Biology subjects

Mishra, A.

Publications and source records attributed to Mishra, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Unravelling the plausible metal-dependent catalytic mechanism of Inositol monophosphatase ortholog from Pseudomonas aeruginosa through the lenses of macromolecular crystallography and enzyme kinetics

The inositol monophosphatase (IMPase) orthologue is pivotal for virulence, pathogenesis, and biofilm regulation, and is therefore considered a potential drug target in Pseudomonas aeruginosa and other bacterial pathogens. The mammalian IMPase orthologue is an established drug target for bipolar disorder. The precise catalytic mechanism in this class of enzymes remains obscure despite five to six decades of extensive efforts and detailed studies of substrate, transition-state analogue, and product-bound structures. Here, we have solved the crystal structures of the IMPase orthologue from Pseudomonas aeruginosa (PaIMPase), capturing pre- and post-catalytic snapshots of metal-substrate- and metal-product-mimic-bound states. Moreover, we solved the metal-substrate transition-state-analogue-bound crystal structure of the enzyme. Critical evaluation of these high-resolution crystal structures of PaIMPase complexed with substrate, transition-state analogue, and product mimic (myo-inositol and phosphate) supports three Mg2+-dependent catalytic mechanisms of PaIMPase. The structural snapshots indicate that, at the enzyme active site, a metal (Mg2+)-coordinating water molecule, activated by two bound Mg2+ ions and the active-site-proximal Threonine/Aspartate dyad, attacks the central phosphorus atom of the bound substrate, leading to formation of a trigonal bipyramidal transition state. Following that, the immediate breakdown of the P-O bond results in the formation of inositolate and phosphate ions. The second water molecule, activated by another Mg2+ dyad, facilitates the departure of myo-inositol and phosphate from the active site. The detailed mechanistic insights gained from this work may offer a foundation for the rational design of precise inhibitors against PaIMPase.

biophysics↗

bioRxiv2026

Plasmodium Protein Kinase 2 is required for ookinete to oocyst transition, and parasite transmission by the mosquito.

Plasmodium spp., the parasites that are the causative agents of malaria, encode a repertoire of divergent protein kinases that coordinate essential processes including cell division and host cell invasion, yet the functions of many kinases are poorly defined. Plasmodium Protein Kinase 2 (PK2) is essential for asexual blood-stage proliferation and has been implicated in P. falciparum merozoite invasion of red blood cells. However, its role in the sexual stages of the Plasmodium life cycle responsible for transmission is unknown. Here, using live cell imaging, functional analyses, ultrastructure microscopy and phosphoproteomics, we demonstrate that PK2 has a significant role in the Plasmodium berghei life cycle in the mosquito. We show that PK2 is expressed in merozoites, ookinetes and sporozoites - the invasive stages of the parasite life cycle. A conditional knockdown approach revealed that PK2 is required for the ookinete to oocyst transition in the mosquito midgut, potentially associated with altered microneme positioning. Using haemocoel injection to bypass the midgut barrier revealed that PK2 is also required for sporozoite development after midgut invasion. Following PK2 knockdown, global proteome abundance was largely unaffected at 24 h post activation, whereas phosphoproteomics identified changes in phosphorylation of proteins linked to midgut traversal, parasite architecture, and gene regulation. These studies provide insight into the importance of PK2 function in Plasmodium sexual stages and parasite transmission through the mosquito, highlighting its essential function during the three invasive stages of the parasites life cycle.

microbiology↗

bioRxiv2026

Integration of QTL Mapping, Transcriptomics, and Genome Resequencing Identifies Yield-Associated Genes for Salt Stress in Rice

Salinity and sodicity stresses adversely affect rice growth and yield. To overcome yield losses, suitable tolerant rice cultivars can be developed through a marker-assisted breeding (MAB) program. In the present study, genomic regions associated with sodicity stress tolerance at the reproductive stage were identified using a high-density 50kSNP array in a recombinant inbred line (RIL) population derived from the contrasting rice genotypes CSR11 and MI48. A total of 50 QTLs were detected for various yield-related traits; further, 19 QTLs with [≥]15% of phenotypic variance were selected for integrated (omics) analysis. RNA sequencing of leaves and panicles at the reproductive stage under sodic stress conditions was employed to find differentially expressed genes. A total of 1368 and 1410 SNPs; 104 and 144 indels were found for MI48 and CSR11, respectively, within the QTL regions from resequencing. At chromosomes 1 and 6, colocalized QTLs (qPH1-1/qGP1-1 and qGP6-2/qSSI6-2) were discovered. Differentially expressed genes (DEGs) were mapped over the QTL regions selected, and SNP variations and indels were screened for colocalized QTLs. Potential candidate genes, namely Os-pGlcT1 (Os01g0133400), OsHKT2;1 (Os06g0701600) and OsHKT2;4 (Os06g0701700), OsANTH12 (Os06g0699800), and OsPTR2 (Os06g0706400), were identified as being responsible for glucose transport, ion homeostasis, pollen germination, and nitrogen use efficiency, respectively, under salt stress. Finally, our study provides important insights into the genes and potential mechanisms affecting grain yield under sodic stress in rice, which will contribute to the development of molecular markers for rice breeding programs.

plant biology↗

bioRxiv2026

GAPMs form a heterotrimeric complex bridging the gliding machinery and the cytoskeleton across Plasmodium species

Apicomplexan parasites, such as malaria-causing Plasmodium spp., use a specialised actomyosin motor system known as the glideosome to drive movement through host tissue and invade host cells. This system is anchored to the inner membrane complex (IMC), a series of flattened vesicles located beneath the plasma membrane, and thought to be linked to the underlying cytoskeleton by the GAPM protein family. However, it is not known how these GAPM proteins are localised across the Plasmodium life cycle, and whether different family members function alone or together. Here, we show that in two Plasmodium species GAPM2 is an IMC component whose recruitment and organisation are tightly coordinated with nuclear and cytoskeletal dynamics during parasite replication and differentiation. We find that the GAPM2 interactome remodels between asexual and sexual stages using mass spectrometry. To understand the molecular relationship between three GAPM paralogues, we solved a cryo-electron microscopy structure of the GAPM complex. This revealed an obligate heterotrimeric architecture that forms an asymmetric platform, likely to serve as a docking interface for other components of the glideosome. Finally integrating our GAPM heterotrimer structure with mass spectrometry data allowed us to propose a unified structural model of the glideosome that is conserved across apicomplexan parasites.

microbiology↗

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

Techno-functional properties of clover grass protein and the effect of different process technologies

This study investigated the effects of different downstream processes for protein isolation on the bulk properties and composition of clover grass protein prototypes (CGPs). A clarified clover grass juice, obtained using membrane filtration (MF), underwent precipitation by acid (AP), heat (HP), or acid+heat (AHP), or underwent ultra- and diafiltration to produce a concentrate (DC) as well as subsequent tryptic hydrolysis of DC (DCH). HP had the highest protein content (p<0.05) and was whiter than other CGPs, although it showed lower aqueous solubility. In contrast, DC showed excellent solubility across a broad pH range. CGPs efficiently decreased oil-water interfacial tension (16-13 mN/m) and displayed viscoelastic and solid-like interfacial behavior. CGPs-stabilized emulsions displayed low physical stability with larger droplets despite high absolute {zeta}-potentials. CGPs were rich in RuBisCO (37-47%) but had varying levels of other proteins. Despite significant protein-level differences, overall protein composition of CGPs was comparable, highlighting that protein state governs bulk functionality more than subtle compositional changes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/701969v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@f37756org.highwire.dtl.DTLVardef@1fb5beorg.highwire.dtl.DTLVardef@1d4efe2org.highwire.dtl.DTLVardef@d11ef8_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com HighlightsO_LIThe effect of different processes on functional properties of CGPs was explored. C_LIO_LIHeat treatment increased protein purity and whiteness at the expense of solubility. C_LIO_LICGPs efficiently reduced O/W interfacial tension but produced unstable emulsions. C_LIO_LICGPs were found rich in RuBisCO (34-47%) using quantitative proteomics. C_LIO_LIProtein state had larger influence on functionality than protein-level composition. C_LI

bioengineering↗

bioRxiv2026

Origin-1: a generative AI platform for de novo antibody design against novel epitopes

0Generative artificial intelligence has advanced antibody discovery, yet de novo design of therapeutic antibodies against targets with "zero-prior" epitopes remains a fundamental challenge. We define "zero-prior" epitopes as target sites lacking structural data from any reported antibody-antigen or protein-protein complex involving the target. Here we present Origin-1, a generative AI platform that overcomes this by integrating epitope-conditioned all-atom structure generation, paired complementarity determining region sequence design, and a specialized co-folding-based scoring protocol to select antibody designs predicted to be high-confidence, specific binders with favorable developability. We evaluated Origin-1 on a panel of ten targets selected to have no available protein-protein complex structures and minimal homology ([≤]60% sequence identity) to proteins with known complexes, creating stringent design conditions. In fewer than one hundred design attempts per target, we identified developable, specific antibodies, validated across multiple biophysical and developability assays, for four targets: COL6A3, AZGP1, CHI3L2, and IL36RA, with functional inhibition demonstrated for IL36RA. Cryogenic electron microscopy confirmed the atomic accuracy of our designs, revealing complexes that closely matched the computational models with high structural fidelity (3.0-3.3 [A] resolution; 0.83-0.91 DockQ). Furthermore, we employed AI-guided affinity maturation to optimize a de novo antibody binder against IL36RA, producing functional antagonists with sub-nanomolar affinities and a top EC50 of 12.3 nM. These results demonstrate a framework for targeting epitopes without structural precedent, expanding the programmable therapeutic antibody landscape.

molecular biology↗

bioRxiv2026

Investigating Quinclorac Binding to Human Serum Albumin using Spectroscopy and Molecular Docking

Human serum albumin (HSA) is the most abundant plasma protein and serves as a major transporter and reservoir for a wide range of endogenous ligands, including fatty acids, heme, bilirubin, prostaglandins, and metal ions, as well as numerous exogenous compounds, such as pharmaceuticals. HSA is a 66 kDa monomeric, multidomain protein containing two principal ligand-binding sites, Sudlow sites I and II. Sudlow site I contains Trp214, the sole tryptophan residue in HSA, whose intrinsic fluorescence provides a sensitive probe for studying ligand-protein interactions. In this study, the interaction between HSA and the persistent organochlorine herbicide quinclorac (QNC) was investigated using steady-state fluorescence spectroscopy and molecular docking. The binding of QNC to HSA is characterized by concentration-dependent quenching of HSAs intrinsic tryptophan fluorescence. Quantitative analysis revealed a high affinity of QNC for HSA, with [~] 1 M dissociation constant (Kd). Temperature-dependent fluorescence quenching experiments indicate a static quenching mechanism. Moreover, a competitive displacement assay using site-specific markers identified Sudlow site I as the primary binding site for QNC in HSA. Induced-fit docking further demonstrated that QNC is accommodated and stabilized by polar interactions, {pi}-stacking, and/or hydrophobic interactions within the Sudlow I binding pocket. Together, these results provide a biochemical and molecular understanding of how QNC, a persistent pesticide, binds to HSA.

biochemistry↗

bioRxiv2025

A bifunctional optical reporter for tracking estrogen response dynamics in neurons

Estrogens are inherently dynamic signaling molecules whose fluctuations induce profound shifts in physiology and behavior. However, methods for tracking the dynamics of estrogen action in vivo are limited and not tissue-specific, making it difficult to directly relate dynamics to ongoing physiological, behavioral, and neural changes. Traditionally, estrogen sensitive cells have been identified by metrics such as receptor expression or radioactive ligand binding, but these measures do not capture the dynamic nature of hormone response. In addition, current methods for assessing the dynamics of estrogens in an individual, including microdialysis and vaginal cytology, lack temporal and spatial resolution.To address this need we developed a bifunctional reporter called neuro-seeER (neuronal see Estrogen Response) that can be used to track changes in exogenous and endogenous estrogen dynamics in vitro and in vivo, including longitudinally in behaving animals. We confirmed that the fluorescent response requires estrogen receptor expression, is specific to activation with estradiol, and is consistent with the timescale of transcriptional induction. Neuro-seeER expression in the hypothalamus of Esr1-Cre mice revealed dynamic labeling of estrogen-responsive cells following treatment with exogenous estradiol, and fluorescence-aided cell sorting followed by RNA-sequencing confirmed that high neuro-seeER response is associated with enriched expression of genes associated with endogenous estrogen responses. Using a novel "snapshot" photometry method to track the dynamics longitudinally in vivo, we demonstrate that we can robustly detect exogenous estrogen response across multiple hypothalamic sites simultaneously. Finally, we demonstrate that this tool is uniquely suited to capturing endogenous estrogen response dynamics in vivo across the long timescale of the estrous cycle, revealing individual differences in neural estrogen dynamics. Together, these findings reveal unexpected cellular and temporal heterogeneity of the transcriptional response and demonstrate the feasibility of tracking the dynamics of hormonal response alongside additional neural, cell signaling, or behavioral measures.

neuroscience↗

bioRxiv2025

Shaping the active site from a distance: Unravelling the regulatory role of the conserved N-terminal β-flap of thiol peroxidases through structure-function characterization of the Staphylococcal ortholog

Bacterial thiol peroxidases (Tpxs) are members of atypical two-cysteine peroxiredoxin, which detoxify hydroperoxides during host-pathogen interactions. Despite extensive research on bacterial Tpxs, the precise structure-based functional characterization of Staphylococcal Tpx (SaTpx) remains elusive. Herein, we cloned and purified SaTpx along with its plausible physiological redox partners to reconstitute its electron relay system. We solved the high-resolution crystal structure of SaTpx, revealing the essential active-site catalytic triad (Cys 60, Thr 57, Arg 128). The crystal structure of SaTpx reveals the presence of the highly conserved N-terminal {beta}-flap, absent in its mammalian orthologs (Peroxiredoxin 5). To investigate the plausible role of this highly conserved {beta}-flap, we cloned and characterized a deletion mutant, N{Delta}15-SaTpx, lacking this region. N{Delta}15-SaTpx showed reduced ability to mitigate organic hydroperoxides in vitro; partially impaired to prevent ROS-mediated ds-DNA nicking and failed to protect host E. coli cells from exogenous ROS stress. The ultra-high-resolution crystal structures of N{Delta}15-SaTpx and N{Delta}15-SaTpx with substrate mimic revealed a distorted catalytic triad (with flipped Arg 128), explaining its partially impaired catalytic activity. This study, for the first time, elucidates the critical regulatory role of the N-terminal {beta}-flap in stabilizing the catalytic triad of bacterial Tpx, providing insights for future inhibitor designing. HighlightsO_LIUltra high-resolution crystal structures of SaTpx and N{Delta}15-SaTpx C_LIO_LIUltra-high resolution crystal structure of hydroperoxide substrate mimic bound N{Delta}15-SaTpx C_LIO_LI{beta}-flap deletion mediated distortion of catalytic triad in N{Delta}15-SaTpx C_LIO_LIThe novel regulatory role of the conserved N-terminal {beta}-flap of Thiol peroxidases. C_LI

biophysics↗

bioRxiv2025

HOXA10 is a Temporal Switch in Controlling Decidual Inflammation and Its Dysregulation is Associated with Early Pregnancy Loss

Successful implantation requires precisely timed endometrial inflammation. Although an initial inflammatory burst is essential for implantation, this response must be rapidly resolved for placentation and pregnancy to progress. The mechanisms that coordinate this temporal switch remain poorly understood. Here, we identify the transcription factor HOXA10 as a key regulator of inflammatory transitions in decidual stromal cells and examine how its dysregulation contributes to implantation failure and early pregnancy loss. In mice, HOXA10 expression decreases transiently at implantation and rises again post-implantation. Silencing HOXA10 in human decidualized stromal cells induced a robust pro-inflammatory state, altered integrin and cytoskeletal gene expression, and impaired stromal substrate adhesion. In non-pregnant Hoxa10 hypomorphs, stromal cells exhibited elevated IL1β and TXNIP, activation of the NLRP3/ASC inflammasome, and dysregulation of receptivity markers. During pregnancy, persistent HOXA10 deficiency prevented the resolution of inflammation, resulting in disorganized decidua, defective placentation, infertility, or progressive reproductive decline. To assess translational relevance, we analyzed publicly available bulk and single-cell RNA-seq datasets from first-trimester human decidua and from women with recurrent pregnancy loss (RPL). Single-cell analysis revealed that HOXA10 is selectively low in inflammatory decidual stromal cell clusters, which display concordant upregulation of IL1B, PYCARD, TXNIP, and inflammasome components. Consistently, both bulk and single-cell datasets from women with RPL showed reduced HOXA10 accompanied by increased inflammatory gene expression. Overall, HOXA10 functions as a temporal switch that enables the initial inflammatory activation required for implantation and subsequently suppresses inflammation to support decidual organization, adhesion, and placentation. Loss of this switch leads to persistent decidual inflammation and is associated with pregnancy loss in both mouse models and humans. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/691844v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@ee81b6org.highwire.dtl.DTLVardef@85d84eorg.highwire.dtl.DTLVardef@13c1b6aorg.highwire.dtl.DTLVardef@12bed9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Apicortin defines the Plasmodium apical conoid body during transmission but is dispensable for the parasite life cycle

Apicomplexan parasites such as Plasmodium spp. and Toxoplasma gondii possess unique tubulin-based structures, including subpellicular microtubules and apical polar rings, which are essential for parasite motility, host cell invasion, and replication. How the stability of these structures is maintained is poorly understood, but it may involve Apicortin, a microtubule-associated protein, so-far found only in apicomplexans and the placozoan Trichoplax adhaerens. Apicortin contains a doublecortin (DC) domain and a partial tubulin polymerisation-promoting protein (TPPP) domain, both implicated in microtubule binding and stabilization. In this study, we investigated the location and function of Apicortin in Plasmodium berghei. Live cell imaging of a transgenic parasite line expressing GFP-tagged Apicortin showed that it was present at the apical end of invasive parasites only during development of transmission stages within the mosquito vector. High-resolution imaging using super-resolution and expansion microscopy, revealed that Apicortin forms a distinct ring-like structure in the apical complex region at the apical end of ookinetes and sporozoites. However, deletion of the Apicortin gene had no effect on parasite development and transmission through the mosquito, indicating that this protein is not essential. This suggests that there may be redundancy or compensatory functions in the mechanisms that stabilise the apical complex.

cell biology↗

bioRxiv2025

Ridge-assisted Micro Positioning of Cells and Particles in a Microchannel

The capability to deterministically and precisely control the lateral position of focused cell streams in a microchannel provides diverse opportunities for biomedical applications, including cell concentration, imaging flow cytometry, and cell-based liquid biopsy platforms. Inertial microfluidics introduced various high-throughput strategies for ordering particles and cells within microchannels. However, existing approaches do not permit precise control over the lateral focusing position of cells. By leveraging engineered microvortices generated by channel ridges and fluidic lift forces, we present a microfluidic method for deterministically positioning focused cell streams to desired lateral streamlines. Unlike inertial focusing, the ridge-assisted micro positioning (RAMP) is independent of particle size and flow rate, enabling polydisperse particles (10 to 30 m) to be focused to the same streamline across a broad range of flow rates (250-1000 L/min). The focusing position can be precisely adjusted by altering ridge placement and geometry, achieving both small (5 m) and large ([≥]15 m) lateral shifts in a controlled manner. Applying the RAMP concept, we developed clog-free microfluidic cell concentrators that can enrich single cells and clusters of cells to desired concentration factors and demonstrate the ability to focus particles in undiluted whole blood. Together, these results establish RAMP as a versatile platform for precise cell positioning in complex biological fluids. TeaserUse of designer vortices produced by ridges allows cells to be focused in user-defined streamlines across a microchannel over a wide range of flow rates.

bioengineering↗

bioRxiv2025

Oxidative stress-induced proteolytic activation of polyphenol oxidase triggers an oxidized flavonoids-mediated stress signaling in Camellia sinensis

Environmental perturbations often increase reactive oxygen species (ROS) production, inducing oxidative damage to various biomolecules. The cellular system utilizes ROS or ROS-generated metabolites to instigate signaling pathways, resulting in acclimation, growth inhibition, or programmed cell death (PCD) for sustaining stress. Various stress-generated or stress-activated signaling components and downstream pathways are identified in model plants; however, they are largely unexplored in non-model plants. Here, we report a stress-induced proteolytic activation of an evolutionarily conserved chloroplast-localized enzyme, polyphenol oxidase (PPO), that oxidizes catechins into theaflavins (TFs) and initiates a stress signaling under drought in Camellia sinensis (Tea). Germplasm-based analysis revealed a heightened proteolytic activation of PPO and consequent TFs accumulation in drought-susceptible genotypes. Transcriptome analysis revealed that PPO activation and TFs accumulation were linked to the activation of UPR(unfolded protein response)-like response, which was reinforced by virus-induced silencing and overexpression of PPO, and direct feeding of TFs in tea plants. Pharmacological treatments revealed that TFs interact with HSP90, activating a canonical IRE-bZIP60-dependent ER stress pathway resulting in PCD. Similar proteolytic activation of PPO and subsequent instigation of stress signaling in other plant species (tomato and wheat) demonstrated that PPO acts as an evolutionarily conserved stress sensor, instigating an inter-organelle communication in plants. Significance statementPPO, an evolutionarily conserved and chloroplast/plastid localized enzyme, senses stress and undergoes proteolytic activation to generate oxidized flavonoids/quinones that function as signaling molecules in Tea and likely in other plants. The oxidized flavonoids modulate protein folding machinery and augment folding stress, especially in the ER, inducing canonical IRE1-bZI60-dependent PCD. The finding shows that specific secondary metabolites likely have roles in instigating intra- and intercellular communication to sustain the adversities of stress in different plant species.

plant biology↗

bioRxiv2025

The cow udder is a potential mixing vessel for influenza A viruses

The incursion of high pathogenicity avian influenza A virus (IAV) into US dairy cows is unprecedented in the era of molecular diagnosis and pathogen sequencing. This raises questions over the likelihood of further outbreaks and whether dairy cattle could be a "mixing vessel" for novel strains of IAV. Using a panel of BSL2-safe reassortant viruses representing clade 2.3.4.4b H5 epizootic lineages circulating since 2020, we found that a cow B3.13 isolate displayed enhanced replication in cow mammary gland cells, along with increased viral polymerase activity and stronger interferon antagonism in cow cells compared to an earlier EA-2020-C genotype virus. However, multiple avian and mammalian IAV strains, including other clade 2.3.4.4b high pathogenicity genotypes, were replication competent in bovine cells, particularly those of the mammary gland, suggesting that there is a diverse circulating IAV pool with the potential to infect cows. Moreover, we show that cow mammary cells co-express -2,3 and -2,6 - linked sialic acids, and are susceptible to co-infection with human and avian IAVs. We conclude that the US cow influenza outbreak does not simply reflect a unique adaptation of the B3.13 genotype virus; rather, the bovine udder represents a permissive niche for IAV and a plausible site for reassortment, underscoring its potential role in generating novel influenza viruses with pandemic risk.

microbiology↗

bioRxiv2025

Plasmodium ARK1 regulates spindle formation during atypical mitosis and forms a divergent chromosomal passenger complex

Mitosis in Plasmodium spp., the causative agent of malaria, is fundamentally different from model eukaryotes, proceeding via a bipartite microtubule organising centre (MTOC) and lacking canonical regulators such as Polo kinases. During schizogony, asynchronous nuclear replication produces a multinucleate schizont, while rapid male gametogony generates an octaploid nucleus before gamete formation. Here, we identify Aurora-related kinase 1 (ARK1) as a key component of inner MTOC and spindle formation, controlling kinetochore dynamics and driving mitotic progression. Conditional ARK1 depletion disrupts spindle biogenesis, kinetochore segregation, karyokinesis and cytokinesis in both stages, and affects parasite transmission. Interactome analysis shows that ARK1 forms the catalytic core of a non-canonical chromosomal passenger complex (CPC) containing two highly divergent inner centromere proteins (INCENPs), which we term INCENP-A and INCENP-B, and lacking the canonical chromatin-targeting subunits Survivin and Borealin. Comparative genomics suggests that apicomplexan INCENPs arose through recurrent lineage-specific duplications, reflecting an evolutionary rewiring of CPC architecture in this eukaryotic lineage. Together, these findings reveal key adaptations in Plasmodium mitosis involving ARK1 and its INCENP scaffolds, and identify the ARK1-INCENP interface as a potential multistage target for antimalarial intervention.

microbiology↗

bioRxiv2025

Calcium chelation promotes microtubule regrowth and axonal recovery after laser-induced axonal injury

Traumatic stretch or crush injury to axons causes widespread and often irreversible damage to the axonal cytoskeleton, in which calcium-mediated breakdown is known to play a central role. Unlike complete transection, where recovery must proceed through formation of a new growth cone, milder injury can disrupt the axonal cytoskeleton while leaving the plasma membrane intact. How the cytoskeleton fails, and how it can recover, under these conditions remains unclear. Here we address this using a partial laser-ablation method that damages the cytoskeleton and evokes a calcium transient while preserving membrane continuity. We show that the ensuing cytoskeletal retraction is set by a mechanical balance between acto-myosin contractility and microtubule stability: stabilizing microtubules or inhibiting acto-myosin contractility suppresses retraction. Moreover, chelating extracellular calcium mitigates degeneration and, in a subset of axons, permits complete recovery. We also show that microtubules and actin filaments show distinct loss and recovery dynamics and provide a hypothesis for the "burning-fuse" -like depolymerization of the microtubule bundle. These findings provide insights into how the axonal cytoskeleton collapses and recovers after injury and suggest strategies for mitigating damage.

neuroscience↗

bioRxiv2025

A 3D Human Neuron-on-Chip Platform to Monitor Neuronal Injury Responses

Traumatic brain injury (TBI) is a major cause of neurological dysfunction and long-term neurodegeneration, yet the intrinsic neuronal contributions to TBI pathophysiology remain incompletely defined. Here, we present a novel Neuron-on-Chip microfluidic platform that can be used to mechanically injure mature human prefrontal cortex neurons (hPFCs) embedded in three-dimensional (3D) hydrogels, enabling the study of injury responses in pure neuronal cultures. We assessed real-time calcium dynamics across 13 metrics of single-cell and network activity, revealing a biphasic injury response: an early phase (0.5-24 hr) characterized by excitotoxicity, hyper-synchronized bursting, and network collapse; and a late phase (8 d) marked by sustained depolarization and structural remodeling. Secretome profiling uncovered progressive elevations in extracellular pT181 and total Tau from days 1 to 5 post-injury. Cytokine analyses identified early (24 hr) elevations in IP-10, IL-10, IFN2, and NCAM, and late increases (8 d) in CXCL9 and MPO, linking neuronal activity changes to stage-specific inflammatory signaling. Immunocytochemistry and immunoblotting confirmed temporally ordered upregulation of calpain-1 and active caspase-3 (days 1-3), phosphorylated Tau (AT8+, days 5-8), and neurofibrillary tangle-like Tau aggregates (NFT+, day 8). These findings establish our platform as a scalable microphysiological model for probing the dynamic cellular and molecular sequelae of neuronal response to injury, offering insights into neurodegeneration and opportunities for therapeutic discovery.

neuroscience↗