Biology subjects

Bhattacharjee, T.

Publications and source records attributed to Bhattacharjee, T..

12 recordsLinked to original sources

bioRxiv2026

Quantifying punctate morphology in mesenchymal stem cells from single cell images provides a definitive quality assessment pipeline for direct correlation to osteogenic lineage differentiation

Mesenchymal stem cells (MSCs) exhibit unique immunological properties and are classified as multipotent stem cells. Considering their immunosuppressive and immunoenhancing properties, they have been used adequately for tissue regeneration across allogeneic barriers. MSCs are propagated mainly using in vitro methods of cell culture and thereby exhibit heterogeneity in a wide spectrum. Such stem cell heterogeneity can arise due to donor, tissue and cellular variability. Studies have shown that functional variances in MSCs derived from the same tissue source across different donors may be influenced by age, gender, and physiological condition. In contrast to their mature counterparts, mesenchymal stem cells exhibit a relative resilience to cellular senescence; yet they remain vulnerable to both intrinsic and extrinsic stress. Cellular senescence can be induced by exposure to cellular stress or a reduction in replicative capacity. Cellular structure, telomere length, and senescence-associated {beta}-galactosidase (SA-{beta}-gal) activity are some of the hallmark observations signifying the onset of senescence in cells. Such a biological state in mesenchymal stem cells diminishes the overall effectiveness of the cells as candidates for biotherapeutics. Although MSCs towards their later passages are known to show drop in proliferative properties and in their regenerative potential, direct correlation of passage related onset of cellular senescence and lineage differentiation at the single cell precision remains largely unexplored. To close this gap in stem cell research, we have developed a single cell image-based pipeline exclusively for human MSCs, which addresses immune-heterogeneity features using both the bright field and fluorescence-based images of stem cells. The MSCProfiler or the single cell image-based pipeline can analyze and quantify feature descriptors of the MSCs, across tissues and passages in vitro. We have extrapolated the pipeline to address a critical biological state like senescence in MSCs to quantify this multi-variable property of stem cells and check the correlation with cellular differentiation, if any. To address the properties of replicative senescence and study it at the single cell level, we wanted to study the senescence-associated {beta}-galactosidase activity in human dental pulp derived MSCs (hDPSCs). Further to these analyses, we wanted to assess if quantifying the punctate morphology in single stem cells can establish any direct correlation of senescence with osteogenic lineage differentiation in case of the hDPSCs. To achieve our hypothesis, we used the MSCProfiler and extended the pipeline to incorporate the expression profiles of senescence-associated {beta}-galactosidase across the early, mid and late passages of hDPSCs. The pipeline was modified to incorporate bright field image features such as cell size, shape and eccentricity and fluorescence images from the SA- {beta}-galactosidase-substrate reactions. We classified the puncta morphology across passages of hDPSCs and checked for osteogenic lineage differentiation abilities in these MSCs. This could prove to be definitive quality assessment pipeline to assess the biological state of all types of MSCs before their use in allogenic transplantations.

cell biology↗

bioRxiv2026

Modeling Dynamics of Contact Inhibition of Proliferation and Structural Order in a Confluent Epithelium

Contact inhibition of proliferation (CIP) enables epithelial tissues to self-regulate growth and maintain tissue homeostasis. However, how cell-level mechanical contact, tissue-scale structural order, and proliferation kinetics interplay remains a fundamental open question in living matter physics. Here, we present a particle-based model of a confluent epithelial monolayer governed by overdamped dynamics, where individual cells interact via a two-dimensional hard core- soft shoulder potential. By comparing structural evolution during quasistatic densification with previously reported experimental division kinetics, we find that the dynamics of proliferation arrest mimics the onset of direct steric contacts between the hard cores of the shell. Identifying hard core contacts as the physical driver of CIP, we couple our mechanical model with a stochastic Monte Carlo division scheme in which the instantaneous division rate decreases to zero from an intrinsic value as the number of hard core contact increases to six from zero. We demonstrate that for high intrinsic division rates, the cellular densification outpaces mechanical relaxation. This kinetic mismatch drives premature hard-core contact formation, shifts the onset of jamming and contact inhibition to lower packing fractions, and induces increasingly disordered transient configurations before the tissue universally converges to a hexagonal close-packed limit. Our model's predicted division kinetics and structural order evolution are consistent with epithelial monolayer experiments, both reported and our own. This minimal physical framework links single-cell steric contact mechanics directly to tissue-scale growth regulation and structural evolution.

biophysics↗

bioRxiv2026

An oxo-mechanical coupling determines cell state

Across myriad habitats and diverse lifeforms, oxygen and mechanics are the most ubiquitously varying and profoundly influential environmental regulators. While physiological niches feature both varying oxygen levels and heterogeneous mechanics, laboratory experiments typically interrogate these as independent variables. Here, we show that combinatorial regimes defined by varying oxygen partial pressures and environmental mechanics--an oxo-mechanical cue--induce functionally-distinct cellular states in 3D ECM-like contexts. Single-cell morphometrics combined with multi-omics reveal that cellular response to oxygen deprivation depends on external mechanical milieus, whereas, cellular engagement with different mechanical microenvironments depends on oxygen availability. Independently perturbing both hypoxic signaling and cytoskeletal activity further reveals a reciprocal oxo-mechanical regulatory coupling, which operates by differentially altering the global chromatin accessibility for transcriptional regulation in response to specific combinations of oxygen partial pressures and external mechanical milieus. Together, our findings establish that a coupling between oxygen and mechanics drives the emergence of microenvironmentally-defined cell states.

cell biology↗

bioRxiv2025

Biophysical Design Space for Cellular Self-assembly and Dynamics

In natural biological systems, cells organize into tissues through interactions of several processes, including cellular signaling, collective migration, contractile activity of cytoskeletal elements and interactions with their surroundings. In recent decades, advancements in microscopy, genetic engineering, biochemistry, and computational modeling have enabled a more quantitative understanding of these processes. In this article, we present an integrated computational framework that couples various physical mechanisms such as cell-cell adhesion, strength and persistence of cellular motility, and the background stiffness. We use this framework to study how they collectively interact to determine the self-organization of the cells from a pseudo-random structure as well as the migration behavior of the cells. Notably, our simulations predict that motility has a two-way effect on cellular self-assembly: it promotes aggregation at moderate levels but disrupts clusters when excessively strong, yielding an optimal motility for formation of multicellular clusters. On the other hand, adhesion shows a two-stage effect: At lower value it self-assembles the structure, at higher value it compacts it. Furthermore, we experimentally demonstrate the motility-assisted self-aggregation of cells using cancer cells in a granular mechanical milieu. Finally we show that cell-cell adhesion and background medium tune the strength and persistence of cellular migration. Altogether, this work presents a computational framework that allows us to design phase behavior of collective of cells tuning their interaction, motility, and the background mechanics.

biophysics↗

bioRxiv2025

Dissecting the root-fungal interface in 3D reveals spatially distinct signalling landscapes

Plant rhizospheric interactions represent intricate relationships that determine plant fitness and are crucial for interrogating host-pathogen dynamics, with significant fundamental and translational implications. Most fungal-plant interactions occur in soil - a disordered and granular 3D environment - and hence remain challenging to unravel due to complex regulatory networks. Our current body of evidence characterizing these molecular dialogues largely stems from experimental systems employing soil or in vitro 2D flat plates, hydroponics and gnotobiotic systems. Soil itself features widely varying visco-elasto-plastic material properties, and its inherent opacity precludes direct visualization of the infection progression in complex diseases such as wilts and root rots. Here, we introduce the first such optically transparent, 3D granular growth matrix to recapitulate complex properties of the soil microenvironment, which enables direct, cellular-level visualization of the plant-fungal interface. Our mechanically tunable 3D matrices support long-term co-culture of plants and fungi with compatibility to classical molecular and physiological assays for unravelling the early signalling events and inter-kingdom crosstalk. By leveraging the optical transparency of this matrix, we track fungal development in response to host signals ex-planta with 3D resolution, to report pioneering evidence of hyphal reprogramming preferentially towards the root tips during the early stages of infection. Crucially, we integrate spatiotemporal transcriptomic analyses and discover distinct pathogen-host ex- and in-planta modules during early signalling, which are likely associated with biomimetic soil-like environments. Together, our findings establish an integrable and versatile 3D platform offering an unprecedented view of the pathogen infection processes, which enables fundamental discoveries into the biological regulation of growth and infection. These insights hold immense potential for advancing our understanding of host immune responses and adaptation of filamentous pathogens, as well as open avenues to decipher drought and disease-resistance mechanisms with major agricultural benefits.

plant biology↗

bioRxiv2025

3D confinement physically regulates cell cycle progression in budding yeast

Our understanding of cell division control traditionally comes via using liquid broths or 2D flat-plate cultures -- which cannot recapitulate the complex visco-elasto-plastic properties of natural habitats such as tissues, mucus, and soil. Consequently, how such regimes of physical confinement influence proliferative growth remains unknown. Here, using engineered, mechanically tunable and transparent growth matrices, we directly visualize yeast budding and division across 3D viscoelastic regimes. We discover that elevated physical confinement drastically prolongs budding intervals without any physiological defects or activating global regulatory programs. Remarkably, extended cell division times are not associated with transcriptional or proteomic signatures of mechanosensation or cell cycle regulation. Rather, 3D confinement physically constrains the volumetric growth of incipient buds -- manifesting as delayed cell cycle progression. Hence, our findings establish that physical constrainment regulates eukaryotic cell division.

biophysics↗

bioRxiv2025

Physical confinement regulates transition in nematode motility

How do worms navigate their complex natural surroundings? Undulatory microswimmers such as nematodes typically inhabit environments such as soil, vegetable matter, and host tissues. While the natural habitats of nematodes are often three-dimensional granular niches with spatiotemporally varying visco-elasto-plastic material properties that impose physical constraints on their motion, current knowledge about nematode motility patterns broadly comes from investigating model organisms such as Caenorhabditis elegans either inside liquid cultures or the surface of soft agar pads. How nematodes move through 3D granular niches across different degrees of physical confinement remains poorly understood due to a lack of optically transparent 3D granular matrices. We bridge this gap by engineering an optically transparent granular matrix to directly visualise and quantitatively analyse nematode motion. Importantly, nematodes can freely move through this matrix by generating a minimal yield stress; once the nematode moves away, the matrix self-heals to ensure the material properties remain invariant. Using these platforms, we observe that the propulsive speed of nematodes shows a non-monotonic relation with the yield stress of their microenvironment. This non-monotonicity emerges as nematodes optimize for efficient navigation at higher yield stress, wherein, their forward propulsive speed matches the wave speed along their body. This regulation of locomotory behaviour is purely dictated by the physical interaction of the nematode with its environment without involving soft-touch sensory neurons. Remarkably, predictions from a slender body theory of undulatory motion exactly capture the scaling behaviour for both efficiency and mode of motion as obtained from the experimental data. Finally, in a phase space described by non-dimensional propulsive efficiency and a non-dimensional time scale of motility, we capture a gait transition from poorly efficient thrashing under low confinement to more efficient crawling under high confinement. Thus, our work establishes a new regulatory paradigm describing how distinct modes of undulatory motion emerge under different degrees of physical confinement.

biophysics↗

bioRxiv2024

Physical confinement selectively favours bacterial growth based on cell shape

How are bacterial communities altered by changes in their microenvironment? Evidence from homogeneous liquid or flat plate cultures implicates biochemical cues -- such as variation in nutrient composition 1,2, response to chemoattractants and toxins 3,4, and inter-species signalling 5,6 -- as the primary modes of bacterial interaction with their microenvironment. However, these systems fail to capture the effect of physical confinement on bacteria in their natural habitats. Bacterial niches like the pores of soil, mucus, and infected tissues are disordered microenvironments with material properties defined by their internal pore sizes and shear moduli7-11. Here, using three-dimensional matrices that match the viscoelastic properties of gut mucus, we test how altering the physical properties of their microenvironment influences bacterial growth under confinement. We find that low aspect-ratio bacteria form compact, spherical colonies under confinement while high aspect-ratio bacteria push their progenies further outwards to create elongated colonies with a higher surface area, enabling increased access to nutrients. As a result, the population level growth of high aspect-ratio bacteria is more robust to increased physical confinement compared to that of low aspect-ratio bacteria. Thus, our results capture experimental evidence showing that physical constraints can play a selective role in bacterial growth based on cell shape.

biophysics↗

bioRxiv2024

Interplay of geometry and mechanics in epithelial wound healing

Wound healing is a complex biological process critical for maintaining an organisms structural integrity and tissue repair following an infection or injury. Recent studies have unveiled the mechanisms involving the coordination of biochemical and mechanical responses in the tissue in wound healing. In this article, we focus on the healing property of an epithelial tissue as a material while the effects of biological mechanisms such as cell crawling and tissue proliferation is minimal. We present a mathematical framework that predicts the fate of a wounded tissue based on the wounds geometrical features and the tissues mechanical properties. Precisely, adapting the vertex model of tissue mechanics, we predict whether a wound of a specific size in an epithelial monolayer characterized by certain levels of acto-myosin contractility and cell-cell adhesion will heal (i.e., close), shrink in size, or rupture the tissue further. Moreover, we show how tissue-mediated mechanisms such as purse-string tension at the wound boundary facilitate wound healing. Finally, we validate the predictions of our model by designing an experimental setup that enables us to create wounds of specific sizes in MDCK monolayers. Altogether, this work sets up a basis for interpreting the interplay of mechanical and geometrical features of a tissue in the process of wound healing.

biophysics↗

bioRxiv2023

Jammed microgel growth medium prepared by flash-solidification of agarose for 3D cell culture and 3D bioprinting

1. Introduction ABSTRACT 1. Introduction 2. Materials and methods 3. Results and discussion 4. Conclusion Author contributions Supplementary Information References Cells grown as monolayers on conventional two-dimensional (2D) culture plates are significantly different from their in vivo counterparts in many different ways [1]. In standard flat plate cultures, not only do they exhibit altered morphologies and dynamics [2-4], their gene expression and signal transduction profiles are dramatically altered [5]. Furthermore, cells in vivo are exposed to more complex mechanical cues and chemical fields due to their three-dimensional (3D) packing and access to systemic circulation [ ...

bioengineering↗

bioRxiv2022

Roughening instability of growing 3D bacterial colonies

How do growing bacterial colonies get their shapes? While colony morphogenesis is well-studied in 2D, many bacteria grow as large colonies in 3D environments, such as gels and tissues in the body, or soils, sediments, and subsurface porous media. Here, we describe a morphological instability exhibited by large colonies of bacteria growing in 3D. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria--Escherichia coli, Vibrio cholerae, Pseudomonas aeruginosa, and Komagataeibacter sucrofermentans--generically roughen as they consume nutrients and grow beyond a critical size, eventually adopting a characteristic branched, broccoli-like, self-affine morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between 2D and 3D colonies: while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient-limited in its interior, driving a transition to rough growth at its surface. We elucidate the onset of roughening using linear stability analysis and numerical simulations of a continuum model that treats the colony as an active fluid whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the growing colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies--as well as other forms of growing active matter, such as tumors and engineered living materials--in 3D environments.

biophysics↗

bioRxiv2020

Chemotactic Migration of Bacteria in Porous Media

Chemotactic migration of bacteria--their ability to direct multicellular motion along chemical gradients--is central to processes in agriculture, the environment, and medicine. However, studies are typically performed in homogeneous media, despite the fact that many bacteria inhabit heterogeneous porous media such as soils, sediments, and biological gels. Here, we directly visualize the migration of Escherichia coli populations in 3D porous media. We find that pore-scale confinement is a strong regulator of chemotactic migration. Strikingly, cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Further, confinement markedly alters the dynamics and morphology of the migrating population--features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous environments. Statement of SignificanceTypical studies of bacterial motility focus on cells in homogeneous media; however, many bacteria inhabit tight porous media such as soils, sediments, and biological gels. This paper demonstrates how confinement in a porous medium fundamentally alters the chemotactic migration of Escherichia coli. We find that cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Further, confinement markedly alters the overall dynamics and morphology of a migrating population--features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values. This work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous porous environments.

biophysics↗