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Sadhukhan, S.

Publications and source records attributed to Sadhukhan, S..

13 recordsLinked to original sources

Shear effects in active models of normal and cancer cells

Mechanical properties of biological tissues, driven by passive and active forces, play a vital role in several processes ranging from development to cancer metastasis. However, the dynamical responses of cells in tissues, subject to mechanical deformations such as shear and the associated rheological properties, are not well characterized. Here, we use three-dimensional agent-based models for normal and cancer tissues to investigate their responses to simple shear as a function of cell stiffness and stochastic active forces. In the normal epithelium, with uniform strength of active force, the yield stress as a function of shear rate follows the Herschel-Bulkley form over a range of cell volume fraction. Strikingly, the shear rate dependence and the elasticity-dependent changes in the yield stress fall on master curves upon suitable scaling. To model cancer-like behavior, a certain fraction (Np) of cells was chosen to have enhanced activity and decreased stiffness. As Np increases, the extent of collective cell movement decreases, transitioning from affine (collective) to non-affine (individualistic) movement, a finding that is in accord with imaging experiments. Simulations of a model of a stiff solid tumor, with radius Rs embedded in normal tissue, show that as Rs increases, the yield stress increases. Interestingly, the cells migrate collectively as Rs increases. A Gaussian Mixture Model (GMM) and a mean field theory quantitatively account for the simulation as well as experimental results on cancerous, non-cancerous, and a mixture of these two types. The combined theoretical and experimental study establishes that heterogeneity in stiffness and activity determines non-affine movements in normal and cancer tissues.

biophysics↗

A minimal physical model of adhesion-dependent protrusion explains confined haptotaxis and oscillatory cell migration

Haptotaxis is the directed migration of cells along gradients of substrate adhesion, and is an important guidance mechanism in biology. Recent experiments on fibronectin-patterned tracks show that cells typically migrate toward higher adhesion, then oscillate around the adhesion maximum, with substantial variability in speed and cell length. To explain these cellular shape and migration dynamics we present a minimal model for confined haptotaxis, built around one key physical ingredient: local adhesion strength directly enhances the recruitment of protrusive actin polymerization activity at the cell edge. This coupling creates a front-rear difference in protrusive activity, biasing the cell towards polarization in the direction of the higher adhesion. Quantitative comparison with experiment shows strong agreement at multiple levels: cell population-level directionality statistics and position-dependent changes in cell length and velocity. At the single-cell level, the model reproduces the full diversity of experimentally observed trajectories, including haptotactic bias and its dependence on adhesion-gradient strength, initial position, length and speed variations, myosin II inhibition, and migration on inverted adhesion gradients. Variability in experimental trajectories and migration speed is explained by differences in intrinsic actin polymerization activity and stochastic fluctuations, accounting for the full spectrum of observed migration patterns. Together, our results identify adhesion-dependent amplification of protrusive activity as a minimal and sufficient physical mechanism for understanding haptotaxis.

biophysics↗

Characterization of Chromatin-Associated Circular RNAs (cacRNAs)

HighlightsO_LIIdentified hundreds of potential chromatin-associated circRNAs in HEK293 cells, H9, and HeLa cells C_LIO_LIThe first report suggesting global interaction of circular RNAs with chromatin C_LIO_LIChromatin-associated circular RNAs interact with various RBPs involved in RNA splicing or processing C_LI Circular RNAs (circRNAs) have emerged as novel regulators of gene expression by interacting with various proteins and RNAs in a spatiotemporal manner. CircRNAs localized in the cytoplasm regulate mRNA translation or stability by binding to microRNAs and RNA-binding proteins (RBPs), while circRNAs in the nucleus regulate transcription and pre-mRNA splicing by associating with transcription factors and splicing factors. In this study, we sought to explore the interaction between circRNAs and chromatin. Analyzing published RNA-seq data from chromatin fractions identified hundreds of chromatin-associated circRNAs (cacRNAs) in various human cells. We validated the enrichment of a subset of circRNAs in the chromatin fraction and established the direct interaction of circDYNC1H1 and circKIF2C with chromatin in HEK293T cells. Furthermore, cacRNAs were found to interact with RBPs. Together, our research demonstrates the global association of hundreds of circRNAs with chromatin and expands our understanding of novel functional aspects of the circRNAs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/739476v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@804151org.highwire.dtl.DTLVardef@405206org.highwire.dtl.DTLVardef@c9373borg.highwire.dtl.DTLVardef@4903ea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

molecular biology↗

Proliferative and Motile Cell Interplay in Glioma Invasion: Go-or-Grow Switching Caps the Invasion Speed

On the cellular level, glioma cells seem to be either in a "go" state or in a "grow" state. It is observed that the outer edge of the tumor grows over time. A general rule c [≤] 1/2c_F was proven by Thiessen, Conte, Stepien, and Hillen via a substitution argument; however, they weren't able to derive the exact formula for the tumor's speed or determine exactly what conditions would cause a tumor to reach its maximum speed. In this article, it is assumed that the cells switch back and forth between moving and growing very fast, and the exact equation for the speed of the tumor expansion is c* = 2{surd}{phi}i_m {phi}_p rD. It is found that the same rate of maximum possible growth occurs when cells move for 50\% of the time and grow for 50% of the time. If the cells spend more of their time doing one than the other, it grows even more slowly. Moreover, a dimensionless parameter is introduced: {chi} = c/2{surd}rD, to determine the exact hidden phenotype balance through plugin the speed at which one individual cell moves (D), the cell division rate (r), and the tumor expansion rate (c). The outcome will be near 1 if the old standard tumor model is correct. If it is 0.5 or below, our model is correct; it is either a "go" or "grow" state. In addition, the exact number indicates the percentage of tumour cells that are moving. In the human brain, tumors do not spread evenly in a circle; they spread much faster along with the white-matter tracts apparent through diffusion tensor imaging (DTI). It is shown that our 50% speed limit remains valid along these "brain highways" a result that has not been previously shown in a mathematical study. Lastly, we address a theoretical question that was left unanswered by past studies using computer simulations and discuss the implications for clinical interpretation of MRI growth rates from real patients using our results.

biophysics↗

From biting to engulfment: curvature-actin coupling controls phagocytosis of soft, deformable targets

Phagocytosis is a core innate immune process that clears targets spanning a wide range of mechanical properties, yet the role of target mechanics in recognition and engulfment remains unclear. Here, we combine theoretical modeling and experiments to reveal how target stiffness governs distinct modes of phagocyte-target interaction. We develop a membrane-based simulation framework in which both the engulfing cell and its target are deformable and undergo large shape changes, while actin-driven protrusions are regulated by curvature-sensitive membrane complexes. The model predicts three mechanical regimes with increasing target stiffness: (i) biting (trogocytosis), where part of the target is extracted; (ii) pushing, where the target is displaced rather than engulfed; and (iii) complete engulfment. We validate these predictions in epithelial clearance of apoptotic targets in vivo and macrophage engulfment of Giant Unilamellar Vesicles (GUVs) and lymphoma cells. Together, our results identify target mechanics as a key regulator of clearance and cell-cell interactions. Significance statementPhagocytosis is essential for immune defence, yet the physical principles governing engulfment of deformable targets remain poorly understood. Most theoretical models assume rigid particles, appropriate for phagocytosis of bacteria or fungi. When phagocytes engage dying cells or antibody-opsonised cancer cells, these targets undergo substantial shape changes during phagocytosis. We develop a theoretical model to simulate cell-cell interactions, enabling a mechanistic exploration of phagocytosis of soft targets. We utilize a model in which cytoskeletal protrusive activity is guided by curvature-sensitive membrane complexes, and show that target membrane rigidity dictates whether targets are fully engulfed, pushed away, or partially bitten. These mechanically driven dynamic regimes are validated experimentally using artificial elastic beads, GUVs, and lymphoma cells, both in vivo and in vitro.

biophysics↗

Modelling how lamellipodia-driven cells maintain persistent migration and interact with external barriers

Cell motility is fundamental to many biological processes, and cells exhibit a variety of migration patterns. Many motile cell types follow a universal law that connects their speed and persistency, a property that can originate from the intracellular transport of polarity cues due to the global actin retrograde flow. This mechanism was termed the "Universal Coupling between cell Speed and Persistency"(UCSP). Here we implemented a simplified version of the UCSP mechanism in a coarse-grained "minimal-cell" model, which is composed of a three-dimensional vesicle that contains curved active proteins. This model spontaneously forms a lamellipodia-like motile cell shape, which is however sensitive and can depolarize into a non-motile form due to random fluctuations or when interacting with external obstacles. The UCSP implementation introduces long-range inhibition, which stabilizes the motile phenotype. This allows our model to describe the robust polarity observed in cells and explain a large variety of cellular dynamics, such as the relation between cell speed and aspect ratio, cell-barrier scattering, and cellular oscillations in different types of geometric confinements. Significance StatementCoupling curved membrane proteins to active protrusive forces that arise from recruited actin polymerization, can lead, in the presence of adhesion, to self-organization of a leading-edge cluster and a motile "minimal-cell". However, this polarized and motile shape can become unstable, and due to fluctuations or interactions with external perturbations transform to an immotile, symmetric shape. Here we couple the spatial organization of the curved active proteins to a global advection of a polarity cue along the cells activity axis. Introducing long-range inhibition, the resultant gradient of the polarity-cue stabilizes the motile, polarized "minimal-cell" vesicle. We thereby present a robust model of cell motility that can explain a variety of cellular shape-migration relations, cell-barrier scattering and spontaneous oscillations of confined cells.

biophysics↗

Glucose-regulated circular RNA Rabep1 regulates pancreatic beta-cell growth by modulating miR-335-3p/PTEN axis

HighlightsO_LIIdentified circRNAs expressed in {beta}TC6 cell line C_LIO_LIFirst report identifying glucose-regulated circRNAs in pancreatic {beta}-cell C_LIO_LICircRabep1 regulates {beta}-cell growth by binding to miR-335-3p C_LI Circular RNAs (circRNAs) are a large family of closed-loop RNA molecules emerging as novel regulators of gene expression. Although several circRNAs are known to regulate various biological processes, the functions of most circRNAs expressed in pancreatic {beta}-cells remain to be discovered. Since short-term glucose treatment induces pancreatic {beta}-cell growth and promotes insulin production, we wanted to explore the role of glucose-regulated circRNAs in pancreatic {beta}-cell physiology. Our RNA-seq analysis identified more than 300 differentially expressed circRNAs in high-glucose compared to low-glucose treated {beta}TC6 cells. A subset of differentially expressed and abundant circRNAs was validated by various biochemical methods, including circular RNA Rabep1 (circRabep1). Moreover, the downregulation of circRabep1 in high glucose-treated {beta}TC6 cells suggested a possible function in {beta}-cell physiology. Furthermore, analysis of the circRabep1-miRNA-mRNA regulatory network discovered the association of circRabep1 with miR-335-3p, a suppressor of Pten expression. Importantly, inhibition of miRNA function by miR-335-3p inhibitor results in upregulation of PTEN levels, suppressing {beta}-cell growth and proliferation. Furthermore, silencing circRabep1 decreased PTEN expression by sponging miR-335-3p, promoting cell proliferation. We propose that the downregulation of circRabep1 in high-glucose treated {beta}-cell leads to an increase in {beta}-cell proliferation by suppressing PTEN expression through derepression of miR-335-3p. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/600308v1_ufig1.gif" ALT="Figure 1"> View larger version (10K): org.highwire.dtl.DTLVardef@542b03org.highwire.dtl.DTLVardef@1d3f3faorg.highwire.dtl.DTLVardef@36b476org.highwire.dtl.DTLVardef@181c7b4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Schematic showing the molecular function of glucose-regulated circRabep1 in pancreatic -cell growth by binding to miR-335-3p. C_FIG

molecular biology↗

How motility drives the glassy dynamics in confluent epithelial monolayers?

As wounds heal, embryos develop, cancer spreads, or asthma progresses, the cellular monolayer undergoes glass transition between solid-like jammed and fluid-like flowing states. During some of these processes, the cells undergo an epithelial-to-mesenchymal transition (EMT): they acquire in-plane polarity and become motile. Thus, how motility drives the glassy dynamics in epithelial systems is critical for the EMT process. However, no analytical framework that is indispensable for deeper insights exists. Here, we develop such a theory inspired by a well-known glass theory. One crucial result of this work is that the confluency affects the effective persistence time-scale of active force, described by its rotational diffusivity, [Formula]. [Formula] differs from the bare rotational diffusivity, Dr, of the motile force due to cell shape dynamics, which acts to rectify the force dynamics: [Formula] is equal to Dr when Dr is small and saturates when Dr is large. We test the theoretical prediction of [Formula] and how it affects the relaxation dynamics in our simulations of active Vertex model. This novel effect of [Formula] is crucial to understanding the new and previously published simulation data of active glassy dynamics in epithelial monolayers.

biophysics↗

Influence of co-occurring weakly pathogenic bacterial species on bacterial spot disease dynamics on tomato

Mixed infections caused by multiple pathogenic and/ weakly pathogenic strains inhabiting the same host plants are common in nature and may modify pathogen dynamics. However, traditional plant pathogen studies have mostly focused on the binary interaction between a single host and a single pathogen. In this study, we have looked beyond this binary interaction and evaluated the impact of co-infection on disease dynamics on tomato using bacterial spot pathogen, Xanthomonas perforans (Xp) and two co-occurring weakly pathogenic strains of X. arboricola (Xa) and Pseudomonas capsici (Pc). Time-series greenhouse co-infection experiments monitoring disease severity and within-host population dynamics revealed higher disease severity in co-infection by three species compared to infection by Xp alone. However, co-infection by dual species, Xp and Pc or Xa resulted in lower disease severity compared to Xp alone. Thus, co-infection outcomes depend on interacting species. Weak pathogens could exploit Xp to colonize the host plant as indicated by their higher populations in co-infection. However, Xp population dynamics was dependent on co-infecting partner. While resource competition might be a possible explanation for lower Xp population in dual co-infection, interaction of Pc with the host was found to influence Xp population. Interestingly, Xp population was higher in presence of three-species interaction compared to Xp and Xa co-infection, suggesting potential modulation of co-operative interactions among Xp and Xa in three-species co-infection rather than competitive interactions. Humidity played a significant role in population dynamics of the three species. Overall, this study highlighted importance of co-infection dynamics in studying plant disease outbreaks.

ecology↗

Modelling how curved active proteins and shear flow pattern cellular shape and motility

Cell spreading and motility on an adhesive substrate are driven by the active physical forces generated by the actin cytoskeleton. We have recently shown that coupling curved membrane complexes to protrusive forces, exerted by the actin polymerization that they recruit, provides a mechanism that can give rise to spontaneous membrane shapes and patterns. In the presence of an adhesive substrate, this model was shown to give rise to an emergent motile phenotype, resembling a motile cell. Here, we utilize this "minimal-cell" model to explore the impact of external shear flow on the cell shape and migration on a uniform adhesive flat substrate. We find that in the presence of shear the motile cell reorients such that its leading edge, where the curved active proteins aggregate, faces the shear flow. The flow-facing configuration is found to minimize the adhesion energy by allowing the cell to spread more efficiently over the substrate. For the non-motile vesicle shapes, we find that they mostly slide and roll with the shear flow. We compare these theoretical results with experimental observations, and suggest that the tendency of many cell types to move against the flow may arise from the very general, and non-cell-type-specific mechanism predicted by our model.

biophysics↗

The origin of universal cell shape variability in a confluent epithelial monolayer

Cell shape is fundamental in biology. The average cell shape can influence crucial biological functions, such as cell fate and division orientation. But cell-to-cell shape variability is often regarded as noise. In contrast, recent works reveal that shape variability in diverse epithelial monolayers follows a nearly universal distribution. However, the origin and implications of this universality are unclear. Here, assuming contractility and adhesion are crucial for cell shape, characterized via aspect ratio (AR), we develop a mean-field analytical theory for shape variability. We find that a single parameter, , containing all the system-specific details, describes the probability distribution function (PDF) of AR; this leads to a universal relation between the standard deviation and the average of AR. The PDF for the scaled AR is not strictly but almost universal. The functional form is not related to jamming, contrary to common beliefs, but a consequence of a mathematical property. In addition, we obtain the scaled area distribution, described by the parameter {micro}. We show that and {micro} together can distinguish the effects of changing physical conditions, such as maturation, on different system properties. The theory is verified in simulations of two distinct models of epithelial monolayers and agrees well with existing experiments. We demonstrate that in a confluent monolayer, average shape determines both the shape variability and dynamics. Our results imply the cell shape variability is inevitable, where a single parameter describes both statics and dynamics and provides a framework to analyze and compare diverse epithelial systems.

biophysics↗

Glassiness in cellular Potts model of biological tissue is controlled by disordered energy landscape

Glassy dynamics in a confluent monolayer is indispensable in morphogenesis, wound healing, bronchial asthma, and many others; a detailed theoretical understanding for such a system is, therefore, important. We combine numerical simulations of a cellular Potts model and an analytical study based on random first order transition (RFOT) theory of glass, develop a comprehensive theoretical framework for a confluent glassy system, and show that glassiness is controlled by the underlying disordered energy landscape. Our study elucidates the crucial role of geometric constraints in bringing about two distinct regimes in the dynamics, as the target perimeter P0 is varied. The extended RFOT theory provides a number of testable predictions that we verify in our simulations. The unusual sub-Arrhenius relaxation results from the distinctive interaction potential arising from the perimeter constraint in a regime controlled by geometric restriction. Fragility of the system decreases with increasing P0 in the low-P0 regime, whereas the dynamics is independent of P0 in the other regime. The mechanism, controlling glassiness in a confluent system, is different in our study in comparison with vertex model simulations, and can be tested in experiments.

biophysics↗

Characterising the vocal repertoire of the Indian wolf (Canis lupus pallipes)

Vocal communication in social animals plays a crucial role in mate choice, maintaining social structure, and foraging strategy. The Indian grey wolf, among the less studied subspecies, is a social carnivore that lives in groups called packs and has many types of vocal communication. In this study, we characterise harmonic vocalisation types in the Indian wolf using howl survey responses and opportunistic recordings from captive and nine packs (each pack contains 2-9 individuals) of free-ranging Indian wolves. Using principal component analysis, hierarchical clustering, and discriminant function analysis, we found four vocal types using 270 recorded vocalisations (Average Silhouette width Si = 0.598) which include howls and howl-bark (N=238), whimper (N=2), social squeak (N=28), and whine (N=2). Although having a smaller body size, Indian wolf howls have an average mean fundamental frequency of 0.422KHz ({+/-}0.126), which is similar to other Holarctic clade subspecies. The whimper showed the highest frequency modulation (37.296{+/-}4.601 KHz) and the highest mean fundamental frequency (1.708{+/-}0.524 KHz) compared to other call types. Less information is available on the third vocalisation type, i.e. Social squeak or talking (Mean fundamental frequency =0.461{+/-}0.083 KHz), which is highly variable (coefficient of frequency variation = 18.778{+/-}3.587 KHz). Our studys characterisation of the Indian wolfs harmonic vocal repertoire provides a first step in understanding the function and contextual use of vocalisations in this social mammal.

animal behavior and cognition↗