Biology subjects

Acharya, B.

Publications and source records attributed to Acharya, B..

7 recordsLinked to original sources

bioRxiv2026

Origins Anywhere and Everywhere: Genome replication requires cooperative activation of thousands of origins in each cell

Our model of replication dynamics in a single eukaryotic cell supplants current population-based models. Long-read sequencing reveals cooperative activation of ~8400 closely spaced origins in every S.cerevisiae cell. Origins with bidirectional forks of comparable velocities are evenly distributed across the genome. The probability of early origin activation directly correlates with the average density of ORC (Origin Recognition Complex) binding motifs in a 10-20kbp region. We propose that 3D chromosome folding creates genomic pockets that act as ORC traps to increase local concentrations of pre-RC (Replication Complexes) and favor origin activation. Our results indicate that efficient replication through chromatin requires the activation of thousands of origins spanning the entire genome. This is consistent with genome instability being caused by insufficient origin activation rather than by perturbations in the replication timing program.

genomics↗

bioRxiv2026

Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments

The mycobacterial outer membrane (MOM) constitutes an asymmetric permeability barrier that influences lipid organization and transport in Mycobacterium tuberculosis. In this study, we have developed MARTINI 3 coarse-grained (CG) lipid models of the MOM, incorporating -mycolic acids, 5 different trehalose-based lipids, and PDIM (phthiocerol dimycocerosate). The CG models were parameterized and validated using all-atom simulations of symmetric inner- and outer-leaflet membranes, as well as fully asymmetric MOM models. Bonded parameters were optimized through an iterative refinement procedure targeting atomistic bonded distributions. The CG simulations show good agreement with the all-atom simulation data and available experimental measurements in terms of the membrane thickness, solvent accessible surface area, lipid density profiles, and the outer-leaflet-induced lipid disorder in -mycolic acids at the inner leaflet. The model reproduces the temperature-dependent phase behavior of all-atom -mycolic acid membranes. Using this model, we demonstrate that PDIM localization, diffusion, and aggregation are strongly modulated by membrane fluidity and lipid composition, with enhanced translocation and clustering in liquid disordered environments. Our CG MOM lipid models provide a validated platform for large-scale simulations of mycobacterial membranes and enable mechanistic studies of lipid organization, membrane dynamics, and protein-membrane and membrane-drug interactions.

biophysics↗

bioRxiv2025

Label-Free Fluorescence Microscopy Reveals Multiphase Organization in Biomolecular Condensates

Phase transitions of proteins and nucleic acids (NA) leading to the formation of biomolecular condensates have been linked to various biological functions. Given the growing number of proteins/NA predicted to undergo liquid-liquid phase separation (LLPS), efficient tools to investigate this behavior are critical to advancing our understanding of biomolecular condensate function. The current standard used to study LLPS involves techniques that utilize exogenous fluorophore labels. The labeling process is often costly and time-consuming and comes with associated complexity that arises from unknown interactions from the bulky fluorescent tags. These aspects limit high throughput analysis of protein/NA phase separation based on external fluorophore labeling. Here, we report the discovery that intrinsic fluorescence, well into the visible spectrum, arises as an emergent property of biomolecular condensates. Leveraging this intrinsic fluorescence, we study condensate formation, directly measure their internal dynamics via Fluorescence Recovery after Photobleaching (FRAP), and examine the 3D morphology and transitions to various multiphase architectures. Through this approach, we find that a variety of G-quadruplex DNA readily form droplets with histone H1 and display dynamic exchange. In addition, we directly demonstrate that the 3D morphology, core-shell architecture, and sub-compartmentalization of condensate droplets are tunable via the charge ratio of components in solution and NA hybridization. Our method utilizes an inherent property of condensates, thus is broadly applicable to any phase-separated systems and can advance our understanding of biological phase transition.

biophysics↗

bioRxiv2023

Dissecting Metabolic Landscape of Alveolar Macrophage

The highly plastic nature of Alveolar Macrophage (AM) plays a crucial role in the defense against inhaled particulates and pathogens in the lungs. Depending upon the signal, AM acquires either classically activated M1 phenotype or alternatively activated M2 phenotype. These phenotypes have specific functions and unique metabolic traits such as upregulated glycolysis and pentose phosphate pathway in M1 phase and enhanced oxidative phosphorylation and tricarboxylic acid cycle during M2 phase that help maintain the sterility of the lungs. In this study, we investigate the metabolic shift in the activated phases of AM (M1 and M2 phase) and highlight the roles of pathways other than the typical players of central carbon metabolism. Pathogenesis is a complex and elongated process where the heightened requirement for energy is matched by metabolic shifts that supplement immune response and maintain homeostasis. The first step of pathogenesis is fever; however, analyzing the role of physical parameters such as temperature is challenging. Here, we observe the effect of an increase in temperature on pathways such as glycolysis, pentose phosphate pathway, oxidative phosphorylation, tricarboxylic acid cycle, amino acid metabolism, and leukotriene metabolism. We report the role of temperature as a catalyst to the immune response of the cell. The activity of pathways such as pyruvate metabolism, arachidonic acid metabolism, chondroitin/heparan sulfate biosynthesis, and heparan sulfate degradation are found to be important driving forces in the M1/M2 phenotype. We have also identified a list of 34 reactions such as nitric oxide production from arginine and the conversion of glycogenin to UDP which play major roles in the metabolic models and prompt the shift of the M2 phenotype to M1 and vice versa. In future, these reactions could further be probed as major contributors in designing effective therapeutic targets against severe respiratory diseases. Author SummaryAlveolar macrophage (AM) is highly plastic in nature and has a wide range of functions including invasion/killing of bacteria to maintaining the homeostasis in the lungs. The regulatory mechanism involved in the alveolar macrophage polarization is essential to fight against severe respiratory conditions (pathogens and particulates). Over the years, experiments on mouse/rat models have been used to draw insightful inferences. However, recent advances have highlighted the lack of transmission from non-human models to successful in vivo human experiments. Hence using genome-scale metabolic (GSM) models to understand the unique metabolic traits of human alveolar macrophages and comprehend the complex metabolic underpinnings that govern the polarization can lead to novel therapeutic strategies. The GSM models of AMs thus far, has not incorporated the activated phases of AM. Here, we aim to exhaustively dissect the metabolic landscape and capabilities of AM in its healthy and activated stages. We carefully explore the changes in reaction fluxes under each of the conditions to understand the role and function of all the pathways with special attention to pathways away from central carbon metabolism. Understanding the characteristics of each phase of AM has applications that could help improve the therapeutic approaches against respiratory conditions.

systems biology↗

bioRxiv2023

Multi-organ Metabolic Model of Zea mays Connects Temperature Stress with Thermodynamics-Reducing Power-Energy Generation Axis

Global climate change has severely impacted maize productivity. A holistic understanding of metabolic crosstalk among its organs is essential to address this issue. Thus, we reconstructed the first multi-organ maize genome-scale metabolic model, iZMA6517, and contextualized it with heat and cold stress-related transcriptomics data using the novel EXpression disTributed REAction flux Measurement (EXTREAM) algorithm. Furthermore, implementing metabolic bottleneck analysis on contextualized models revealed fundamental differences between these stresses. While both stresses had reducing power bottlenecks, heat stress had additional energy generation bottlenecks. To tie these signatures, we performed thermodynamic driving force analysis, revealing thermodynamics-reducing power-energy generation axis dictating the nature of temperature stress responses. Thus, for global food security, a temperature-tolerant maize ideotype can be engineered by leveraging the proposed thermodynamics-reducing power-energy generation axis. We experimentally inoculated maize root with a beneficial mycorrhizal fungus, Rhizophagus irregularis, and as a proof of concept demonstrated its potential to alleviate temperature stress. In summary, this study will guide the engineering effort of temperature stress-tolerant maize ideotypes.

plant biology↗

bioRxiv2021

Deltamethrin contact exposure mediated toxicity and histopathological aberrations in tissue systems of cockroach species Periplaneta americana and Blatella germanica

Cockroach species Periplaneta americana and Blatella germanica potentially survive in locations close to human activity. Besides spoiling food material, cockroaches also transfer pathogens of different diseases among human. Since the insecticides have been used extensively to control cockroaches, information on their insecticide susceptibility and toxicity at cellular level may be crucial. In the study, deltamethrin toxicity as well as the deltamethrin-mediated cytomorphological changes in brain, ovary and midgut of the two important cockroach species has been assessed. Different concentrations [0.00025% (0.0025mg/ml), 0.0025% (0.025mg/ml), 0.025 (0.25mg/ml), 0.25% (2.5mg/ml), 0.5% (5mg/ml), 1% (10mg/ml)] of deltamethrin in acetone were used to expose test species in WHO bottle assay. Knockdown was recorded after 5 min interval while delayed mortality was observed after 24 hr. Brain, ovary and gut were dissected post 1 hr exposure and 24 hr holding (for 0.25%, 0.5% and 1% concentration), and tissues were processed for microscopic analysis. Deltamethrin exposed cockroaches and dissected tissues were used to estimate deltamethrin using HPLC. At 0.00025% (lowest concentration), the percentage knock-down observed was 66.7% for P. americana and 80% B. germanica respectively (R2= 0.78; p=0.0001) in 1 hr. KDT50 value was found to be 8.7 min (95% CI: 7.3-10.2), while KDT99 was 20.7 min (95% CI: 16.0-35.7) in P. americana at 1% concentration. Whereas, the KDT50 and KDT99 values for B. germanica were 7.4 min (95% CI: 5.4-9.1) and 27.4 min (95% CI: 18.2-80.0) at similar concentration. LD50 and LD95 values (for 60 min standard exposure) were 0.0006 % (95% CI: 0.00-0.001) and 0.034% (95% CI: 0.013-0.49) respectively for P. americana, while these values were 0.0005 (95% CI: 0.00-0.001) and 0.04 (95% CI: 0.01-0.23) for B. germanica. Exposure to 1% deltamethrin induced considerable toxic effect in the epithelial cells in the midgut. HPLC estimated 0.21{+/-}0.05 mg (95% CI - 0.18-0.25; CoV 23.9%) deltamethrin in P. americana post 1% exposure. Even short term exposure of low concentration of synthetic pyrethroid deltamethrin displayed immediate knockdown and delayed mortality in both the test species. Considerable histological damage was observed in both the insects at 1% exposure. In India, resistance to deltamethrin may have been reported among different insects due its extensive use, however the formulations such as insecticide paints, attractant baits etc. developed using deltamethrin as active ingredient could be useful in cockroach control operations.

zoology↗

bioRxiv2019

Confirmation of local transmission of Orientia tsutsugamushi during scrub typhus outbreaks in Nepal

BackgroundScrub typhus is a severely ignored tropical disease and a leading cause of undifferentiated febrile illness worldwide caused by infection of an obligate intracellular bacteria Orientia tsutsugamushi. It has been rapidly expanding in South Asian countries, although clear epidemiological information is not available from Nepal. After the 2015 earthquake in Nepal, a sudden upsurge in scrub typhus cases was reported. The objective of this study was to investigate scrub typhus and its causative agents in human, rodent and chigger mites to better understand the ongoing transmission ecology. MethodsScrub typhus cases with confirmed diagnosis throughout the country were included in the analysis. Studies were concentrated in the Chitwan district, the site of a major outbreak in 2016. Additional country-wide data from 2015 to 2017 was made available from the government database to analyse the disease distribution using geographical mapping. ResultsDuring 2015-2017, 1,239 scrub typhus cases were confirmed with the largest outbreak occurring in 2016 with 831 (67.1%) cases. The remainder 267 cases were reported in 2017. The case fatality rate was 5.7% in 2015 and declined to 1.1% in 2017. Nationwide outbreak of scrub typhus was identified as the cases were found from 52 of the 75 districts of Nepal. A seasonal trend was observed with a peak during August and September (p = 0.01). In addition to the human cases, the presence of O. tsutsugamushi was also confirmed in rodents and chigger mites from the outbreak areas of southern Nepal. ConclusionThe detection of O. tsutsugamushi in human, rodent, and chigger mites from outbreak locations and wide-spread reports of scrub typhus throughout the country over two years confirms the ongoing transmission of O. tsutsugamushi with a firmly established ecology in Nepal. The countrys health system needs to be strengthened for systematic surveillance, early outbreaks detection, and immediate response actions including treatment and preventive measures. Author SummaryScrub typhus is a disease caused by a bacteria called Orientia tsutsugamushi and transmitted to people through bites of infected chiggers (larval mites). After the 2015 Gorkha earthquake in Nepal, a sudden upsurge in scrub typhus cases was reported with repeated outbreaks from different parts of the country. This study has documted epidemiology of scrub typhus and its causative agents in human, rodent and chigger mites confimring the local transmission O. tsutsugamushi with a firmly established ecology in Nepal. The local transmission of the diseases from most parts of the country demands strengthening for systematic surveillance, early outbreaks detection, and immediate response actions including treatment and preventive measures.

pathology↗