Biology subjects

Parmar, B.

Publications and source records attributed to Parmar, B..

9 recordsLinked to original sources

bioRxiv2026

Smartphone-Validated Portable Paper-Based Device Integrated with an Electropolymerized Molecularly Imprinted Polymer for Serotonin Detection in Serum Samples

Accurate and decentralized quantification of serotonin, also known as 5-hydroxytryptamine (5-HT), in biological fluids is critically important for the diagnosis, prognosis, and therapeutic monitoring of neurological and psychiatric disorders. However, conventional analytical methods generally rely on centralized laboratory infrastructure, skilled personnel, and labor-intensive sample processing, which restrict their applicability in rapid near-patient and point-of-care settings. Herein, we report a portable molecularly imprinted polymer (MIP)-based electrochemical sensing platform for selective and on-site detection of serotonin using screen-printed carbon electrodes (SPCEs). The biomimetic recognition interface was fabricated through direct electropolymerization of a polydopamine recognition layer in the presence of serotonin as the template molecule, followed by template extraction to generate complementary recognition cavities for selective rebinding. The sensor fabrication parameters, including monomer concentration, electropolymerization cycles, template-to-monomer stoichiometry, and electrolyte pH, were systematically optimized to achieve improved sensitivity, selectivity, and signal stability. Under optimized conditions, the MIP/SPCE sensor exhibited a broad linear response from 10 pM -10 {micro}M in phosphate buffer, with a correlation coefficient of R2 = 0.974 and an ultralow limit of detection of 0.16 pM. The analytical applicability of the platform was further validated in spiked artificial serum, where the sensor achieved an LOD of 0.12 pM, satisfactory recovery values of 88.66-96.02%, and acceptable precision with RSD values [≤] 8.43% (n=3), confirming its reliability in a complex biological matrix. The developed sensor demonstrated excellent selectivity toward serotonin against physiologically relevant interferents, maintaining signal retention between 99% and 101%. In addition, the platform showed high operational repeatability with an RSD of 0.45%, good inter-electrode reproducibility with an RSD of 6.3%, and long-term storage stability, retaining 90-110% of its initial response over 28 days. Importantly, cross-platform validation using a smartphone-coupled potentiostat demonstrated strong analytical agreement with laboratory-grade instrumentation, as evidenced by R2 = 0.9967 and a slope of 1.023. These findings establish the proposed MIP/SPCE platform as a simple, low-cost, portable, and smartphone-compatible electrochemical device for field-deployable serotonin monitoring in clinically relevant samples.

bioengineering↗

bioRxiv2026

Rationally Anchored Geometry-Controlled DNA Tetrahedral Nanostructures for Attomolar Impedimetric IL-6 Detection

Interleukin-6 (IL-6) is a pleiotropic cytokine whose aberrant elevation drives life-threatening conditions, including sepsis, cytokine storm, and autoimmune disorders, yet existing clinical detection methods demand centralized laboratory infrastructure and multi-hour assay times incompatible with rapid point-of-care decision-making. Here, we report an impedimetric aptasensor built on a programmable tetrahedral DNA nanostructure (TDN) interface anchored to a disposable gold screen-printed electrode (Au-SPE) for the ultrasensitive, label-free detection of IL-6. By systematically varying the number of thiolated base vertices from zero to three, we establish a clear and previously unreported structure-function relationship between multipodal anchoring geometry and charge-transfer resistance modulation: tripodal thiolation yields the most rigid, upright, and electrochemically responsive interface, producing the steepest analytical signal gain upon IL-6 binding at the apex-localised aptamer. Under optimised conditions (pH 7.0, 0.05 {micro}M TDN, MCH passivation), the aptasensor exhibits a linear dynamic range of 0.0001-0.001 pg/mL, a limit of detection of 55 ag/mL , and a sensitivity of 1.55x107 {Omega} (pg mL-1)-1. Selectivity evaluation against seven physiologically relevant interferents such as TNF-, BSA, glucose, urea, ascorbic acid, glycine, and cysteine confirms negligible cross-reactivity, with relative responses ranging from 0.57% to 14.35% of the IL-6 signal. Spike-recovery experiments in human serum yield recoveries of 74.0-87.6% (%RSD < 4.5%), and the sensor retains functional activity for at least 21 days under refrigerated storage. This work demonstrates that thiolated vertex number is a critical and tunable design parameter for TDN-based biosensors, offering a modular, disposable platform for sub-femtogram cytokine detection with direct applicability to early sepsis diagnosis and inflammatory disease monitoring.

bioengineering↗

bioRxiv2026

Green Solvothermal Synthesis of Nitrogen-Doped Chamomile-Derived Carbon Dots with Superior Quantum Yield and Bioimaging Potential: A Comparative Physicochemical Evaluation

Conventional fluorescent imaging probes, including organic dyes and semiconductor quantum dots, suffer from inherent limitations such as photobleaching, cytotoxicity, poor aqueous dispersibility, and complex synthetic routes, necessitating the development of next-generation nanoscale fluorophores suitable for biological imaging. Carbon dots (CDs) have emerged as a compelling alternative owing to their nanoscale dimensions, tunable photoluminescence, excellent biocompatibility, and amenability to green synthesis from biomass-derived precursors. Herein, we report a comparative synthesis and systematic physicochemical evaluation of nitrogen-doped and undoped carbon dots derived from chamomile (Matricaria chamomilla L.) extract, prepared via solvothermal and microwave-assisted routes. Among the four synthesized variants--CM ST-U, CM ST-N, CM MW-U, and CM MW-N--the solvothermally synthesized nitrogen-doped carbon dots (CM ST-N) exhibited markedly superior optical performance, characterized by a high fluorescence quantum yield of 57.2%, which is among the highest reported for biomass-derived nitrogen-doped carbon dots. Comprehensive characterization using UV-visible spectroscopy, photoluminescence (PL) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), dynamic light scattering (DLS), zeta potential analysis, and atomic force microscopy (AFM) confirmed the nanoscale dimensions (~8.3 nm), surface-rich functional groups, successful nitrogen incorporation (10.86 %), and moderate colloidal stability (zeta potential: -17.3 mV). Photoluminescence stability studies across seven solvent systems including biologically relevant media--phosphate-buffered saline (PBS), Dulbeccos modified Eagles medium (DMEM), and serum-free medium (SFM) demonstrated sustained fluorescence emission over 72 hours. In vitro cytotoxicity assessment using the MTT assay on RPE-1 retinal pigment epithelial cells confirmed high cell viability (>70%) across a broad concentration range (10-500 {micro}g mL-1) over multiple exposure durations. Collectively, these results establish CM ST-N as a highly fluorescent, biocompatible, and colloidally stable nanoprobe with strong potential for fluorescence-based bioimaging applications.

bioengineering↗

bioRxiv2026

Green Synthesis of Fluorescent Carbon Quantum Dots from Bearberry Extract via Hydrothermal and Microwave-Assisted Routes: Comparative Physicochemical Characterisation, Antioxidant Activity, and Biocompatibility Evaluation

Producing photoluminescent nanomaterials with controllable surface chemistry and predictable biological activity remains one of the outstanding problems in green nanoscience. The present study shows that, even when the same bearberry (Arctostaphylos uva-ursi) extract precursor is used, the mode of energy delivery during synthesis plays a determining role in shaping the surface composition, photophysical properties, and biological activity of the resulting carbon quantum dots (CQDs). Hydrothermal processing at 160 {degrees}C for 6 h yielded CQDs with an average particle size of 7.13 nm. Surface characterisation indicated abundant hydroxyl- and carbonyl-containing functionalities, while XPS analysis showed a comparatively higher proportion of graphitic sp2 carbon (43.06%). These structural features were accompanied by strong DPPH free-radical scavenging activity. Microwave-assisted synthesis, by contrast, yields 9.65 nm particles carrying a substantially greater surface carboxylate content (O-C=O: 19.06%), a higher fluorescence quantum yield, and enhanced intracellular uptake statistically significant in retinal epithelial cells at 200 {micro}g/mL (p < 0.001) and showing concentration-dependent accumulation in zebrafish larvae from 100 {micro}g/mL onwards (p < 0.05). XPS C 1s deconvolution, interpreted alongside FTIR difference spectroscopy, points to incomplete decarboxylation under microwave conditions as the primary mechanistic origin of these divergent properties. Cytocompatibility was uncompromised for both formulations across the full concentration range tested (10-250 {micro}g/mL) in RPE-1 and HeLa cells, with no statistically significant loss of viability at any concentration. Taken together, these results define a synthesis-route-encoded structure-property relationship that permits rational selection between an antioxidant-optimised and an imaging-optimised CQD formulation from the same green precursor feedstock.

bioengineering↗

bioRxiv2026

Membrane sialylation orchestrates cellular gateways: A spatiotemporal analysis of cellular transport using DNA nanocages via membrane charge modulation

Negatively charged DNA nanostructures, such as tetrahedral nanocages, are internalized by cells despite the electrostatic repulsion from the anionic cell membrane, and, paradoxically, cancer cells, which carry intrinsically higher negative charge due to overexpression of sialic acids on their cell surface, show markedly higher uptake than normal cells. This contradiction exposes a fundamental gap in our understanding of how these anionic nanostructures overcome this repulsion. Using chemical modulation of cell-surface sialylation in RPE1 cells to create three groups with altered sialylation levels, together with inhibitor-based dissection of endocytic pathways, we demonstrate that an increase in cell surface sialylation governs the uptake of DNA tetrahedra not through electrostatics but by structurally remodeling the cell membrane via rearrangement of the GM1 lipid raft microdomain, recruiting caveolae-mediated endocytosis as an additional pathway alongside clathrin-mediated endocytosis, thereby increasing the intake of the nanostructure. These findings reframe tumor hyper-sialylation as a determinant of the uptake of anionic nanostructures, such as DNA tetrahedra, and as a targetable parameter for rational optimization of DNA-based nanotherapeutics against cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/722926v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@10eede7org.highwire.dtl.DTLVardef@124dd56org.highwire.dtl.DTLVardef@13f5355org.highwire.dtl.DTLVardef@780ecf_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Evaluation of deep and dynamic proteomic screening strategies at sub-50Hz scan rate and without automation.

Advances in ultra-fast mass analyzer technology and procedural automation have enabled proteomics screening at the throughput of hundreds of proteomes per day. However, these approaches often require expensive instrumentation upgrades and robotic automation that remain inaccessible to many research laboratories and core facilities. In this study we address the feasibility of scaling up proteomic screening capabilities with minimal upgrade cost by focusing on (a) strategies for non-automated high-throughput sample preparation from 96-well cell culture, (b) data acquisition on sub-50Hz scan speed hybrid and tribrid Orbitrap instruments and (c) data analysis strategies for label-free and labeled proteomic screening. We find that the 96-well format STrap, in combination with C18 plates, provides the most robust throughput for a non-automated sample preparation workflow. Furthermore, we show that for static proteomes, an isobaric tandem mass tag-based (TMT) multiplexing approach provides deeper and more precise proteome coverage whereas label-free data-independent acquisition (DIA) is more accurate, albeit with a reduced dynamic range and more missing values. Finally, we extend the optimized workflow to proteome turnover studies using pulsed stable isotope labeling by amino acids in cell culture (pSILAC), highlighting the key advantages and trade-offs of DIA and TMT data-dependent acquisition strategies for capturing protein translation. Together, these results provide a practical framework for designing high-throughput proteomics experiments that balance throughput, depth, and quantitative accuracy using existing instrumentation, without requiring major hardware upgrades or automation.

molecular biology↗

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↗

bioRxiv2022

A novel overlapping gene azyx-1 affects the translation of zyxin in C. elegans

Overlapping genes are widely prevalent, however, their expression and consequences are poorly understood. Here, we describe and functionally characterize a novel zyx-1 overlapping gene, azyx-1, with distinct regulatory functions in C. elegans. We observed conservation of alternative open reading frames overlapping the 5 region of zyxin family members in several animal species, and find shared sites of azyx-1 and zyxin proteoform expression in C. elegans. In line with a standard ribosome scanning model, our results support cis regulation of zyx-1 long isoform(s) by upstream initiating azyx-1a. Moreover, we report on a rare observation of trans regulation of zyx-1 by azyx-1, with evidence of increased ZYX-1 upon azyx-1 overexpression. Our results suggest a dual role for azyx-1 in influencing zyx-1 proteoform heterogeneity and highlights its impact on C. elegans muscular integrity and locomotion.

genetics↗

bioRxiv2020

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation

Once described as mere "bags of enzymes", bacterial cells are in fact highly organized, with many macromolecules exhibiting non-uniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid-liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in E. coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and suggests that this process serves as a universal mechanism for intracellular organization across the tree of life. SignificanceBacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid-liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid-liquid phase separation is a universal mechanism for intracellular organization that extends across the tree of life.

cell biology↗