Biology subjects

Kadam, S.

Publications and source records attributed to Kadam, S..

15 recordsLinked to original sources

bioRxiv2026

Data-driven polymer modeling reveals how scale-dependent active fluctuations shape chromatin organization

The nature of the chromatin polymer and its properties are tightly coupled to its function. By analyzing recent microscopy data, we show that chromatin segments at [~] 10-100 kb scales exhibit anomalously broad bond-length fluctuations and acute local angles beyond the scope of existing polymer models. Using polymer simulations at nucleosome resolution and systematic coarse-graining, we show that chromatin at these scales requires a non-equilibrium description. We develop a data-constrained non-equilibrium model that explains these anomalous fluctuations, in which coarse-grained beads experience extensile, angular, and stochastic active forces. Our work provides an experimentally guided framework for incorporating active processes and suggests that the nature of activity is scale-dependent. The model quantitatively reproduces three-dimensional distance distributions across scales and enables inference of effective elastic and active parameters, providing a unified framework for active chromatin simulations and the study of its 3D organization.

biophysics↗

bioRxiv2026

Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism of Xist

The fundamental process of X-chromosome inactivation (XCI) involves silencing one X chromo-some in female mammals by the Xist gene within the X-inactivation center (Xic). While experiments have identified key regulatory elements controlling Xist expression, mechanistic details are unknown. By combining nucleosome-resolution and coarse-grained polymer modeling, we reveal multiscale Xic reorganization during XCI driven by loop extrusion and epigenetic modifications, including methylation. At the nucleosome level, inactive X shows differential gene organization, where Xite is buried and compacted but Xist folds into a fragmented open structure; clutch patterns also change upon inactivation, and changes in methylation (in Xite) and NFRs (in Xist) explain the reorganization. At the megabase scale, our simulations reveal spatial rewiring: Linx -Tsix contacts are disrupted, isolating Tsix from its activator, while Xist, Jpx, and Ftx coalesce into an active compartment. This hierarchical and differential reorganization creates a chromatin architecture with an active domain for Xist favoring its expression, while a repressed Xite prevents Tsix reactivation. These general principles of how 3D genome organization directs development have implications for diseases related to XCI and extend beyond XCI to gene regulation broadly.

biophysics↗

bioRxiv2025

Predicting statistics of gene translocation events: role of chromatin compaction and double-strand DNA break

How the 3D organization of chromatin affects gene translocation is an open question. By Monte Carlo simulation of translocation events in folded chromatin, we examine how the probability of translocation (Tij) is influenced by chromatin compaction and the occurrence of double-stranded DNA breaks (DSBs). Our results show that, beyond the two-segment contact probability, Tij depends on the overall compaction of the polymer and has a non-trivial contribution from multi-bead contacts and the probability of DSBs. We propose an empirical formula and provide analytical arguments for simple cases.

biophysics↗

bioRxiv2024

Interplay between cohesin kinetics and polymer relaxation modulates chromatin-domain structure and dynamics

Even though the three-dimensional static organization of chromatin is highly studied, chromatin is a dynamic structure, and time-dependent changes are crucial for biological function. While it is known that both intra-chromatin interaction and loop extrusion are crucial to understanding chromatin organization, what is their respective role in deciding the nature of spatial and temporal organization is not clear. Simulating a model with active loop extrusion and intra-chromatin interactions, we show that under certain conditions, the measurable dynamic quantities are dominated by the loop extrusion, even though the population-averaged contact map (structure) can be dominated by intra-chromatin interactions, with loop extrusion playing no major role. Our results show that the dynamic scaling exponents with loop extrusion are consistent with the experimental observations and can be very different from those predicted by existing fractal-globule models for chromatin. We argue that one needs to measure both the structure and dynamics simultaneously to unambiguously interpret the organization of chromatin.

biophysics↗

bioRxiv2023

Nonequilibrium switching of segmental states can influence compaction of chromatin

Knowledge about the dynamic nature of chromatin organization is essential to understand the regulation of processes like DNA transcription and repair. While most models assume protein organization and chemical states along chromatin as static, experiments have shown that these are dynamic and lead to the switching of chromatin segments between different physical states. To understand the implications of this inherent nonequilibrium switching, we present a diblock copolymer model of chromatin, with switching of its segmental states between two states, mimicking active/repressed or protein unbound/bound states. We show that competition between switching timescale Tt, polymer relaxation timescale{tau} p, and segmental relaxation timescale{tau} s can lead to non-trivial changes in chromatin organization, leading to changes in local compaction and contact probabilities. As a function of the switching timescale, the radius of gyration of chromatin shows a non-monotonic behavior with a prominent minimum when Tt {approx}{tau} p and a maximum when Tt {approx}{tau} s. We find that polymers with a small segment length exhibit a more compact structure than those with larger segment lengths. We also find that the switching can lead to higher contact probability and better mixing of far-away segments. Our study also shows that the nature of the distribution of chromatin clusters varies widely as we change the switching rate. Significance statementDifferent cells in multicellular organisms have the same DNA but different functions. The function of any given cell type can be time-dependent. The current understanding is that differences in gene expression arising from local compaction and the probability for far-away regulatory segments to come in contact play an important role in establishing these differences. The necessary structural variations are achieved through a combination of changes in the chemical and physical states of chromatin regions. In this paper, we present a model for chromatin accounting for the dynamic switching of chromatin regions between different chemical and physical states. We demonstrate the implications of such switching in determining the local 3D structure of chromatin.

biophysics↗

bioRxiv2023

Talk To A Scientist: A Framework for a Webinar-Based Science Outreach Platform for Children

Given their future roles as citizens and decision makers, science outreach focused on children is important and relevant. We describe a scientist-led outreach platform (Talk To A Scientist), that uses a webinar-based approach to discuss a range of science topics with children (6-16 years). Based in India and led by two working scientists, Talk To A Scientist has been running for nearly 3 years, with a large and diverse reach across school students. In addition to webinars, the platform regularly hosts archived video content and weekly science activities, along with occasional summer family quizzes and age-specific webinars. We outline the framework used to build Talk To A Scientist, and discuss key considerations and challenges in the development and expansion of the program. We believe that the Talk To A Scientist outreach model focused on children can serve as a guideline for the implementation of similar platforms across diverse settings, and is amenable to a range of modifications to enhance engagement, sustain interest, and tailor outreach to specific groups.

scientific communication and education↗

bioRxiv2022

Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

Simulating chromatin is crucial for predicting genome organization and dynamics. Even though coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using publicly available nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions between neighboring bonds giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show that there are two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.

biophysics↗

bioRxiv2022

Biofilms with a dash of color: A hands-on activity for school students to build a biofilm model, and use it to understand antibiotic tolerance in biofilms

It is increasingly recognized that microbes, such as bacteria, exist in communities or biofilms, both in the environment and human body. However, school biology curriculum continues to focus on the free-floating form of bacterial life, with minimal descriptions of biofilms. Consequently, there is a need to introduce biofilms to school students, to not only to develop a fundamental understanding of microbial life, but to also highlight the challenges posed by biofilm infections to antibiotic treatment. We have developed a hands-on activity in which students build a biofilm model, and use it to understand the role of the extracellular matrix in the antibiotic tolerance of biofilms. The activity uses simple, easy to obtain supplies, and can be conducted in an in-person or virtual format, with students participating from school or home. We conducted the activity in virtual mode for a group of 59 school students across India, and present feedback and learnings that could be used to execute and adapt this accessible and engaging science experience.

scientific communication and education↗

bioRxiv2021

Of Biofilms and Beehives: An Analogy-Based Instructional Tool to Introduce Biofilms to High-School and Undergraduate Students

The concept of biofilms and biofilm-based research is largely absent or minimally described in high school and undergraduate life science curriculum. While it is well-established that microbes, such as bacteria and fungi most often exist in multicellular biofilm communities, descriptions in standard biology textbooks continue to focus on the single-celled form of microbial life. We have developed an analogy-based instructional tool to introduce and explain biofilms to high school and undergraduate students. The module employs an analogy with beehives, given that biofilms and beehives are both superorganism states, to explain key biofilm features such as development and structure, chemical communication, division of labor and emergent properties. We delivered this analogy based learning tool to a cohort of 49 high school and undergraduate students, and based on participant feedback and learnings, present a formal evaluation of the instructional tool. Further, we outline prerequisites and learning approaches that can enable the delivery of this module in classroom and virtual learning settings, including suggestions for pre-lesson reading, student-centred interactive activities, and specific learning objectives. Taken together, this instructional analogy holds potential to serve as an educational tool to introduce biofilms in high school and undergraduate curricula in a relatable and comprehensible manner.

scientific communication and education↗

bioRxiv2021

Spatiotemporal solidification of α-synuclein inside the liquid droplets

Liquid-liquid phase separation (LLPS) and subsequent liquid-to-solid transition is implicated in membraneless organelles formation as well as disease associated protein aggregation. However, how liquid-to-solid transition is initiated inside a liquid droplet remains unclear. Here, using studies at single droplet resolution, we show that liquid-to-solid transition of -synuclein (-Syn) liquid droplets is associated with significant changes in the local microenvironment as well as secondary structure of the protein, which is prominently observed at the center of the liquid droplets. With the ageing of liquid droplets, the "structured" core at the center gradually expands and propagates over entire droplets. Further, during droplet fusion, smaller, homogeneous droplets progressively dissolve and supply proteins to the larger, heterogeneous droplets containing solid-like core at their center. The present study will significantly help to understand the physical mechanism of LLPS and liquid-to-solid transition in biological compartmentalization as well as in protein aggregation associated with human neurodegenerative disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/465113v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@2a3406org.highwire.dtl.DTLVardef@bd8148org.highwire.dtl.DTLVardef@172b4eaorg.highwire.dtl.DTLVardef@1c3965f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

AMPing up the search: An in silico approach to identifying Antimicrobial Peptides (AMPs) with potential anti-biofilm activity

Antibiotic resistance is a public health threat, and the rise of multidrug-resistant bacteria, including those that form protective biofilms, further compounds this challenge. Antimicrobial peptides (AMPs) have been recognized for their anti-infective properties, including their ability to target processes important for biofilm formation. However, given the vast array of natural and synthetic AMPs, determining potential candidates for anti-biofilm testing is a significant challenge. In this study, we present an in silico approach, based on open-source tools, to identify AMPs with potential anti-biofilm activity. This approach is developed using the sortase-pilin machinery, important for adhesion and biofilm formation, of the multidrug-resistant, biofilm-forming pathogen C. striatum as the target. Using homology modeling, we modeled the structure of the C. striatum sortase C protein, resembling the semi-open lid conformation adopted during pilus biogenesis. Next, we developed a structural library of 5544 natural and synthetic AMPs from sequences in the DRAMP database. From this library, AMPs with known anti-Gram positive activity were filtered, and 100 select AMPs were evaluated for their ability to interact with the sortase C protein using in-silico molecular docking. Based on interacting residues and docking scores, we built a preference scale to categorize candidate AMPs in order of priority for future in vitro and in vivo biofilm studies. The considerations and challenges of our approach, and the resources developed, which includes a search-enabled repository of predicted AMP structures and protein-peptide interaction models relevant to biofilm studies (B-AMP), can be leveraged for similar investigations across other biofilm targets and biofilm-forming pathogens.

bioinformatics↗

bioRxiv2021

Milieu matters: An in vitro wound milieu to recapitulate key features of, and probe new insights into, polymicrobial biofilms

Bacterial biofilms are a major cause of delayed wound healing. Consequently, the study of wound biofilms, particularly in host-relevant conditions, has gained importance. Most in vitro biofilm studies employ refined laboratory media to study biofilms, conditions that are not relevant to the infection state. To mimic the wound milieu, in vitro biofilm studies often incorporate serum or plasma in growth conditions, or employ clot or matrix-based biofilm models. While incorporating serum or plasma alone is a minimalistic approach, the more complex in vitro wound models are technically demanding, and poorly compatible with standard biofilm assays. Based on previous reports of clinical wound fluid composition, we have developed an in vitro wound milieu (IVWM) that includes, in addition to serum (to recapitulate wound fluid), matrix elements and biochemical factors. In comparison with Luria-Bertani broth and Fetal Bovine Serum (FBS), the IVWM was used to study planktonic growth and biofilm features, including interspecies interactions, of common wound pathogens, Staphylococcus aureus and Pseudomonas aeruginosa. We demonstrate that the IVWM recapitulates widely reported in vivo biofilm features such as metabolic activity, increased antibiotic tolerance, 3D structure, and interspecies interactions for single- and co-species biofilms. Further, the IVWM is simple to formulate, uses laboratory-grade components, and is compatible with standard biofilm assays. Given this, it holds potential as a tractable approach to study wound biofilms under host-relevant conditions.

microbiology↗

bioRxiv2020

Continuous variable response, kinetic gating and connectivity that govern IS topology are perturbed in hyperinsulinemia

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin-signaling (IS) is central for almost all metazoans and its perturbations are associated with various diseases and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood. Our iterative experimental and mathematical simulation-based approaches reveal novel kinetic parameters that encode concentration and nutrient dependent information. Further, we find that pulsatile fasting insulin rewires IS akin to memory and in anticipation of a fed response. Importantly, selective kinetic gating of signals and maximum connectivity, between metabolic and growth-factor arms under normo-insulinemic states, maintains network topology. In addition to unraveling kinetic constraints that determine cascade architecture, our findings will help in identifying novel therapeutic strategies that conserve coupling between metabolic and growth-factor arms, which is lost in diseases and conditions of hyperinsulinemia.

bioinformatics↗

bioRxiv2020

Continuous variable response, kinetic gating and connectivity that determine topology of insulin signaling are perturbed in hyper-insulinemic states

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin signaling (IS) is central for almost all metazoans and its perturbations are associated with various diseases and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood. Our iterative experimental and mathematical simulation-based approaches reveal novel kinetic parameters of IS that encode concentration and nutrient dependent information. Further, we find that pulsatile fasting insulin rewires IS akin to memory and in anticipation of a fed response. Importantly, selective kinetic gating of signals and maximum connectivity, between metabolic and growth-factor arms under normo-insulinemic states, maintains network topology. In addition to unraveling kinetic constraints that determine cascade architecture, our findings will help in identifying novel therapeutic strategies that conserve coupling between metabolic and growth-factor arms, which is lost in diseases and conditions of hyperinsulinemia.

systems biology↗

bioRxiv2020

Towards 'Ancientbiotics' for Biofilms: How can we bring traditional medicinal remedies out of treatise and into contemporary science?

IntroductionTraditional medicinal remedies hold vast potential as novel antimicrobial agents, particularly for recalcitrant infection states such as biofilms. To explore their potential, it is important to bring these remedies out of ancient treatise and into present-day scientific evaluation. For traditional medical practices, this development pipeline starts with probing treatise for potential remedies and testing them for anti-biofilm effects, or the treatise to test phase. AimThe aim of this work is to present a primer for developing ancientbiotics against biofilms, that focuses on the treatise to test phase of the pipeline. Based on our approach and results, we provide insights into the considerations and challenges relevant to evaluating traditional remedies as anti-biofilm agents. MethodologyWe identified and reconstituted plant-based medicinal formulations from historical treatises of Indian traditional medicine, and analyzed their efficacy using widely-employed microtiter based assays, that constitute the cornerstone of biofilm studies. Measuring biomass and metabolic activity, we evaluated effects on biofilm formation and eradication of pre-formed biofilms, of Pseudomonas aeruginosa and Staphylococcus aureus. ResultsBased on recipes and preparation practices across several texts, and with modifications to ensure compatibility with modern scientific practices, three plant-based traditional remedies were identified and formulated in sesame oil (Bryophyllum pinnatum, Cynodon dactylon, and Ocimum tenuiflorum). We observed differential effects on biomass and metabolic activity on the biofilm formation and eradication of P. aeruginosa and S. aureus; highlighting the value of the microtiter-based assays as an initial screening tool for traditional remedies. ConclusionThrough this study, we provide insights into considerations relevant to the treatise to test phase of the ancientbiotics pipeline, such as identifying ancient remedies, reconstituting them with present-day modifications, and using in vitro assay formats for evaluation. The learnings in this primer will be relevant to both contemporary scientists and practitioners of ancient medicine, and will serve as a starting point for future studies exploring anti-biofilm approaches at the interface of historical and modern medicine.

microbiology↗