Biology subjects

Roy, A. K.

Publications and source records attributed to Roy, A. K..

4 recordsLinked to original sources

bioRxiv2025

Understanding the selectivity of lysine negatively charged acyl modifications by OsCobB and its link with different plant stress condition

Recent proteomic studies have found several different lysine modifications in plants related to various important metabolic pathways. Lysine deacylation is a key feature of sirtuins for the regulation of several cellular processes in mammals. This may be involved in the tolerance against different stress conditions in case of plants. In this study, we deliver a comprehensive structural and kinetic analysis describing the selection of lysine acidic acyl groups by OsCobB. The catalytic efficiency (kcat/Km) of OsCobB to erase glutaryl, succinyl, and malonyl groups from the designated lysine site is favored due to the presence of Tyr55 and Arg58 at the active site. The selectivity of the substrate is further based on the OsCobB active site residues as well as residues next to the modified lysine. These modifications can be further linked to the plants mechanism to cope with stress due to dehydration, cold temperature and different metal toxicities.

plant biology↗

bioRxiv2022

Cryo-EM-based structural insights into supramolecular assemblies of γ-Hemolysin from Staphylococcus aureus reveal the pore formation mechanism.

{gamma}-hemolysin ({gamma}-HL) is a hemolytic and leukotoxic bicomponent {beta}-pore-forming toxin ({beta}-PFT), a potent virulence factor from Staphylococcus aureus Newman strain. In this study, we performed single particle cryo-EM of {gamma}-HL in a lipid environment. We observed clustering and square lattice packing of octameric HlgAB pores upon membrane bilayer, and an octahedral superassembly of octameric pore complexes, that we resolved at resolution 3.5 [A]. Our atomic model further demonstrated the key residues involved in hydrophobic zipping between the rim domains of adjacent octameric pore complexes, thus providing first evidence of additional structural stability in PFTs upon membrane lysis. We also observed lipid densities at the octahedral and octameric interfaces, providing critical insights into the lipid-binding residues involved for both HlgA and HlgB components. Furthermore, the hitherto elusive N-terminal region of HlgA has also been resolved in our cryo-EM map and an overall mechanism of pore formation for bicomponent {beta}-PFTs is proposed.

biophysics↗

bioRxiv2020

Decomposing complex links between the childhood environment and brain structure in school-aged youth

Childhood experiences play a profound role in conferring risk and resilience for brain and behavioral development. However, how different facets of the environment shape neurodevelopment remains largely unknown. Here we sought to decompose heterogeneous relationships between environmental factors and brain structure in 989 school-aged children from the Adolescent Brain Cognitive Development Study. We applied a cross-modal integration and clustering approach called Similarity Network Fusion, which combined two brain morphometrics (i.e., cortical thickness and myelin-surrogate markers), and key environmental factors (i.e., trauma exposure, neighborhood safety, school environment, and family environment) to identify homogeneous subtypes. Depending on the subtyping resolution, results identified two or five subgroups, each characterized by distinct brain structure-environment profiles. Notably, more supportive caregiving and school environments were associated with increased myelination, whereas less supportive caregiving, higher family conflict and psychopathology, and higher perceived neighborhood safety were observed with increased cortical thickness. These subtypes were highly reproducible and predicted externalizing symptoms and overall mental health problems. Our findings support the theory that distinct environmental exposures differentially influence neurodevelopment. Delineating more precise associations between risk factors, protective factors, and brain development may inform approaches to enhance risk identification and optimize interventions targeting specific experiences.

neuroscience↗

bioRxiv2020

Isolation and characterization of two bacterial strains from textile effluents having Malachite Green dye degradation ability

Water pollution from textile effluent is now one of the major issues all over the world. Malachite Green dye of the triphenylmethane group is a key component of textile effluents. This study aimed to isolate and identify potential Malachite Green dye degrading bacteria from textile effluents. Different growth and culture parameters such as temperature, pH, inoculum-size and dye concentration were optimized to perform the dye-degradation assay using different concentrations of Malachite Green dye in mineral salt medium. A photo-electric-colorimeter was used to measure the decolorizing activity of bacteria at different time intervals after aerobic incubation. Two competent bacterial strains of Enterobacter spp. (CV-S1 and CM-S1) were isolated from textile effluents showing potential degradation efficiency against Malachite Green dye. The RAPD analysis and 16S rRNA sequencing confirmed the genetical difference of the isolated strains Enterobacter sp. CV-S1 and Enterobacter sp. CM-S1. The two bacterial strains CV-S1 and CM-S1 showed complete Malachite Green dye degradation up to 15 mg/l under shaking condition with 5% (v/v) inoculums at pH 6.50 and temperature 35{degrees}C within 72 and 144 hours respectively. These findings indicate that the two potential bacterial strains can be used in large scale treatment of textile effluents in the future.

microbiology↗