Biology subjects

Rizvi, M. S.

Publications and source records attributed to Rizvi, M. S..

10 recordsLinked to original sources

bioRxiv2026

Length scale of cellular activity determines signatures of epithelial remodeling

Cellular activity drives epithelial fluidization -- a widespread phenomenon observed during tissue development, remodeling, and repair both in vivo and in vitro. Yet the physical origins and spatial organization of active forces vary widely across biological systems and are often represented by a single generic mechanism in theoretical models. Here, using an active vertex model, we systematically compare four modes of epithelial activity spanning subcellular to tissue scales: apolar motility, polar motility, fluctuating contractility, and mechanochemical regulation. Although all four mechanisms drive the same global transition from a solid-like rectangular tissue to a fluid-like circular morphology, they reach this state through distinct pathways -- differing in the rates and topology of junctional rearrangements, cell elimination, and collective motion and leave distinguishable signatures in tissue architecture, cell dynamics, and mechanical relaxation. Among these observables, spatial velocity correlations directly capture the spatial organization of activity: their correlation length and functional form together resolve all four mechanisms. The robustness of these signatures across activity strengths suggests that spatial velocity correlations offer an experimentally accessible means of identifying the physical origin of epithelial activity from live-cell imaging alone.

biophysics↗

bioRxiv2026

SARS-CoV-2 PLpro Drives Epithelial Barrier Disruption Across Drosophila and Mammalian Epithelia

Severe SARS-CoV-2 infection manifests as a systemic disorder characterized by catastrophic loss of epithelial homeostasis and dysregulated host inflammation. However, which specific viral factors initiate this tissue damage in intact, living organisms remains unresolved. Using a comprehensive in vivo screen of all 25 SARS-CoV-2 nonstructural proteins (NSPs) and accessory factors (ORFs) in the Drosophila wing imaginal epithelium, here we have identified NSP5 (Main protease, Mpro) and NSP3--specifically its papain-like protease (PLpro) domain--as individual triggers of tissue injury. Focusing further on PLpro, we demonstrate that its expression initiates a self-amplifying host cell stress signaling circuit driven by metabolic overdrive, oxidative stress, and hyperactivation of Akt, JNK, and JAK-STAT signaling. However, this pathogenic loop is fragile; genetic suppression of any of the hyperactivated signaling nodes collapses this network, thereby restoring epithelial homeostasis. This organ-intrinsic, PLpro-induced epithelial vulnerability is also seen in the adult midgut and larval respiratory system. Notably, in the larval respiratory system, PLpro drives compartment-specific pathologies: it induces fibrosis-like remodeling in terminally differentiated squamous tracheal tubes, while catastrophically depleting the progenitor-competent tracheoblasts and air sac precursors (ASP). Both these defects are reversed by the genetic knockdown of PLpro-induced JAK-STAT signaling. Finally, we show that PLpro expression in mammalian MDCK epithelia similarly triggers junctional remodeling and inflammatory stress signaling. Our findings position PLpro as a central driver of COVID-19 pathogenesis through a self-amplifying epithelial stress circuit that compromises epithelial homeostasis across organs and species.

cell biology↗

bioRxiv2025

Motility-Driven Viscoelastic Control of Tissue Morphology in Presomitic Mesoderm

During development, embryonic tissues experience mechanical stresses ranging from cellular to supracellular length scales. In response, cells generate active forces that drive rearrangements, allowing the tissue to relax accumulated stresses. The nature of these responses depends strongly on the magnitude and duration of the deformation, giving rise to the tissues characteristic viscoelastic behavior. Although experiments have characterized tissue rheology in various contexts, simpler theoretical approaches that directly connect cellular activity to emergent rheological behavior are still limited. In this study, we employ a vertex-based model of epithelial tissue incorporating active force fluctuations in cell vertices to represent cell motility. We capture distinct rounding dynamics and motility-dependent timescales by benchmarking against experimental observations such as the bulging of presomitic mesoderm (PSM) explants driven by Fibroblast Growth Factor(FGF) gradients. Stress relaxation tests reveal rapid short-timescale relaxation alongside persistent longtimescale residual stresses that decrease from anterior to posterior (AP) region of the PSM. By applying oscillatory shear, we analyzed the resulting elastic and viscous responses, revealing motility dependence of storage and loss modulus. Finally, we introduce spatially patterned cues applied in a temporally pulsed manner, mimicking dynamic biochemical or mechanical signals during development. Our results show that while higher motility promotes tissue remodeling in response to these cues, this response is constrained by spatial scale; cellular-scale perturbations are relaxed irrespective of motility strength, preventing complete morphological adaptation.

developmental biology↗

bioRxiv2025

Modeling the role of ATP metabolism in articular cartilage and osteoarthritis

Osteoarthritis, a prevalent degenerative joint disease, is characterized by progressive degradation of articular cartilage. The avascular nature of articular cartilage makes it vulnerable to metabolic disruptions under hypoxic conditions. Central to this process is the role of ATP metabolism in chondrocytes, which generally maintains a delicate balance between glycolysis and oxidative phosphorylation. To investigate the balance between these two mechanisms and their regulation, we developed a comprehensive mathematical model simulating ATP metabolism in chondrocytes. The model incorporates key metabolic regulators, capturing the bistable switching between glycolysis and oxidative phosphorylation under varying nutrient conditions. Our simulation also accounts for stochastic fluctuations in oxygen and glucose levels, mimicking physiological conditions during mechanical loading, and their impact on articular cartilage dynamics. The results demonstrate that chronic hypoxia induces an irreversible metabolic shift to glycolysis, leading to sustained reductions in ATP levels and progressive ECM loss. Interestingly, the model predicts that physiological stochasticity in oxygen levels, representative of mechanical loading during physical activity, enhances metabolic flexibility and promotes ATP synthesis. When testing therapeutic interventions, we found that while exogenous ECM supplementation provides transient matrix restoration, only approaches targeting metabolic dysfunction - either through enhanced ATP synthesis or controlled suppression of regulatory factors - successfully reverse the pathological glycolytic shift. Our model suggests that optimal therapeutic approaches should combine ATP metabolic modulation with structural support to maintain beneficial nutrient fluctuations. The framework provides a basis for the development of personalized treatment strategies that address both the metabolic and structural aspects of osteoarthritis, offering new possibilities for restoring cartilage homeostasis and preventing disease progression.

systems biology↗

bioRxiv2025

Fluid flow induced biomechanical origin of collagen architecture in articular cartilage

The zonal collagen architecture of articular cartilage (AC) is essential for its mechanical function and long-term homeostasis. While its structural organization is well established, the mechanistic basis for the emergence and maintenance of this architecture remains unresolved. In this study, we propose a fluid flow-driven mechanism for the evolution of collagen fiber orientation in AC, using both a continuum orientation field model and a discrete three-dimensional fiber network model. Joint movements, shear-dominated during embryogenesis and combined shear-compression postnatally, induce synovial fluid flow, which guides collagen alignment through preferential fiber deposition. Our models reproduce the characteristic Benninghoff architecture observed in mature AC and are validated against experimental data across multiple species, joint types, and developmental stages. We demonstrate how joint- and organism-specific mechanical loading leads to diverse collagen arrangements and zonal organization. Further, by systematically varying shear and compressive loading durations to mimic different physical activities, we show that the collagen architecture, mechanical stiffness, and effective synovial fluid viscosity of AC adapt in an activity-dependent manner. Finally, we simulate osteoarthritic remodeling as a localized disruption to fluid flow and show how it leads to progressive collagen disorganization. These findings offer a unifying biomechanical framework for AC development, function, and degeneration, with implications for tissue engineering and rehabilitation strategies.

biophysics↗

bioRxiv2023

Cortical ductility governs cell-cell adhesion mechanics

This paper challenges our understanding of cell-cell adhesion by emphasising the role of mechanical dissipation at the cellular level. We have developed new microdevices to measure the energy dissipated during the rupture of junctions between cell-cell doublets. Using a synthetic cadherin approach, we decoupled the role of cadherin binding energy, signalling and downstream regulation of cytoskeletal architecture. This yielded a phase diagram in which cell junctions transition from a ductile to a brittle fracture mode based on their ratio of cortical tension and shape relaxation time. We recapitulated our results using a descriptive mechanical simulation approach. Our results shift our understanding of cell-cell adhesion from the current focus on bond energy and tension to the key role played by energy dissipation in the cytoskeleton during junction deformation and its active mechanosensitive regulation.

cell biology↗

bioRxiv2021

Emergence of planar cell polarity from the interplay of asymmetric interaction and tissue-level gradients

Planar cell polarity (PCP) - tissue-scale alignment of the direction of asymmetric localization of proteins at cell-cell interface - is essential for embryonic development and physiological functions. Abnormalities in PCP can lead to neural tube closure defects and misaligned hair follicles. Decoding the mechanism responsible for PCP establishment and maintenance remains a fundamental open question. While the roles of various molecules - broadly classified into "global" and "local" modules - have been well-studied, their necessity and sufficiency in explaining PCP and connecting their perturbations to experimentally observed patterns has not been examined. Here, we develop a minimal model that captures the proposed features of these modules - a global tissue-level gradient and local asymmetric distribution of protein complexes. Our model suggests that while polarity can emerge without a gradient, the gradient can provide the direction of polarity and maintain PCP robustly in presence of stochastic perturbations. We also recapitulated swirling patterns seen experimentally and features of domineering non-autonomy, using only three free model parameters - protein binding rate, concentration of proteins forming heterodimer across cell boundaries and gradient steepness. We explain how self-stabilizing asymmetric localizations in presence of tissue-level gradient can lead to robust PCP patterns and reveal minimal design principles for a polarized system.

systems biology↗

bioRxiv2021

Continuum Theory for Planar Cell Polarity

Planar Cell Polarity (PCP), characterized by asymmetric localization of proteins at the cell membrane within the epithelial plane, plays essential roles in embryonic development and physiological functions. The significance of PCP can be appreciated by the outcomes of its failure in the form of defects in neural tube formation, tracheal malfunctions, organ shape misregulation, hair follicle misalignment etc. Extensive experimental works on PCP in fruit fly Drosophila melanogaster have classified the proteins involved in PCP into a core module, acting locally by inter-cellular protein interactions, and a global module, responsible for the alignment of cell polarities with that of the tissue axis. Despite the involvement of different molecular players the asymmetric localization of the proteins of the two modules on cell membrane primarily involves inter-cellular dimer formations. We have developed a continuum model of the localization of PCP proteins on the cell membrane and its regulation via intra- and inter-cellular protein-protein interactions. We have identified the conditions for the asymmetric protein localization, or PCP establishment, for uniform and graded protein expression levels in the tissue. We have found that in the absence of any tissue level expression gradient polarized state of the tissue does not arise. However, in the presence of tissue-level expression gradients of proteins the polarized state remains stable. We have also looked at the influence of the loss of PCP proteins from a select region of the tissue on the polarization of the cells outside of that region. This continuum theory of planar cell polarity can be coupled with active-matter hydrodynamics to study cell flows and their regulation by genetic machinery.

biophysics↗

bioRxiv2020

Degenerating Drosophila Larval Epidermal Cells Drive Thorax Closure

Adult thorax formation in Drosophila begins during pre-pupal development by fusion of its two contralateral progenitor halves, the heminotal epithelia (HE). HEs migrate and replace an underlying cell layer of thoracic larval epidermal cells (LECs) during a morphogenetic process called thorax closure. The LEC layer has so far been proposed to be a passive substrate over which HEs migrate before their zipping. By contrast, here we show that the pull forces generated within the LEC layer drive HE migration. During thorax closure, the LECs display actomyosin-mediated contraction, via enrichment of non-muscle myosin-II and actin, besides squamous-to-pseudostratified columnar epithelial transition and tissue shrinkage. This shrinkage of the LEC layer is further accompanied by cell extrusion and death, that prevent overcrowding of LECs, thereby promoting further shrinkage. The pull forces thus generated by the shrinking LEC layer are then relayed to the HEs by their mutual adhesions via {beta}PS1 (Mys) and PS3 (Scb) integrins. Suppression of cell death in the LEC layer by a gain of p35 leads to cell overcrowding, which impedes HE migration and zipping. Further, knockdown of sqh, the light chain of non-muscle myosin II, in LECs or integrins (mys or scb) in either the LEC layer or in the HEs, or both abrogate thorax closure. Mathematical modeling also reveals the biophysical underpinnings of the forces that drive this tissue closure process wherein a degenerating LEC layer mediates its succession by the future adult primodia. These essential principles of thorax closure appear ancient in origin and recur in multiple morphogenetic contexts and tissue repair.

developmental biology↗

bioRxiv2018

Speed-detachment tradeoff and its effect on track bound transport of single motor protein

The transportation of the cargoes in biological cells is primarily driven by the motor proteins on filamentous protein tracks. The stochastic nature of the motion of motor protein often leads to its spontaneous detachment from the track. Using the available experimental data, we demonstrate a tradeoff between the speed of the motor and its rate of spontaneous detachment from the track. Further, it is also shown that this speed-detachment relation follows a power law where its exponent dictates the nature of the motor protein processivity. We utilize this information to study the motion of motor protein on track using a random-walk model. We obtain the average distance travelled in fixed duration and average time required for covering a given distance by the motor protein. These analyses reveal non-monotonic dependence of the motor protein speed on its transport and, therefore, optimal motor speeds can be identified for the time and distance controlled conditions.

biophysics↗