Biology subjects

Jahagirdar, D.

Publications and source records attributed to Jahagirdar, D..

5 recordsLinked to original sources

bioRxiv2025

Exploring the effect of dynamic deformation on the tight junctions of endothelial cells

Atherosclerosis (Ath) is a leading cause of cardiovascular deaths, accounting for approximately 17.1 million fatalities annually. This condition arises from plaque-induced arterial narrowing, which obstructs blood flow. Traditional animal models face ethical, economic, and translational limitations, while current in vitro models often oversimplify plaque formation by using fixed channels and neglecting the dynamic effects of narrowing on endothelial junctions. The study addresses the limitations by developing a microfluidic device that mimics human-relevant stenosis with dynamic channel narrowing under continuous perfusion. Endothelial cells, which are crucial for maintaining barrier integrity through tight junctions, are subjected to physiological shear stress and hyperlipidaemic conditions by administering free fatty acids. The model evaluates cell alignment, junctional stability, and disease progression under mechanically deformed static conditions. To validate the translational potential of this system, ROS scavenging drug, quercetin is tested for its ability to reverse oxidative stress and barrier dysfunction. This innovative microphysiological system offers a robust platform for investigating endothelial dysfunction in Ath and provides a valuable alternative to animal models for cardiovascular drug testing. By integrating both biochemical and mechanical cues in a controllable environment, this model aims to enhance our understanding of Ath and facilitate the development of more effective therapeutic strategies.

bioengineering↗

bioRxiv2025

High-Fidelity Simulation of Cell Adhesion and Flow with Coarse Grain Modelling: A Numerical and Experimental Approach

A coupled CFD-DEM framework was developed to investigate red blood cell (RBC) transport and cellular adhesion in constricted microchannels, with a primary objective of reducing computational cost while preserving physiological accuracy. Initially, numerical softening factors were implemented, allowing greater overlap between particles to expedite computations, with an optimal value of 0.03 selected. Adhesion forces between RBCs and the channel wall were incorporated, with a minimum effective distance of 0.4{square}{micro}m identified as computationally feasible. However, RBC-RBC adhesion led to artificial clustering and was therefore omitted. Coarse-graining methods were applied up to a factor of 2 to further reduce simulation time, with a value of 1.8 chosen based on consistent cell-free layer (CFL) thickness and drag force characteristics. To correct for the increased drag in coarse-grained models, rolling resistance (Type C) with a coefficient of 0.8 was employed, bringing deviations within 10%. The validated model was then extended to simulate the detachment of adherent C2C12 myoblasts under physiological flow. Experimental validation showed increasing cell retention with seeding time, and simulations reproduced this trend with <5% deviation. The resulting Detachment Force Ratio (DFR) at 6 hours indicates near-equivalence between adhesion and hydrodynamic forces, establishing the models robustness for cell-substrate interaction studies in microfluidics.

cell biology↗

bioRxiv2022

KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion

Ribosome assembly is orchestrated by many assembly factors, including ribosomal RNA methyltransferases whose precise role is poorly understood. Here, we leverage the power of cryo-EM and machine learning to discover that the bacterial methyltransferase KsgA performs a novel "proofreading" function in assembly of the ribosomal small subunit by recognizing and partially disassembling particles that have matured but are not competent for translation. We propose that this activity allows inactive particles an opportunity to reassemble into an active state, thereby increasing overall assembly fidelity. Detailed structural quantifications in our datasets additionally enabled expansion of the Nomura assembly map to highlight rRNA helix and r-protein interdependencies, which newly details how binding and docking of these elements are tightly coupled. These results have wide-ranging implications in our understanding of the quality control mechanisms governing ribosome biogenesis, and showcase the power of heterogeneity analysis in cryo-EM to unveil functionally relevant information in biological systems.

biochemistry↗

bioRxiv2020

Alternative Conformations and Motions Adopted by 30S Ribosomal Subunits Visualized by Cryo-Electron Microscopy.

It is only after recent advances in cryo-electron microscopy that is now possible to describe at high resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between the "active" and "inactive" conformations. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6[A] resolution and study its motions. In the inactive conformation, three nucleotides at the 3 end of the 16S rRNA cause the region of helix 44 forming the decoding center to adopt an unlatched conformation and the 3 end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42 {degrees}C reverts these structural changes. The position adopted by helix 44 dictates the most prominent motions of the 30S subunit. We found that extended exposures to low magnesium concentrations induces unfolding of large rRNA structural domains. The air-water interface to which ribosome subuints are exposed during sample preparation also peel off some ribosomal proteins. Overall this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution.

molecular biology↗

bioRxiv2019

Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit

To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains were able to fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Eras role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.

molecular biology↗