Mastodawn

📰 "Diatom Endosymbionts have Shrinking but Stable Genomes Despite Low Coding Density"
https://www.biorxiv.org/content/10.64898/2026.03.19.712447v1?rss=1 #CellDivision #Cell

Diatom Endosymbionts have Shrinking but Stable Genomes Despite Low Coding Density

Successful establishment of long-term, obligate endosymbiotic relationships requires integration of hosts and endosymbionts across multiple levels. For example, highly integrated, host-beneficial endosymbionts typically have extremely reduced genomes and metabolisms. However, we do not yet fully understand the specific mechanisms that drive this integration or if there is a specific order in which these changes must occur. To investigate the early stages of endosymbiont genome reduction, we greatly expanded available whole genome data for the nitrogen-fixing endosymbionts (spheroid bodies, SBs) of diatoms in the family Rhopalodiaceae. We used these data to reconstruct SB evolutionary history and to characterize SB core metabolic capacity. We found two key genes missing from all SB genomes, mltA and dnaA , which could provide points of host control over SB cell division. Although most of the SB core genome is experiencing moderately strong purifying selection, we identified 54 genes under positive selection. Eighteen of these are peripheral proteins or involved in cell wall and cell membrane metabolism and could be involved in direct interactions with the host. Unexpectedly, we also found three nif genes under positive selection that are core to the central nitrogen-fixing enzyme. Overall, our results provide early insights into how SBs and their hosts interact, showing that SBs are still in the early stages of endosymbiont genome reduction, but they differ in key ways from current models, including the early loss of all mobile elements. ### Competing Interest Statement The authors have declared no competing interest. NSF, 2222944 Montana Institute on Ecosystems, https://ror.org/0591pcw70

bioRxiv

Rxiv mechanobio 15h ago

📰 "Cell Cycle-Dependent Chromatin Motion: A Role for DNA Content Doubling Over Cohesion"
https://www.biorxiv.org/content/10.64898/2026.03.19.712877v1?rss=1 #Dynamics #Cell

Cell Cycle-Dependent Chromatin Motion: A Role for DNA Content Doubling Over Cohesion

The spatiotemporal organisation of chromatin in the eukaryotic nucleus is fundamental for genome regulation. Chromatin undergoes rapid remodelling and rearrangements within minutes, altering its diffusion properties. Considering the tight coupling between genome function and nuclear architecture, a key question is how chromatin dynamics adapt to or promote nuclear processes. To elucidate the underlying physical principles, we employed High-resolution Diffusion mapping (Hi-D) to track chromatin motion throughout interphase in live human cells. Our analysis, that considers both diffusive motion and drift generated by active forces, re-vealed that chromatin dynamics are heterogeneous, with distinct behaviours in different subnuclear zones. Notably, both diffusive and processive contributions to chromatin motion progressively decrease from G1 to G2 phase, with this reduction occurring uniformly across all subzones. This suggests a global mechanism driving the observed decrease in chroma-tin mobility during cell cycle progression. By combining genetic knockout experiments and polymer modelling, we demonstrate that the doubling of DNA content, rather than cohesin-mediated sister chromatid entrapment, is responsible for the gradual decrease in chromatin motion during the cell cycle in human nuclei. These findings provide new insights into the physical and functional organisation of chromatin and its regulation during cellular proliferation. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-22-EXES-0015 La Ligue Contre le Cancer, https://ror.org/00rkrv905 Institut Universitaire de France, https://ror.org/055khg266

bioRxiv

Rxiv mechanobio 15h ago

📰 "One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization"
https://www.biorxiv.org/content/10.64898/2026.03.19.710883v1?rss=1 #Forces #Cell

One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization

Understanding how chromatin folds in three dimensions remains challenging because most experimental assays capture low-dimensional projections of an underlying, highly heterogeneous polymer. Here we present an ensemble-based interpretive framework built on the previously introduced Self-Returning Excluded Volume (SR-EV) model, a minimal generator of nucleosome-resolution chromatin conformations based on stochastic return rules and excluded-volume geometry. Despite its simplicity, SR-EV reproduces key experimental signatures across scales: heterogeneous nanoscale packing domains resembling ChromEMT and ChromSTEM observations, sparse and highly variable single-configuration contact patterns analogous to single-cell chromosome conformation capture (Hi-C), and robust ensemble-level contact enrichment consistent with topologically associating domains (TADs). In this framework, Hi-C loop and TAD signatures are interpreted as ensemble-level statistical enrichments rather than invariant features of single-cell conformations. SR-EV is explicitly designed to generate large ensembles of complete three-dimensional chromatin configurations that can be projected consistently onto two-dimensional contact maps and one-dimensional genomic profiles. By introducing architectural-protein effects only through ensemble selection rather than explicit forces, SR-EV supports a separation between intrinsic polymer geometry and regulatory bias and suggests that TAD-like features can emerge as statistical enrichments rather than deterministic three-dimensional structures. Coordination number and probe-based accessibility computed directly from SR-EV provide a unified link between three-dimensional packing, two-dimensional contact maps, and one-dimensional genomic profiles. Together, these results establish SR-EV as a minimal and physically grounded reference framework for interpreting how heterogeneous chromatin ensembles give rise to multimodal experimental observables, while remaining consistent with the fact that chromatin organization is realized in individual cells. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, https://ror.org/01cwqze88, R01CA228272, U54 CA268084, T32AI083216, K23DK144661 Northwestern University, Starzl Scholarship

bioRxiv

Rxiv mechanobio 1d ago

📰 "Logic of optimal collective migration in heterogeneous tissues"
https://www.biorxiv.org/content/10.64898/2026.03.19.712843v1?rss=1 #CellMigration #Cell

Logic of optimal collective migration in heterogeneous tissues

Collective cell migration is a critical process in embryogenesis and cancer invasion. Recent work has shown that uniform tissues can undergo sharp rheological transitions, with collective motion emerging above a critical cell motility. In vivo, however, migration typically involves multiple populations with distinct motile and adhesive properties, and how this heterogeneity shapes collective dynamics remains unclear. Here, using two different vertex model implementations, we show that migration of heterogeneous clusters through tissues is maximized at intermediate adhesion strength: too little and the cluster fragments, too much and cluster cell cohesion suppresses the rearrangements needed for forward motion. We test our model against recent and new data on zebrafish mesendoderm invasion, where graded Nodal signalling regulates both motility and adhesion differences. By mapping measured Nodal levels to mechanical parameters, the model not only reproduces migration outcomes across homogeneous and heterogeneous clusters, but also discriminates between alternative adhesion rules. Strikingly, the inferred parameters place the system near the predicted optimum, where adhesion is strong enough to maintain cohesion yet graded enough to allow selective coupling among heterogeneous neighbors. These results identify an optimal balance between cohesion and interfacial remodeling as a general principle coordinating collective invasion in heterogeneous tissues. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, 101116586

bioRxiv

Rxiv mechanobio 1d ago

📰 "Morphotype-Resolved 3D Morphometry Reveals a Structure-Density-Location Coupling in Mitochondrial Networks"
https://www.biorxiv.org/content/10.64898/2026.03.19.712811v1?rss=1 #Dynamics #Cell

Morphotype-Resolved 3D Morphometry Reveals a Structure-Density-Location Coupling in Mitochondrial Networks

Mitochondrial architecture plays a critical role in cellular function, yet how organelle structure, metabolic density, and subcellular position are jointly remodeled across whole cells remains poorly understood. We applied quantitative 3D soft X-ray tomography to analyze intact INS-1E cells in a native, cryo-hydrated state. By integrating morphometric profiling with voxel-level linear absorption coefficients (LAC) and contour-based radial mapping, we tracked the structural, biochemical, and spatial remodeling of fragmented, intermediate, and interconnected mitochondrial morphotypes under high glucose and Exendin-4 stimulation. High glucose induces morphotype-specific hypertrophy, fission, and perinuclear redistribution of low-density fragments. Co-stimulation with Exendin-4 stabilizes interconnected networks and increases metabolic density at the cell periphery. Morphotype-resolved analysis uncovers a structure-density-location coupling in which mitochondrial shape, macromolecular packing, and radial position shift in concert. These results offer a quantitative framework and high-resolution spatial constraints for whole-cell modeling of organelle dynamics. ### Competing Interest Statement The authors have declared no competing interest.

bioRxiv

Rxiv mechanobio 1d ago

📰 "Differences in Cellular mechanics and ECM dynamics shape differential development of wing and haltere in Drosophila"
https://doi.org/doi:10.1016/j.ydbio.2026.03.012
https://pubmed.ncbi.nlm.nih.gov/41862115/
#Mechanical #Mechanics #Cell #Ecm

Rxiv mechanobio 1d ago

📰 "Subdiffusive random growth of bacteria"
https://www.biorxiv.org/content/10.64898/2026.03.19.712816v1?rss=1 #Dynamics #Cell

Subdiffusive random growth of bacteria

While the regulation of bacterial cell size is widely studied across generations, the stochastic nature of cell volume growth remains elusive within a cell cycle. Here, we investigate the fluctuations of cell volume growth and report a deviation from standard white-noise models: the random growth rate exhibits subdiffusive dynamics. Specifically, the mean square displacement of the growth-rate noise scales as Δt^α with an anomalous exponent α≈0.27. This low exponent implies strong negative temporal correlations in growth rate noise on timescales of minutes, which are significantly faster than those of gene expression dynamics. We attribute this phenomenon to the physical mechanics of the cell wall. By modeling the peptidoglycan network as a complex viscoelastic material with power-law-distributed relaxation times, we successfully recapitulate the observed subdiffusive behavior. Our results suggest that the heterogeneous mechanical constraints of the peptidoglycan network, rather than biological regulatory programs,govern the short-timescale fluctuations of bacterial growth. ### Competing Interest Statement The authors have declared no competing interest. National Key Research and Development Program of China

bioRxiv

Rxiv mechanobio 1d ago

📰 "Systematic identification of tissue-conserved m6A sites reveals a stable epitranscriptomic regulatory layer controlling essential genes"
https://www.biorxiv.org/content/10.64898/2026.03.19.713046v1?rss=1 #Dynamics #Cell

Systematic identification of tissue-conserved m6A sites reveals a stable epitranscriptomic regulatory layer controlling essential genes

Chemical modifications to RNA are fundamental regulators of cellular identity and function. Among these, N6-methyladenosine (m6A) is the most abundant mRNA modification in mammalian cell, governing major post-transcriptional processes. While conditional m6A dynamics are well studied, the extent and function of condition-independent, tissue-conserved (TC) m6A in humans remain unclear. Here we show that 5,945 TC sites are consistently methylated across 24 human tissues. These sites are enriched near stop codons, evolutionarily conserved, and characterized by distinct sequence signatures. RBM15/B are identified as candidate mediators of TC m6A deposition, and YTHDF1-3 and UPF1 are preferentially enriched at TC sites, supporting their role for m6A-linked mRNA decay. TC m6A sites mark 1,386 genes essential for core cellular processes like autophagy and homeostasis, showing stable expression and evolutionary constraint. Pan-cancer analysis reveals that TC m6A genes are disproportionately differentially expressed, alongside with altered RBM15/B expression, suggesting that disruption of this stable m6A layer may contribute to transcriptional changes in cancer. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, https://ror.org/01cwqze88, U01CA279618, R21GM155774 National Institutes of Health, CA096512, CA284554, CA278812, CA291244, CA124332 UPMC Hillman Cancer Center Startup Fund, P30CA047904

bioRxiv

Rxiv mechanobio 1d ago

📰 "Non-Equilibrium Spatial Encoding of Nanoscale Mechanical Relaxation in Growing Plant Epithelial cells"
https://www.biorxiv.org/content/10.64898/2026.03.18.712596v1?rss=1 #Mechanical #Cell

Non-Equilibrium Spatial Encoding of Nanoscale Mechanical Relaxation in Growing Plant Epithelial cells

A central problem in soft and biological physics is how molecular-scale activity and remodelling coarse-grain into emergent mechanical laws at larger scales. In growing cell walls (polymeric composite materials that surround 90% of living organisms' cells) irreversible deformation is not controlled by elastic stress alone. Instead, growth depends on the interplay between energy storage, dissipation, and the local timing of viscoelastic relaxation. Although dynamic atomic force microscopy (AFM) resolves storage and loss moduli (E', E'') of living walls at nanometre resolution, these observables have remained phenomenological and disconnected from constitutive field variables. Here we introduce a physics-based inversion framework that converts AFM measurements of epidermal cells of living Arabidopsis plants into spatially resolved fields of stiffness k, viscosity η, and relaxation time τ. By analysing the spatial gradients of E' and E'', we uncover organized mechanical heterogeneities governed by cellular confinement and stress focusing. We demonstrate that the local relaxation time is encoded directly in the coupling between storage and dissipation, yielding the pointwise relation τ = (1/ω)∂ E'/∂ E'' is the indentation frequency. This relation enables model-independent extraction of mechanical timescales and establishes a general route from nanoscale non-equilibrium rheology to continuum descriptions of growth in living and active soft materials. ### Competing Interest Statement The authors have declared no competing interest. BBSRC, BB/P01979X/1

bioRxiv

Rxiv mechanobio 1d ago

📰 "The limits of information in precise regulation of early multicellular life cycles"
https://www.biorxiv.org/content/10.64898/2026.03.19.712848v1?rss=1 #Mechanical #Cell

The limits of information in precise regulation of early multicellular life cycles

A key step in the evolution of complex multicellularity is the emergence of regulated life cycles that coordinate growth and reproduction. One potential route toward regulation involves co-opting intrinsic information: cues generated by routine cellular activities such as aging or mechanical stress from growth. Here, we model the simplest form of multicellular organization, linear filaments, to investigate whether intrinsic information can be harnessed to produce regular multicellular life cycles. Based on our analyses, we find that these information sources face an inherent trade-off between flexibility and regularity. Some sources, such as mechanical stress, precisely regulate when reproduction occurs but generate only a single reproductive mode. Others, such as cell age, can in principle produce diverse life cycles but fail to generate any of them reliably. Combining information sources through simple genetic circuits reduces variance in some cases, but the range of achievable life cycles remains constrained. Together these results suggest that while intrinsic information may facilitate early multicellular evolution, there are significant limitations on the degree to which it can be harnessed to evolve tightly-regulated, flexible life cycles. Our work highlights the constraints faced by nascent multicellular organisms and the evolutionary innovations likely required for coordinated multicellular development. ### Competing Interest Statement The authors have declared no competing interest. Swedish Research Council, https://ror.org/03zttf063, 2022-04124 NIH Common Fund, R35GM138030

bioRxiv