Biology subjects

Dmitrieff, S.

Publications and source records attributed to Dmitrieff, S..

12 recordsLinked to original sources

bioRxiv2026

The Endoplasmic Reticulum as a Cytoplasmic Anchor for Microtubule-Driven Aster Centration

The proper positioning of microtubule (MT) asters is essential to regulate division positioning and multi-cellular morphogenesis, yet the mechanisms regulating this process remain poorly understood. Using sea urchin zygotes as a model, we combined high-resolution imaging, perturbation assays, and 3D modeling to investigate the nature of forces driving sperm aster centration after fertilization. We show that centering asters are highly anisotropic, featuring long microtubules extending at the aster front that may engage with organelles in bulk cytoplasm to generate pulling forces. While vesicular compartments, like acidic organelles, mitochondria or yolk, contributed minimally, we found that the endoplasmic reticulum (ER) undergoes a massive compaction around the centering aster and drags cytosol to produce a reactive centering force on the aster. Perturbing ER organization by cytoplasmic stratification or Atlastin-mediated fragmentation disrupted aster centration. A two-fluid model suggests that the frictional interaction between the compacting ER and cytosol fluid is sufficient to recapitulate key features of aster centration. These findings identify the ER as an important cytoplasmic anchor for MT force exertion in bulk cytoplasm, to guide aster centering motion and influence early embryonic division geometries. More broadly, our results highlight the role of cytoplasmic architecture in shaping the mechanics of organelle positioning during development.

cell biology↗

bioRxiv2026

A Composite Endomembrane Suspension Governs Cytoplasm Rheology

The cytoplasm of eukaryotic cells is populated by dense disordered suspensions of filamentous and granular endomembranes, yet how they contribute to the mechanical behavior of the cell interior remains unknown. We combined active micro-rheology, cell-like encapsulation and simulations to study the material properties of marine egg extract fractions enriched in distinct endomembrane components. We characterized the cytoplasm as a composite suspension made of yolk granules interspaced by sheets and tubules of endoplasmic reticulum (ER) bathed in cytosolic fluid, that occupies [~]38% of cell volume. Remarkably, while isolated cytosol, yolk or ER fractions had characteristics of Newtonian fluids, their combination yielded the emergence of viscoelasticity and glass-like dynamics closely resembling that of in vivo cytoplasm. Our data suggest that the ER acts as a sterically excluding backbone that drives the formation of load-bearing yolk flocculation structures to endow the cytoplasm with solid-like properties at volume fractions far below random close packing. This work establishes a generic framework to understand the material properties of composite endomembrane suspensions, and delineates a novel strategy by which eukaryotic cells may tune the physical state of their cytoplasm.

biophysics↗

bioRxiv2025

Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation

Chromosome segregation during anaphase occurs through two mechanistically distinct processes: anaphase A, in which chromosomes move toward spindle poles, and anaphase B, in which the anaphase spindle elongates through cortical astral microtubule pulling forces. Caenorhabditis elegans embryos have been thought to rely primarily on anaphase B, with little to no contribution from anaphase A. Here, we uncover a novel anaphase A mechanism in C. elegans embryos, driven by the kinesin-13 KLP-7MCAK and opposed by the kinesin-12 KLP-18. We found that the extent of chromosome segregation during anaphase A is asymmetrically regulated by cell polarity cues and modulated by mechanical tension within the spindle, generated by opposing forces acting on chromosomes and spindle poles. Additionally, we found that the contribution of anaphase A to chromosome segregation increases progressively across early embryonic divisions. These findings uncover an unexpected role for anaphase A in early C. elegans development and reveal a KLP-7MCAK-dependent mechanical coordination between anaphase A and anaphase B driven chromosome segregation. eTOC summaryDias Maia Henriques et al. uncover an anaphase A pathway, driven by the kinesin-13 KLP-7 and opposed by the kinesin-12 KLP-18, that contributes to chromosome segregation in early C. elegans embryos. Its activity is regulated by spindle tension, cell polarity cues, and progressively increases during early embryonic divisions.

cell biology↗

bioRxiv2024

A physical model for M1-mediated influenza A virus assembly

Influenza A virus particles assemble at the plasma membrane of infected cells. During assembly all components of the virus come together in a coordinated manner to deform the membrane into a protrusion eventually forming a new, membrane-enveloped virus. Here we integrate recent molecular insights of this process, particularly concerning the structure of the matrix protein 1 (M1), within a theoretical framework describing the mechanics of virus assembly. Our model describes M1 polymerization and membrane protrusion formation, explaining why it is efficient for M1 to form long strands assembling into helices in filamentous virions. Eventually, we find how the architecture of M1 helices is controlled by physical properties of viral proteins and the host cell membrane. Finally, by considering the growth force and speed of viral filaments, we propose that the helical geometry of M1 strands might have evolved to optimize for fast and efficient virus assembly and growth. SignificanceInfluenza A virus remains a major threat to public health. Its most abundant viral protein, matrix protein 1 (M1), forms an endoskeleton underneath the viral membrane, but how this endoskeleton contributes to the virus lifecycle is poorly understood. Combining cryo-electron tomography data and structural data with theoretical predictions, we explain how the energetically favorable polymerization of M1 into helical strands mediates the membrane deformations that permit the virus to exit infected cells. Our analysis of M1s variable architecture provides insights into adaptive strategies of the virus for efficient growth under variable local conditions. The quantitative framework developed in this study could be extrapolated to other enveloped viruses and generally applied to protein-driven membrane deformations.

biophysics↗

bioRxiv2023

Cell shape anisotropy enhances cytoplasm viscoelastic resistance to stabilize mitotic spindle position during early embryo development

Cell geometry is a key parameter for the regulation of mitotic spindle positioning during early embryo development and tissue morphogenesis. To date, however, we still lack an understanding for how intracellular forces that position, orient or hold mitotic spindles depend on cell geometry. Here, we used in vivo magnetic tweezers to directly measure the forces that maintain the mitotic spindle in the center of sea urchin cells that adopt different shapes during early embryo development. We found that spindles are held by viscoelastic forces that progressively increase in amplitude as cells become more elongated during early development. By coupling direct cell shape manipulations and in vivo force measurements, we establish how spindle associated forces increase in dose dependence with cell shape anisotropy. Cytoplasm flow analysis and hydrodynamic simulations suggest that this geometry-dependent mechanical enhancement results from a stronger hydrodynamic coupling between the spindle and cell boundaries, which dampens cytoplasm flows and spindle mobility as cells become more elongated. These findings establish how cell shape affects spindle associated forces, and suggest a novel mechanism for shape-sensing and division positioning mediated by intracellular hydrodynamics with functional implications for early embryo morphogenesis.

cell biology↗

bioRxiv2022

Size and position dependent cytoplasm viscoelasticity through hydrodynamic interactions with the cell surface

Many studies of cytoplasm rheology have focused on small components in the sub-micrometer scale. However, the cytoplasm also baths large organelles like nuclei, microtubule asters or spindles that often take significant portions of cells and move across the cytoplasm to regulate cell division or polarization. Here, we translated passive components of sizes ranging from few up to ~50 percent of the cell diameter, through the vast cytoplasm of live sea urchin eggs, with calibrated magnetic forces. Creep and relaxation responses indicate that for objects larger than the micron size, the cytoplasm behaves as a Jeffreys material, viscoelastic at short time-scales and fluidizing at longer times. However, as components size approached that of cells, cytoplasm viscoelastic resistance increased in a non-monotonic manner. Flow analysis and simulations suggest that this size-dependent viscoelasticity emerges from hydrodynamic interactions between the moving object and the static cell surface. This effect also yields to position-dependent viscoelasticity with objects initially closer to the cell surface being harder to displace. These findings suggest that the cytoplasm hydrodynamically couples large organelles to the cell surface to restrain their motion, with important implications for cell shape sensing and cellular organization. Significance StatementLarge-sized organelles like nuclei or mitotic spindles typically translocate through the cytoplasm to regulate cell division or polarity, but their frictional interaction with the cytoplasm and the cell surface remain poorly addressed. We used in vivo magnetic tweezers, to move passive components in a range of size in the cytoplasm of living cells. We found that the mobility of objects with sizes approaching that of cells, can be largely reduced as a result of hydrodynamic interactions that couple objects and the cell surface through the cytoplasm fluid.

biophysics↗

bioRxiv2021

Elasticity of dense actin networks produces nanonewton protrusive forces

Actin filaments assemble into force-generating systems involved in diverse cellular functions, including cell motility, adhesion, contractility and division. It remains unclear how networks of actin filaments, which individually generate piconewton forces, can produce forces reaching tens of nanonewtons. Here we use in situ cryo-electron tomography to unveil how the nanoscale architecture of macrophage podosomes enables basal membrane protrusion. We show that the sum of the actin polymerization forces at the membrane is not sufficient to explain podosome protrusive forces. Quantitative analysis of podosome organization demonstrates that the core is composed of a dense network of bent actin filaments storing elastic energy. Theoretical modelling of the network as a spring-loaded elastic material reveals that it exerts forces of up to tens of nanonewtons, similar to those evaluated experimentally. Thus, taking into account not only the interface with the membrane but also the bulk of the network, is crucial to understand force generation by actin machineries. Our integrative approach sheds light on the elastic behavior of dense actin networks and opens new avenues to understand force production inside cells.

biophysics↗

bioRxiv2019

The perinuclear ER scales nuclear size independently of cell size in early embryos

SUMMARYNuclear size plays pivotal roles in gene expression, embryo development, and disease. A central hypothesis in organisms ranging from yeast to vertebrates is that nuclear size scales to cell size. This implies that nuclei may reach steady state sizes set by limiting cytoplasmic pools of size-regulating components. By monitoring nuclear dynamics in early sea urchin embryos, we found that nuclei undergo substantial growth in each interphase, reaching a maximal size prior to mitosis that declined steadily over the course of development. Manipulations of cytoplasmic volume through multiple chemical and physical means ruled out cell size as a major determinant of nuclear size and growth. Rather, our data suggest that the perinuclear endoplasmic reticulum, accumulated through dynein activity, serves as a limiting membrane pool that sets nuclear surface growth rate. Partitioning of this local pool at each cell division modulates nuclear growth kinetics and dictates size scaling throughout early development.

cell biology↗

bioRxiv2018

Cytoskeleton mechanics determine resting size and activation dynamics of platelets.

Platelets are cell fragments of various size that help maintain hemostasis. The way platelets respond during a clotting process is known to depend on their size, with important physiological consequences. We characterized the cytoskeleton of platelets as a function of their size. In resting Human and Mice platelets, we find a quadradic law between the size of a platelet and the amount of microtubule polymer it contains. We further estimate the length and number of microtubules in the marginal band using Electron and Super-resolution microscopy. In platelets activated with ADP, the marginal band coils as a consequence of cortical contraction driven by actin. We observe that this elastic coiling response is accompanied by a reversible shortening of the marginal band. Moreover, larger platelets have a higher propensity to coil. These results establish the dynamic equilibrium that is responsible for platelet size and differential response on a more quantitative level.\n\nHighlightsO_LIPlatelet size scales consistently with amount of polymerized tubulin in both mouse and human.\nC_LIO_LIPolymerized actin is required for ADP-induced marginal band coiling.\nC_LIO_LIUpon activation, the marginal band exhibits a reversible visco-elastic response involving shortening.\nC_LIO_LILarger marginal bands have a higher propensity to coil than shorter ones.\nC_LI\n\nIn briefThe cytoskeleton is adapted to platelet size and its mechanical properties determine propensity of a platelet to undergo morphological changes in response to agonists.

cell biology↗

bioRxiv2017

Systematic analysis of the molecular architecture of endocytosis reveals a nanoscale actin nucleation template that drives efficient vesicle formation

Clathrin-mediated endocytosis is an essential cellular function in all eukaryotes that is driven by a self-assembled macromolecular machine of over 50 different proteins in tens to hundreds of copies. How these proteins are organized to produce endocytic vesicles with high precision and efficiency is not understood. Here, we developed high-throughput superresolution microscopy to reconstruct the nanoscale structural organization of 23 endocytic proteins from over 100,000 endocytic sites in yeast. We found that proteins assemble by radially-ordered recruitment according to function. WASP family proteins form a circular nano-scale template on the membrane to spatially control actin nucleation during vesicle formation. Mathematical modeling of actin polymerization showed that this WASP nano-template creates sufficient force for membrane invagination and substantially increases the efficiency of endocytosis. Such nanoscale pre-patterning of actin nucleation may represent a general design principle for directional force generation in membrane remodeling processes such as during cell migration and division.

cell biology↗

bioRxiv2016

ConfocalGN : a minimalistic confocal image simulator.

We developed a user-friendly software to generate synthetic confocal microscopy images from a ground truth specified as a 3D bitmap with pixels of arbitrary size. The software can analyze a real confocal stack to derivate noise parameters and will use them directly to generate new images with similar noise characteristics. Such synthetic images can then be used to assert the quality and robustness of an image analysis pipeline, as well as be used to train machine-learning image analysis procedures. We illustrate the approach with closed curves corresponding to the microtubule ring present in blood platelets.\n\nAvailability and implementationConfocalGN is written in MATLAB but does not require any toolbox. The source code is distributed under the GPL 3.0 licence on https://github.com/SergeDmi/ConfocalGN.

bioinformatics↗

bioRxiv2016

Balance of microtubule stiffness and cortical tension determines the size of blood cells with marginal band across species

The fast blood stream of animals is associated with large shear stresses. Consequently, blood cells have evolved a special morphology and a specific internal architecture allowing them to maintain their integrity over several weeks. For instance, non-mammalian red blood cells, mammalian erythroblasts and platelets have a peripheral ring of microtubules, called the marginal band, that flattens the overall cell morphology by pushing on the cell cortex. In this article, we model how the shape of these cells stems from the balance between marginal band elasticity and cortical tension. We predict that the diameter of the cell scales with the total microtubule polymer, and verify the predicted law across a wide range of species. Our analysis also shows that the combination of the marginal band rigidity and cortical tension increases the ability of the cell to withstand forces without deformation. Finally, we model the marginal band coiling that occurs during the disc-to-sphere transition observed for instance at the onset of blood platelet activation. We show that when cortical tension increases faster than crosslinkers can unbind, the marginal band will coil, whereas if the tension increases slower, the marginal band may shorten as microtubules slide relative to each other.\n\nSignificance StatementMany blood cells have a discoidal shape, which is essential for them to function properly within the organism. For some cells, such as blood platelets, this shape is due to the interplay between the elasticity of the marginal band, which is a closed ring of stiff filaments called microtubules, and the tension of the cell cortex, a polymer scaffold associated with the plasma membrane. Dmitrieff et al. examined how cell size is determined by the mechanical balance between these two components. Remarkably, the theory is confirmed over nearly three orders of magnitudes, by data collected from 25 species. The theory also shows how the composite structure is adapted to resist transient mechanical challenges, as encountered in the blood stream.

biophysics↗