Biology subjects

Kumari, A.

Publications and source records attributed to Kumari, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Site, Fertilization and Season Structure the Soil Microbiome and its Interactions with Bdellovibrio and Like Organisms Predators

The contribution of predation between bacteria to microbial community dynamics in agricultural fields has hardly been investigated. Here. dynamics of general prokaryotes (GEP) and of the predators Bdellovibrionales (Bd) and Bacteriovoracales (Bac) (Bdellovibrio-and-Like Organisms, BALOs) were studied in two agricultural fields differing in organic and mineral input regimes, for one year. Season, but not fertilization, affected absolute sizes of GEP and of BALO communities. 16S rRNA gene community analysis identified numerous novel Bd and Bac lineages, with none of the dominant BALOs related to characterized isolates. A few dominant BALO amplicon sequence variants (ASVs) persisted year-round, whereas others showed seasonal- or treatment specific responses. GEP, Bd, and Bac ASV -diversity was mostly influenced by season, with some changes due to fertilization in Bd, and Bac communities. Seasonal changes, site, and fertilization regimes influenced {beta}-diversity of GEP, Bd and Bac communities and determined the structure of BALO-gram-negative bacteria interaction networks, signaling that niche segregation acts at the microbiome-BALO interface. Accordingly, we suggest that shifts in GEP community structure triggered by environmental changes and agricultural practices cascade to BALO predators, in turn affecting BALO-microbiome interactions. These dynamics may be harnessed to manipulate the soil microbiome to benefit sustainable environmental and agricultural outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/735237v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@ee25dcorg.highwire.dtl.DTLVardef@f79940org.highwire.dtl.DTLVardef@16e48a2org.highwire.dtl.DTLVardef@1628c9e_HPS_FORMAT_FIGEXP M_FIG The soil microbiome and the microbial predators Bdellovibrio and Like Organisms (BALOs) are influenced by environmental parameters (season) and agricultural practice (fertilization) in their population dynamics, diversity and interactions. BALO diversity is high, and novel clades are found with BALOs differing in abundance and persistence. Microbiome-BALO interactions suggest environment and agricultural practice-dependence of niche segregation in BALOs. BALOs - and other micro-predators-may thus be integrated in the development of soil microbiome manipulations for environmental and agricultural applications. C_FIG

microbiology↗

bioRxiv2026

Mechanistic basis of EMRE's essential role in the regulation of mitochondrial calcium uniporter complex

Mitochondrial Ca2+ uptake through the mitochondrial calcium uniporter complex (MCUcx) is a critical determinant of cellular metabolism, integrating Ca2+ signaling with ATP production and redox control. Yet how MCUcx activity is constrained to prevent Ca2+ overload and cell injury, and how the essential MCU regulator (EMRE), a subunit required for channel activity, mechanistically supports MCUcx function remains incompletely defined. Here, using a newly developed high-sensitivity assay to quantify MCUcx function in intact mitochondria, we uncover two fundamental roles of EMRE. First, EMRE is required for robust matrix Ca2+-dependent inhibition of MCUcx, acting through a juxtamembrane site via a mechanism distinct from MICU1-mediated inhibition at low cytosolic Ca2+. Second, by decoupling channel function from regulation, we demonstrate that EMRE promotes robust ion permeation through MCUcx, elevating its role from a structural scaffold to an active determinant of channel throughput. Together, our findings refine current models of mitochondrial Ca2+ regulation, establish EMRE as an essential multifunctional regulator of uniporter activity, and highlight the utility of our assay for probing MCUcx biophysical mechanisms and enabling the discovery of uniporter modulators. Significance StatementMitochondria use Ca2+ signals to adjust energy production to cellular demand, but excessive Ca2+ entry can trigger cell death. How the mitochondrial calcium uniporter balances these opposing needs remains fundamentally unresolved. Using a high-sensitivity approach that isolates uniporter permeation from Ca2+-dependent confounders in intact mitochondria, we characterize a matrix Ca2+-dependent inhibitory mechanism that depends on EMRE and is functionally distinct from MICU1-mediated regulation. We further show that EMRE, a small regulatory subunit unique to higher organisms, not only enables channel function but promotes robust ion permeation through the pore. Together, these findings refine current models of mitochondrial Ca2+ regulation and provide a unified framework for understanding EMRE-dependent uniporter regulation in intact mitochondria.

biophysics↗

bioRxiv2026

CDK1 facilitates RAD51-mediated DNA repair to protect dictyate stage arrested oocytes from genotoxic stress

Oocytes arrested at the dictyate stage of meiosis I must maintain genomic integrity for prolonged periods to preserve female fertility. During this extended arrest, DNA lesions arising from endogenous and exogenous sources threaten oocyte survival, yet the molecular mechanisms coordinating DNA repair in dormant oocytes remain poorly understood. Here, we identify cyclin-dependent kinase 1 (CDK1) as a critical regulator of the oocyte DNA damage response and homologous recombination (HR) repair under genotoxic stress. Using cisplatin-induced DNA damage models in fetal goat ovaries and neonatal mouse ovaries, we investigated repair mechanisms operating within the ovarian reserve. Label-free proteomic profiling revealed significant enrichment of DNA damage response pathways following cisplatin exposure, with CDK1 emerging as one of the most prominently upregulated kinases. Pharmacological inhibition of CDK1 had little effect on follicle survival under physiological conditions but aggravated oocyte and follicle loss following DNA damage, indicating a stress-dependent role for CDK1 in preserving ovarian follicle pool integrity. Mechanistically, DNA damage activated a Chk2-dependent signaling pathway that promoted p63 phosphorylation and altered the WEE1-CDK1 regulatory axis, resulting in reduced inhibitory CDK1 phosphorylation (Thr14/Tyr15) and increased activating phosphorylation (Thr161). Activated CDK1 was associated with enhanced RAD51 phosphorylation and accumulation at DNA damage foci, supporting homologous recombination (HR)-mediated repair in dictyate-arrested oocytes. In contrast, CDK1 inhibition reduced phospho-RAD51 levels, impaired RAD51 localization, increased persistent {gamma}H2AX accumulation, and elevated oocyte apoptosis. Notably, suppression of CDK1 was accompanied by increased expression of the non-homologous end joining (NHEJ) marker Ku80 and the nucleotide excision repair (NER) factor XPA, suggesting increased engagement of alternative DNA repair pathways. Furthermore, inhibition of Chk2 abolished the DNA damage-associated CDK1 activation signature and restored WEE1 expression, supporting a model in which CDK1 functions downstream of Chk2 signaling during the oocyte DNA damage response. Collectively, our findings identify a previously unrecognized Chk2-CDK1-RAD51 signaling axis that coordinates homologous recombination repair in dormant oocytes and safeguards ovarian follicular pool integrity under genotoxic stress. These findings provide new mechanistic insight into how dictyate-arrested oocytes maintain genome stability during prolonged meiotic arrest.

Cell Biology↗

bioRxiv2026

Exploring the Structural and Functional role of α,β-unsaturated Ketoesters as Anti-Staphylococcal Agents Targeting Glutathione Peroxidase

Multiple-drug resistant (MDR) Staphylococcus aureus strains (like methicillin-resistant S. aureus or MRSA) uses an arsenal of antioxidant enzymes to mitigate host-induced oxidative stress. Among them the non-canonical Staphylococcal glutathione peroxidase (SaGpx) plays a crucial role in bacterial redox homeostasis by reducing peroxides via thioredoxin-dependent pathways. Thus, enabling oxidative stress mitigation during host infection. Despite its importance in S. aureus, its role in bacterial pathogenesis remains unexplored. This study aimed to elucidate the possible role of SaGpx in Staphylococcal virulence. First, we determined the high-resolution crystal structure of SaGpx (at 1.65 [A] resolution) using X-ray crystallography. Guided by the catalytic cleft architecture of SaGpx, small-molecule based inhibitors were then rationally designed and synthesized. These inhibitors exhibited good binding affinity to SaGpx and complete enzymatic blockade. These inhibitors exhibited potent anti-S. aureus activity (MICs 6.25-31.25 M) along with no cytotoxicity in L929 fibroblast wound-healing assays. Furthermore, the in vivo antibacterial ability of these inhibitors was evaluated using S. aureus-infected skin wound mouse model, where these compounds show potent antibacterial and wound healing ability supported by subsequent histological as well as immunohistochemical analysis. These findings suggest SaGpx as a possible virulence determinant in S. aureus and position these synthesized inhibitors as promising antivirulence therapeutics. HighlightsO_LIThe high-resolution crystal structure of Staphylococcal glutathione peroxidase is solved. C_LIO_LIBased on the SaGpx catalytic site, ,{beta}-unsaturated ketoesters derivatives are synthesized. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives inhibit SaGpx activity and binds the protein at M range. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives show in vitro antibacterial activity against S. aureus at low M range. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives show in vivo antibacterial and wound healing ability S. aureus-infected skin wound mouse model. C_LI

biophysics↗

bioRxiv2026

Integrative genomics reveals shared and stress-specific adaptive pathways underlying acidic soil-associated metal toxicity in rice

Soil acidity-associated toxicities of aluminum (Al), cadmium (Cd), and manganese (Mn) severely constrain rice productivity in upland ecosystems. To investigate the genomic basis of adaptation to acidic soil-related metal stress, we conducted an integrated meta-QTL (M-QTL) and functional genomics analysis in rice. Meta-analysis of 681 QTLs and MTAs from 53 QTL mapping and GWAS studies identified 79 robust M-QTLs, including ten overlapping regions associated with Al-, Cd-, and Mn-responsive traits. A multi-criteria prioritization framework identified 98 candidate genes supported by positional overlap, transcriptomic recurrence, and functional annotation, enriched for ion transport, detoxification, and redox regulation pathways. M-QTL10.9 emerged as a major hotspot enriched for glutathione-S-transferase genes, whereas M-QTL9.5 contained the highest density of prioritized candidates linked to Al and Cd responses. Comparative physiological & biochemical analyses of the contrasting rice genotypes Sahasarang and IR64 revealed genotype-dependent differences in antioxidant responses, metal partitioning, metabolic regulation, and cell wall remodeling under individual and combined metal stresses. Expression profiling of prioritized candidate genes, including OsACO family genes, OsZIP10, and OsGSTU10, further revealed genotype-dependent transcriptional divergence under combined stress. The identification of overlapping M-QTLs across Al, Cd, and Mn datasets suggests both shared and stress-specific adaptive responses to acidic soil-associated metal stress in rice.

genomics↗

bioRxiv2026

In silico characterization of unique fungal modular rhodopsin expands the horizon of novel optobiological and biomedical applications

Microbial modular rhodopsins, in which light-sensing rhodopsin domains are fused with effector modules, have emerged as promising tools for optogenetic regulation in algae and other systems. However, the diversity and potential regulatory roles of fungal modular rhodopsins remain largely unexplored. Here, we performed a comprehensive in-silico analysis to identify previously uncharacterized fungal modular-rhodopsins that pair a conserved light-sensing core with diverse effector domains, including RPEL-motif, NADP-binding Rossmann fold domain, MCM (Mini-Chromosome Maintenance) domain, and GC-cAT (Carnitine O-Acetyltransferase) modules. In Aureobasidium pullulans, the representative modular rhodopsin (ApRh-RPEL) contains RPEL-motif associated with actin-related and transcriptional regulatory processes, suggesting light-driven fungal signaling pathway involved in transcriptional and cellular regulation, respectively. Rhodopsins fused with NADP-binding Rossmann fold and MCM domains further indicate possible applications in light-programmable metabolic and cell-cycle signaling. Genome mining additionally revealed that A. pullulans harbours a diverse but underexplored array of biosynthetic gene clusters (BGCs), raising the intriguing possibility that light perception may regulate secondary metabolite pathways. Supporting this, multisource protein-protein interaction network analysis links ApRh-RPEL to enzymes involved in terpenoid and sphingolipid biosynthesis, indicating potential cross-talk between light-sensing module and metabolic regulation. These findings outline a computationally derived model in which fungal modular rhodopsins (ApRh-RPEL) function as opto-synthetic regulators of biosynthetic processes. Structural predictions confirmed conserved Schiff-base lysine and retinal-binding pocket, highlighting functional diversity across fungal rhodopsins. Together, these findings expand the optogenetic toolkit and provide a framework for engineering light-driven signaling in fungi, with applications in optobiological and biomedical applications.

bioinformatics↗

bioRxiv2026

Antiviral Potential of Lauric Acid against Dengue Virus 2: Evidence from a Luciferase-Based Replicon Assay

Dengue virus (DENV) infection generates a significant health burden throughout the world, and there are no clinically approved antiviral drugs, as of now. The virus also depends on lipid metabolism in the host to conduct effective replication and this makes lipid-directed compounds promising as therapeutic options. We assessed the antiviral effect of lauric acid, a 12-carbon medium-chain fatty acid, against DENV serotype 2 (DV2) in the presence of a stable cell line, DV2-replicon, expressing all the non-structural proteins (NS1-NS5) and a luciferase reporter. Active viral replication in replicon cells was established by morphological examination and immunofluorescence of cells. The MTT assay was used to determine the cytotoxicity of lauric acid revealing the LD50 of 2.52 uM, so higher concentrations were toxic as the effect of the drug is dose-related. The antiviral effect was tested through replicon inhibition (luciferase) assay which showed an incredible inhibition of viral RNA replication with a IC50 of 1.70 uM and this is equivalent to antiviral mycophenolphycic acid. The cytopathic effects, as well as a decrease in the activity of luciferase, proved the presence of viral translation and replication inhibition within the process of the treatment of the lauric acid. These results propose that lauric acid has cytotoxic and antiviral dual effect and can be a possible inhibitor of DENV replication. The toxicity needs to be reduced and future research is necessary to explain its molecular pathway and also to come up with the best delivery methods. IMPORTANCEDengue virus (DENV) remains a significant health challenge to the world since there are no effective antiviral agents. This work will recognize lauric acid as a possible dengue virus replication inhibitor in a model of a DV2 replicon, exhibiting antiviral action that is similar to that of mycophenolic acid. These results support lipid-directed compounds as potential dengue antiviral targets, but more research is needed to minimize toxicity and better understand the molecular mechanism of action.

molecular biology↗

bioRxiv2026

HIPK2-and IKKβ-dependent phosphorylation stabilizes TAp63α during the oocyte DNA damage response

TAp63, a member of the p53 family, serves as a central quality control factor in oocytes, safeguarding genomic integrity during the prolonged dictyate arrest of meiosis. In healthy oocytes, TAp63 is maintained in an inactive dimeric state; upon DNA damage, it undergoes phosphorylation-dependent tetramerization, enabling transcriptional activation of pathways that determine oocyte fate. While the upstream activation cascade of TAp63 has been well characterized, the mechanisms that regulate its stability during the DNA damage response remain incompletely understood. Here, we identify the kinases HIPK2 and IKK{beta} as key regulators of TAp63 stability. We show that TAp63 interacts with both kinases and is phosphorylated at distinct residues, T452 by HIPK2 and S4/S12 by IKK{beta} in vitro and in vivo, in addition to previously described CHK2 and CK1-mediated phosphorylation. Functionally, these phosphorylation events do not primarily contribute to activation, but instead stabilize TAp63 by limiting MDM4-dependent ubiquitination and subsequent proteasomal degradation. Mechanistically, our data support a model in which CHK2 and CK1 initiate TAp63 phosphorylation, while HIPK2 and IKK{beta} act in a complementary manner to maintain protein stability during genotoxic stress. Disruption of HIPK2 or IKK{beta} activity reduces TAp63 stability, whereas their inhibition in vivo attenuates oocyte loss following DNA damage, resulting in increased preservation of the follicle pool. Importantly, these effects are observed across multiple systems, including mouse models and ex vivo goat ovary cultures, supporting an evolutionarily conserved role for this regulatory axis. Together, our findings uncover a previously unidentified layer of TAp63 regulation, in which phosphorylation not only contributes to its activation but also enhances protein stability, thereby fine-tuning oocyte responses to DNA damage. Our results further indicate that HIPK2 and IKK{beta}-mediated phosphorylation modulates oocyte survival under genotoxic stress, highlighting this pathway as a potential target for strategies aimed at limiting oocyte loss.

cell biology↗

bioRxiv2026

Meiotic cohesin paralogs govern cell survival by exhibiting flexibility in partner choice

Erroneous loading of the ring-shaped cohesin complex, especially at centromeres, cause chromosomal segregation defects in both mitosis and meiosis. Mitotic cohesin subunits of this complex, either get replaced or co-exist with their meiotic paralogs during meiosis and also in certain cancers. However, it is unclear whether meiotic paralogs can partner mitotic subunits to form hybrid complexes in somatic cells and if there are any functional consequences on cancer progression. Here, we provide a conceptual framework for the principles of cohesin complex assembly involving non-canonical subunits in proliferating Schizosaccharomyces pombe. We show that chromosome loading, segregation fidelity and cellular proliferation are critically affected by the composition of the available cohesin complexes. We find stark differences in the ability of the meiotic kleisin subunit Rec8 to support robust centromere loading, irrespective of its partner, when compared to the canonical mitotic paralog Rad21. Such variations in cellular growth can be explained by different dwell times of these cohesin complexes on the chromosomes as determined by single-molecule tracking and altered chromatin enrichment. We also discover a unique feature of Rec8, in stabilizing chromatin-bound hypomorphic cohesin mutants that aid in cell survival under restrictive conditions. Overall, we highlight the flexibility of meiotic cohesins in restoring function, albeit at a fitness cost, in the presence of inactivating cohesin mutations. Such imbalances could be exploited by cancers to aid cell survival, but at the expense of increased aneuploidy and genomic instability.

molecular biology↗

bioRxiv2026

Diet-conditioned microbiota enhances fecal microbiota transplantation efficacy in alcoholic liver disease through caproic acid-PPARα signaling

Background and AimFecal microbiota transplantation (FMT) in Alcohol-related liver disease (ALD) has shown therapeutic potential, with variable efficacy and unclear mechanism. Because dietary protein influences gut microbiota composition, we hypothesized that donor dietary preconditioning could enhance FMT efficacy. We therefore examined in a murine ALD model if high-protein donor diet improves FMT outcome. MethodsALD was induced in C57BL/6N mice using a Lieber-DeCarli ethanol diet combined with thioacetamide administration for 12 weeks. FMT was performed using stool from diet-modulated donors, and recovery was assessed on day7 post-FMT. Multi-omics analysis using 16s rRNA and mass spectroscopy was performed for Gut microbiota composition, plasma- and stool-metabolome, and hepatic proteomes. Multi-omics outcomes were validated in ALD animal and Huh7 hepatocytes. ResultsBoth protein-based FMTs improved ALD recovery; Veg-FMT demonstrated superior efficacy, significantly reducing hepatic injury (AST 1.2-fold, p=0.002; bilirubin 1.2-fold, p=0.03; steatosis 1.7-fold,p=0.01) and restoring gut barrier integrity (occludin 1.5-fold,p=0.04; mucin 2 2.2-fold, p=002; and plasma endotoxin 1.7-fold, p=0.02). A significant 2-fold increase was observed in Lachnospiraceae NK4A136, Coriobacteriaceae UCG-002, and short-chain fatty acids, particularly caproic acid. Functional validation confirmed that caproic acid promoted hepatic fatty acid {beta}-oxidation through PPAR-dependent mechanisms, reducing triglyceride accumulation and lipogenesis in both cellular and animal models. ConclusionDonor preconditioning with a plant-protein enriched diet enhances FMT efficacy in ALD by gut microbiota modulation with increased metabolites like caproic acid. These findings highlight a microbiota-metabolite-host axis through which diet-modulated FMT improves hepatic lipid metabolism and injury, and identifies a pathway via which FMT imparts its effect. SignificanceThis study identifies a mechanistic basis for improving fecal microbiota transplantation (FMT) efficacy in alcohol-related liver disease (ALD) by demonstrating that dietary preconditioning of donor microbiota improves therapeutic outcomes. We show that plant protein-modulated donor microbiota supplements abstinence-associated recovery through increased production of the microbial metabolite caproic acid, which promotes hepatic fatty acid {beta}-oxidation via PPAR signaling. These findings highlight donor dietary conditioning and microbiota-derived metabolites, rather than microbial composition alone, as important determinants of FMT efficacy. The results suggest that microbial metabolites such as caproic acid may represent potential therapeutic targets or biomarkers to enhance and standardize microbiota-based interventions in ALD. Although the current work is based on a murine model, the identified microbiota-metabolite-host metabolic axis provides a framework for future translational studies aimed at optimizing FMT strategies in liver disease.

microbiology↗

bioRxiv2026

SUMO modulates meiotic crossover rates between and within vertebrate species

Crossing over during meiosis drives genetic diversity and ensures the accurate segregation of homologous chromosomes. Variation in the rate of crossing over has been linked to evolutionary divergence and environmental adaptability, shaping fitness and responses to selective pressures. Despite its significance, the molecular mechanisms underlying this variation remain poorly understood. Crossover sites are selected from a large pool of potential sites initiated by programmed DNA double-strand breaks. Post-translational modification by SUMO (Small Ubiquitin-like Modifier) has been implicated in this process. Here, we show that crossover rate, chromosome length, and abundance of chromosome-associated SUMO are positively correlated across a range of vertebrate species, including mouse, chicken, pig, cattle, sheep, and goat. Crossover variation between goat breeds across the Indian subcontinent was also positively correlated with chromosomal SUMO level. Furthermore, modulating SUMO levels in cultured goat spermatocytes altered crossover frequency. Cumulatively, these observations point to a central role for SUMO in mediating crossover variation both between and within vertebrate species.

cell biology↗

bioRxiv2026

Excessive Ca2+-dependent ER-mitochondrial contact stabilization by EFHD1 drives liver injury

Metabolic-associated steatohepatitis (MASH) involves hepatocyte damage that cannot be explained solely by lipid accumulation. Here, to discover injury-specific pathways, we focused on a gene of uncertain function, EF-Hand Domain Family Member D1 (EFHD1), identified in human genome-wide association studies of liver injury but not liver fat. We show that EFHD1, a Ca2+-dependent actin crosslinker, stabilizes endoplasmic reticulum-mitochondria contact sites (ERMCS), detecting spatiotemporal coincidence of inter-organellar proximity and ER Ca2+ release. During MASH, EFHD1 upregulation drives pathological mitochondrial fragmentation via excessive contact persistence. This structural failure promotes mitochondrial double-stranded RNA escape and activation of a maladaptive antiviral PKR-dependent stress response, a causal relationship also supported by Mendelian randomization in humans. Consequently, inhibiting EFHD1 in human and mouse models blunts hepatocyte damage. These findings identify EFHD1 as a Ca2+-dependent ERMCS stabilizer, reveal a hepatocyte-intrinsic injury pathway, and suggest EFHD1 inhibition as a therapeutic strategy.

cell biology↗

bioRxiv2026

Gut microbiota-derived indole-3 acetic acid mitigates key hallmarks of metabolic dysfunction-associated steatotic liver disease (MASLD) in an NLRP3-dependent manner in in vitro and diet-induced mouse models

BackgroundMetabolic-dysfunction associated steatotic liver disease(MASLD) is a global epidemic affecting >30 % global population with no approved therapies till date. Recent reports suggest that activation of NLRP3 inflammasome may be involved in the pathogenesis of MASLD. We, therefore, aimed to identify small molecule inhibitor(s) of NLRP3 inflammasome as a potential therapeutic strategy to manage MASLD and validate their efficacy using in vitro and in vivo models of MASLD. MethodologyWe screened an in-house library of natural products using an in vitro phenotypic assay and identified a gut microbiota derived metabolite of dietary Tryptophan; indole-3 acetic acid (I3A) for its ability to inhibit the levels of IL-1{beta} and IL-18, which are elevated as a result of activation of NLRP3 inflammasome in differentiated THP1 cells. Subsequently, we carried out several in vitro and in vivo studies to confirm the mechanism of action of I3A and its ability to mitigate the key hallmarks of MASLD ResultsOur in vitro data suggest that I3A is an inhibitor of NLRP3 inflammasome. I3A was also found to improve the blood glucose level, plasma lipid profile, hepatic fat, and liver function in high-fat-high-fructose diet induced model of MASLD using C57BL/6 mice. ConclusionOur results show that I3A, which has been previously reported to be a gut microbiota-derived metabolite of dietary tryptophan, mitigates the key hallmarks of MASLD in an NLRP3 dependent manner. A dedicated structure-activity-relationship (SAR) study around the I3A chemotype may be carried out in future to identify novel NLRP3 inhibitors with desirable pharmacological profile.

pharmacology and toxicology↗

bioRxiv2026

Root-Suppressed Phenotype of Tomato Rs Mutant is Seemingly Related to Expression of Root-Meristem-Specific Sulfotransferases

Root development and growth are governed by a complex interplay between a plants genetic makeup and its ambient environment. In this study, we characterised a radiation-induced root-suppressed (Rs) mutant mapped on chromosome 4 of tomato. Rs seedlings had a dwarf stature, and mature plants exhibited abnormalities in their leaves, flowers, and fruits. The partial rescue of seedling root elongation by H2S donors or L-cysteine hinted that its root defect is linked to disrupted sulfur metabolism. The metabolite profiling of organs revealed altered homeostasis, analogous to that of plants subjected to sulfur starvation. Whole-genome sequencing revealed that the Rs genome was replete with genetic lesions; therefore, the pleiotropic morphological abnormalities likely emanate from mutations in other genes, including those related to sulfur. Among S-related genes, two sulfotransferase genes (Solyc04g028380 and Solyc04g028390) localised on chromosome 4 showed mutations in their promoters. The expression of both sulfotransferases is confined to the root meristem, suggesting a causal connection with the suppression of root growth. These sulfotransferases belonged to a distinct subset exclusively expressed in the root meristem and were distinct from the tyrosine sulfotransferase involved in the sulfation of root growth factors. Our study suggests that a sulfur-related module, other than tyrosine sulfotransferase, may regulate root development.

plant biology↗

bioRxiv2025

Aging increases ovarian cancer growth, metastasis and immunosuppression that can be alleviated by inhibiting hedgehog signaling

Ovarian cancer incidence and mortality increase with age, yet how aging shapes tumor progression and the immune microenvironment remains poorly defined. Using orthotopic syngeneic models of distinct cellular origins (ovarian surface epithelial and fallopian tube-derived) in young versus aged mice, we show that aged hosts exhibit higher tumor burden, metastasis and ascites. Follicle depletion in young mice did not recapitulate these effects, indicating contributions beyond hormonal decline. Spatial transcriptomics revealed distinct age dependent intratumoral heterogeneity, with Hedgehog signaling enrichment in CD45+ cells from aged tumors, alongside elevated CD206+ tumor-associated macrophages and FoxP3+ regulatory T cells. Pharmacologic Hedgehog inhibition in aged mice suppressed tumor growth, reduced metastasis, and decreased CD206+ macrophages and FoxP3+ T cells while preserving CD8+T cells. In human ovarian cancer, Hedgehog activation correlated with immunosuppressive and immune checkpoint resistance signatures. We propose Hedgehog inhibition as an immunomodulatory strategy for Hedgehog activated or post menopausal ovarian cancer.

cancer biology↗

bioRxiv2025

Lipid Droplet Remodeling Safeguards Redox Balance through the DGAT1-PANK2-NRF2 Axis in Mammalian Oocytes and Drives Age-Associated Decline

How lipid droplets (LDs) buffer metabolic stress and redox imbalance in aging oocytes remains poorly understood. Here, we identify de novo LD remodeling as a metabolic capacitor that couples lipid storage to mitochondrial fitness and oxidative resilience in mammalian oocytes. Live imaging revealed pronounced LD dynamics, with LD number peaking at metaphase I and declining by metaphase II, while LD area shifted inversely. Despite stable triacylglyceride and free fatty acid pools, {beta}-oxidation increased sharply, indicating elevated lipid turnover during meiotic progression. Spatial mapping and fatty-acid tracing demonstrated that newly synthesized lipids are actively incorporated into LDs, which arise primarily from the endoplasmic reticulum and engage with lysosomes and mitochondria. Acute inhibition of DGAT1, the rate-limiting enzyme of LD biogenesis, disrupted meiotic maturation and triggered oxidative stress, mitochondrial aggregation, and ultrastructural damage. Proteomic profiling revealed robust PANK2 upregulation and suppression of NRF2-linked antioxidant pathways. Mechanistic analyses showed that {beta}-oxidation blockade, PANK2 inhibition, antioxidant supplementation, or NRF2 activation each partially rescued DGAT1-dependent defects, and genetic validation in NRF2-null oocytes confirmed pathway dependence. Notably, aged oocytes exhibited reduced de novo LD biogenesis and impaired DGAT1-ER organization despite increased LD accumulation, resulting in smaller, metabolically inert droplets and a mismatch between lipid formation and utilization. Inhibiting PANK2 alleviated oxidative stress in aged oocytes, further implicating the DGAT1-PANK2-NRF2 axis in redox control and oocyte quality. Together, these findings establish LD biogenesis as a core metabolic capacitor safeguarding mitochondrial and organelle integrity during meiosis and reveal dysfunction of the DGAT1-PANK2-NRF2 axis as a mechanistic driver of reproductive aging.

cell biology↗

bioRxiv2025

Intraflagellar transport-20 coiled-coil domain mediates the channelrhodopsins trafficking to the cilia in Chlamydomonas reinhardtii

The primary cilium is a microtubule-based organelle essential for cellular signaling, whose assembly depends on intraflagellar transport (IFT). IFT20, a unique IFT-B component, localizes to both Golgi and cilium/flagellum, and plays a role in ciliary membrane protein trafficking. Here, we analyzed IFT20-mediated ciliary membrane trafficking of channelrhodopsin-1 (ChR1) in Chlamydomonas reinhardtii. IFT20 and ChR1 was found to be co-localized throughout the cilia of C. reinhardtii wild-type strain. In bbs1 mutants, IFT20 exhibited distribution along the flagellar length and basal body region. In contrast, ChR1 was found to be accumulating in the distal region of the cilia. Further, protein interaction network analysis reveals that IFT20 serves as a central adaptor, interfacing ancillary ciliary trafficking components, including Arf, the IFT complex, and BBSome subunits. The Arf co-localized with IFT20 in the cilia of the wild-type strain, suggesting a potential interaction. The fluorescence spectroscopic analysis shows that upon GTP binding, IFT20 undergoes concentration-dependent fluorescence quenching. From the far-UV CD spectroscopic analysis, it was observed that recombinant IFT20 has a predominantly helical structure, which does not change upon GTP binding. These findings extend the mechanistic understanding of ciliary membrane protein delivery in C. reinhardtii and reveal a conserved role of IFT20 in photoreceptor trafficking.

cell biology↗

bioRxiv2025

OpEnHiMR: Optimization based Ensemble Model for Prediction of Histone Modification in Rice

Histone modifications are central to gene regulation, yet their systematic identification in plants remains limited due to the complexity of epigenomic landscapes. We present OpEnHiMR, an optimization-based ensemble learning framework for multiclass prediction of three key histone modifications, H3K4me3, H3K27me3, and H3K9ac, in rice. The framework integrates Support Vector Machines, Random Forest, and Gradient Boosting models, optimized via Ant Colony Optimization to maximize performance. Biologically meaningful features, including mononucleotide binary encoding, nucleotide chemical properties, GC content, and k-mer frequencies, were used for training after rigorous data curation and redundancy removal. OpEnHiMR achieved a classification accuracy of 77.54%, outperforming individual models and ensuring improved recall, specificity, and Matthews correlation coefficient. Model interpretability was enhanced using SHAP analysis, which highlighted critical sequence features influencing prediction outcomes. To promote community-wide adoption, a user-friendly webserver (https://dipro-sinha.shinyapps.io/OpEnHiMR/) and R package (https://cran.r-project.org/web/packages/OpEnHiMR/index.html) were developed. OpEnHiMR thus provides a scalable, accurate, and interpretable tool for histone modification prediction in plants, advancing epigenomics research and supporting data-driven crop improvement strategies.

bioinformatics↗