Biology subjects

Kumar, V.

Publications and source records attributed to Kumar, V..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Targeting Galectin-3 C-epitope oligomers associated maladaptive mechanotransductive signaling in pressure-overload induced left ventricular cardiac hypertrophy

BackgroundAging and various pathological conditions lead to pressure-overload in the left ventricle, promoting maladaptive hypertrophic remodeling and subsequent cardiac dysfunction, ultimately increasing the risk of heart failure. Galectin-3 (Gal-3) plays a central role in this process; however, its critical intracellular functions complicate direct therapeutic targeting. Notably, pathological microenvironments trigger the proteolytic cleavage of Gal-3 into distinct N- and C-terminal fragments. The specific contributions of these cleaved epitope forms to adverse cardiomyocyte mechanotransduction, and their potential as precision therapeutic targets in contrast to the full-length protein, remain unresolved. MethodsTo address this gap, we combined rodent models of aging and pressure-overload (PO) -induced cardiac hypertrophy with PO mechanobiology-driven in vitro assays and validation in human cardiac tissue and serum. Gal-3 epitope abundance, localization, phosphorylation, oligomerization, and downstream signaling were quantified using biochemical, imaging, and functional approaches. ResultsWe found that extracellular oligomers of the Gal-3 C-terminal epitope accumulated in serum and on cardiomyocyte surfaces in hypertrophic rodents and human subjects, where they correlated with adverse remodeling and cardiomyocyte loss. Treatment with Amalaki Rasayana (AR), a standardized nutraceutical-based cardioprotective Ayurvedic phytomedicine, and its bioactive component gallic acid (GA) significantly reduced circulating and surface-associated Gal-3 C-epitope oligomers and attenuated hypertrophy-associated cytotoxic signaling. Mechanistically, AR/GA enhanced Ser6 phosphorylation of Gal-3, promoting intracellular retention, while limiting pathological secretion and deleterious extracellular oligomerization. Following AR/GA treatment, the binding of preformed Gal-3 C-epitope oligomers to cardiomyocyte surfaces were further inhibited, thereby suppressing maladaptive mechanotransductive signaling. Importantly, circulating Gal-3 C-epitope oligomers, together with atrial natriuretic peptide (ANP), constituted a drug-responsive biomarker panel that accurately tracked hypertrophy regression, serving as an indicator of drug efficacy. ConclusionsIn summary, Gal-3 C-epitope oligomers represent pathogenic signaling, drug-responsive therapeutic targets and circulating biomarkers of cardiac hypertrophy, with broader relevance to other Gal-3-driven neoplastic, fibrotic, and inflammatory diseases. HighlightsO_LIGalectin-3 C-epitope forms pathogenic extracellular oligomers in pressure-overload induced cardiac hypertrophy. C_LIO_LISurface binding of excess C-epitope oligomers triggers an adverse mechanotransductive remodelling in cardiomyocytes. C_LIO_LIPhytomedicine -Amalaki Rasayana (AR) and its key bioactive compound, gallic acid (GA), effectively inhibit the surface binding and mitigate harmful effects of Gal-3 C-epitope oligomers. C_LIO_LIAR/GA induces the phosphorylation of Gal-3, limiting pathological secretion, extracellular oligomer assembly, and glycan-mediated surface binding. C_LIO_LIIntracellular retention of Gal-3 preserves its crucial cellular functions. C_LIO_LICirculating levels of Gal-3 C-epitope oligomers can be used to monitor the therapeutic regression of cardiac hypertrophy, serving as an indicator of drug efficacy C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=164 HEIGHT=200 SRC="FIGDIR/small/704762v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@4702e9org.highwire.dtl.DTLVardef@10361eorg.highwire.dtl.DTLVardef@51118eorg.highwire.dtl.DTLVardef@57ba37_HPS_FORMAT_FIGEXP M_FIG C_FIG Pressure-overload induces excessive secretion of Galectin-3 and triggers its proteolytic cleavage into the N- and C-terminal epitopes. The extracellular oligomerization of the C-terminal epitope facilitates high-affinity glycan binding and promotes pathological mechanotransductive signaling in cardiomyocytes. Phytochemical modulation by Amalaki rasayana and its bioactive component, gallic acid, induces the phosphorylation of Gal-3, limiting pathological secretion, extracellular oligomer assembly, and glycan-mediated surface binding, while preserving intracellular function. Circulating levels of Gal-3 C-epitope oligomers can be used to monitor the therapeutic regression of cardiac hypertrophy, serving as an indicator of drug efficacy.

cell biology↗

bioRxiv2026

Image-Guided Injectable Niche for Hepatocyte Transplantation

Liver transplantation remains the standard of care for end-stage liver failure, yet it is constrained by donor scarcity, surgical complexity, and restricted access for many patients. Cell-based therapies offer a potential alternative, yet their translation has been hindered by low engraftment, poor localization, and a lack of delivery strategies that are both effective and minimally invasive. To address these challenges, we developed a new approach termed INSITE (Injected Self-assembled Image-guided Tissue Ensembles), an injectable platform composed of primary human hepatocytes and hydrogel microspheres that can be delivered by image-guided injection and assembled in situ into supportive, vascularizable scaffolds. In vivo, ultrasound-guided delivery into an ectopic site enabled precise graft localization, persistent visibility under noninvasive imaging, and vascular integration. Hepatocytes within these niches remained confined to the scaffold and maintained long-term functional activity. Furthermore, tuning material properties allowed control over scaffold remodeling and vascular recruitment, providing a means to enhance graft function. By integrating image-guided delivery with a modular and supportive scaffold, INSITE establishes a clinically compatible strategy for advancing minimally invasive cell therapies.

bioengineering↗

bioRxiv2026

STMN2 protein depletion via translation deficits and stress granules and its compensation in ALS

STMN2 is an abundant neurospecific protein dysregulated in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). We previously reported that cellular stress can lead to STMN2 loss due to TDP-43 nuclear condensation. Here, using human and murine neuronal cell models, multiple pharmacological tools, single-molecule in situ analysis of mRNA localisation and translation, and longitudinal analysis of neuronal fitness/survival, we establish TDP-43-independent mechanisms of STMN2 depletion linked to stress response. We find that human STMN2 protein is extremely labile under acute high-magnitude stress. Early in stress, STMN2 is suppressed via activated proteasomal degradation, phosphorylation and translational repression by stress granules, independently of TDP-43 loss of function in splicing. We further show that STMN2 protein level is highly sensitive to chronic translation deficits, such as those elicited by prolonged low-grade stress. Finally, we demonstrate that STMN2 mRNA is upregulated in non-TDP ALS such as ALS-FUS, which may compensate for translation/stress granule defects in these disease subtypes. Consistent with the compensation hypothesis, STMN2 mRNA is also upregulated in the relatively spared (cortex), but not severely affected (spinal cord), CNS regions in ALS-TDP. In conclusion, our study implicates two common hallmarks of neurodegeneration, translation impairment and abnormal stress granules, in STMN2 depletion and reports an RNA-level compensation that fails in neurons with TDP-43 pathology. Our study supports the development of stress response targeting therapies in ALS with and without TDP-43 pathology.

cell biology↗

bioRxiv2026

Neuronal microscale biophysical instability mediates macroscale network dynamics shaping pathological manifestations

Subtle changes in membrane excitability may contribute to neurological disease, but disease-relevant dynamical signatures that generalize across models remain poorly defined. Here, we quantified variability in action potential initiation in Drosophila neurons expressing tauopathy- or epilepsy-associated mutations and in human iPSC-derived neurons from patients with Alzheimers disease or epilepsy. Across these models, disease-associated neurons exhibited increased instability in spike timing relative to controls. In Drosophila neurons, this phenotype was accompanied by increased variability in voltage-gated sodium currents during non-stationary inactivation, identifying a candidate biophysical contributor to altered spike initiation. Antiepileptic drugs reduced sodium-current variability and stabilized spike initiation in fly neurons, and similarly improved spike-timing instability in patient-derived human neurons. In the fly models, neuronal instability was also associated with altered circuit- and brain-state readouts. Together, these findings identify unstable spike initiation as a conserved electrophysiological phenotype across distinct neurological disease models and suggest that sodium-channel-dependent variability may contribute to this phenotype. Rather than establishing a complete multiscale causal framework, our study defines a tractable cellular and dynamical entry point for investigating how subtle perturbations in intrinsic excitability may scale toward circuit dysfunction and disease-relevant phenotypes. Significance StatementLinking microscale neuronal changes to macroscale disease phenotypes remains a key challenge in neuroscience biophysics. Here, we show that neurons from Drosophila models of tauopathy and epilepsy and human iPSC-derived neurons from patients with Alzheimers disease and epilepsy share increased biophysical instability in their local neural activities. In fly neurons, this phenotype is associated with increased variability in voltage-gated sodium currents and is reduced by antiepileptic treatment. These findings define unstable local spike variability as a conserved dynamical signature across distinct disease models and nominate sodium-current variability as a mechanistically testable, pharmacologically reversible contributor to pathological excitability.

neuroscience↗

bioRxiv2026

Searching for a New Home or Rare Dispersal? Habitat Suitability and Landscape Connectivity of the Tibetan Brown Bear across the Indian Cold Deserts and the Tibetan Plateau

Understanding habitat suitability and landscape connectivity is essential for conserving wide-ranging carnivores in climate-sensitive high-altitude mountain ecosystems. The first occurrence record of the Tibetan brown bear (Ursus arctos pruinosus) from the Changthang region of Ladakh, India, has raised questions about whether this individual represents an isolated dispersal event or reflects functional connectivity with source populations on the Tibetan Plateau. To evaluate potential habitat suitability and transboundary connectivity, we compiled species occurrence records and associated environmental predictors and developed an ensemble species distribution model using biomod2. We then assessed landscape connectivity using circuit theory implemented in Circuitscape to identify potential ecological corridors. Our models indicate that approximately 1,011,818 km{superscript 2} (21.34%) of the combined Ladakh (India) and the Tibetan Plateau landscape is currently suitable for the species, of which only [~]207,000 km{superscript 2} represents highly suitable habitat. Annual precipitation, precipitation of the wettest month, and precipitation of the warmest quarter were the most influential predictors of habitat suitability. Connectivity analysis identified potential corridors linking the eastern Changthang region of Ladakh with suitable habitat on the Tibetan Plateau, suggesting plausible transboundary ecological connectivity. These results indicate that the recent record from Changthang is more likely driven by landscape-scale functional connectivity than by an isolated dispersal event. Although the mapped corridors represent probable connectivity pathways rather than confirmed movement routes, this study provides the first spatially explicit assessment of habitat suitability and potential transboundary connectivity for the Tibetan brown bear across the Ladakh and Tibetan Plateau landscape.

ecology↗

bioRxiv2026

ThermiQuantTM AquaStream: A Portable Instrument for Quantitative Colorimetric Isothermal Nucleic Acid Amplification Reactions in Paper and Tube Formats

Microfluidic paper-based analytical devices ({micro}PADs) are an attractive format for colorimetric nucleic acid amplification tests (NAATs) because they enable low-cost, portable diagnostics in resource-limited settings. However, researchers often optimize colorimetric assays in liquid reactions in tubes before translating them to {micro}PADs. Since both formats require separate instruments for incubation and real-time sensing, direct comparison of reactions between the two formats is difficult. To address these cross-platform limitations, we developed ThermiQuant AquaStream, a portable benchtop device (15 x 20 x 16 cm, [~]5 kg; cost: USD 327) that supports seamless colorimetric loop-mediated isothermal amplification (LAMP) reactions in both {micro}PADs and tubes under a common workflow. The system enables real-time reaction tracking (every 30 seconds) through onboard image processing, precise isothermal control ({+/-}0.5 {degrees}C) using a repurposed consumer-grade sous-vide heater, and medium-throughput (24 tubes or 42 {micro}PADs). Testing with synthetic SARS-CoV-2 orf7ab DNA fragments demonstrated a limit of detection corresponding to a 95% probability of detection (LOD95) of 110 copies per reaction in tube (22 copies/{micro}L) and 39 copies per reaction in {micro}PADs (5 copies/{micro}L), estimated using probit regression. In both formats the limit of quantification (LOQ), defined as the lowest concentration yielding a coefficient of variation (CV) of Tq [≤] 10%, was 250 copies/reaction resulting in a strong linear (R2 = 0.98 & R2 = 0.96 respectively for tube and {micro}PADs) standard calibration curves. ThermiQuant AquaStream provides an affordable and versatile benchtop platform capable of supporting both tube- and {micro}PAD-based colorimetric LAMP assays, serving as a proof-of-concept research tool for assay development and molecular diagnostics in One Health settings such as clinics, farms, and field environments.

bioengineering↗

bioRxiv2026

Chronic ER Stress Disrupts Mitochondrial-Associated ER Membrane Integrity in Corneal Endothelial Cells.

PurposeFuchs endothelial corneal dystrophy (FECD) is an age-related degenerative disease of the corneal endothelium cells (CEnCs), affecting 4% of the US population over 40. While Endoplasmic reticulum (ER) and mitochondrial stress have been independently associated with FECD pathogenesis, few studies have examined ER-mitochondrial interactions/ER-mitochondrial contact sites/mitochondria-associated ER membrane (MAM), or MAM proteins, and their contribution to ER and mitochondrial stress in FECD. This study aims to characterize alterations in MAMs and identify key MAM proteins associated with ER and mitochondrial stress in FECD. MethodHuman corneal endothelial cell line (HCEnC-21T) and Fuchs corneal endothelial cell line (F35T) were cultured and subjected to ER stressor tunicamycin (1, 10 g/ml) for 6 and 24 hours. MAM proteins were isolated by subcellular fractionation, and key ER and mitochondrial-damage-sensor proteins, such as PERK and Parkin, respectively, were identified by immunoblotting. ER-mitochondrial contact sites were quantified using the MAM plasmid and transmission electron microscopy (TEM) in normal and Fuchs cell lines, as well as in human tissues under chronic ER stress. ResultsER-mitochondrial contact distance significantly increased in Fuchs tissues compared with normal tissues, and a similar increase was observed in 21T cell line after tunicamycin treatment. There was a significant increase in the intensity of the MAM plasmid upon tunicamycin treatment at 6 hours in the 21T cell line compared to the non-treated control. However, MAM plasmid intensity significantly decreased at 24 hours compared to 6 hours post-tunicamycin treatment in 21T cell line. Analysis of MAM function by quantifying phosphatidylserine synthase 1 (PSS1 [gene PTDSS1]) expression in 21T cells showed a reduction in PTDSS1 expression after 24 hours of tunicamycin treatment. ER stress protein PERK and mitochondria damage sensor protein (Parkin) significantly increased in the MAM fraction after tunicamycin at 24 hours in 21T cell line. ConclusionsFuchs cell lines and tissues demonstrate decreased ER-mitochondrial interactions/MAMs, which are also seen in 21T cell line after chronic ER stress. Under chronic ER stress, ER and mitochondrial stress mediator proteins are translocated to MAM. This study highlights the importance of MAMs as a potential mediator of ER-mitochondria crosstalk in degenerating corneal endothelial cells for FECD.

cell biology↗

bioRxiv2026

ThermiQuant(TM) MegaScan: High-throughput isothermal reactor with quantitative colorimetric readout for paper-based nucleic acid amplification tests

Isothermal nucleic acid amplification tests (NAATs), such as loop-mediated isothermal amplification (LAMP) implemented on microfluidic paper-based analytical devices ({micro}PADs), enable inexpensive and rapid ([≤]60 min) colorimetric molecular diagnostics; however, no existing instrument supports high-throughput (>100 reactions) quantitative analysis of colorimetric isothermal assays on paper substrates under controlled laboratory conditions. To address this gap, we developed ThermiQuant MegaScan, a scanner- and water-bath-based platform that accommodates a 160-reaction {micro}PAD cartridge, maintains uniform incubation at 65 {+/-} 0.5 {degrees}C, and enables real-time imaging every 30 s. We also developed accompanying software, Amplimetrics, for automated {micro}PAD detection and kinetic colorimetric analysis. Using paper-based colorimetric LAMP targeting the SARS-CoV-2 orf7ab region, the assay achieved a limit of detection at 95% probability (LOD95) of 34 copies per reaction (5 copies/{micro}L) and a limit of quantification (LOQ) of 250 copies per reaction (33 copies/{micro}L) using purified synthetic DNA targets, and achieved 72% sensitivity and 100% specificity relative to digital PCR (dPCR) for diluted human nasopharyngeal (NP) swab virus samples. We further evaluated the effects of viral and universal transport media (VTM/UTM) on assay performance and found that linear calibration derived from synthetic targets do not reliably translate to clinical samples in these media. Together, these results establish ThermiQuant MegaScan as a high-throughput laboratory research platform for standardized evaluation, optimization, and benchmarking of paper-based colorimetric nucleic acid amplification assays.

bioengineering↗

bioRxiv2025

Synthetic Control of Implanted Engineered Liver Tissue Growth

Despite the promise of engineered tissue implants for the treatment of organ failure, scaling of these constructs to sizes of therapeutic relevance remains a barrier to clinical translation. Here, we propose a strategy to circumvent this limitation: to instead implant a small-scale construct and then induce it to grow in situ after its engraftment into a host. Using engineered liver tissue as a proof-of-concept application, we integrated synthetic biology and tissue engineering tools to build liver tissues that can be expanded on-demand after implantation in vivo. To achieve this goal, we first identified the combination of YAP and growth factor signaling as sufficient to drive human hepatocyte proliferation in dense, 3D engineered tissues. We then engineered control of these signaling axes using synthetic biology tools to drive human liver tissue expansion both in vitro and in vivo. As such, this work establishes a genetic strategy for generating large organ implants through bioengineered, on-demand outgrowth using synthetic triggers (BOOST). TeaserPresenting bioengineered on-demand outgrowth via synthetic biology triggering (BOOST) for in situ solid cell therapy scale up.

bioengineering↗

bioRxiv2025

Osteoblasts Exert a Pro-Tumorigenic Effect on Breast Cancer Spheroids Through CXCL5/CXCR2 Signaling In 2D And 3D Bone Mimetic Cultures

Bone provides a favorable niche for breast cancer colonization and metastatic progression. Breast cancer cells are attracted to the bone microenvironment where they induce bone cells to resorb bone, which enhances tumor cell proliferation in a positive feedback loop often referred to as the vicious cycle. While this phenomenon is established, the molecular interactions between cancer cells and bone cells are not well defined. CXCL5/CXCR2 signaling has recently been shown to promote breast cancer colonization to the bone. Here, we investigate the effects of osteoblasts and osteocytes on breast cancer cell proliferation in engineered two- and three-dimensional models. We observed that osteoblasts and osteocytes induce proliferative effects on cancer cells. Specifically, bone cells increase cancer proliferation in 2D culture and osteoblasts increase cancer growth more than osteocytes in 3D models. Moreover, osteocyte interaction with cancer cells in 3D models are stiffness dependent. We show that these effects depend on the CXCL5/CXCR2 signaling axis. Taken together, we demonstrate that osteoblasts drive cancer growth in a bone metastatic niche and that this effect can be rescued with CXCL5/CXCR2 inhibition.

bioengineering↗

bioRxiv2025

Mosquito NF-κB-mediated innate immunity exerts arbovirus-specific antiviral effects at multiple stages of the viral life cycle

One third of all emerging infectious diseases are vector-borne, with the vectors ecology and physiology playing key roles in determining whether viruses can access new vertebrate host species and spread globally. Innate immunity is a known barrier to virus replication in mosquito vectors that influences arboviral vector tropism. We here generated novel CRISPR-Cas9-mediated knockouts of the NF-{kappa}B family transcription factor Rel2 in Aedes aegypti-derived Aag2 cells and tested the impact on the replication of a diverse range of arboviruses in the Flaviviridae and Togaviridae families and the class Bunyaviricetes. We found that NF-{kappa}B-mediated innate immunity has broad antiviral activity against the Ae. aegypti-borne orthoflaviviruses dengue virus (DENV), yellow fever virus (YFV) and Zika virus (ZIKV) in mosquito cells. In contrast, little impact of NF-{kappa}B-loss-of-function was observed for the alphavirus chikungunya virus (CHIKV) or phlebovirus Rift Valley fever virus (RVFV), indicating specificity in the antiviral effects of NF-{kappa}B-mediated immunity. By comparing orthoflaviviruses with different transmission routes (mosquito-borne, tick-borne, no known vector), we demonstrated that NF-{kappa}B-mediated immunity exerts its antiviral effects both early and late in the viral replication cycle, and that NF-{kappa}B-mediated immunity is not the only molecular barrier influencing the ability of orthoflaviviruses to replicate in Ae. aegypti cells. Overall, our work demonstrates the importance of mosquito NF-{kappa}B-mediated innate immunity in suppressing arbovirus replication, and shows that the barriers for arboviruses to adapt to new vector species are multifactorial and virus-specific. Our findings increase our understanding of the molecular barriers influencing arboviral emergence, and could inform the development of refractory mosquitoes incapable of transmitting human pathogens. Author SummaryMosquito-borne viruses are causing an increasing global disease burden due to urbanisation, globalisation, changing land use and the climate change-driven invasion of mosquitoes into new locations. Few vaccines and no medicines for mosquito-borne viral infections are licensed for human use. Historically, the most effective way to reduce human disease has been to kill mosquitoes using insecticides, which also harms beneficial insects and is leading to resistance. Newer technologies with lower ecological impacts are being developed, including genetically modified mosquitoes with a reduced ability to transmit viruses. Like humans, mosquitoes have an immune system that protects against viral infections, and strengthening this immune system through genetic modification has shown promise for reducing virus transmission. We here expand our understanding of the ways in which mosquito immunity could be harnessed by demonstrating that a gene called "Rel2" helps the mosquito fight mosquito-borne virus infection. Unlike previously studied mosquito immune responses, Rel2 has a very broad (but not universal) protective capacity against viruses. Our work also indicates that Rel2 works in concert with other arms of the mosquito immune system, highlighting a need for further research to fully realise the potential of genetically modifying mosquito immune responses for the prevention of human disease.

microbiology↗

bioRxiv2025

Interlocus gene conversion causes mosaic divergence in tandem paralogues - simulating HMA4 evolution in Arabidopsis halleri

Following gene duplication, the evolutionary trajectories of gene copies can be shaped by various processes including mutation, selection, recombination and interlocus gene conversion (IGC). To explore their dynamics and consequences, we developed a mathematical model that simulates the early evolution of recently duplicated, tandemly arrayed gene families with positive selection on the new gene copy. We compared the results of our model to sequence variation of the three tandemly arrayed HEAVY METAL ATPase 4 (HMA4) gene copies of Arabidopsis halleri, which are known to undergo IGC. However, rate and efficacy of IGC vary within genes, resulting in a mosaic pattern of divergence. Informed by empirical data, our model captures the impact of IGC and unequal crossing-over on the diversity within each gene copy and the divergence among them. By tailoring the model to the HMA4 gene copies, we demonstrate the models flexibility and its potential to provide insights into the evolutionary dynamics driving the evolution of tandemly arrayed paralogues. This study enhances our understanding of the balance between homogenization and divergence of gene family evolution.

evolutionary biology↗

bioRxiv2025

PEX11β-mediated improvement of mitochondrial dysfunction restores behavioral defect and cellular viability in neuropathological conditions

Peroxisomal biogenesis factor 11 beta (Pex11{beta}) is a key regulator of peroxisome proliferation, functioning in coordination with mitochondrial fission proteins. Recent human proteome co-regulation mapping has revealed a distinctive co-expression pattern between Pex11{beta} and components of the mitochondrial respiratory chain complex at the peroxisome-mitochondria interface. In neurodegenerative disorders, such as Huntingtons disease (HD) and Alzheimers disease (AD), mitochondrial dysfunction is primarily associated with impairments in the respiratory chain complexes, particularly Complex II. However, the role of Pex11{beta} in maintaining mitochondrial homeostasis in these two disease conditions remains largely unexplored. In this study, using both in vitro and in vivo models, we identify Pex11{beta} as a critical modulator of mitochondrial dynamics, influencing the balance between fission and fusion. Through targeted knockdown and overexpression experiments, we demonstrate a direct link between Pex11{beta} level and mitochondrial dysfunction, mediated by transcriptional dysregulation of nuclear-encoded Complex II and mitochondrial fusion genes. Restoration of Pex11{beta} expression, along with Complex II and fusion gene level in striatal brain via a peroxisome proliferator & chemical chaperone, significantly alleviates motor and cognitive deficits in 3-NP-induced HD mouse model indicating better mitochondrial health in striatal brain. Furthermore, in silico analysis and ChIP-qPCR reveal Yin Yang 1 (YY1) is a critical transcription factor governing the co-expression of Pex11{beta} and Complex II genes. This establishes a novel transcriptional axis that orchestrates inter-organellar communication. Collectively, our findings position Pex11{beta} as a pivotal mediator of mitochondrial fission-fusion dynamics, linking mitochondrial morphology and oxidative phosphorylation (OXPHOS) to behavioural outcomes, and offering mechanistic insights relevant to amyloid-associated neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Open Raman Microscopy (ORM): A Modular Hardware and Software Framework for Accessible Raman Imaging

Raman microscopy is a label-free, non-destructive imaging tool for spatially resolved chemical fingerprinting. Its powerful ability to reveal molecular information has driven rapid growth in applications across fields as varied as materials science, environmental analysis, and biomedical research. Despite its versatility, the accessibility of Raman microscopy is limited by expensive commercial setups and the technical barriers faced by researchers attempting to build custom systems. Here, we introduce an Open Raman Microscopy (ORM) framework based on a readily accessible modular microscopy platform. The ORM platform provides configurations for both high-throughput imaging and confocal imaging. We developed a dedicated python-based control and acquisition software, the ORM-Integrated Raman and Imaging Software (ORM-IRIS) designed to accommodate modular integration and control of components, including the laser source, spectrometer, and translational stages. Implemented across three institutions we demonstrate the ORM platform for high-throughput imaging of articular cartilage tissue, confocal three-dimensional imaging of a zebrafish embryo, and imaging of gold colloid decorated surfaces for surface enhanced Raman spectroscopy. Together, this open-source hardware and software framework enhances the accessibility of Raman microscopy across an expanding range of scientific applications.

biophysics↗

bioRxiv2025

Glycan recognition by a plant sentinel immune receptor

Pathogens target and degrade the extracellular matrix surrounding plant cells. A central question is how cell wall-derived damage-associated molecular patterns (DAMPs) are recognized and integrated to trigger immune responses. We address this question by determining the structure of the multidomain receptor IGP1 in both apo form and bound to the cellulose-derived DAMP cellotriose. Structural analyses reveal that constitutive Leucine Rich Repeat-malectin interactions preconfigure IGP1 for ligand recognition and that the receptor features a highly specific sugar-binding pocket in the LRR domain capable of distinguishing fine variations in glycan structures. By directly sensing cello-oligomers, IGP1 acts as a cell wall sentinel that links pathogen-induced wall degradation to immune alerting, equipping plants to mount rapid and robust defense responses.

plant biology↗

bioRxiv2025

Integrative Microbiome Profiling of Colorectal Cancer Across South Asian and Western Cohorts Using Interpretable Machine Learning

The incidence of colorectal cancer (CRC) cases has been steadily rising in South Asian countries compared to western countries. Microbiome dysbiosis has been strongly associated with CRC development, with diet and demographic factors playing an important role in shaping gut microbial composition. Since most CRC cases are diagnosed at advanced stages, early detection remains critical for improving patient outcomes. Machine learning (ML) approaches provide a promising strategy to identify predictive microbial biomarkers for early CRC detection. In this study, we have analyzed publicly available 16S rRNA datasets comprising CRC patients and controls from South Asian cohorts (India and Sri Lanka) and compared them with Western cohorts (USA). Our findings revealed a higher relative abundance of Prevotella in South Asian cohorts, whereas Bacteroides predominated in the USA cohort. Across all three datasets, Fusobacterium, Escherichia-Shigella, and Akkermansia were consistently elevated in CRC cases. We evaluated multiple ML algorithms, including Decision Tree, Random Forest, AdaBoost, LogitBoost, XGBoost, Support Vector Machine (SVM), and k-Nearest Neighbors (KNN) and proposed stacked ensemble model to differentiate between CRC and controls. Stacked ensemble model has higher accuracy compared to base models. To improve models interpretability and transparency SHAP (SHapley Additive exPlanations) analysis were performed to identify key taxa influencing model predictions. These results underscore the utility of ML-based microbiome analysis for identifying robust CRC-associated microbial signatures, with potential application in developing generalizable early detection tools.

microbiology↗

bioRxiv2025

BenchIDPs: Evaluation of Conformational Preferences Molecular Mechanics and Solvent Interactions of IDPs across popular Force Fields and Water Models

Intrinsically disordered proteins (IDPs), unlike globular proteins, lack stable secondary structure and exist as dynamic ensembles of conformations in physiological conditions. These conformations allow them to adapt to many roles while interacting with other proteins, forming partially folded soluble oligomers or insoluble plaques rich in {beta}-sheet, and are responsible for different pathological diseases. The dynamic nature of IDPs and the lack of well-defined binding sites make drug discovery and development both challenging. Although computational protocols, predominantly involving molecular dynamics (MD) simulations studies, have been complementing in understanding the structure and dynamics of IDPs, the choice of force fields become important in reproducing experimental observations. We herewith provide a systematic study to investigate the structural propensity of four IDPs (A{beta}42, Tau43, amylin and S), using 13 combinations of force field-water models (FF-wm). In addition to validating with NMR observables, we also examine the water dynamics surrounding the chosen IDPs to underscore the generalizability of chosen FF-wms. C36-IDPSFF with amber99sb-dispersion water model (A99SB-disp) is found to perform optimal in simulating IDPs in comparison with other FF-wm combination based on structural propensity and comparison with experimental NMR 3JHN-H-Coupling data as well as dynamical observables.

biophysics↗

bioRxiv2025

Electrical stimulation directs formation of perfused vasculature in engineered tissues

Effective, rapid and functionally perfusable vascularization remains a major challenge in tissue engineering. Current approaches to generate vasculature in vitro require multipart fabrication methods or complex and costly media supplements, limiting their scalability. Here, we demonstrate that exogenous electrical stimulation (estim) offers a promising alternative by enhancing 3D vasculogenesis in engineered human tissues. Exposing 3D endothelial-fibroblast cocultures to pulsed estim promoted the formation of dense and branched vascular networks. In a microfluidic device model, we show that estim induces the formation of an interconnected vascular network that can be perfused, whereas unstimulated control networks remained less mature. Importantly, we demonstrate that upon implantation, estim-pretreated vascular grafts exhibit elevated anastomosis with host and perfusion with blood relative to the untreated grafts. In addition, we use estim to promote engraftment of a vascularized 3D liver construct. Mechanistically, we find that estim induces membrane hyperpolarization in endothelial cells via voltage-gated potassium (KV) channels. Inhibiting KV channels abrogated estims pro-vasculogenic effects in endothelial cells. Conversely, pharmacologically activating hyperpolarization induced endothelial responses even without estim, directly linking KV channel-mediated hyperpolarization as a key mechanism by which estim drives vascular assembly and function. Ultimately, our work establishes estim as a new orthogonal approach to promote formation of perfusable vasculature in engineered tissues.

bioengineering↗