Biology subjects

Mishra, H.

Publications and source records attributed to Mishra, H..

8 recordsLinked to original sources

bioRxiv2025

Prediction of Piconewton Receptor Tension Images using Deep Learning

Piconewton (pN) receptor forces govern many biological processes, but measuring these forces remains challenging. Molecular tension probes (MTPs) provide a sensitive means to measure pN cellular forces via fluorescence microscopy; however, MTPs are challenging to use and only forces transmitted through the probes are reported, complicating their use in heterogenous environments. Here, we present Tension Deep Learning (TensionDL), which leverages convolutional neural networks and image-to-image translation to predict pN receptor tension maps from images of cell morphology and the force-transducing protein vinculin. We validate the accuracy of TensionDL at the subcellular and cellular scales, demonstrate model accuracy across different substrate stiffnesses and cell types, and leverage TensionDL to make semi-quantitative predictions of cell mechanical output. Finally, TensionDL enables long-term mapping of pN receptor tension and infers tension distributions in heterogeneous environments in which some forces are not transduced through MTPs.

bioengineering↗

bioRxiv2024

Sustainable in situ extraction of microalgae-derived terpenoids using functionalized silica microparticles

Chlamydomonas reinhardtii is a green microalga that has been genetically engineered to produce heterologous terpenoid metabolites. While this green biochemical approach for producing high-value chemicals holds tremendous potential, the current in situ extraction methods, utilizing traditional solvents such as dodecane and perfluorinated chemicals, present separation challenges, unfavorable economics, and risk of cell toxicity. Here, we develop a low-cost solvent-free approach based on silanized silica particles to fill the technology gap. We determine the feasibility and specificity of three differently coated (C11, C16, C18) silica particles to extract nine terpenoid metabolites from C. reinhardtii cultures during cultivation. The results reveal that the extraction efficiencies of functionalized particles, particularly those coated with C18, demonstrated high potential as an alternative to traditional extraction methods. While the extraction efficiencies of coated microparticles are for most compounds lower than those observed for dodecane-based extractions, it holds higher potential for larger-scale cultivations where the use of dodecane is restricted due to its flammability and tendency to form emulsions. In addition, the present study provides insights into the optimization of particle-to-culture volume ratio, particle saturation, and the required number of product elution steps, and proves the feasibility of an upscaled extraction of the sesquiterpenoid patchoulol as a representative metabolite in 5 L hanging bag reactors. This study paves the way for a circular bioprocess where product capture with traditional solvent overlays is impractical due to the formation of emulsions, and at the same time allows for an easy product recovery (solid-liquid separation) and reuse of functionalized particles over numerous cycles.

bioengineering↗

bioRxiv2024

Superhydrophobic Sand Mulch and Date Palm Biochar Dramatically Boost Growth of Moringa oleifera in Sandy Soil: Insights into Evapotranspiration Budgeting and Metabolomic Profiling

In response to the challenge of nutrient-deficient sandy soils and water scarcity due to excessive evaporative water loss in arid regions, we developed and tested two complementary soil amendment technologies: Superhydrophobic sand (SHS) mulch and an enriched date palm biochar. In a greenhouse pot experiment, we investigated the stand-alone and synergistic effects of SHS mulch (10 mm-thickness) and biochar (2% w/w) on Moringa oleifera plants under normal (N, 100% field capacity) and reduced (R, 50% of N) irrigation scenarios. Under N and R, SHS mulch reduced evaporation by 71% and 64%, respectively; while SHS+biochar reduced evaporation by 61% and 47%, respectively, in comparison with the control (p < 0.05). Total transpiration significantly increased in SHS plants by 311% and 385% under N and R, respectively. Compared with the control, transpiration increased in biochar-amended plants by 103% and 110%; whereas, its combination with SHS increased transpiration by 288% and 301% under N and R, respectively (p < 0.05). Irrespective of the irrigation regimes, we found superior effects of SHS, biochar, and their combination on plant height (62-140%), trunk diameter (52-91%), leaf area index (57-145%), leaf chlorophyll content index (11-19%), stomatal conductance (51-175%), as well as shoot (390-1271%) and root (52-142%) biomass, in comparison with the controls. Metabolomics analysis showed significantly higher relative abundance of amino acids, sugars, fatty acids, and organic acids in the leaves of control plants relative to other treatments, as a response to water or nutrient stress induced by excessive water loss through evaporation. Next, we found a higher concentration of D-Mannose, D-Fructose, glucose, and malic acid in plants grown with SHS or biochar treatment under N and R irrigation, attributed to increased water/nutrient-use efficiency and carbon assimilation because of higher photosynthesis rates than in the control plants. Our results show that, our complementary technologies could address the challenge of water loss via evaporation from soil and maximize soil nutrient retention for improving plant growth in arid regions. This could underscore the success and sustainability of irrigated agriculture and greening efforts in arid lands.

plant biology↗

bioRxiv2023

Endosome dysfunction leads to gain-of-function TLR7 and human lupus

Hyperactive Toll-like receptor (TLR) 7 signaling has long been appreciated as a driver of autoimmune disease by breaking tolerance to self-nucleic acids in mouse models1-5. Recently, mutations in TLR7 or its associated regulator UNC93B16, 7, were identified as monogenic causes of human lupus; the unifying feature of these mutations being TLR7 gain-of-function. TLR7 is an intracellular transmembrane receptor, sensing RNA breakdown products within late endosomes8, 9. Hence, its function depends on intricate transport mechanisms and membrane interactions within the endomembrane network. Whether perturbations of any of these endosome-related processes can give rise to TLR7 gain-of-function and facilitate self-reactivity has not been investigated. Here, we show that a dysregulated endosomal compartment leads to unrestricted TLR7 signaling and human lupus. The late endosomal BLOC-1-related protein complex (BORC) together with the small Arf1-like GTPase Arl8b controls TLR7 protein levels, and a direct interaction between Arl8b and Unc93b1 is required to regulate TLR7 turnover. We identified an amino acid insertion in UNC93B1 in a patient with childhood-onset lupus, which reduces the interaction with the BORC-Arl8b complex and leads to endosomal TLR7 accumulation. Therefore, a failure to control the proper progression of TLR7 through its endocytic life cycle is sufficient to break immunological tolerance to nucleic acids in humans. Our results highlight the importance of an intact endomembrane system to prevent autoimmune disease. As the cellular mechanisms restricting TLR7 signaling can be manifold, identifying and stratifying lupus patients based on a TLR7-driven pathogenesis could be a viable strategy towards a targeted therapy.

immunology↗

bioRxiv2021

Effects of Superhydrophobic Sand Mulching on Evapotranspiration and Phenotypic Responses in Tomatoes (Solanum lycopersicum) under Normal and Reduced Irrigation

Irrigated agriculture in arid and semi-arid regions is a vital contributor to the global food supply; however, these regions endure massive evaporative losses that are compensated by unsustainable freshwater withdrawals. Plastic mulches have been used to curtail evaporation, improve water-use efficiency, and ensure food-water security, but they are non-biodegradable and their disposal is unsustainable. We recently developed superhydrophobic sand (SHS), which comprises sand grains with a nanoscale wax coating that could offer a more sustainable mulching solution. Here, the effects of adding a 1.0 cm-thick layer of SHS mulch on the evapotranspiration and phenotypic responses of tomato (Solanum lycopersicum) plants are studied under normal and reduced irrigation. Under both irrigation regimes, SHS mulching suppressed evaporation and enhanced transpiration by 78% and 17%, respectively relative to the bare soil. Overall, SHS mulching enhanced root xylem vessel diameter, stomatal aperture, stomatal conductance, and chlorophyll content index by 21%, 25%, 28%, and 23%, respectively. Total fruit yields, total dry mass, and harvest index increased in SHS-mulched plants by 33%, 20%, and 16%, respectively than in bare soil. These findings demonstrate the potential of SHS to boost irrigation efficiency in water-limited environments and provide mechanistic insights behind yield enhancement by SHS mulching.

plant biology↗

bioRxiv2021

Evaluation of in vitro and in vivo toxicity of pristine molybdenum disulphide nanosheets in Swiss albino mice

The Molybdenum disulfide nanosheets (MoS2-NSs) thin films has received increasing attention recently due to their versatile multi functionality including catalytic properties, photoluminescence and flexibility, which suggests their future, uses for biomedical applications. However, there are no studies in detail related with biocompatibility of MoS2 thin sheets. Here, weevaluated the dose-dependent effects of MoS2-NSs on cell viability (MTT assay) and release of lactate dehydrogenase (LDH) into culture media using MG-63 cells, as well as haemolysis, hematological, serum biochemical, antioxidants and histopathological parameters in Swiss albino mice. The MoS2-NSs was synthesized via facile hydrothermal method and characterized using XRD, Raman, SEM, TEM and HRTEM. The in vitro study results suggest that at lower concentration MoS2-NSs does not causes any toxicity. The lethal dose (LD50) was evaluated by intraperitoneal administration with different concentrations and estimated as ~1.0 mg kg-1. The higher dose (1.5 mg kg-1) of MoS2-NSs showed significant alteration in hematological markers and serum biochemical enzymes, as compared to control. Lipid peroxidation also shows significant alteration with respect to the control. Histopathological, hematological and biochemical examination, revealed no remarkable changes at lower concentration (less than 1.0 mg kg-1), however, higher concentration (1.5 mg kg-1) causes significant histopathological, antioxidants and biochemical alterations in tissues and serum, respectively. The results suggest that the lower concentration of MoS2-NSs can be used in future biomedical applications.

bioengineering↗

bioRxiv2020

Unique mutational changes in SARS-CoV2 genome of different state of India

COVID-19 is a global pandemic causing more than 8 million deaths till mid-August, 2020. In India, more than 3 million confirmed cases have been reported although with relatively low death rate of 1.8%. In this study, we sequenced 47 genomes of SARS-CoV-2 from the patients of 13 districts of Uttar Pradesh (UP), the largest state of India using third-generation sequencing technique. The phylogenetic clustering revealed that no UP sample was aligned with the previously defined USA clade, where the mortality was high. We identified 56 distinct SNP variations in the genomes of UP resulting in a unique mutation rate of 1.19% per sequence, which is greater than the value 0.88% obtained for the rest of India. The relatively less death rate in UP indicates that the mutation in the virus is deleterious. Further investigation is required with larger sample size to determine the degree of virulence vis-a-vis SNP variation.

bioinformatics↗

bioRxiv2018

Expression of a recombinant high affinity IgG Fc receptor by engineered NK cells as a docking platform for therapeutic mAbs to target cancer cells

Anti-tumor mAbs are the most widely used and characterized cancer immunotherapy agents. Despite having a significant impact on some malignancies, most cancer patients respond poorly or develop resistance to this therapy. A known mechanism of action of these therapeutic mAbs is antibody-dependent cell-mediated cytotoxicity (ADCC), which is a primarily effector function of NK cells. CD16A on human NK cells has an exclusive role in binding to tumor-bound IgG antibodies. Though CD16A is a potent activating receptor, it is a low affinity Fc{gamma}R and its cell surface levels can be rapidly downregulated by a proteolytic process involving ADAM17 upon NK cell activation, which are likely to limit the efficacy of tumor-targeting therapeutic mAbs in the tumor environment. We sought to enhance NK cell binding to anti-tumor mAbs by engineering these cells with a recombinant Fc{gamma}R consisting of the extracellular region of CD64, the highest affinity IgG Fc receptor expressed by leukocytes, and the transmembrane and cytoplasmic regions of CD16A. This novel recombinant Fc{gamma}R (CD64/16A) was expressed in the human NK cell line NK92 and in induced pluripotent stem cells from which primary NK cells were derived. CD64/16A also lacked the ADAM17 cleavage region in CD16A and it was not rapidly downregulated in expression following NK cell activation during ADCC. CD64/16A on NK cells facilitated conjugation to antibody-treated tumor cells, ADCC, and cytokine production, demonstrating functional activity by its two components. Unlike NK cells expressing CD16A, CD64/16A captured soluble therapeutic mAbs and the modified NK cells mediated tumor cell killing. Hence, CD64/16A could potentially be used as a docking platform on engineered NK cells for therapeutic mAbs and IgG Fc chimeric proteins, allowing for switchable targeting elements, and a novel cancer cellular therapy.

immunology↗