Biology subjects

Balakrishnan, S.

Publications and source records attributed to Balakrishnan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Nondimensional nucleus shape parameters reveal mechanostasis during confined migration

Nucleus shape is a sensitive indicator of cell state, influenced by numerous bio-chemical and physiological factors. While prior work has cataloged how perturbations alter nucleus morphology, we address the inverse: inferring underlying molecular changes from nucleus shape alone. We previously developed a mechanical model yielding two nondimensional parameters: flatness index and scale factor, which are surrogate measures for cortical actin tension and nuclear envelope compliance respectively. In this study, we apply these parameters to investigate the dynamics in cellular mechanics during confined migration. We fabricated polydimethylsiloxane (PDMS) microchannels with widths of 3 {micro}m (high confinement) and 10 {micro}m (low confinement) and tracked cells migrating through them. We captured high-frequency 3D nucleus shapes via double fluorescence exclusion microscopy and custom image analysis. Fitting the model and estimating flatness index and scale factor to time-resolved shapes revealed dynamic regulation in 3 {micro}m channels: actin tension decreased and nucleus compliance increased immediately before nucleus entry into the constriction, with rapid restoration to baseline upon exit. No such changes occurred in 10 {micro}m channels, indicating active, confinement-dependent cytoskeletal adaptation. Immunostaining for YAP and lamin-A,C confirmed these model inferences. Our results uncover mechanostasis, active mechanical homeostasis, during confined migration and establish the combination of double fluorescence exclusion microscopy and nondimensional nucleus shape parameters as a powerful, non-invasive tool for single-cell mechanobiology studies.

biophysics↗

bioRxiv2026

Mechanical Signaling Drives Tunneling Nanotubes to Preserve Cytoskeleton Tension and Lamin Integrity Against α-Synuclein-Induced Senescence in Astroglia

Astroglia can counteract the harmful effects of -synuclein (-SYN) protofibrils and reverse premature cellular senescence by promoting tunneling nanotubes (TNTs). However, the mechanism behind this recovery is unknown. This study is the first to examine TNT-mediated mechanical stability in senescent astroglial recovery. We demonstrate that disruption of Lamin A/C in -SYN-protofibrils-treated senescent cells reduces actin-cytoskeleton stress, as measured by nucleus flatness index and isometric scale factor from quantitative microscopy. ROCK (Rho-associated kinase) inhibition, which is crucial for reducing actin-cytoskeleton tension, promotes TNTs. Small molecules like Cytochalasin-D, Nocodazole, and Jasplakinolide, which inhibit TNTs by altering actin tension other than ROCK pathway, cannot reverse senescence. RNA-sequence heatmaps reveal changes in senescence-, integrin-, and ROCK-pathway genes; STRING links these to the Hippo pathway. Experimental results show that cytosolic YAP translocation, a key regulator of Hippo pathway, is vital for TNT formation and actin-based stability in U87-MG astrocytoma and primary astrocytes. Interestingly, TNTs form between two cells with different actin tensions: one exhibits low actin tension with Hippo signaling on, while the other has higher actin tension with Hippo signaling off. The most notable observation is the high abundance of YAP inside the TNTs, along with actin. The study shows that TNTs maintain mechanical stability through Lamin A/C integrity and actin tension in -SYN-induced senescent astroglia, thereby protecting the cells, reversing senescence. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/711517v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@192307dorg.highwire.dtl.DTLVardef@ad8b75org.highwire.dtl.DTLVardef@19ece78org.highwire.dtl.DTLVardef@1056395_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Identification and Characterization of a Small Molecule Ligand for the Huntingtin-HAP40 Complex

Huntingtons disease (HD) is caused by a CAG repeat expansion mutation, giving rise to a polyglutamine expansion in the huntingtin (HTT). However, the explicit molecular functions of HTT and opportunities for direct pharmacological modulation remain incompletely understood. Here, we report the discovery of a small molecule ligand for the full-length HTT protein in complex with its partner, HAP40. Using affinity selection mass spectrometry (AS-MS), we identified a stereoselective binder, whose binding was characterized by surface plasmon resonance, hydrogen-deuterium exchange mass spectrometry, and cryo-electron microscopy at 2.3 [A] resolution. The ligand binds HTT-HAP40 in vitro with single-digit micromolar affinity and one-to-one stoichiometry at a druggable interface previously predicted computationally. In silico studies predicted and experimental analyses confirmed the (R)-enantiomer as the eutomer and initial structure activity relationship was established experimentally. This work details a structurally-validated chemical scaffold and highlights a ligandable pocket which could enable development of chemical probes for probing HTT biology, as well as therapeutics such as degraders and imaging agents for HD.

pharmacology and toxicology↗

bioRxiv2025

High-Affinity, Structure-Validated and Selective Macrocyclic Peptide Tools for Chemical Biology Studies of Huntingtin

Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the Huntingtin (HTT) gene, with no disease-modifying therapies currently available. The precise molecular function of the HTT protein is unclear, and the lack of selective chemical tools has limited functional studies. We have identified and characterized macrocyclic peptide binders targeting HTT. These binders exhibit low-nanomolar affinity in vitro and engage distinct HTT and HTT-HAP40 interfaces, as revealed by hydrogen-deuterium exchange mass spectrometry and cryo-electron microscopy. Chemoproteomics confirmed selective binding in cell extracts from wildtype but not HTT-null cell lines. HAP40 consistently and stoichiometrically co-purified with HTT across cell lines, including with HTT variants containing different CAG repeat lengths, highlighting the broad presence of the HTT-HAP40 complex. Significance StatementHuntingtin (HTT) is a large, essential protein with conserved roles in development, intracellular trafficking, and protein homeostasis, yet its precise molecular functions remain incompletely defined. Here, we report the first high-affinity, selective, and structurally validated macrocyclic peptide ligands for HTT. These chemical tools bind HTT and its complex with HAP40 across polyglutamine repeat lengths, enabling direct interrogation of HTT structure and function in health and disease contexts. By overcoming longstanding barriers to studying HTT at the molecular level, these ligands open new avenues for discovery in neurobiology, cell biology, and offer opportunities for therapeutic development. This study delivers urgently needed tools to both the Huntingtons disease field and the broader scientific community seeking to understand this elusive and biologically fundamental protein.

biochemistry↗

bioRxiv2025

Estimating anisotropy of single cells using a compliant biaxial stretcher

Understanding the mechanical properties of single cells is essential for elucidating their responses to mechanical cues and plays a critical role in development, disease progression, and mechanotransduction. However, probing these properties at the single-cell level remains technically challenging. Traditional methods for probing cellular mechanics are often restricted to a single deformation mode and rely on complex instrumentation, limiting their adaptability. Hence, no single platform currently offers multi-modal cell manipulation, which motivates the development of more versatile tools. Towards this, we are developing an ensemble of compliant micromechanisms that enables diverse modes of cell manipulation on a single chip. Building on our earlier work with a uniaxial stretcher, here we demonstrate estimation of cellular anisotropy using a biaxial stretcher. Since the mechanism transforms motion using deformation, cell stretching forces can be estimated through image-based displacement measurements, without additional sensing modalities, considerably simplifying the device fabrication and operation. By assembling these uniaxial and biaxial stretching micromechanisms on a single chip, we can establish a multi-modal manipulation platform for single cells, which can be augmented with shearing and twisting modes in the future. Such a simple and versatile platform presents a paradigm shift in mechanical testing of single cells.

bioengineering↗

bioRxiv2025

Valve endothelial monolayer fissuring via RhoA activity induces 3D calcific aortic valve lesion emergence as revealed by a longitudinal live-imaging platform

Calcific aortic valve disease (CAVD) is a degenerative disease with wide prevalence in the aging population and a low survival rate after onset of symptoms, yet there are no effective pharmacological treatments. Many patients present to the clinic with symptoms at end-stages of CAVD, when the disease may be irreversible. The ability to identify and live-trace calcific lesion emergence in-vivo would allow for the identification of disease biomarkers and discovery of therapeutic targets at earlier, more treatable stages. In this work, we establish a new multimodal in-vitro CAVD platform consisting of lineage traced-VEC and VIC cells in a 3D model combined with live optical coherence and fluorescence microscopy to unravel VEC, VIC, and matrix transitional events during calcific lesion formation. We discover that fissuring of the endothelial monolayer combined with the formation of dense aggregates in adjacent regions is a key biomarker of the onset of lesion formation. This coincides with the formation of dense VIC and ECM conglomerates under endothelial aggregates, an additional biomarker of pathogenesis. Further, we discover that fibrotic tissue compaction is correlated with but not necessary for lesion formation. Additionally, we identify RhoA activation in disease-treated samples. We demonstrate that RhoA inhibition through ROCK, but not Rac1 inhibition, prevents delamination of the endothelial monolayer, fibrotic remodeling, and emergence of calcific lesions. Together, this work establishes a new longitudinal live-imaging platform that identifies emergent cell and matrix biological signatures of CAVD onset and enables the evaluation of therapeutic interventions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/660489v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@dc378org.highwire.dtl.DTLVardef@19c37d5org.highwire.dtl.DTLVardef@11581c6org.highwire.dtl.DTLVardef@fb0a6a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting and inadequate model documentation of model results. Addressing this gap, we introduce FROG analysis, a community-driven initiative aimed at standardizing reproducibility assessments of CBMs and GEMs. The FROG framework encompasses four key analyses--Flux variability, Reaction deletion, Objective function, and Gene deletion--to produce standardized, numerically reproducible FROG reports. These reports serve as reference datasets, enabling model evaluators, curators, and independent researchers to verify the reproducibility of GEMs systematically. BioModels, a leading repository of systems biology models, has integrated FROG analysis into its curation workflow, enhancing the reproducibility and reusability of submitted GEMs. In our study evaluating 65 GEM submissions from the community, approximately 40% reproduced without intervention, 28% requiring minor adjustments, and 32% needing input from authors. The standardization introduced by FROG analysis facilitated the detection and resolution of issues, ultimately leading to the successful reproduction of all models. By establishing a standardized and comprehensive approach to evaluating GEM reproducibility, FROG analysis significantly contributes to making CBMs and GEMs more transparent, reusable, and reliable for the broader scientific community.

systems biology↗

bioRxiv2023

S100A8/A9 predicts triple-negative breast cancer response to PIM kinase and PD-1/PD-L1 inhibition

It remains elusive why some triple-negative breast cancer (TNBC) patients respond poorly to existing therapies while others respond well. Our retrospective analysis of historical gene expression datasets reveals that increased expression of immunosuppressive cytokine S100A8/A9 in early-stage tumors is robustly associated with subsequent disease progression in TNBC. Although it has recently gained recognition as a potential anticancer target, S100A8/A9 has not been integrated into clinical study designs evaluating molecularly targeted therapies. Our small molecule screen has identified PIM kinase inhibitors as capable of decreasing S100A8/A9 expression in multiple cell types, including TNBC and immunosuppressive myeloid cells. Furthermore, combining PIM inhibition and immune checkpoint blockade induces significant antitumor responses, especially in otherwise resistant S100A8/A9-high PD-1/PD-L1-positive tumors. Importantly, serum S100A8/A9 levels mirror those of tumor S100A8/A9 in a syngeneic mouse model of TNBC. Thus, our data suggest that S100A8/A9 could be a predictive and pharmacodynamic biomarker in clinical trials evaluating combination therapy targeting PIM and immune checkpoints in TNBC and encourage the development of S100A8/A9-based liquid biopsy tests.

cancer biology↗

bioRxiv2023

Structure of RADX and mechanism for regulation of RAD51 nucleofilaments

Replication fork reversal is a fundamental process required for resolution of encounters with DNA damage. A key step in the stabilization and eventual resolution of reversed forks is formation of RAD51 nucleoprotein filaments on exposed ssDNA. To avoid genome instability, RAD51 filaments are tightly controlled by a variety of positive and negative regulators. RADX is a recently discovered negative regulator that binds tightly to ssDNA, directly interacts with RAD51, and regulates replication fork reversal and stabilization in a context-dependent manner. Here we present a structure-based investigation of RADXs mechanism of action. Mass photometry experiments showed that RADX forms multiple oligomeric states in a concentration dependent manner, with a predominance of trimers in the presence of ssDNA. The structure of RADX, which has no structurally characterized orthologs, was determined ab initio by cryo-electron microscopy (EM) from maps in the 2-3 [A] range. The structure reveals the molecular basis for RADX oligomerization and binding of ssDNA binding. The binding of RADX to RAD51 filaments was imaged by negative stain EM, which showed a RADX oligomer at the end of filaments. Based on these results, we propose a model in which RADX functions by capping and restricting the growing end of RAD51 filaments. SignificanceDespite the central role of RAD51 in DNA replication and repair processes, the mechanisms of action of its many modulators are poorly understood. Here we combine structural and biophysical data to determine how the negative regulator RADX functions. We show that RADX oligomerizes upon binding DNA, and caps RAD51 filaments at the ends to prevent extension. This work advances knowledge of how RAD51 filaments can be modulated to regulate replication fork reversal and maintain genomic stability.

biophysics↗

bioRxiv2023

Disentangling gene expression burden identifies generalizable phenotypes induced by synthetic gene networks

Large-scale genetic circuits are rapidly becoming critical components for the next generation of biotechnologies and living therapeutics. However, the relationship between synthetic and host gene expression is poorly understood. To reveal the impact of genetic circuits on their host, we measure the transcriptional response of wild-type and engineered E. coli MG1655 subject to seven genomically integrated circuits and two plasmid-based circuits across 4 growth time points and 4 circuit input states resulting in 1007 transcriptional profiles. We train a classifier to distinguish profiles from wild-type or engineered strains and use the classifier to identify synthetic construct burdened genes, i.e., genes whose dysregulation is dependent on the presence of a genetic circuit and not what is encoded on the circuit. We develop a deep learning architecture, capable of disentangling influence of combinations of perturbations, to model the impact that synthetic genes have on their host. We use the model to hypothesize a generalizable, synthetic cell state phenotype and validate the phenotype through antibiotic challenge experiments. The synthetic cell state results in increased resistance to {beta}-lactam antibiotics in gram-negative bacteria. This work enhances our understanding of circuit impact by quantifying the disruption of host biological processes and can guide the design of robust genetic circuits with minimal burden or uncover novel biological circuits and phenotypes.

systems biology↗

bioRxiv2023

CRISPR-dependent base editing screens identify separation of function mutants of RADX with altered RAD51 regulatory activity

RAD51 forms nucleoprotein filaments to promote homologous recombination, replication fork reversal, and fork protection. Numerous factors regulate the stability of these filaments and improper regulation leads to genomic instability and ultimately disease including cancer. RADX is a single stranded DNA binding protein that modulates RAD51 filament stability. Here, we utilize a CRISPR-dependent base editing screen to tile mutations across RADX to delineate motifs required for RADX function. We identified separation of function mutants of RADX that bind DNA and RAD51 but have a reduced ability to stimulate its ATP hydrolysis activity. Cells expressing these RADX mutants accumulate RAD51 on chromatin, exhibit replication defects, have reduced growth, accumulate DNA damage, and are hypersensitive to DNA damage and replication stress. These results indicate that RADX must bind RAD51 and promote RAD51 ATP turnover to regulate RAD51 and genome stability during DNA replication.

molecular biology↗

bioRxiv2022

Learning transcriptome dynamics for discovery of optimal genetic reporters of novel compounds

A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, we develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery of analyte-responsive promoters. This provides a set of biomarkers that act as a proxy for the transcriptional state referred to as cell state. We construct low-dimensional models of gene expression dynamics and rank genes by their ability to capture the perturbation-specific cell state using a novel observability analysis. Using this ranking, we extract 15 analyte-responsive promoters for the organophosphate malathion in the underutilized host organism Pseudomonas fluorescens SBW25. We develop synthetic genetic reporters from each analyte-responsive promoter and characterize their response to malathion. Furthermore, we enhance malathion reporting through the aggregation of the response of individual reporters with a synthetic consortium approach, and we exemplify the librarys ability to be useful outside the lab by detecting malathion in the environment. The library of living malathion sensors can be optimized for use in environmental diagnostics while the developed machine learning tool can be applied to discover perturbation-inducible gene expression systems in the compendium of host organisms.

synthetic biology↗

bioRxiv2022

NETISCE: A Network-Based Tool for Cell Fate Reprogramming

The search for effective therapeutic targets in fields like regenerative medicine and cancer research has generated interest in cell fate reprogramming. This cellular reprogramming paradigm can drive cells to a desired target state from any initial state. However, methods for identifying reprogramming targets remain limited for biological systems that lack large sets of experimental data or a dynamical characterization. We present NETISCE, a novel computational tool for identifying cell fate reprogramming targets in static networks. In combination with machine learning algorithms, NETISCE estimates the attractor landscape and predicts reprogramming targets using Signal Flow Analysis and Feedback Vertex Set Control, respectively. Through validations in studies of cell fate reprogramming from developmental, stem cell, and cancer biology, we show that NETISCE can predict previously identified cell fate reprogramming targets and identify potentially novel combinations of targets. NETISCE extends cell fate reprogramming studies to larger-scale biological networks without the need for full model parameterization and can be implemented by experimental and computational biologists to identify parts of a biological system relevant to the desired reprogramming task.

systems biology↗

bioRxiv2021

Metabolic modeling of the International Space Station microbiome reveals key microbial interactions

BackgroundRecent studies have provided insights into the persistence and succession of microbes aboard the International Space Station (ISS), notably the dominance of Klebsiella pneumoniae. However, the interactions between the various microbes aboard the ISS, and how it shapes the microbiome remain to be clearly understood. In this study, we apply a computational approach to predict possible metabolic interactions in the ISS microbiome and shed further light on its organization. ResultsThrough a combination of a systems-based graph-theoretical approach, and a constraint-based community metabolic modelling approach, we demonstrated several key interactions in the ISS microbiome. These complementary approaches provided insights into the metabolic interactions and dependencies present amongst various microbes in a community, highlighting key interactions and keystone species. Our results showed that the presence of K. pneumoniae is beneficial to many other microorganisms it coexists with, notably those from the Pantoea genus. Species belonging to the Enterobacteriaceae family were often found to be the most beneficial for the survival of other microorganisms in the ISS microbiome. However, K. pneumoniae was found to exhibit parasitic and amensalistic interactions with Aspergillus and Penicillium species, respectively. To prove this metabolic prediction, K. pneumoniae and Aspergillus fumigatus were co-cultured under normal and simulated microgravity, where K. pneumoniae cells showed parasitic characteristics to the fungus. The electron micrography revealed that the presence of K. pneumoniae compromised the morphology of fungal conidia and its biofilm biofilm-forming structures. ConclusionsOur study underscores the importance of K. pneumoniae in the ISS, and its potential contribution to the survival (mutualism) and eradication (parasitism) of other microbes, including potential pathogens. This integrated modelling approach, combined with experiments, demonstrates immense potential for understanding the organization of other such microbiomes, unravelling key organisms and their interdependencies.

systems biology↗

bioRxiv2021

Inhibition of BMP and FGF signaling prior to wound epithelium formation leads to an aberrant regenerative response in teleost fish Poecilia latipinna

The BMP and FGF pathways play a pivotal role in the successful regeneration of caudal fin of teleost fish. Individual inhibition of these pathways led to impaired caudal fin regeneration until the pharmacologic inhibitor of FGF (SU5402) and BMP (LDN193189) were metabolized off. Therefore, in the current study both these pathways were inhibited collectively wherein inhibition of BMP and FGF during the wound epithelium formation led to stalling of the process by bringing down the established levels of shh and runx2. In members of the treatment group, it was observed that, each blastema grows crouched rather than linear and the regrown lepidotrichia therefore remain tilted down. Amongst the other irregularities observed, the transition from epithelial to mesenchymal cells was found hindered due to down-regulation of snail and twist, brought about by BMP and FGF inhibition. Compromised expression of Snail and twist deranged the normal levels of cadherins causing disruption in the transition of cells. Lastly, blocking BMP and FGF delayed blastema formation and proliferation due to diminished levels of fgf2, fgf8, fgf10 and bmp6, while casp3 and casp9 levels remained heightened causing accelerated cell death. This study not only highlights the axial role of BMP and FGF pathways in regeneration but also accentuates the collaboration amongst the two. This ingenious coordination of signalling further reinforces the involvement of relaying messenger molecules between these crucial pathways. Summary StatementBMP and FGF collectively control the process of blastema formation in fish and inhibiting them prior to wound epithelium stage leads to irrevocable damage to the regenerating caudal fin.

developmental biology↗

bioRxiv2020

Predicting the tension in actin cytoskeleton from the nucleus shape

Tension in actin cytoskeleton regulates many cellular processes and nuclear morphology. Here, we demonstrate a simple computational method for estimating actin cytoskeletal tension from nucleus shape. We first note that mechanics-based modeling defines a relationship among the volume, surface area, and projected area of the nucleus and hence a specific surface in the three-parameter space of the aforementioned geometric quantities. Data of nuclei from multiple cell types lie on such a surface. Furthermore, nuclei from a given cell population lie on a straight line on the surface. The location and orientation of the line varies with cell type. By using a mechanical model, we present two non-dimensional parameters, namely, the flatness and stretch indicators, which serve as curvilinear coordinates on the surface. Flatness indicator defines the extent of nuclear flattening due to actin cytoskeletal tension and the stretch indicator captures the effect of the elastic modulus of the nuclear envelope. We validate our assertions by modulating the actin cytoskeletal tension using three independent mechanisms: (i) direct downregulation by Cytochalasin D, (ii) indirect upregulation using Nocodazole, and (iii) mechanical stimulation by varying substrate stiffness. We also infer that the flatness indicator is equivalent to the ratio of the height to diameter of the nucleus and is related to the Vogel number. By using this geometric insight, we validate the predictions of our model with data from many previous studies. Finally, we present an analytical formula and a correlation for estimating actin cytoskeletal tension from nuclear projected area and volume.

biophysics↗

bioRxiv2019

Glutathione Peroxidase 8 (GPX8)-IL6 axis is essential in maintaining breast cancer mesenchymal stem-like state and aggressive phenotype

Metabolic reprogramming as a downstream result of oncogenic signaling pathways has been described as a hallmark of cancer. Here, we describe a reverse scenario in which a metabolic enzyme regulates cancer cell behavior by triggering a signaling pathway. We find that glutathione peroxidase 8 (GPX8), a poorly characterized redox enzyme that resides in the endoplasmic reticulum, is upregulated during the epithelial-to-mesenchymal (EMT) program in HMLE and A549 cells. In cancer patients, high tumor levels of GPX8 correlate with mesenchymal markers and poor patient outcome. Strikingly, GPX8 knockout in mesenchymal-like cells results in an epithelial-like morphology, downregulation of EMT characteristics, loss of cancer stemness features, and impeded tumor initiation in mice. We determine the mechanism governing this reduction in cancer aggressiveness is through the repression of crucial autocrine factors, in particular, interleukin-6 (IL-6). Specifically, GPX8 knockout impairs IL-6-driven activation of the JAK-STAT3 signaling pathway, a critical regulator of a cancer-aggressive state. Altogether, we uncover the GPX8-IL-6 axis as a novel metabolic-inflammatory pathway that acts as a robust EMT activator and program to induce aggressive cancer cell characteristics.

cancer biology↗

bioRxiv2018

A non-dimensional, two-parameter mechanical model reveals alterations in nuclear mechanics upon Hepatitis C Virus infection

Morphology of the nucleus is an important regulator of gene-expression. Nuclear morphology is in turn a function of the forces acting on it and the mechanical properties of the nuclear envelope. Here, we present a two-parameter, non-dimensional mechanical model of the nucleus that reveals a relationship among nuclear shape parameters such as projected area, surface area and volume. Our model fits the morphology of individual nuclei and predicts the ratio between forces and modulus in each nucleus. We analyzed the changes in nuclear morphology of liver cells due to Hepatitis C Virus (HCV) infection using this model. The model predicted a decrease in the elastic modulus of the nuclear envelope and an increase in the pre-tension in cortical actin as the causes for the change in nuclear morphology. These predictions were validated biomechanically by showing that liver cells expressing HCV proteins possessed enhanced cellular stiffness and reduced nuclear stiffness. Concomitantly, cells expressing HCV proteins showed down-regulation of lamin-A,C and up-regulation of actin, corroborating the predictions of the model. Our modelling assumptions are broadly applicable to adherent, monolayer cell cultures making the model amenable to investigate changes in nuclear mechanics due to other stimuli by merely measuring nuclear morphology. Towards this, we present two techniques, graphical and numerical, to use our model for predicting physical changes in the nucleus.

biophysics↗