Biology subjects

Inamdar, M. M.

Publications and source records attributed to Inamdar, M. M..

12 recordsLinked to original sources

bioRxiv2026

Actin cross-linking organizes basal body patterning through anomalous diffusion transitions

Subcellular protein complexes and organelles exhibit diverse dynamic behaviors that reflect the mechanical constraints and organization of the intracellular environment. Although some structures follow classical Brownian motion, many display anomalous dynamics, including subdiffusion and superdiffusion, driven by viscoelasticity, molecular crowding, and cytoskeletal interactions. Transitions between these regimes are increasingly recognized as critical for subcellular organization, yet how they are regulated and influence pattern formation remains unclear. Here, we investigate the spatial arrangement of cilia on the apical surface of multiciliated cells (MCCs) in developing Xenopus laevis embryos, where coordinated ciliary beating depends on the precise organization of hundreds of centriole-derived basal bodies (BBs). Using quantitative confocal, high-resolution and high-speed TIRF imaging together with theoretical modeling, we show that BB trajectories undergo time-resolved transitions between diffusive and anomalous motion, with distinct regimes that correlate with apical surface expansion. During the early stages, actin remodeling facilitates the dispersal of BBs by providing a permissive, low-confinement environment. As development progresses, the actin network becomes increasingly cross-linked, forming a dense meshwork that constrains BB movement and promotes uniform spacing across the apical domain. Disruption of -actinin-1, a major actin cross-linking protein, impairs the integrity of the apical actin meshwork, weakens BB confinement, and disrupts regular spatial patterning, ultimately compromising the spatial arrangement of BBs required for proper cilia alignment. Together, we show that progressive apical actin cross-linking coordinates BB positioning and regulates their dynamic state, guiding the shift from diffusive to confined motion. This transition in dynamics enables the emergence of a uniform BB pattern, which in turn ensures the aligned deployment of motile cilia necessary for effective directional fluid flow.

biophysics↗

bioRxiv2026

Developmental regulation of progenitor aging shapes long-term intestinal homeostasis in Drosophila

Aging causes a progressive loss of tissue homeostasis, with stem cell exhaustion as a major hallmark. Age-associated decline in organ function is widely perceived as emanating from progressive accumulation of cellular damage in adult tissues. However, whether aging trajectories are established early on during development remains an open question. Here, we demonstrate that genetic modulation of cellular aging pathways in larval adult midgut progenitors (AMPs), which serve as the precursors of adult intestinal stem cells and differentiated epithelial cells, dictates the long-term trajectory of intestinal aging in Drosophila. Accelerated cellular aging by genetic perturbation employing Toll or Imd pathway overactivation or elevation of reactive oxygen species (ROS) using ND42 (mitochondrial complex I) knockdown in the AMPs results in aberrant progenitor proliferation, skewed lineage allocation, epithelial barrier dysfunction, and genomic instability. These alterations are accompanied by marked destabilization of AMP islet architecture and widespread changes in age-related molecular signatures, as revealed by bulk transcriptomic analysis. In contrast, decelerated cellular aging mediated by Foxo or Atg8a overexpression results in a decrease in enteroendocrine population and the intestinal barrier remained unaffected. Intriguingly, early-life activation of immune and oxidative stress signaling manifested later in the adult gut as elevated enteroendocrine differentiation, highlighting lasting effects on intestinal regenerative capacity and lineage balance. Together, our findings demonstrate that cellular aging is tightly regulated early on in development and its perturbation can cause developmental disruption hampering adult gut homeostasis, establishing AMPs as key developmental determinants that regulate the trajectory of intestinal aging in Drosophila.

developmental biology↗

bioRxiv2024

Mechanics of E. coli cell width homeostasis and bulging dynamics from MreB and septum inhibition

The mechanobiology of cytoskeleton and cell envelope play a vital role in cell shape homeostasis. In the gram-negative model rod-shaped bacterium Escherichia coli antibiotics that weaken the cell envelope are seen to result in bulges that eventually lead to lysis. Here, we quantify the shape dynamics of E. coli treated with cephalexin, a PBP3 inhibitor and A22, an MreB polymerization inhibitor from single cell microscopy. We find low concentrations of both inhibitors result in bulge formation with multiple cell shapes observed: rugby, large bacilli and rods with two and three bulges. We quantify the parameters of cell envelope rigidity, pressure and fluidity obtained from fitting a computational model of shell-mechanics to length and width dynamics from experiment. Using this optimized model we estimate the turgor and growth pressures of untreated growing cells as {approx}0.15 MPa and {approx}0.4 MPa. The bulge expansion dynamics correlate most prominently with a change in bending rigidity of the cell wall and cytoskeleton. Simulations predict a threshold behavior in response to envelope bending rigidity that is validated by comparison with experiments of E. coli treated with A22 either in isolation or in combination, resulting in loss of width control and cell shape change.

cell biology↗

bioRxiv2024

The life history traits of phages in a cocktail determine coinfection dynamics and efficacy

Phage cocktails are preferred over single phages for efficacious and broader-spectrum therapy. An ideal phage cocktail should have a minimum number of phages with efficient infection kinetics and delay the emergence of resistance in bacterial populations. This study examined population dynamics of the common host and combinations of two phages (N4, KKE5P, and Ec_YwIITB1) through experimental and modeling approaches to gaining insights into how phage life history traits influence the outcome of infection in the short-term of approximately an infection cycle, and whether it is informative for developing efficacious cocktails. We tested the killing efficacy of a cocktail containing two divergent phages (N4 and Ec_YwIITB1) with similar adsorption rates but differed in their latency period. Because of the shorter latency period, phage N4 dominated under all conditions tested. The cocktail essentially behaves as a single phage. When two phages (N4 and KKE5P), with similar adsorption rates and latency periods but targeted different host receptors were used, it not only resulted in the efficient replication of both phages but also improved the suppression of the emergence of resistance when compared to the N4 and Ec_YwIITB1 combination, thus behaving like an ideal cocktail. The ODE-based mathematical model demonstrated predictive capabilities consistent with experimental observations and offered insights into infection dynamics. The model may aid in phage selection and optimizing cocktail formulation based on phage life history traits. This study highlights the need for thorough characterization of phage growth parameters and informed combinations of phages, as random combinations could lead to undesirable outcomes.

microbiology↗

bioRxiv2024

Differences in Cellular mechanics and ECM dynamics shape differential development of wing and haltere in Drosophila

Diverse organ shapes and sizes arise from the complex interplay between cellular properties, mechanical forces, and gene regulation. Drosophila wing-a flat structure and the globular haltere are two homologous flight appendages emerging from a similar group of progenitor cells. The activity of a single Hox transcription factor, Ultrabithorax (Ubx), governs the development of these two distinct organs-wing and haltere with different cell and organ morphologies. Our work reported here on differential development of wing and haltere suggest that the localisation and abundance of actomyosin complexes, apical cell contractility, properties of extracellular matrix, and cell size and shape, which is a result of various cell intrinsic and extrinsic forces, plausibly influence the flat vs. globular geometry of these two organs. We followed the three-dimensional architecture of developing wing and halteres during early pupal morphogenesis, indicating the role of the above-mentioned factors in force generation and in driving differential morphogenesis, leading to different organ shapes. Loss of Ubx function led to wing cell-like cellular features in haltere discs, and corresponding changes at the level of adult organs. We also observed that RNAi-mediated downregulation of Atrophin or Pten, in the background of downregulated Expanded (or elevated Yki), gave rise to varying degrees of haltere to wing homeotic transformations at the cellular as well as adult organ levels. Finally, we provide simulated scenarios based on computational modelling that propose key ingredients required for producing wing- or haltere-like morphologies in Drosophila.

developmental biology↗

bioRxiv2023

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data of S. pombe.

biophysics↗

bioRxiv2022

Actomyosin cables position cell cohorts during Drosophila germband retraction by entraining their morphodynamic and mechanical properties

The unfolding and displacement of the germband during Drosophila germband retraction (GBR) accomplish the straightening of the embryonic anterior-posterior axis. The failure of GBR reduces embryonic viability and results in the mispositioning of the embryonic segments and the gastrointestinal tract. Despite its importance, the cellular, molecular and physical mechanisms that govern the unfolding of the germband and ensure the accurate positioning of cell fields within it remain poorly understood. Here, we uncover the requirement of planar polarized, supracellular, tensile actomyosin cables for entraining cellular morphodynamics, cell field positioning and retraction kinematics. Circumferential, non-constricting cables that form during early retraction ensure the coherence of placode-like cell cohorts, pattern medio-lateral gradients in cell shape and sidedness within it, and dampen retraction speed. Linear, constricting cables that power displacement at the end of retraction enable sequential, multi-tissue, collective T1 transitions to reposition medial cell fields to more posterior locations. Together, our results reveal how the spatiotemporally regulated deployment of actomyosin structures, functioning either as barricades or as purse strings, modulate the speed of tissue unfolding and enable cell field positioning by influencing the morphodynamic and mechanical properties of cell cohorts during morphogenesis.

cell biology↗

bioRxiv2022

Interplay between cell height variations and planar pulsations in epithelial monolayers

Biological tissues change their shapes through collective interactions of cells. This coordination sets length and time scales for dynamics where precision is essential, in particular during morphogenetic events. However, how these scales emerge remains unclear. Here we address this question using the pulsatile domains observed in confluent epithelial MDCK monolayers where cells exhibit synchronous contraction and extension cycles of {approx}5 hours duration and {approx}200 m length scale. We report that the monolayer thickness changes gradually in space and time by more than two folds in order to counterbalance the contraction and extension of the incompressible cytoplasm. We recapitulate these pulsatile dynamics using a continuum model and show that incorporation of cell stiffness dependent height variations is critical both for generating temporal pulsations and establishing the domain size. We propose that this feedback between height and mechanics could be important in coordinating the length scales of tissue dynamics.

biophysics↗

bioRxiv2022

Role of Delta-Notch signalling molecules on cell-cell adhesion in determining heterogeneous chemical and cell morphological patterning

Cell mechanics and motility are responsible for collective motion of cells that result in overall deformation of epithelial tissues. On the other hand, contact-dependent cell-cell signalling is responsible for generating a large variety of intricate, self-organized, spatial patterns of the signalling molecules. Moreover, it is becoming increasingly clear that the combined mechanochemical patterns of cell shape/size and signalling molecules in the tissues, for example, in cancerous and sensory epithelium, are governed by mechanochemical coupling between chemical signalling and cell mechanics. However, a clear quantitative picture of how these two aspects of tissue dynamics, i.e., signalling and mechanics, lead to pattern and form is still emerging. Although, a number of recent experiments demonstrate that cell mechanics, cell motility, and cell-cell signalling are tightly coupled in many morphogenetic processes, relatively few modeling efforts have focused on an integrated approach. We extend the vertex model of an epithelial monolayer to account for contact-dependent signalling between adjacent cells and between non-adjacent neighbors through long protrusional contacts with a feedback mechanism wherein the adhesive strength between adjacent cells is controlled by the expression of the signalling molecules in those cells. Local changes in cell-cell adhesion lead to changes in cell shape and size, which in turn drives changes in the levels of signalling molecules. Our simulations show that even this elementary two-way coupling of chemical signalling and cell mechanics is capable of giving rise to a rich variety of mechanochemical patterns in epithelial tissues. In particular, under certain parametric conditions, bimodal distributions in cell size and shape are obtained, which resemble experimental observations in cancerous and sensory tissues.

biophysics↗

bioRxiv2020

Role of cell polarity dynamics and motility in pattern formation due to contact dependent signalling

A key challenge in biology is to understand how spatiotemporal patterns and structures arise during the development of an organism. An initial aggregate of spatially uniform cells develops and forms the differentiated structures of a fully developed organism. On the one hand, contact-dependent cell-cell signalling is responsible for generating a large number of complex, self-organized, spatial patterns in the distribution of the signalling molecules. On the other hand, the motility of cells coupled with their polarity can independently lead to collective motion patterns that depend on mechanical parameters influencing tissue deformation, such as cellular elasticity, cell-cell adhesion and active forces generated by actin and myosin dynamics. Although modelling efforts have, thus far, treated cell motility and cell-cell signalling separately, experiments in recent years suggest that these processes could be tightly coupled. Hence, in this paper, we study how the dynamics of cell polarity and migration influence the spatiotemporal patterning of signalling molecules. Such signalling interactions can occur only between cells that are in physical contact, either directly at the junctions of adjacent cells or through cellular protrusional contacts. We present a vertex model which accounts for contact-dependent signalling between adjacent cells and between non-adjacent neighbours through long protrusional contacts that occur along the orientation of cell polarization. We observe a rich variety of spatiotemporal patterns of signalling molecules that is influenced by polarity dynamics of the cells, relative strengths of adjacent and non-adjacent signalling interactions, range of polarized interaction, signalling activation threshold, relative time scales of signalling and polarity orientation, and cell motility. Though our results are developed in the context of Delta-Notch signalling, they are sufficiently general and can be extended to other contact dependent morpho-mechanical dynamics.

biophysics↗

bioRxiv2020

Control and mechanisms of pulsatile flows in epithelial monolayers

Collective motions of epithelial cells in vivo are essential for morphogenesis in developmental biology. Tissues elongate, contract, flow, and oscillate, thus sculpting embryos. These tissue level dynamics are known, but the physical mechanisms at the cellular level are unclear, with various behaviors depending on the tissues and species. Moreover, investigations on in vitro tissue behavior usually focus on only one type of cell dynamics and use diverse theoretical approaches, making systematic comparisons between studies challenging. Here, we show that a single epithelial monolayer of Madin Darby Canine Kidney (MDCK) cells can exhibit two types of local tissue kinematics, pulsations and long range coherent flows. We analyzed these distinct motions by using quantitative live imaging. We also report that these motions can be controlled with internal and external cues such as specific inhibitors, and friction modulation of the substrate by microcontact printing method. We further demonstrate with a unified vertex model that both behaviors depend on the competition between velocity alignment and random diffusion of cell polarization. When alignment and diffusion are comparable, a pulsatile flow emerges, whereas the tissue undergoes long-range flows when velocity alignment dominates. We propose that environmental friction, acto-myosin distributions, and cell polarization kinetics are important in regulating the dynamics of tissue morphogenesis.

biophysics↗

bioRxiv2019

Elongations of epithelial colony in vitro: symmetry breaking through collective effects

Epithelial tissues of the developing embryos elongate by different mechanisms, such as neighbor exchange, cell elongation, and oriented cell division. Since autonomous tissue self-organization is influenced by external cues such as morphogen gradients or neighboring tissues, it is difficult to distinguish intrinsic from directed tissue behavior. The mesoscopic processes leading to the different mechanisms remain elusive. Here, we study the spontaneous elongation behavior of spreading circular epithelial colonies in vitro. By quantifying deformation kinematics at multiple scales, we report that global elongation happens primarily due to cell elongations, and its direction correlates with the anisotropy of the average cell elongation. By imposing an external time-periodic stretch, the axis of this global symmetry breaking can be modified and elongation occurs primarily due to orientated neighbor exchange. These different behaviors are confirmed using a vertex model for collective cell behavior, providing a framework for understanding autonomous tissue elongation and its origins.

biophysics↗