Biology subjects

Deshpande, A. P.

Publications and source records attributed to Deshpande, A. P..

4 recordsLinked to original sources

bioRxiv2025

Matrix compliance regulates cellular and nuclear confinement of fibroblasts in tunable protein-based hydrogel microenvironments

The extracellular matrix (ECM) influences cellular behavior, fate, and various mechanisms underlying homeostasis, development, and disease. Biophysical and biochemical properties of the ECM are known to affect three-dimensional (3D) cellular behavior, and phenotype that regulate a wide range of pathological conditions. Tunable biomimetic hydrogels are extensively employed to regulate cellular dynamics in defined 3D microenvironments, enabling detailed investigation of cell-matrix interactions. This study aims to establish the relationship between varying hydrogel properties (adhesivity, degradability, porosity, and stiffness, hereby collectively referred to as matrix compliance) and fibroblast morphology at the cellular and nuclear levels. Poly(ethylene glycol diacrylate)-fibrinogen (PF)-based hydrogels were fabricated and their matrix properties were tuned using two different non-degradable co-monomers of varying molecular weights and concentrations. NIH3T3 mouse fibroblasts were cultured in 3D hydrogels for 10 days and their cellular and nuclear morphology was analyzed via confocal imaging. Cells in degradable, soft, porous, and adhesive hydrogels displayed higher degree of spreading, higher cell density, longer protrusions, and elongated and larger nuclei compared to those in less degradable, stiffer, less porous, and less adhesive hydrogels. Matrix compliance conjointly regulated cell density, protrusion length, and protrusion frequency (collectively referred to as cellular confinement) and nuclear volume (referred to as nuclear confinement). These results highlight the complex interplay and interdependence of these cellular and nuclear morphological features as regulated by engineered tunable matrices, providing guidance for future studies of 3D cell behavior in novel biomaterials. Statement of significanceBiomimetic tunable hydrogels are commonly used to support, and control, three-dimensional (3D) cellular behavior to recapitulate various developmental processes and disease states. Specific biophysical and biochemical characteristics of the extracellular matrix (ECM) can be modeled using these hydrogels by controlling the compositions and crosslinking mechanisms. Using this approach, the behavior of cells in 3D hydrogel matrices can be correlated with the matrix properties, thereby providing mechanistic insights into cell-matrix interactions. This study assesses the variations in the morphological features of fibroblasts encapsulated in 3D protein-based hydrogel matrices with varying crosslinking mechanisms. Our results reveal the combinatorial role of matrix adhesivity, degradability, porosity, and stiffness in regulating cellular and nuclear confinement of fibroblasts in 3D microenvironments. Overall, this study elucidates how matrix characteristics influence cellular behavior, serving as a practical guide for researchers developing innovative biomaterial matrices for 3D cell culture applications.

bioengineering↗

bioRxiv2024

How mucilage helps seeds from being washed away? A mechanical interpretation of myxodiaspory using rheology

Cellulosic, hemicellulosic and pectinaceous mucilages produced by certain angiosperms as adaptation in myxodiaspory are investigated in the past for seed dispersal. The present understanding of zoochory and telechory are based on mucilage amount, state of hydration and to a limited extent, role of mucilage microstructure studied using adhesion and friction. Pectinaceous mucilages have less adhesion and supports dispersal by zoochory. However, in the case of cellulosic mucilages, the role played by the cellulosic fibrils in seed dispersal is not clear, especially, since they have a negative correlation with endozoochory. Using fresh cellulosic seed mucilages from, sweet basil (Ocimum basilicum) and chia (Salvia hispanica) we investigate the role of microstructure of the mucilage in two key behaviours: anchoring and adhesion properties of the seeds through rheology. We report a special large deformation mechanism triggered through strain stiffening operational in these cellulosic mucilages. In many biopolymers semi-flexible polymer chains and other aligning elements contribute to the strain stiffening. However, the strain stiffening and strong wet adhesion observed in these mucilages have a significant role from the cellulosic components. This behaviour is more pronounced in basil seeds and presents a plausible structure-property mechanism for anti-telechory favoured by plant species found in arid habitats.

physiology↗

bioRxiv2021

Pectin self-assembly and its disruption by water: Insights into plant cell wall mechanics

Plant cell walls undergo multiple cycles of dehydration and rehydration during their life. Calcium crosslinked low methoxy pectin is a major constituent of plant cell walls. Understanding the dehydration-rehydration behavior of pectin gels may shed light on the water transport and mechanics of plant cells. In this work, we report the contributions of microstructure to the mechanics of pectin-Ca gels subjected to different extents of dehydration and subsequent rehydration. This is investigated using a pectin gel composition that forms egg-box bundles, a characteristic feature of the microstructure of low methoxy pectin-Ca gels. Large Amplitude Oscillatory Shear (LAOS) rheology along with Small Angle Neutron Scattering and Near Infrared (NIR) spectroscopy on pectin gels are used to elucidate the mechanical and microstructural changes during dehydration-rehydration cycles. As the extent of dehydration increase, the reswelling ability, strain-stiffening behavior and the yield strain decreases. These effects are more prominent at faster rates of dehydration and are not completely reversible upon rehydration to the initial undried state. Microstructural changes due to the aggregation of egg-box bundles and single chains and the associated changes in the water configurations lead to these irreversible changes.

plant biology↗

bioRxiv2019

Reevaluation of the RNA binding properties of the Tetrahymena thermophila telomerase reverse transcriptase N-terminal domain

Telomerase restores chromosome-capping telomeric repeats lost with each round of genome replication by DNA-templated DNA polymerases. The telomerase reverse transcriptase (TERT) N-terminal (TEN) domain is a peripheral, telomerase-specific, processivity-stimulatory addition to more conserved domains that encircle the active site cavity. Reports of ciliate, yeast, and mammalian telomerase TEN domain associations with the telomerase RNA subunit (TR) describe low affinity interactions of uncertain specificity. Unfortunately two cryo-EM structures of synthesis-paused telomerase holoenzymes lack sufficient resolution to discriminate molecular specificity of possible TR contact(s) with the TEN domain, and there is no assigned density for the TEN domain termini implicated in RNA binding. Furthermore, studies have revealed alternative secondary structures for TR regions that could interact with TERT prior to TR folding into active conformation. Informed by recent advances in knowledge of telomerase structure, we returned to the investigation of Tetrahymena thermophila TERT TEN domain interaction with TR. Instead of finding specificity for a particular TR sequence or structure, we discovered that the tagged TEN domain used in previous characterizations has trace contamination with a bacterial RNA-interacting protein not detectable by SDS-PAGE. By resolving this interference, we show that the TEN domain binds RNAs dependent on RNA length rather than sequence.

biochemistry↗