Biology subjects

Solanki, R.

Publications and source records attributed to Solanki, R..

9 recordsLinked to original sources

bioRxiv2026

Bioactive Spermidine-Crosslinked DNA Hydrogel for rapid homeostasis and accelerated wound healing

Damage to the skin by trauma, burns, or surgical procedures often results in uncontrolled bleeding, which remains a leading cause of preventable death following injury, yet most conventional hemostatic materials are engineered solely to arrest bleeding and often adhere strongly to the wound bed, causing pain, rebleeding, and disruption of newly formed tissue upon removal. Here, we report a DNA hydrogel that structurally mimics neutrophil extracellular traps (NETs) and is crosslinked using a bioactive small molecule with potent autophagy-inducing, cardioprotective, anti-inflammatory, antioxidant, and mitochondria-protective properties, integrating rapid hemostasis with active support for tissue regeneration in a single biomaterial. The DNA network provides an intrinsically biocompatible, biodegradable scaffold capable of recruiting platelets and erythrocytes to achieve rapid clot formation, while the bioactive crosslinker is released as the network degrades, delivering a sustained cytoprotective and anti-inflammatory stimulus directly at the wound site. The hydrogel was characterised physiochemically and evaluated for cytocompatibility, hemolytic potential, hemostatic efficacy, and wound-healing performance in a murine model. Results demonstrate that the bioactive-crosslinked DNA hydrogel achieves rapid, effective hemostasis, while accelerating wound closure and supporting regenerative tissue remodelling. This dual-function platform offers a promising strategy for next-generation wound-care biomaterials that unite immediate bleeding control with accelerated, natural tissue healing.

bioengineering↗

bioRxiv2026

Systematic errors in enzymatic conversion limit cell-free DNA methylation specificity

Enzymatic methylation sequencing (EM-seq) converts unmethylated cytosines to uracils while preserving DNA integrity, making it attractive for liquid biopsies. Here we report a reproducible fragment-level over-conversion error in EM-seq, which is not observed in bisulfite-based conversion or in Oxford Nanopore sequencing. While bisulfite and nanopore errors occur at sporadic CpGs, EM-seq generates molecules that appear fully unmethylated, introducing a false-positive background signal that severely limits deconvolution specificity in cfDNA analysis.

genomics↗

bioRxiv2025

Programmable DNA-Silk fibroin hydrogel scaffold with temporal mechanical reinforcement for mesenchymal stem cells differentiation and accelerated wound healing in a full-thickness skin defect mice model

DNA-based hydrogels have attracted significant attention in biomedical applications due to their programmability, biocompatibility, and tunable functionalities. However, their clinical translation is hindered by high synthesis costs, limited mechanical strength, poor stability, and complex synthesis protocols. In this work, we present a novel DNA-silk fibroin hybrid hydrogel that overcomes these limitations by combining the unique biofunctionality of DNA with the superior mechanical and chemical properties of silk fibroin. Salmon-derived DNA, an abundant and low-cost source, was incorporated with silk fibroin to form hybrid networks via a simple, scalable process. Silk fibroin served as a robust scaffold, enhancing mechanical strength, controlling degradability, and improving structural stability, while the entangled DNA-silk network reduced rapid DNA degradation. The resulting hybrid hydrogel demonstrated temporal mechanical reinforcement and prolonged stability, with in vitro studies demonstrating that the developed hybrid hydrogel enhanced the chondrogenic and osteogenic differentiation of Infrapatellar Fat Pad Mesenchymal Stem Cells (IFP-MSCs). Additionally, hemostatic and in vivo studies demonstrated the potential of DNA-silk fibroin hydrogel as a promising biomaterial for rapid hemostasis and accelerated wound healing. Overall, the developed DNA-silk fibroin hybrid hydrogel offers strong potential for mesenchymal tissue engineering, hemostatic adjuvant and wound healing.

bioengineering↗

bioRxiv2025

Protocol for the Synthesis of Green Fluorescence Carbon Quantum Dots and Biological Application

Carbon quantum dots (CQDs) are materials that are made up of particles that are only a few n anometers wide. They have no dimensions and can change their fluorescence qualities. They are also verybiocompatible and have a lot of potential to change the chemistry of their surface. Their eco-friendly synthesis from precursors, like citric acid (CA) and ascorbic acid (AA), provides a sustainable approach to highly fluorescent nanomaterials with promising applications in bioimaging, drug delivery, and other biomedical fields. Green-emitting carbon quantum dots (GCQDs) were synthesized via a simple reflux approach using citric acid and ascorbic acid as biomolecular precursors in a solvent solution of ethanol-water (1:2). The obtained GCQDs solution was purified using a dialysis process. Besides this, pH maintenance, lyophilization, and further submission for detailed physicochemical evaluation and characterization are done. The spectroscopic analysis, including UV-visible spectroscopy, fluorescence spectroscopy, and FTIR, confirmed the presence of surface functional groups and strong fluorescence properties and quantum yield calculations of the synthesized GCQDs. Microscopic and structural analyses using XRD, AFM, and TEM revealed the nanoscale, predominantly spherical morphology of the synthesized GCQDs. In addition, in vitro biological evaluations such as MTT assay and cellular uptake analysis were undertaken to evaluate cytocompatibility and intracellular distribution. We study the endocytosis pathway of these GCQDs, with size variations ranging from 3 to 5 nm, in mouse tissue-derived primary cells, tissues, and zebrafish embryos. GCQDs were internalized into mouse kidney and liver primary cells through a clathrin-mediated pathway. The findings confirmed that the produced GCQDs exhibit good water solubility, favorable biocompatibility, and significant potential as candidates for biomedical imaging applications.

bioengineering↗

bioRxiv2025

Protocol for green synthesis of excellent fluorescent mango leaves-derived carbon for advanced theragnostic in biological applications

Carbon quantum dots (CQDs) are zero-dimensional fluorescence nanoparticles that are less than 10 nm in size. They have unique properties like tunable surface functionality, biocompatibility, fluorescence, and low toxicity. This study outlines a detailed protocol for synthesizing CQDs from mango leaf powder using a reflux method at 160 C and 400 rpm for a duration of two hours. The synthesized CQDs were comprehensively characterized using the following techniques, including UV-visible spectroscopy, fluorescent spectrophotometry, atomic force microscopy, dynamic light scattering and zeta potential measurement, Fourier transform infrared spectroscopy, and scanning electron microscopy. In vitro analysis was conducted through an MTT assay, revealing that the CQDs exhibit reduced toxicity in RPE1 cells compared to the control group. Additionally, a concentration-dependent cellular uptake assay was performed to further evaluate the biological performance of the CQDs. The findings suggest the potential of CQDs as safe and effective nanomaterials for various biological applications, including drug delivery and bioimaging.

bioengineering↗

bioRxiv2025

Human whole epigenome modelling for clinical applications with Pleiades

Gene regulation in humans extends beyond the four-letter genetic code. DNA methylation, in particular, functions as a critical epigenetic regulator, dynamically programming cellular identity, adapting gene expression in response to environmental cues, and underpinning the onset and progression of numerous diseases. Here we present Pleiades, a series of whole-genome epigenetic foundation models spanning three sizes: 90M, 600M, and 7B parameters. Pleiades is trained upon an extensive proprietary corpus of human methylation and genomic data, totalling 1.9T tokens. We introduce alignment embeddings and stacked hierarchical attention techniques to provide precise epigenetic modelling without the need for extended context lengths. Collectively, these advances enable Pleiades to perform a diverse range of down-stream biological and clinical tasks, including genomic regulatory prediction, realistic generation of cell-free DNA fragments and fragment-level cell-type-of-origin classification, within a unified and scalable computational framework. We specifically apply Pleiades to the early detection of clinical Alzheimers disease and Parkinsons disease from plasma cell-free DNA, achieving high-accuracy detection (AUROC 0.89 for AD and 0.84 for PD) using a minimally invasive blood test. Combined with plasma pTau-217, Pleiades reaches an AUROC of 0.97 for AD, underscoring the promise of multimodal epigenomic and proteomic approaches. Using mechanistic interpretability, we ground Pleiades latent features in interpretable biological signals, relating its Alzheimers predictions to fragmentomic and epigenomic properties of cfDNA. These findings demonstrate the potential of genome-wide epigenomic modelling as a clinically translatable paradigm for diagnostics and precision medicine, though prospective validation in larger, more diverse cohorts will be required to confirm clinical utility.

genomics↗

bioRxiv2024

Targeting the acetyltransferase NAT10 corrects pathologies in human frontotemporal neurons and extends lifespan in an in vivo Drosophila tauopathy model

Disruption of the neuronal nuclear membrane and perturbation of nucleocytoplasmic transport are features of neurodegenerative diseases, including Alzheimers disease, that involve the microtubule-associated protein tau (MAPT). We previously identified that missense and splicing mutations in the MAPT gene, causal for frontotemporal dementia, result in nuclear envelope deformation and disrupted nucleocytoplasmic transport in human neurons. This is most likely due to microtubule mechanical stress, similar to that observed in Hutchinson-Gilford Progeria Syndrome (HGPS). A small molecule inhibitor of the acetyltransferase NAT10 has been shown to correct nuclear membrane defects in HGPS by modulating microtubule dynamics. We report here that NAT10 inhibition alters microtubule dynamics and corrects nuclear lamina defects and aberrant nucleocytoplasmic transport in human iPSC-derived FTD-MAPT neurons. Similarly, NAT10 inhibition and haploinsufficiency correct neuronal nuclear shape defects and extend lifespan in vivo in a Drosophila model of tauopathy. Our results show that NAT10 mediates neuronal pathologies in tauopathies and is a promising new therapeutic target in these diseases.

neuroscience↗

bioRxiv2021

Using polyacrylamide hydrogels to model physiological aortic stiffness reveals that microtubules are critical regulators of isolated smooth muscle cell morphology and contractility.

Vascular smooth muscle cells (VSMCs) are the predominant cell type in the medial layer of the aortic wall and normally exist in a quiescent, contractile phenotype where actomyosin-derived contractile forces maintain vascular tone. However, VSMCs are not terminally differentiated and can dedifferentiate into a proliferative, synthetic phenotype. Actomyosin force generation is essential for the function of both phenotypes. Whilst much is already known about the mechanisms of VSMC actomyosin force generation, existing assays are either low throughput and time consuming, or qualitative and inconsistent. In this study, we use polyacrylamide hydrogels, tuned to mimic the physiological stiffness of the aortic wall, in a VSMC contractility assay. Isolated VSMC area decreases following stimulation with the contractile agonists angiotensin II or carbachol. Importantly, the angiotensin II induced reduction in cell area correlated with increased traction stress generation. Inhibition of actomyosin activity using blebbistatin or Y-27632 prevented angiotensin II mediated changes in VSMC morphology, suggesting that changes in VSMC morphology and actomyosin activity are core components of the contractile response. Furthermore, we show that microtubule stability is an essential regulator of isolated VSMC contractility. Treatment with either colchicine or paclitaxel uncoupled the morphological and/or traction stress responses of angiotensin II stimulated VSMCs. Our findings support the tensegrity model and we demonstrate that microtubules act to balance the actomyosin-derived traction stress generation and regulate the morphological responses of VSMCs.

cell biology↗

bioRxiv2018

Abnormal microtubule dynamics disrupt nucleocytoplasmic transport in tau-mediated frontotemporal dementia

The neuronal microtubule-associated protein tau (MAPT) is central to the pathogenesis of many dementias, including Alzheimers disease. Autosomal dominant mutations in MAPT cause inherited frontotemporal dementia (FTD), but the underlying pathogenic mechanisms are unclear. Using human stem cell models of FTD due to MAPT mutations, we find that tau becomes hyperphosphorylated and mislocalises to neuronal cell bodies and dendrites in cortical neurons, recapitulating a key early event in FTD. Mislocalised tau in the cell body leads to abnormal microtubule dynamics in FTD-MAPT neurons that grossly deform the nuclear membrane, resulting in defective nucleocytoplasmic transport. Neurons in the post-mortem human FTD-MAPT cortex have a high incidence of nuclear deformation, indicating that tau-mediated nuclear membrane dysfunction is an important pathogenic process in FTD. Defects in nucleocytoplasmic transport in FTD point to important commonalities in the pathogenic mechanisms of both tau-mediated dementias and ALS-FTD due to TDP-43 and C9orf72 mutations.

neuroscience↗