Biology subjects

Deguchi, S.

Publications and source records attributed to Deguchi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Mechanoadaptive focal adhesion-actomyosin coupling organizes diverse modes across ECM stiffness

Focal adhesions mechanically couple the actomyosin cytoskeleton to the extracellular matrix (ECM), contributing to mechanosensing and mechanical homeostasis. They span diverse states in response to the mechanical environment, from nascent adhesions and focal complexes to mature and supermature adhesions, undergoing dynamic remodeling. However, how ECM-dependent force generation and internal mechanoadaptation jointly shape the emergence and stability of these states remains unclear. Here, we develop a four-variable dynamical model comprising adhesion state, transmitted force, reinforcement activity, and an adaptive mechanical stress target. As ECM stiffness varies, the model generates distinct modes while regulating mechanical stress toward this target. The force-response timescale further modifies the stability structure, giving rise to a stable oscillatory mode. Within multistable regimes, adhesion-mode selection depends not only on current ECM stiffness but also on its history. These results show that diverse adhesion modes can emerge from a common mechanoadaptive system, with ECM stiffness history influencing mode selection.

biophysics↗

bioRxiv2026

CycloCross: Adversarial single-cell RNA-seq data translation across species

Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cellular heterogeneity, yet most datasets are limited to a handful of model organisms, leaving critical gaps in cross-species biology. Existing computational methods for integrating multi-species scRNA-seq data often rely on one-to-one ortholog mapping, which fails to account for gene duplications, losses, or functional divergences. To address these challenges, we introduce CycloCross, an adversarial method based on the CycleGAN architecture, designed to translate scRNA-seq data between species without requiring a priori gene correspondences. Unlike generative models that synthesize data from noise, CycloCross leverages real data from a source species, enabling more realistic and data-efficient translations. We demonstrate its effectiveness in germ cell development, translating data between mouse, macaque, and human with conserved yet divergent transcriptional programs. CycloCross not only preserves temporal dynamics but also enables interpolation and extrapolation of gene expression at missing time points, offering predictions for experimentally inaccessible states. Furthermore, CycloCross generates biologically plausible samples even with limited data, outperforming traditional generative models.

bioinformatics↗

bioRxiv2026

SERPINE1-AP2A1 interplay links substrate stiffness to fibroblast senescence

Cellular senescence is characterized by stable cell-cycle arrest, cytoskeletal remodeling, and altered secretion of senescence-associated secretory phenotype (SASP) factors, including SERPINE1/plasminogen activator inhibitor-1 (PAI-1). Although extracellular matrix (ECM) stiffening has been linked to fibroblast mechanotransduction and SERPINE1-associated remodeling, the molecular pathway connecting substrate stiffness to SERPINE1 regulation in senescent fibroblasts remains incompletely understood. Here, we investigated how defined substrate stiffness affects fibroblast morphology, mechanical phenotype, and SERPINE1 expression, and examined whether the clathrin adaptor AP2A1 participates in this response in replicative senescent human fibroblasts. Using tunable polyacrylamide hydrogels, we found that increasing substrate stiffness enhanced fibroblast spreading, stress fiber thickening, focal adhesion maturation, cellular stiffness, and senescence-associated marker expression. Stiff substrates also increased SERPINE1 expression and its colocalization with actin fibers, with stronger responses observed in senescent than in young fibroblasts. Functional perturbation experiments further suggested that SERPINE1 contributes to stress fiber organization in senescent cells. In addition, AP2A1 colocalized with SERPINE1, and modulation of AP2A1 under knockdown and overexpression conditions altered SERPINE1 signal intensity. Conversely, perturbation of SERPINE1 also affected AP2A1, supporting a potential bidirectional relationship between these two components. Together, these findings identify SERPINE1 as a stiffness-responsive factor associated with senescence-linked cytoskeletal remodeling and support a functional relationship between AP2A1 and SERPINE1 in senescent fibroblasts. These results suggest that the AP2A1-SERPINE1 axis may contribute to the link between extracellular mechanical cues and senescence-associated fibroblast remodeling.

cell biology↗

bioRxiv2026

Mechanical contributions of the Myp2 tail revealed by coiled-coil force sensors

Cytokinesis is driven by the constriction of an actomyosin contractile ring, yet how forces generated by individual myosin molecules are transmitted within the ring remains poorly understood. In fission yeast Schizosaccharomyces pombe, the type II myosin Myp2 plays a key role in ring constriction and stability, particularly under stress conditions. Unlike typical type-II myosins, Myp2s tail contains two coiled coils. Although numerous studies have revealed the structure and molecular function of Myp2, the mechanical contribution of its unique tail region has remained unclear. Here, we directly measured forces acting on Myp2 in living cells using genetically encoded coiled-coil force sensors. Insertion of force sensors into the neck region revealed that Myp2 experiences forces of approximately 6.6 pN within the contractile ring. To dissect the contribution of the tail region, we systematically analyzed tail-deletion mutants. Deletion of the proximal tail had little effect on force levels, whereas deletion of the distal C-terminal tail significantly reduced the forces experienced by Myp2. Quantitative analysis of force distributions further showed that truncation of the C-terminal tail reduces the characteristic force by approximately half, demonstrating a major mechanical contribution of the distal tail to the forces experienced by Myp2 at the molecular scale. Deletion of the C-terminal tail slowed the growth rate, consistent with previous macroscopic observations that this region is required for robust ring constriction under stress conditions. We further found that the C-terminal tail forms clusters, which require full-length Myp2 for proper localization to the ring. These findings, together with molecular force measurements and quantitative analysis, demonstrate that the Myp2 tail is not merely a structural or regulatory domain but functions as a load-bearing component in vivo, with its C-terminal region playing a central role in force transmission across scales.

Cell Biology↗

bioRxiv2026

Energetically constrained turnover drives the emergence of aging

Aging is characterized by progressive functional decline, yet why such decline is observed broadly across living systems remains unclear. While molecular and cellular mechanisms describe how aging progresses, they do not explain why functional decline should arise as a natural consequence of living organization. Here, we show that aging naturally emerges from three general features of life: unavoidable damage, turnover-mediated maintenance, and the energetic constraint of turnover. We develop a hierarchical damage-turnover model in which component-level damage and energetically constrained turnover jointly determine whole-system performance. In the model, damage stochastically converts functional components into non-functional components, whereas turnover restores component performance at a rate coupled to whole-system performance. Analytical and Monte Carlo analyses reveal two regimes: a non-aging regime, in which performance remains finite, and an aging regime, in which performance progressively collapses toward zero. Performance-independent turnover always maintains a positive steady state, whereas performance-dependent turnover generates irreversible decline when reduced performance weakens maintenance capacity. Stochastic fluctuations further promote collapse near the transition boundary, even when deterministic analysis predicts a nonzero steady state. These results indicate that unavoidable damage and energetically constrained turnover are sufficient to generate aging-like decline, providing a minimal theoretical explanation for long-term irreversibility in biological systems.

biophysics↗

bioRxiv2026

Mechanical stretch disrupts intracellular structures under impaired actin integrity in vascular smooth muscle cells

Actin-bundle organization is essential for vascular smooth muscle cell mechanics and is implicated in actin-related diseases. However, it remains unclear how cell stretching affects intracellular actin bundles when actin polymerization is impaired. Here, we performed live imaging of Latrunculin A-treated A7r5 vascular smooth muscle cells in a stretch chamber. GFP--actinin imaging showed that Latrunculin A reduced actin-bundle coverage while periodicity was maintained. Subsequent mechanical stretch disrupted both actin-bundle coverage and periodicity. We constructed a stochastic filament bundle model in which actin filament length, actin crosslinking protein dynamics, external stretch, and myosin-driven contractile shortening determine bundle connectivity. The model generated non-spanning, collapse, and persistent states based on spanning connectivity before and after stretch, shaped by filament length and applied strain. A reduced model further showed that these states are governed by a balance between connectivity formation and stretch-induced loss. Together, our results suggest that reduced actin polymerization destabilizes intracellular actin-bundle organization under mechanical stretch, providing a mechanism linking actin polymerization defects to mechanical fragility in vascular smooth muscle cells.

biophysics↗

bioRxiv2026

A closed-loop mathematical structure of mechanics-turnover coupling for mechanical adaptation in living systems

Mechanical adaptation underlies mechanical homeostasis by allowing living systems to restore characteristic mechanical variables under sustained perturbations. Across biological scales, turnover-mediated remodeling enables mechanical adaptation by continuously renewing internal structures under load. Despite extensive progress in this field, it remains to be established what closed-loop mathematical structure of mechanics-turnover coupling is sufficient to guarantee homeostasis and how the characteristic adaptation timescale emerges from this coupling. Here, we identify the minimal mathematical structure of closed-loop mechanics-turnover coupling, providing a unifying description of mechanically adaptive remodeling across scales. We derive an analytical expression for the adaptation timescale as a function of the coupling between internal mechanical parameters and turnover kinetics, enabling direct cross-system comparison. To isolate this structure, we formulate a dynamical model linking mechanics and turnover, and establish conditions under which the closed-loop dynamics exhibit integral action. Specifically, our model describes how deviations in the mechanical state modulate the turnover of an internal structural state, and the renewed structure feeds back onto mechanics in a negative-feedback direction, driving recovery toward a reference state. We define systems satisfying this structure as Feedback Adaptive Turnover-mediated Environment-Dependent (FATED) systems. As an experimental example, we formulate mechanical adaptation in terms of mechanically regulated actin turnover. With the generalization of this architecture, we evaluate cross-system consistency by comparing reported adaptation and turnover timescales across representative remodeling systems.

biophysics↗

bioRxiv2025

A dual-domain chitinase mechanism enables marine bacteria tosense and localize sparse crystalline chitin in the ocean

Chitin is one of the most abundant biopolymers in the ocean, and its remineralisation underpins major pathways of marine carbon cycling. A central challenge for chitinolytic bacteria is to locate and remain associated with sparsely distributed crystalline chitin particles. Here, we show that the GH18 chitinase VpChi1 from Vibrio parahaemolyticus possesses a dual-domain architecture that enhances particle encounter and retention. Full-length VpChi1 displayed much higher catalytic efficiency than a CBD-truncated mutant at low chitin concentrations, whereas substrate inhibition occurred at higher concentrations. Single-molecule fluorescence imaging demonstrated that the additional C-terminal chitin-binding domain (CBD) enables selective binding to the hydrophobic surface of crystalline chitin and substantially prolongs enzyme residence time. Kinetic simulations using experimentally determined dissociation rates showed that this extended residence arises from CBD-assisted rebinding of the catalytic domain. High-speed atomic force microscopy confirmed that the CBD does not alter stepping velocity or travel distance along individual crystals, indicating that substrate inhibition likely results from CBD engagement with neighbouring particles rather than impaired motility. Screening of seawater and marine sediments across multiple depths identified Vibrio and Pseudoalteromonas species as dominant chitin degraders, many encoding GH18 chitinases with dual CBDs, whereas terrestrial bacteria generally lacked this architecture. We propose that this two-domain configuration confers an ecological advantage by increasing enzyme retention on particulate chitin and enabling sustained production of chitobiose, a potent chemotactic signal for marine bacteria. These findings reveal a mechanistic basis for how bacteria sense and exploit particulate chitin and highlight an adaptive strategy for resource acquisition in the ocean.

molecular biology↗

bioRxiv2025

Dissecting Molecular Origins of the Mechano-Adaptive Behaviors of Actomyosin Bundles

Actomyosin bundles, composed mainly of actin filaments, myosin II filaments, and actin cross-linking proteins, are central to force generation and maintenance in non-striated muscle cells. Actomyosin bundles exhibit diverse mechano-adaptive responses to external mechanical cues. However, the molecular mechanisms underlying such adaptability remain poorly understood. In this study, we employed experiments and agent-based simulations to illuminate how actomyosin bundles adapt to complex mechanical perturbations. Our experiments revealed that individual stress fibers isolated from cells, and thus operating independently of cellular regulation, exhibited buckling in response to rapid compressions following stretch, accompanied by gradual recovery to a straight configuration. Such buckling was not observed under slow compression, indicating that the bundles exhibit rate-dependent adaptive responses. These findings demonstrate that mechano-adaptive behavior is an intrinsic property of actomyosin bundles. Simulations successfully reproduced these rate-dependent behaviors intrinsic to actomyosin bundles and identified key factors determining the dependence. Bundle stiffness influenced the buckling-induced curvature but had little effect on the time required for recovery to straight configuration. Motor density did not alter the recovery time but significantly influenced the magnitude of tensile forces developed after full recovery. The recovery time was primarily governed by the motor walking rate and the applied compressive strain rate. This work reveals how intrinsic mechanics and motor activity drive actomyosin bundle behavior in cellular mechano-adaptation.

biophysics↗

bioRxiv2025

A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity

The global circulation of SARS-CoV-2 in human populations has driven the emergence of Omicron subvariants, which have become highly diversified through recombination. In late 2024, SARS-CoV-2 Omicron XEC variant emerged from the recombination of two JN.1 progeny, KS.1.1 and KP.3.3, and became predominant worldwide. Here, we investigated virological features of the XEC variant. Epidemic dynamics modeling suggested that spike substitutions in XEC mainly contribute to its increased viral fitness. Additionally, four licensed antivirals were effective against XEC. Although the fusogenicity of XEC spike is comparable to that of the JN.1 spike, the intrinsic pathogenicity of XEC in hamsters was significantly higher than that of JN.1. Notably, we found that the nucleocapsid R204P mutation of XEC enhanced inflammation through NF-{kappa}B activation. Recent studies suggest that the evolutionary potential of spike protein is reaching its limit. Indeed, our findings highlight the critical role of non-spike mutations in the future evolution of SARS-CoV-2.

microbiology↗

bioRxiv2025

Emergence of Pareto distributions in intracellular protein activity through interaction-driven modulation

The functional activity of proteins within cells is often unequally distributed: only a small subset of molecules tends to account for the majority of cellular work. This skewed contribution pattern, reminiscent of Paretos principle, often known as the 80/20 rule, has been observed across various protein classes, yet its mechanistic origin remains poorly understood. In this study, we present a statistical mechanics-based framework that explains how such disparities naturally emerge from biologically plausible rules of interaction and regulation. By modeling proteins as elements whose activity levels and outputs evolve through mutual comparison and feedback, we demonstrate that power-law distributions can arise without assuming any intrinsic heterogeneity. The model also captures a recursive feature of disparity: even among highly active proteins, a new skewed distribution reappears when a subpopulation is isolated, reflecting the scale-invariant structure commonly observed in complex adaptive systems. We analytically derive these patterns under both positive and negative feedback scenarios and identify key conditions under which long-term functional dominance is established. Our results offer a mechanistic interpretation for the coexistence of active and inactive molecular populations and suggest that functional inequality may reflect an adaptive organizational principle of cellular systems.

biophysics↗

bioRxiv2025

Non-uniform temporal scaling of neurogenesis for species-specific dosing of cortical excitatory subtypes

Mammals share a laminar cerebral cortex, with excitatory neuron subtypes organized in distinct layers. Although this framework is conserved, subtype balance varies markedly between species due to unknown mechanisms. This study shows that species-specific neuronal composition arises from non-uniform scaling of the temporal dynamics of neurogenesis. Comparative histology of eight mammalian species revealed a significant, rat-specific expansion of the cortical deeper layer (DL). This species difference results from a specific extension of the early neurogenetic phase for DL neuron production before transitioning to the upper layer (UL) in rats, as confirmed by birthdating and single-cell transcriptomics. The duration of DL neuron production is regulated by a genetic program controlling progenitor aging, including canonical Wnt signaling. Comparative single-cell transcriptomics revealed that cortical progenitors in rats exhibit significantly elevated Wnt ligand expression. Thus, while sequential cortical neurogenesis is conserved, its progression is non-uniformly scaled in each species. Such precise heterochronic fine-tuning allows evolutionary refinement of cellular configuration without drastic remodeling of the conserved corticogenesis program. TeaserDifferential temporal progression of neural progenitor program contributes to species-specific cellular composition of mammalian cerebral cortex

developmental biology↗

bioRxiv2025

Mapping molecular diffusion across the whole cell with spatial statistics-based FRAP

Understanding molecular diffusion within cells is crucial for gaining insights into cellular biophysical mechanisms. Fluorescence recovery after photobleaching (FRAP) is a powerful technique for assessing molecular diffusion, yet its localized measurement approach hinders whole-cell analysis. To overcome this limitation, we developed Probabilistic FRAP (Pro-FRAP), a novel approach that integrates FRAP with sequential Gaussian simulation (SGS), an advanced spatial statistical method incorporating probabilistic modeling to estimate diffusion in unmeasured regions. Pro-FRAP applies SGS to standardize measured FRAP data, perform conditional simulations based on spatial correlations, and generate statistically robust estimates. In separate analyses, numerical simulations were conducted to optimize the spatial arrangement of measurement points, enhancing data accuracy and coverage. Unlike deterministic interpolation methods, Pro-FRAP captures spatial variability and quantifies uncertainty in intracellular diffusion, providing a more detailed representation of molecular transport. Thus, this framework extends FRAP beyond localized measurements, offering a refined approach for mapping intracellular diffusion with improved spatial coverage and statistical reliability. Significance statementUnderstanding molecular diffusion is essential for deciphering cellular functions and regulation. However, conventional fluorescence recovery after photobleaching (FRAP) techniques are constrained to localized measurements, limiting their ability to capture diffusion dynamics across entire cells. Here, we describe Probabilistic FRAP (Pro-FRAP), a novel framework that integrates FRAP with sequential Gaussian simulation (SGS), a spatial statistical method that enables the estimation of molecular diffusion in unmeasured regions. By incorporating probabilistic modeling, Pro-FRAP generates high-resolution diffusion maps with enhanced statistical reliability. This approach provides a more comprehensive perspective on intracellular transport, allowing for deeper insights into the spatial organization of cellular processes.

biophysics↗

bioRxiv2025

Decoupling diffusion, turnover, and advection in long-term FRAP

Intracellular molecular turnover is a dynamic process governed by diffusion, biochemical reactions, and intracellular transport dynamics. While fluorescence recovery after photobleaching (FRAP) has been widely used to quantify fluorescence recovery mechanisms, conventional models primarily focus on diffusion and reaction kinetics, often overlooking the influence of intracellular advection. However, in cytoskeletal structures such as stress fibers, myosin-driven actin retrograde flow generates a significant advective component, which complicates the interpretation of FRAP data, particularly in long-term observations where advective effects become sufficiently pronounced. Here, we develop an analytical framework that extends FRAP modeling to incorporate the coupled effects of diffusion, turnover, and intracellular advection within the photobleached region of interest. By deriving exact solutions to a reaction-diffusion-advection system, we identify three key dimensionless parameters that govern fluorescence recovery dynamics: the turnover-to-diffusion ratio, the monomer-to-filament ratio, and the advection magnitude. Our results demonstrate that, even in the absence of biochemical reactions, fluorescence recovery in a fixed region can occur due to advection, leading to potential misinterpretations of molecular exchange rates. The model provides a theoretical foundation for distinguishing these effects and offers a practical tool for long-term FRAP analysis, where the interplay of diffusion, turnover, and advection becomes increasingly relevant over extended timescales. By systematically characterizing the interplay between molecular diffusion, reaction kinetics, and intracellular transport, our framework provides deeper insight into protein turnover in complex biological environments.

biophysics↗

bioRxiv2024

Impacts of Structural Properties of Myosin II Filaments on Force Generation

Cells need intracellular forces for their physiological functions, such as migration, cytokinesis, and morphogenesis. The actin cytoskeleton generates a large fraction of the forces via interactions between cytoskeletal components, such as actin filament (F-actin), myosin, and actin cross-linking proteins (ACPs). Myosin II plays the most important role in cellular force generation. Myosin II molecules self-assemble into filaments with different structures depending on myosin II isoforms and other conditions such as pH and ionic concentration. It has remained elusive how force generation in actomyosin structures is affected by the architecture of myosin II filaments. In this study, we employed an agent-based model to investigate the effects of the structural properties of myosin II filaments on force generation in disorganized actomyosin structures. We demonstrated that the magnitude of forces and the efficiency of force generation can vary over a wide range depending on the number and spatial distribution of myosin II filaments. Further, we showed that the number of myosin heads and the length of a bare zone at the center of myosin II filaments without heads highly affect the force generation process in bundles and networks. Our study provides insights into understanding the roles of the structural properties of myosin II filaments in actomyosin contractility.

biophysics↗

bioRxiv2023

Mutual interplay of actin meshwork and stress fibers in cellular adaptive response: Insights from percolation dynamics

Cells dynamically remodel their internal structures by modulating the arrangement of actin filaments (AFs). In this process, individual AFs exhibit stochastic behavior without knowing macroscopic higher-order structures they are meant to create or disintegrate. Cellular adaptation to environmental cues is accompanied with this type of self-assembly and disassembly, but the mechanism allowing for the stochastic process-driven remodeling of the cell structure remains incompletely understood. Here we employ percolation theory to explore how AFs interacting only with neighboring ones without recognizing the overall configuration can nonetheless construct stress fibers (SFs) at particular locations. To achieve this, we determine the binding and unbinding probabilities of AFs undergoing cellular tensional homeostasis, a fundamental property maintaining intracellular tension. We showed that the duration required for the assembly of SFs is shortened by the amount of preexisting actin meshwork, while the disassembly occurs independently of the presence of actin meshwork. This asymmetry between the assembly and disassembly, consistently observed in actual cells, is explained by considering the nature of intracellular tension transmission. Thus, our percolation analysis provides insights into the role of coexisting higher-order actin structures in their flexible responses during cellular adaptation.

biophysics↗

bioRxiv2023

Virological characteristics of the SARS-CoV-2 BA.2.86 variant

In late 2023, a lineage of SARS-CoV-2 emerged and was named the BA.2.86 variant. BA.2.86 is phylogenetically distinct from other Omicron sublineages identified so far, displaying an accumulation of over 30 amino acid mutations in its spike protein. Here, we performed multiscale investigations to reveal the virological characteristics of the BA.2.86 variant. Our epidemic dynamics modeling suggested that the relative reproduction number of BA.2.86 is significantly higher than that of EG.5.1. Experimental studies showed that four clinically-available antivirals were effective against BA.2.86. Although the fusogenicity of BA.2.86 spike is similar to that of the parental BA.2 spike, the intrinsic pathogenicity of BA.2.86 in hamsters was significantly lower than that of BA.2. Since the growth kinetics of BA.2.86 is significantly lower than that of BA.2 in both in vitro cell cultures and in vivo, it is suggested that the attenuated pathogenicity of BA.2.86 is due to its decreased replication capacity.

microbiology↗

bioRxiv2023

Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant

In middle-late 2023, a sublineage of SARS-CoV-2 Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. Here, we performed multiscale investigations to reveal virological features of newly emerging EG.5.1 variant. Our phylogenetic-epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T, are critical to the increased viral fitness. Experimental investigations addressing the growth kinetics, sensitivity to clinically available antivirals, fusogenicity and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 is comparable to that of XBB.1.5. However, the cryo-electron microscopy reveals the structural difference between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible at least in our experimental setup. Our multiscale investigations provide the knowledge for understanding of the evolution trait of newly emerging pathogenic viruses in the human population.

microbiology↗