleobase sequences are employed to regulate the segregation dynamics. The experimental results are corroborated in a lattice-based theoretical model which mimics the interactions between the DNA Y-motif populations. Altogether, engineered DNA droplets, reconstituted in GUVs, could represent a strategy towards an entropy-driven DNA segregation module within bottom-up assembled synthetic cells. Table of Contents O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY An entropy-driven DNA segregation module for bottom-up assembled synthetic cells is realized. It is based on DNA droplets that are engineered to segregate upon enzymatic or photocleavage inside giant unilamellar lipid vesicles (GUVs). The segregation kinetics is altered by the confinement, as confirmed by lattice-based numerical simulations. DNA segregation is further controlled by temperature, ionic strengths and nucleobase sequence. C_FIG_DISPLAY

biophysics↗

A pili-driven bacterial turbine

Work generated by self-propelled bacteria can be harnessed with the help of microdevices. Such nanofabricated microdevices, immersed in a bacterial bath, may exhibit unidirectional rotational or translational motion. Swimming bacteria that propel with the help of actively rotating flagella are a prototypical example of active agents that can power such microdevices. In this work, we propose a computational model of a micron-sized turbine powered by bacteria that rely on active type IV pili appendages for surface-associated motility. We find that the turbine can rotate persistently over a time scale that significantly exceeds the characteristic times of the single cell motility. The persistent rotation is explained by the collective dynamics of multiple pili of groups of cells attaching to and pulling on turbine. Furthermore, we show that the turbine can rotate permanently in the same direction by altering the pili binding to the turbine surface in an asymmetric fashion. We thus can show that by changing the adhesive properties of the turbine while keeping its symmetric geometry, we can still break the symmetry of its rotation. Altogether, this study widely expands the range of bacteria that can be used to power nanofabricated microdevices, and, due to high pili forces generated by pili retraction, promises to push the harnessed work by several orders of magnitude.

biophysics↗

RNA polymerase II clusters form in line with liquid phase wetting of chromatin

It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state and subsequent pause release to begin transcript elongation. Pol II associates with macromolecular clusters during recruitment, but it remains unclear how Pol II recruitment and pause release might affect these clusters. Here, we show that clusters exhibit morphologies that are in line with wetting of chromatin by a liquid phase enriched in recruited Pol II. Applying instantaneous structured illumination microscopy and stimulated emission double depletion microscopy to pluripotent zebrafish embryos, we find recruited Pol II associated with large clusters, and elongating Pol II with dispersed clusters. A lattice kinetic Monte Carlo model representing recruited Pol II as a liquid phase reproduced the observed cluster morphologies. In this model, chromatin is a copolymer chain containing regions that attract or repel recruited Pol II, supporting droplet formation by wetting or droplet dispersal, respectively.

biophysics↗

The domain-within-domain packing of euchromatin can be described as multiplicative cascades

The genome is packed into the cell nucleus in the form of chromatin. Biochemical approaches have revealed that chromatin is packed within domains, which group into larger domains, and so forth. Such domain-within-domain packing, also called hierarchical packing, is equally visible in super-resolution microscopy images of large-scale chromatin organization. While previous work has suggested that chromatin is partitioned into distinct domains via microphase separation, it is unclear how these domains organize into a hierarchical packing. A particular challenge is to find an image analysis approach that fully incorporates such hierarchical packing, so that hypothetical governing mechanisms of euchromatin packing can be compared against the results of such an analysis. Here, we obtain 3D STED super-resolution images from pluripotent zebrafish embryos labeled with improved DNA fluorescence stains, and demonstrate how the hierarchical packing of euchromatin in these images can be described as multiplicative cascades. Multiplicative cascades are an established theoretical concept to describe the placement of ever-smaller structures within bigger structures. Importantly, these cascades can generate artificial image data by applying a single rule again and again, and can be fully specified using only four parameters. Here, we show how the typical patterns of euchromatin organization are reflected in the values of these four parameters. In particular, we can pinpoint the values required to mimic a microphase-separated configuration of euchromatin. We suspect that the concept of multiplicative cascades can also be applied to images of other types of chromatin. In particular, cascade parameters could serve as test quantities to assess whether microphase separation or other theoretical models accurately reproduce the hierarchical packing of chromatin. SIGNIFICANCEDNA is stored inside the cell nucleus in the form of chromatin. Chromatin exhibits a striking three-dimensional organization, where small domains group into larger domains, which again group into larger domains, and so forth. While this hierarchical domain-within-domain organization is obvious from microscopy images, it is still not entirely clear how it is established, or how it should be properly characterized. Here, we demonstrate that multiplicative cascades - a concept from theoretical physics used to characterize for example cloud patterns, galaxy locations, or soil patterns - are also ideally suited to describe the domain-within-domain organization of chromatin. This description is rather simple, using only four numbers, and can thus facilitate testing of competing theories for the domain-within-domain organization of chromatin.

biophysics↗

High-precision protein-tracking with interferometric scattering microscopy

The mobility of proteins and lipids within the cell, sculpted oftentimes by the organisation of the membrane, reveals a great wealth of information on the function and interaction of these molecules as well as the membrane itself. Single particle tracking has proven to be a vital tool to study the mobility of individual molecules and unravel details of their behaviour. Interferometric scattering (iSCAT) microscopy is an emerging technique well suited for visualising the diffusion of gold nanoparticle-labelled membrane proteins to a spatial and temporal resolution beyond the means of traditional fluorescent labels. We discuss the applicability of interferometric single particle tracking (iSPT) microscopy to investigate the minutia in the motion of a protein through measurements visualising the mobility of the epidermal growth factor receptor in various biological scenarios on the live cell.

biophysics↗