Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Analysis and design of disordered polypeptides with optimized sequence patterning properties

Intrinsically disordered proteins (IDPs) exhibit phase separation behavior that is closely linked to their degree of single-chain compaction, which in turn is governed by both amino acid composition and sequence patterning. Existing metrics such as sequence charge decoration (SCD) and sequence hydropathy decoration (SHD) describe these effects but are largely limited to describing differences between sequences of similar length and overall composition. In this work, we present a shuffle-based normalization scheme for SCD and SHD, enabling comparison of sequence patterning between very different IDP sequences. Leveraging this normalization scheme toward design space, we develop a Monte Carlo based sequence design algorithm that generates novel IDPs with desired patterning features. Our design framework is further strengthened by incorporating additional metrics such as sequence aromatic decoration (SAD), compositional RMSD, and a previously developed sequence based {Delta}G predictor. We validate our approach through coarse-grained MD simulations, showing that the designed sequences exhibit tunable phase behavior. This strategy lays the groundwork for rational design of IDPs for biomedical and biotechnology applications, as well as basic biophysical research. Author summaryIntrinsically disordered proteins behave similar to polymers in solution, having no defined structure. Their behavior is dictated by the collection of shapes the protein adopts, known as its "conformational ensemble" which is tuned by its amino acid sequence and the solution environment. In this work, we have developed parameters to describe the patterning of charged and hydrophobic amino acids within these protein sequences, which are predictive of their ability to phase separate and form dense liquid-like droplets in solution. Importantly, the parameters we develop are motivated by physics and can be applied across a large number of amino acid sequences rapidly. This will enable researchers to rapidly predict the behavior of large libraries of protein sequences. We have additionally developed a software to design randomized amino acid sequences with desired amino acid composition and patterning properties. Finally, we have tested our design scheme and parameters by running simulations of designed IDP sequences and quantified each of their ability to phase separate.

biophysics↗

bioRxiv2026

Aging associated RNA loss impairs the dynamics of RNA and protein condensates

Altered biomolecular condensate dynamics are increasingly implicated in age-associated neurodegenerative disorders, yet the molecular principles governing these changes remain incompletely understood. Here, we demonstrate that aged cells across diverse cellular and organismal models harbor pre-formed, viscous, and persistent stress granules (SGs), which we term alt-SGs. These persistent condensates confer protection to senescent cells under fluctuating stress conditions. Comparative analyses reveal that alt-SGs exhibit elevated RNA-binding protein (RBP)-to-RNA ratios, underscoring a shift in condensate stoichiometry. By quantifying SG composition and dynamics in live cells and in vitro, we establish that RNA concentration is a key determinant of condensate material properties, molecular composition, and dissolution capacity. Importantly, aging cells display diminished absolute RNA concentrations due to reduced RNA metabolic activity. Reactivation of RNA metabolism restores RNA/RBP ratios within SGs and alleviates aging-associated phenotypes. Together, our findings highlight RNA metabolism as a central regulator of condensate stoichiometry and function, linking metabolic decline to altered phase behavior and cellular aging. Key findingsO_LIAging and senescence have Alt-SGs with increased protein/RNA Ratio C_LIO_LIAlt-SGs are persistent after stress removal in aging C_LIO_LIAging is associated with reduced total cellular RNA C_LIO_LIReactivating RNA metabolism rescues SG phenotypes C_LIO_LIAlt-SGs are protective for senescent cell C_LI

cell biology↗

bioRxiv2026

ADT-030, a novel PDE10 inhibitor, demonstrates potent antitumor activity in pancreatic ductal adenocarcinoma

Phosphodiesterase 10 (PDE10) has been noted to be highly expressed in multiple types of cancer and is crucial for the growth and maintenance of cancer cells found in colon, lung, and ovarian cancers. Here, we studied a novel orally bioavailable PDE10 inhibitor, ADT-030, and found that it potently inhibits the proliferation and clonogenicity of KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) cells at levels that block recombinant PDE10. ADT-030 also inhibited PDAC cell motility and triggered G2/M cell cycle halt and programmed cell death. These impacts were facilitated by raised cAMP/cGMP levels, activation of PKA/PKG, reduced {beta}-catenin and RAS signaling. Notably, ADT-030 diminished the proliferation of PDAC cells with KRASG12D and KRASG12C mutations that were resistant to both allele-specific and pan-RAS inhibitors. When administered orally, ADT-030 markedly decreased tumor growth, lowered the metastasis to the lungs and liver, and enhanced survival rates without causing systemic toxicity in both syngeneic and patient-derived xenograft (PDX) models of PDAC. ADT-030 also increased chemotherapy response in orthotopic PDAC models. Immune phenotyping and single-cell RNA sequencing revealed remodeling of the tumor microenvironment by ADT-030 with a more favorable anti-tumor immune profile. The findings suggest that ADT-030 holds promise as a potential drug development candidate for treating KRAS-mutant PDAC by simultaneously targeting key oncogenic signaling pathways, resulting in tumor-intrinsic and immunomodulatory effects.

cancer biology↗

bioRxiv2026

Cajal-Retzius fate specification is disrupted by constitutive activation of β-Catenin in hem progenitors

Cajal-Retzius cells (CR cells) are the earliest born neurons in the cerebral cortex, and have been implicated in regulating neuronal migration and development of circuitry. A major source of CR cells is the cortical hem, a signaling center at the dorsal telencephalic midline. The hem functions as the hippocampal organizer via canonical WNT signaling and hem progenitors are therefore exposed to high levels of WNT ligands. We tested whether constitutive stabilization of {beta}-Catenin (gain of function, GOF) in the mouse cortical hem progenitors supports CR cell production. We find that although neurons are produced from the hem, they do not acquire molecular features of CR cell identity. The trajectory of differentiation examined using single-cell transcriptomics reveals that immature CR cells normally display a Tbr2+ stage, which is absent upon {beta}-Catenin GOF. These data indicate that CR progenitors in the hem are sensitive to levels of stabilized {beta}-Catenin and that a Tbr2+ stage may be important for the acquisition of CR cell identity.

developmental biology↗

bioRxiv2026

Irrational groups: decoy placement, not group size, shapes collective shoal-size preference in adult zebrafish

Group living often improves decision accuracy in animals, yet whether increasing group size buffers against context-dependent biases remains unexplored. One such bias is the decoy effect, where the presence of a third option shifts preferences between two alternatives. Here, we tested whether introducing a decoy shoal influences collective preference for the larger female shoal in adult male zebrafish (Danio rerio), and whether the strength of this effect depends on group size. Groups of two, three, or four males were presented with female shoals under two choice contexts: a dichotomous contrast (four vs. two fish) and a trichotomous contrast including an additional alternative of one, three, or five fish. The order of presentation (dichotomous-first or trichotomous-first) was counterbalanced, and multi-animal tracking was used to quantify group-level shoal-size preference (time spent near shoals), inter-individual distance (IID), polarization, and swimming speed. In the dichotomous-first order, across all group sizes, subject shoals consistently showed a baseline preference for the larger shoal. Adding a third decoy option altered this preference only when the decoy was extreme (one or five fish relative to the 4 vs. 2 alternatives), reducing relative preference toward indifference. Group IIDs were associated with context-dependent shifts in relative preference in the dichotomous-first order, whereas polarization and swimming speed were not. In the trichotomous-first order, groups showed no preference for the larger shoal, with or without a decoy shoal. Our results demonstrate that context-dependent biases, shape collective shoal choice, with effects driven by choice structure and order of presentation of options than by group size.

animal behavior and cognition↗

bioRxiv2026

Predicting Obstetric and Non-obstetric Diagnoses Co-occurrences during Pregnancy

Pregnancy care often involves simultaneous obstetric and other medical conditions, but their co-occurrence patterns are rarely modeled explicitly in a systematic, network-based approach. In this work, we formulate obstetric and non-obstetric diagnoses co-occurrences as a link prediction problem on a diagnosis-level homogeneous graph constructed from pregnancy encounters. Diagnoses are represented as nodes connected by co-occurrence edges, with node features capturing graph structure and demographic statistics3. We address this challenge by leveraging collected electronic health records data and study several standalone and hybrid graph neural network (GNN) architectures, including GCN, GAT, GraphSAGE, and three hybrid encoders that combine complementary aggregation mechanisms, namely GCN+GraphSAGE, GCN+GAT, and GAT+GraphSAGE. All models used consistent train-validation-test splits and are evaluated on 5- fold cross-validation sets. Among standalone models, GraphSAGE achieved the strongest performance, whereas hybrid GraphSAGE-based models (GCN+GraphSAGE and GAT+GraphSAGE) are best performers. The GCN+GraphSAGE hybrid, reaching an AUROC and AUPRC of approximately 0.90, consistently outperformed all other architectures. Further analysis of top-ranked predicted links revealed clinically plausible associations between pregnancy stage and risk-related diagnoses and common endocrine, metabolic, and hematological conditions. These findings indicate that graph-based link prediction may effectively prioritize obstetric and non-obstetric diagnosis pairs, providing a scalable framework for identifying clinically meaningful comorbidity patterns. They may further support hypothesis generation and downstream obstetric risk stratification efforts. AvailabilityAll codes including data preparation scripts, training and validation recipes, and experimental configurations are available at: https://github.com/kabir-ai2bio-lab/ob-nonob-diagnoses-cooccurrences.

bioinformatics↗

bioRxiv2026

Cellular mechanisms of acquired drug resistance against regorafenib in colon cancer cells.

Colorectal cancer is the third most common cancer across the world. Acquired resistance to therapeutics is one of the major challenges in cancer cure. With the development of resistance to organometallic drugs there was switch for the usage of inhibitors of kinases which play a crucial role in cellular activities. Regorafenib is a multi-kinase inhibitor used as an oral anti-cancer drug for treating advanced colorectal cancer (CRC). With increasing reports of acquired resistance to regorafenib in long-term use it is inevitable to understand the mechanisms underlying in the development of resistance. To understand the molecular mechanism of acquired drug resistance towards regorafenib we have developed a regorafenib resistant HCT116 cell line (Reg-R-HCT116) and an integrated quantitative proteomic and phospho-proteomics approach is used to elucidate the molecular signaling mechanisms that help in drug tolerance. Proteome and Phosphoproteome analysis revealed an extensive remodelling of signaling pathways associated with metabolism, protein synthesis and stress adaptations. This also revealed a large set of phosphorylated proteins as well as proteins that might be associated with aberrant activation or differential alteration of PI3K-AKT-mTOR, EIF2, HIF-1, Apoptosis inhibition, Glucose metabolism, amino acid metabolism and DNA-repair-associated signaling. Differential phosphorylation of downstream molecules of the mentioned pathways NDRG1, ACINUS and RICTOR and enhanced cell survival further confirmed their role in drug tolerance. Targeted inhibition of both the mTOR complexes using Torin1 resensitized the cells to regorafenib. Combination treatment of regorafenib with torin1 showed a synergistic cytotoxicity and attenuated the expression of key survival proteins. These findings provide mechanistic insight into acquired resistance to regorafenib in colorectal cancer and identified mTOR/eIF2 signaling as one of the critical drivers of resistance phenotype. The results suggest combinatorial targeting of these pathways could be an effective strategy to overcome regorafenib resistance and improve clinical outcomes in CRC.

cancer biology↗

bioRxiv2026

A Genetic Mechanism Linking Hippo Signaling to Dorsoventral Patterning for Control of Head and Eye Development

The integration of growth and patterning in developing tissues is a complex process involving both intrinsic and extrinsic cues. The Hippo pathway, a conserved regulator of organ size, controls growth and patterning in Drosophila, including the development of the eye-antennal imaginal disc into adult structures. Defective Proventriculus (Dve), a SATB1/2 ortholog and K-50 type transcription factor regulates dorsal-ventral (DV) patterning during Drosophila eye development. Dve works with Wingless (Wg) to suppress eye development and promote head cuticle fate, thereby influencing the positioning of eyes and interocular distance. Our study investigates the role of the Hippo effector Yorkie (Yki), and dve in coordinating growth and patterning during eye development, specifically focusing on the regulation of the head cuticle domain. Here we show that Hippo signaling, mediated by Yki, regulates the size of the head cuticle domain and morphogenetic furrow (MF) progression, and that Dve suppresses Yki activity in the dorsal head region. Furthermore, Yki regulates several DV patterning genes like pnr, wg and mirr, to coordinate eye and head development. Mutations in mammalian orthologs of yki, dve, pnr and wg are associated with facial dysmorphia and several developmental disorders. Our studies thus reveal new genetic mechanisms by which growth and patterning are coordinated for head and eye development across species.

developmental biology↗

bioRxiv2026

Pol γ possesses separate metal binding sites for polymerase and strand displacement functions

Accurate replication of mitochondrial genome (mtDNA) integrity, which is essential for cellular metabolism and energy supply, relies primarily on DNA polymerase gamma (Pol {gamma}), Twinkle helicase, and mitochondrial single-stranded DNA binding protein (mtSSB). Twinkle alone exhibits little helicase activity while reports indicate that Pol {gamma} displays from modest to limited unwinding activity. This led us to dissect Pol {gamma} strand displacement activity using structural, biochemical and in silico approaches. Here, we show that human Pol {gamma} carries out robust strand displacement synthesis at physiological concentrations of divalent metal ions which reveals that distinct metal-binding sites can independently regulate DNA synthesis and unwinding activities. We further showed that Pol {gamma} can displace RNA/DNA hybrid with comparable efficiency as DNA/DNA duplex, representing a key implication on RNA primer removal to preserve mtDNA integrity. Our cryo-electron microscopy structures of Pol {gamma} complexed with a template containing downstream dsDNA and an incoming nucleotide revealed the structural mechanism for the strand displacement activity. We identified four conformational states that represent successive stages of DNA unwinding, accompanied by coordinated rearrangement of the downstream DNA and Pol {gamma} elements that mediate strand displacement. This work establishes biochemical and structural mechanisms of Pol {gamma} strand displacement activity, providing fundamental insight into human mitochondrial DNA replication and integrity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/701366v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1be1dborg.highwire.dtl.DTLVardef@8912c5org.highwire.dtl.DTLVardef@12f5e75org.highwire.dtl.DTLVardef@e25d2a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Coordinated inhibition of SOX9 and cell cycle progression by microRNA-200 restricts sebaceous gland fate specification

The microRNA-200 family (miR-200s) is widely recognized for their potent role in inhibiting epithelial-to-mesenchymal transition and cell cycle progression in cancer. However, their functional specificity in normal epithelial development remains poorly understood. Here we show that miR-200s are highly enriched in hair matrix progenitors but conspicuously absent from the upper hair follicle (HF), the anatomical location where sebaceous gland (SG) and HF stem cells are specified. We demonstrate that elevated miR-200 expression in this region abolishes SG fate specification while permitting hair morphogenesis. Genome-wide identification of miR-200 targets reveals that miR-200s regulate multiple negative regulators of WNT signaling, in addition to cell cycle regulators. Single-cell and spatial transcriptomic analyses uncover a mutually exclusive expression patterns between WNT activity and SOX9 in the upper HF, which is disrupted by miR-200 induction, resulting in compromised SOX9 function. Mechanistically, genome-wide identification of SOX9 targets uncovers a broad network of lipid and fatty acid metabolism genes critical for the transition of upper HF progenitors to the SG fate. The coordinated inhibition of the SOX9-dependent lipogenic program and the potent restriction of cell cycle progression, both mediated by miR-200s, collectively blocks SG specification. Taken together, this work reveals an unexpected specificity of miR-200 in restricting epithelial plasticity and elucidates a spatially defined SOX9 regulatory network essential for SG development.

developmental biology↗

bioRxiv2026

Circulating miR-4532 is associated with loss of ambulation in dysferlinopathy

BackgroundLimb-girdle muscular dystrophies (LGMDs) are inherited myopathies characterized mainly by progressive weakness of the proximal muscles of the shoulder and pelvic girdle areas, leading to functional decline and eventual loss of independent ambulation. Dysferlinopathy (LGMD2B) is an autosomal recessive LGMD subtype, is caused by mutations in the DYSF gene that lead to lack of dysferlin which results in muscle death and chronic muscle fiber degeneration. Preservation of ambulation is a key clinical milestone, as loss of independent gait markedly reduces quality of life and complicates care management. Although patients often perceive functional decline before their initial clinical presentation, current clinical assessments typically detect disease progression after substantial muscle damage has occurred. MethodsIn this multigroup case-control study, we profiled plasma miRNAs from 49 genetically confirmed dysferlinopathy patients (24 ambulatory, 25 non-ambulatory) and 25 age- and sex-matched healthy controls. Total RNA was extracted from blood samples and hybridized to Affymetrix GeneChip miRNA 3.1 arrays. After quality control and filtering, differential expression analysis was performed using linear models for microarrays, adjusting for age and sex, with a false discovery rate cutoff of 10%. Results14 miRNAs were significantly altered between dysferlinopathy patients and controls. Notably, miR-4532 was upregulated in ambulatory patients relative to controls, whereas it was downregulated in non-ambulatory patients compared with ambulatory patients, although expression levels remained higher than in controls. Levels of miR-4532 were positively associated with circulating monocyte levels in ambulatory patients only. ConclusionThese results suggest that miR-4532 may be a circulating marker associated with ambulatory status in dysferlinopathy. Its known involvement in inflammatory signaling and muscle regeneration pathways underscores its potential as an early indicator for disease activity.

bioinformatics↗

bioRxiv2026

Operations Near the Edge of cognitive decline: Behavioral and Neural Correlates of cognitive load in Mild cognitive impairment

MotivationEarly detection of cognitive strain is essential for identifying Mild Cognitive Impairment (MCI) and its progression to more severe neurodegenerative diseases. This study investigates cognitive strain in MCI by examining both behavioral and neural correlates during a real-world task. MethodsTwenty-four older adults (M=69, 14 male, 10 female), including 11 with MCI and 13 healthy controls (MMSE >22/30), performed a spatial navigation task under varying memory load. We recorded brain activity using electroencephalography (EEG) and a mismatch negativity (MMN) paradigm to capture error-related potentials (ErrPs), which reflect cognitive load and processing errors. ResultsBoth groups showed a decline in working memory performance as cognitive load increased ({beta} = -41.39, SE = 10.73, t(90) = -3.86, p < .001). MCI participants, however, exhibited more efficient use of non-intrinsic (allocentric) reference frames under high cognitive load ({beta} = 2.47, SE = 0.95, t(82) = 2.61, p = .009). MCI individuals also displayed larger ErrPs in central brain regions, indicating greater neural resource allocation. Additionally, MCI participants showed a decrease in parietal-to-frontal theta dominance under high load ({beta} = -0.68, SE = 0.32, t(90) = -2.12, p = .037), and reduced fronto-parietal connectivity. DiscussionThese findings suggest that MCI participants experience greater cognitive strain, evidenced by increased neural resource allocation and strategy-shifting under load. This heightened strain may serve as an early marker of MCI progression, offering potential for early detection of pathological changes.

neuroscience↗

bioRxiv2025

Viscoelasticity and interface properties of multi-component condensates govern protein sequestration and suppression of amyloid formation

Stress granules (SGs) are multi-component biomolecular condensates widely implicated as sites of protein aggregation by virtue of the high concentrations of amyloidogenic RNA-binding proteins they contain. This model, in which SGs are viewed as crucibles for amyloid formation, has not been rigorously tested. Here, we employed twelve multi-component protein-nucleic acid condensate systems as SG-mimics with diverse physicochemical features. Utilizing three fibril-forming proteins, hnRNPA1, Tau, and FUS, which are concentrated more than 50-fold in condensates, we report that multi-component biomolecular condensates robustly suppress, rather than promote, amyloid formation. Multiscale experimental analyses, including quantitative kinetic measurements, rheology, and microscopy, combined with computational modelling, reveal that condensates serve as sinks for soluble protein, and fibrils form in the dilute phase, although interfaces can promote nucleation. Three key physicochemical properties of condensates govern suppression of fibril formation: First, condensate-mediated sequestration lowers the concentration of fibril-forming proteins in the dilute phase. Second, condensate viscoelasticity constrains efflux-driven fibril growth in the dilute phase. And third, dilution of fibril-forming proteins at condensate interfaces mitigates fibril nucleation. The sink potential of SG-mimics is recapitulated in G3BP1-RNA condensates and SGs reconstituted in mammalian cell lysate, suggesting that SGs may have evolved to suppress stress-induced protein aggregation.

biophysics↗

bioRxiv2025

Spontaneous cancer regression as inversion of spontaneous cancer progression: Malignant melanoma remission as a case-study towards clinical applicability

The spontaneous cancer regression process (SCR) a rather rare paradoxical natural phenomenon, shows that malignant tumors can episodically undergo complete permanent elimination without treatment, and thus may be used for gaining clues to incisive therapeutic innovations. SCR of malignant breast tumors occurs subclinically across human populations ([~]22% rate), according to Scandinavian and Wisconsin Screening Registries (monitoring 0.33million and 2.95million population respectively). SCR occurs in discoid melanomas ([~]12% rate). SCR process has high novelty with no toxicity nor recurrence, and duplicating SCR process is indeed clinically desirable. We aim to probe SCR using melanoma as illustrative pilot-study, and identify candidate leads that may mimic SCR on the tumor. We investigated molecular biological of melanoma, finding two reciprocal phases: spontaneous-progression and spontaneous-regression, and showed driver genes for melanoma SCR. Then, we pursued network pharmaco-informatics analysis. We found that spontaneous melanoma eradication shows an unexpected finding, in distinct contrast to the prevalent view that immunological processes and immunotherapy are critical for melanoma regression, than targeting DNA. We found that in contradistinction, it is DNA interference process that is primary route for melanoma regression, while anti-tumor immune activation is only secondarily needed. We observed that targeting two pathways (kinase-system, inositide-system) by inhibiting two genes, arrested melanoma-progression phase, and activated the reverse phase, melanoma-regression. We investigated the interactions of possible candidate leads, indicating significant therapeutic potency. Our findings underscore the high impact possibility for leveraging the anomalous phenomenon of spontaneous cancer regression as a general oncological principle for probing targeted therapeutic interventions, with substantial clinical potentials.

cancer biology↗

bioRxiv2025

A dietary pan-amino acid dropout screen in vivo reveals a critical role for histidine in T-ALL

Dietary interventions show therapeutic potential in cancer, but systematic comparisons are lacking. We performed a dietary pan-amino acid dropout screen in an orthotopic model of NOTCH1-driven T-cell acute lymphoblastic leukemia and identified histidine depletion as uniquely antileukemic. Histidine-restricted diets extended survival of leukemic mice in a dose-dependent manner, while remaining well-tolerated. Mechanistically, multiomic profiling revealed that histidine deprivation-induced ribosome stalling activates GCN2 to suppress cholesterol biosynthesis pathways critical for leukemic proliferation. Dietary cholesterol supplementation partially reverted the antileukemic effects of histidine restriction in vivo. These findings couple histidine levels and translational control to cholesterol metabolism, which can be therapeutically exploited for cancer treatment. Our results suggest that defined dietary amino acid restrictions may expose broader therapeutic opportunities in diseases beyond cancer.

cancer biology↗

bioRxiv2025

Foraging egg parasitoids benefit from the presence of potential competitors

Competition is generally considered a negative interaction that lowers the fitness of individuals. Studies of competition and fitness traits in parasitoids have primarily focused on interference competition, with less attention paid to parasitoids under exploitative competition. Theoretical studies predict that interference competition will decrease the resource utilisation of parasitoids, while exploitative competition will not. In our study, we investigated the impact of intraspecific exploitative competition among parasitoids on fitness traits, including resource utilisation, the percentage of offspring that emerged from parasitised eggs, and the percentage of female offspring produced from parasitised eggs. We investigated whether these fitness traits were influenced by the presence of conspecific foraging females, as well as by parasitoid and resource densities. Since we were studying the effect of exploitative competition, we used Trichogramma chilonis, a non-aggressive egg parasitoid. Corcyra cephalonica, a stored grain pest, was used as the host. We found that T. chilonis resource utilisation increased in the presence of conspecifics. However, the density of those conspecifics and the resource density did not affect resource utilisation. The presence of conspecific foraging females did not affect the rate of offspring survival. However, at a lower resource density, offspring survival was higher than under resource-abundant conditions. We explored this counterintuitive pattern using a simple mathematical model, which shows that superparasitism, occurring at high parasitoid density, can lead to high emergence. This is because, given only some progeny survive, the chance of parasitoid emergence increases with the number of eggs laid in the host. The secondary sex ratio of the progeny was unaffected by the presence of conspecifics or by parasitoid or resource densities. We conclude that for T. chilonis, the presence of competitors has a positive effect. Its high performance under competitive conditions may contribute to its efficiency as a biological control agent.

ecology↗

bioRxiv2025

Outer Membrane Vesicles Hijack TIM-1 for Cellular Uptake

Outer membrane vesicles (OMVs) are nanoscale proteoliposomes shed by Gram-negative bacteria that mediate host-pathogen interactions and hold promise as platforms for vaccines and targeted drug delivery. Despite their biological and translational significance, the cellular mechanisms governing OMV entry into host cells remain poorly understood. Here, we demonstrate that E. coli OMVs are internalized by epithelial cells via clathrin-mediated, receptor-dependent endocytosis. Using a high-throughput screen of over 1,500 human single-pass transmembrane proteins, we identify T-cell immunoglobulin and mucin-domain 1 (TIM-1) as a strong OMV-binding receptor. Functional validation revealed that TIM-1 overexpression markedly increased OMV uptake, whereas TIM-1 knockout and antibody-mediated blockade significantly impaired internalization across multiple cell lines. Mechanistic studies demonstrate that TIM-1 binds to lipopolysaccharide (LPS) on the OMV surface via its known phosphatidylserine-binding domain. Uptake of OMVs by TIM-1 triggers proinflammatory cytokine production which can be reduced by preventing this interaction. Additionally, OMVs from multiple bacterial species hijack TIM-1 for entry, making it an intriguing antivirulence strategy. Our findings establish TIM-1 as a critical host receptor mediating OMV uptake and provide a novel approach to modulate vesicle-driven pathogenesis and enhance OMV-based therapies.

microbiology↗

bioRxiv2025

An Oral Combination therapy against SARS-CoV-2 based on Synergistic Action of Auranofin and Remdesivir.

The combination of direct-acting and host-directed antivirals targeting SARS-CoV-2 represents an attractive treatment strategy to combat COVID-19. In our previous work, we showed that the FDA-approved anti-arthritis drug Auranofin restricts SARS-CoV-2 replication and pathology in an animal model. Here, we report that Auranofin inhibits SARS-CoV-2 by targeting viral entry and main protease (Mpro) activity without affecting viral transcription. Time-of-addition studies combined with functional assays of viral entry, protease activity, and cell-cell fusion delineated its inhibitory effects at both early and late stages of the viral life cycle. Molecular docking and isothermal titration calorimetry analyses of Auranofin and the known Mpro inhibitor Nirmatrelvir indicated competitive binding within the Mpro active-site pocket. In addition, Auranofin attenuated NF-{kappa}B-dependent signalling and suppressed proinflammatory cytokine production. Combination studies with SARS-CoV-2 targeting nucleoside analogues, revealed the strongest synergistic antiviral activity with remdesivir in vitro. Comparable synergy was observed between auranofin and GS-621763, the orally bioavailable derivative of remdesivir, and was further validated in a preclinical animal model. Collectively, these findings provide a rationale for the further development of auranofin-nucleoside analog combinations targeting SARS-CoV-2. FundingThis research has been supported by ICMR (IIRPIG-2023-0000978) and BIRAC grant (BT/CS0070/06/22) to ST. We acknowledge the infrastructure and research support provided to IISc by the Crypto Relief Fund, L&T Trust, DST-FIST program, Institute of Eminence Fund, Ministry of Education, and the DBT-IISc partnership program (Phase II). RN acknowledges DBT-RA fellowship, SK acknowledges PMRF fellowship, and RS acknowledges FICCI-PMRF fellowship. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSMultiple previous studies have provided evidence showing that auranofin is an antiviral agent targeting SARS-CoV-2 through a host-targeting mechanism, involving the inhibition of thioredoxin reductase and redox homeostasis. Mixed results have been reported regarding the effect of this drug on inhibiting virus-induced syncytia. A prior study from our lab demonstrated the drugs effectiveness in reducing SARS-CoV-2 viral loads in both cell and animal models. Added value of the studyOur study firmly establishes the synergistic use of Auranofin and Remdesivir GS 621763 in the treatment of SARS-CoV-2 infection.

microbiology↗