Biology subjects

Ahmad, A.

Publications and source records attributed to Ahmad, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Calcium-activated chloride channels, rather than the voltage-gated ones, regulate sperm capacitation

Background: Ion channels regulate mammalian sperm function, yet chloride channels have received less attention than their cation counterparts. Herein, we investigated the presence, localization, and function of voltage-gated chloride channels (ClC-1, ClC-2, and ClC-K) and calcium-activated channels (ANO1 and ANO2) during sperm capacitation and the acrosome reaction. Results: Using the pig as an animal model, we localized these channels in different sperm regions: ClC-1 in the equatorial and post-acrosomal regions; ClC-2 in the connecting and principal pieces; ClC-K in the acrosome, connecting, and principal pieces; ANO1 in the principal piece; and ANO2 in the mid-piece and post-acrosomal sheath region. Following this, we addressed the roles of these channels in sperm capacitation and acrosome reaction by blocking them with different inhibitors: 9AC, specific for ClCs; BBR, specific for CaCCs; and NPPB, a broad-spectrum blocker that inhibits ClCs, CaCCs, and other chloride channels. Blocking CaCCs with BBR led to a significant reduction in sperm motility and mitochondrial membrane potential, with effects similar to those of the non-selective inhibitor NPPB or to a combination of BBR and NPPB. Moreover, although none of the three inhibitors affected intracellular calcium levels or acrosomal integrity, a significant reduction in protein tyrosine phosphorylation was observed in sperm treated with the combination of NPPB and BBR. Finally, membrane lipid disorder was increased when ClCs were blocked with 9AC and when sperm were incubated with a combination of BBR and NPPB. Conclusions: Our results suggest that CaCCs play a major role in sperm capacitation compared to ClCs. Further research to address the regulatory mechanisms involved and the potential relationship with other ion channels is warranted.

cell biology↗

bioRxiv2026

Genomic Context as a Predictor of Multidrug Resistance in African Klebsiella pneumoniae: A Feasibility Study with Leave-One-Country-Out Validation

Multidrug-resistant (MDR) Klebsiella pneumoniae is a leading cause of healthcare-associated mortality in Africa, yet genomic prediction of resistance has relied almost exclusively on resistance-gene detection validated under random data splits. Whether genomic context lineage, capsule and O-locus background, and virulence loci, with all resistance determinants excluded can predict aggregate MDR status, and whether such signal survives geographic transport, remains untested. As a feasibility study, we built an explainable machine-learning framework with leave-one-country-out (LOCO) cross-validation. Phenotypic linkage proved extremely scarce: only 231 of 9,505 strict-K. pneumoniae African NCBI records (2.43%) carry submitter-supplied antibiograms, necessitating a rule-based genotypic MDR proxy label. Country-sufficiency analysis showed LOCO is feasible on the current snapshot 8 countries at n >= 200 genomes but not on any previously published cohort. In a stratified pilot (175 species-confirmed genomes, 9 countries), tree ensembles reached pooled AUROC 0.85 under random splitting but only 0.66 - 0.69 under LOCO; this ~0.15 AUROC geographic-generalization gap suggests that pooled accuracy overstates transportability, though at pilot fold sizes (n <= 20 test genomes) confidence intervals are wide and overlapping. SHAP attributions implicated the ybt virulence locus and O-serotype background, indicating models exploit lineage-associated population structure. The substantive contribution is a leakage-controlled, fully reproducible pipeline indicating that geographic validation, not pooled accuracy, is the operative test for genomic AMR surveillance models.

bioinformatics↗

bioRxiv2026

Genome-Wide Selection Signatures in Nili-Ravi Buffalo (Bubalus bubalis) Reveal a T-Cell Costimulatory and Cytokine-Signaling Gene Network Distinct from Classical Bovine Tuberculosis Candidate Genes

Genomic signatures of selection can reveal loci underlying adaptation and disease resistance in livestock populations, but such analyses in water buffalo (Bubalus bubalis) have historically been constrained by the absence of a chromosome-level, species-native reference genome for SNP array data. We re-analyzed genotype data from 85 Nili-Ravi buffalo (Axiom Buffalo Genotyping 90K array, originally positioned using bovine (Bos taurus, UMD3.1) proxy coordinates, by performing a full coordinate liftover to the buffalo-native UOA_WB_1 assembly using an independently published SNP remapping resource. Following quality control (51,209 markers retained), haplotype phasing, and genome-wide integrated haplotype score (iHS) and Wrights Fst (case/control) selection scans, we evaluated 14 classical bovine-tuberculosis (bTB) candidate genes and identified six additional genes with putative immune function through an unbiased genome-wide screen. None of the 14 classical candidates (including SLC11A1, the Toll-like receptors, and IFNG) reached genome-wide significance in either scan. In contrast, six novel loci TNFSF18, IL2RB, TNFRSF19, IRF2, IL15, and CD28 showed significant iHS or Fst signals, four of which (TNFSF18, IL2RB, IL15, CD28) converge functionally on T-cell costimulation and cytokine receptor signaling (KEGG pathways map04660 and map04060, Bos taurus proxy annotation). Using extended haplotype homozygosity (EHH) decay, haplotype furcation structure, and per-marker haplotype counts as three independent lines of corroborating evidence, we classified these six genes into confidence tiers: TNFSF18 and IL2RB showed the strongest, most balanced support, while CD28 and IL15 signals were driven by very few haplotypes (3 and 5 of 30, respectively) and should be interpreted cautiously pending replication. These findings suggest that adaptive, cell-mediated immune signaling rather than the innate/macrophage-centred mechanisms emphasized by existing bTB candidate gene panels may be a more productive avenue for future selection studies in Nili-Ravi buffalo, while underscoring the value of buffalo-native coordinate systems for accurate genomic inference in this species.

genomics↗

bioRxiv2026

Industrialization restructures the domestic dog gut microbiome while preserving host specificity

Industrialization has reshaped human gut microbiomes, but its effects on other human-associated mammals remain poorly understood. Domestic dogs provide an informative comparative system because they have shared human environments and food systems for millennia yet retain distinct host biology. However, most canine microbiome studies have focused on industrialized companion animals, limiting our understanding of the ecological range of the domestic dog gut microbiome. We analyzed fecal 16S rRNA gene profiles from 261 dogs sampled across Nepal, Thailand, the United Arab Emirates, and the United States, spanning forager, agrarian, pastoralist, urban, and industrialized lifestyles; 257 dogs remained after excluding recent antibiotic exposure. Lifestyle was the strongest measured correlate of canine gut microbiome composition, and this structure persisted in restricted analyses of mature, non-shelter dogs sampled from temperate climate regions. Industrialized dogs differed from non-industrialized dogs through directional genus-level turnover, restructuring of VANISH- and BloSSUM-like microbial guilds, and shifts in predicted functional potential. Non-industrialized dogs were not microbiologically uniform: pastoralist dogs carried non-industrialized microbiome profiles but diverged from a simple forager-to-industrialized continuum. Cross-species comparisons with humans sampled across matched lifestyle categories showed parallel lifestyle-associated restructuring in both hosts, but host species remained the dominant axis of variation and the genera responding to industrialization were largely host-specific. These findings expand the ecological baseline for the domestic dog gut microbiome and identify industrialization as a major axis of microbiome restructuring in a long-term human-associated mammal. More broadly, they show that shared lifestyle transitions can impose parallel ecological pressures across host species without overriding host-specific community assembly.

microbiology↗

bioRxiv2026

CD248 activates TGF-β receptor I to promote vascular remodeling in pulmonary arterial hypertension

I.BackgroundPulmonary arterial hypertension (PAH) is a debilitating cardiopulmonary disease characterized by progressive remodeling of the pulmonary vasculature. Pathologic transforming growth factor-{beta} (TGF-{beta}) signaling is an essential driver of vascular remodeling in PAH. While global inhibitors of TGF-{beta} exist, their clinical application is limited by systemic adverse effects. Therefore, a critically unmet need in PAH is to identify pulmonary vascular-specific regulators of the TGF-{beta} axis, which would selectively enhance clinical efficacy while minimizing adverse effects. As the clinical care of PAH largely promotes vasodilation, and only one FDA-approved agent targets vascular remodeling, this study aimed to identify selective, therapeutically targetable regulators of the TGF-{beta} axis in the PAH pulmonary vasculature. MethodsCD248 was identified via liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics in human lungs. CD248 levels were assessed across human, rat, and mouse lung tissues using western blotting, RTqPCR, and/or immunofluorescence techniques. CD248-null (CD248-/-) mice were used to study the contribution of CD248 to hypoxia-sugen (H/S)-induced PAH. The mechanistic role of CD248 in PAH vascular remodeling and TGF-{beta} signaling was assessed by genetic (siRNA knockdown; overexpression) and pharmacologic (Ontuxizumab) manipulation of primary human pulmonary vascular cells. ResultsLC-MS/MS proteomics coupled with pathway enrichment analysis of human lung tissue identified CD248 as a putative mediator of vascular remodeling that is elevated in PAH lungs. CD248 was elevated in PAH pulmonary artery smooth muscle cells (PASMCs) across human, rat, and mouse lung tissue. CD248-/- mice were protected from H/S-induced elevations in right ventricular (RV) systolic pressure (RVSP), RV hypertrophy, and pulmonary artery muscularization. CD248 knock-down reduced cell proliferation and migration of primary PAH PASMCs. CD248 was essential for phospho-activation of TGF-{beta} receptor I (T{beta}RI) at S165 and canonical phosphorylation of SMAD3 at S423/425. CD248 loss blunted TGF-{beta}-induced gene expression (FN1, Col11, -SMA) and activated expression of the vasoprotective matrix metalloprotease, MMP-8. Mechanistically, CD248 interacted with and enhanced de novo phosphorylation and stability of T{beta}RI, blocking its ubiquitin-mediated proteasomal degradation. Ontuxizumab promoted T{beta}RI instability and attenuated the production of FN1, Col11, and -SMA in primary PAH PASMCs. ConclusionsThis work identifies CD248 as a previously unrecognized co-activator of T{beta}RI in PAH. As CD248 is largely quiescent in most adult tissues yet pathologically upregulated in the PAH pulmonary vasculature, this study supports the potential of anti-CD248 therapy as a novel pulmonary vascular-specific alternative to systemic TGF-{beta} inhibition.

molecular biology↗

bioRxiv2026

Genome-Wide Linkage Disequilibrium, Haplotype Block Structure, and Population Diversity in Nili-Ravi Buffalo (Bubalus bubalis)

Linkage disequilibrium (LD) and haplotype block structure govern the resolution and utility of genomic selection, marker-assisted selection, and genome-wide association studies (GWAS) in livestock. We performed a comprehensive genome-wide characterization of LD decay, haplotype block architecture, and population diversity across all 24 autosomes in Nili-Ravi buffalo (Bubalus bubalis; n = 85), using 43,543 post-quality-control SNPs. Mean genome-wide r2 was 0.124 (median 0.074) and mean D was 0.540 (median 0.481), with LD half-decay at {approx}70 kb. A total of 133 haplotype blocks encompassing 721 SNPs were identified (Gabriel et al., 2002). Haploview analysis of nine chromosomes harbouring bTB resistance candidate genes revealed contrasting selection signatures: directional selection at innate immune loci (IFNG, TLR1; H < 0.55) versus balancing selection at adaptive immune loci (BoLA-DRB3, SP110; H > 1.0). Critically, BBU15 Block 3 (28.6 kb; OR52E5/NCR1 locus, 47.16 Mb) showed a genome-wide significant integrated haplotype score (iHS; -log1 0 p = 5.408), directly co-localising with the published bTB susceptibility QTL (Bermingham et al., 2014). The TAA haplotype (frequency 53.3%) at this block represents a candidate resistance-associated haplotype for marker-assisted selection. These findings provide essential parameters for SNP panel design and bTB resistance breeding in South Asian buffalo.

genomics↗

bioRxiv2026

Molecular Imaging of Collagen Turnover in Myocardial Infarction

Cardiac fibrosis is a key contributor to cardiomyopathy after myocardial infarction (MI). Existing imaging techniques can detect established fibrotic changes; however, they lack sensitivity for ongoing collagen turnover--a dynamic process involving the denaturation of collagen triple helix. Molecular imaging of this process could enhance risk assessment and aid in the development of anti-fibrotic treatments. This study aimed to evaluate 99mTc-(HE)-(GPO), a radiotracer designed to target denatured collagen, as a biomarker of collagen turnover after MI. Methods99mTc-(HE)-(GPO) incorporates glycine-proline-hydroxyproline (GPO) repeats and can hybridize with denatured single- or double-stranded collagen. MI was induced in mice by ligation of the left anterior descending artery; sham-operated animals served as controls. At 2 weeks post-MI, animals underwent myocardial perfusion imaging or contrast-enhanced CT to detect the infarct zone, followed by SPECT/CT imaging using 99mTc-(HE)-(GPO) or a control scrambled tracer. Tracer uptake was quantified in vivo and ex vivo with gamma counting and autoradiography. Different aspects of fibrosis were examined by tissue analysis, along with autoradiography with a matrix metalloproteinase-targeted radiotracer, 99mTc-RYM1. Tracer binding was also assessed in human cardiac tissue through ex vivo autoradiography. Results99mTc-(HE)-(GPO) SPECT/CT revealed significantly higher tracer uptake in the infarct zone of MI mice compared to the remote zone and sham controls (P < 0.0001 for both). Tracer uptake was confirmed by autoradiography, which showed a strong correlation between SPECT and autoradiography (R = 0.81, P < 0.01). The scrambled tracer exhibited minimal cardiac uptake, demonstrating the specificity of 99mTc-(HE)-(GPO) signal. Denatured collagen staining and 99mTc-RYM1 autoradiography showed similar patterns as ex vivo 99mTc-(HE)-(GPO) autoradiography, while the ratio of denatured collagen to procollagen in the infarct zone significantly increased from day 3 to 2 weeks post-MI. Finally, 99mTc-(HE)-(GPO) bound to human fibrotic (but not normal) cardiac tissue. Conclusion99mTc-(HE)-(GPO) enables non-invasive detection of denatured collagen as a marker of collagen remodeling in vivo, offering a promising tool for assessing fibrotic remodeling after MI. Collagen, procollagen, and denatured collagen, along with MMP activation, exhibit distinct patterns, and their combined imaging may provide a comprehensive molecular fingerprint of cardiac fibrosis, advancing personalized management of cardiomyopathy.

bioengineering↗

bioRxiv2026

Aging, matrix metalloproteinase imaging, and survival prospects in aortic aneurysm

Age is a risk factor for aortic aneurysm (AA), and different segments of the aorta exhibit varying susceptibilities to aneurysm. The specific factors that contribute to the higher incidence of AA and its complications with aging remain unclear. Matrix metalloproteinases (MMPs) are elevated in AA. However, the connection between aging, aortic MMP activity, and the increased prevalence of AA and its complications has not been systematically evaluated. This study leveraged MMP-targeted molecular imaging to investigate how aging affects aortic MMP expression and activity, as well as aneurysm development and survival. MethodsAA development and animal survival were monitored for 28 days after Angiotensin (Ang)-II infusion in 8-10-week-old (young) and >51-week-old (old) Apoe-/- mice. Aortic MMP activation was quantified by PET/CT using an MMP-targeted tracer, 64Cu-RYM2, at baseline and 1 week after Ang II infusion. MMP activity and expression were quantified by tissue zymography and quantitative reverse transcription polymerase chain reaction, and compared between different segments of the aorta in young and old animals, and before and after Ang II infusion. ResultsOld animals survival to 28 days was significantly lower than that of young Ang-II-infused Apoe-/- mice (P < 0.05). 64Cu-RYM2 PET/CT showed significantly higher aortic MMP activation before and 1 week after Ang-II infusion in old compared to young Apoe-/-mice. The 64Cu-RYM2 signal was significantly higher in animals that did not survive 28 days than those that did (P < 0.01). MMP activity significantly increased by 4 days after Ang-II infusion, when dissection was found in a subset of Apoe-/- mice; and was significantly higher in the dissected, compared to adjacent, apparently normal, segments of the aorta. MMP activity was also significantly higher in the ascending thoracic aorta of untreated young and old mice, as well as of Ang-II-treated Apoe-/-mice (which was associated with significantly higher Mmp2 gene expression), and of old wild-type mice. ConclusionAging is associated with increased MMP activity along the aorta and worse AA survival. MMP-targeted molecular imaging can inform the aneurysm survival prospects. Selective MMP inhibitors and tracers may help prevent and track aneurysm growth, dissection, and rupture.

bioengineering↗

bioRxiv2025

Endothelial Adgrl2 expression and alternative splicing controls the cerebrovasculature

Central nervous system development requires parallel but interrelated processes of neural circuit assembly and vascularization. Intersecting between these two processes, the cell-adhesion G-protein coupled receptor Adgrl2 is expressed in select neuron populations where it has been found to localize and control the assembly of specific synaptic sites. Further, Adgrl2 is found to be expressed in select non-neuronal brain cells, where it is restricted to endothelial cells. Testing for Adgrl2 function in these cells, here we find that endothelial cell specific Adgrl2 deletion results in an impairment in cerebrovascular integrity. To understand how it might be possible for Adgrl2 to function independently in neuronal and endothelial contexts, we analyzed single-cell RNA sequencing datasets for differences in transcriptional identity between these cell classes. Doing so, we find that expression of Adgrl2 mRNA is subject to robust cell type-specific alternative splicing, resulting in distinct isoforms being produced in neurons compared to endothelial cells. Investigating the functional implication of this cell type-specific alternative splicing, we find that forced expression of the neuronal isoform of Adgrl2 in endothelial cells leads to alterations in cerebrovascular properties. Morphologically, endothelial cells with the non-native neuronal Adgrl2 isoform induce the formation of ectopic glutamatergic synaptic contacts onto endothelial cells, indicating alterations in the cell-cell recognition process. Functionally, in direct contrast to endothelial Adgrl2 deletion, this genetic expression switch instead enhances blood-brain barrier integrity. This overly restrictive cerebrovascular function results in dysregulation of blood to cerebrospinal fluid homeostasis, enlargement of brain ventricles, and a higher risk of hydrocephalus. As such, alternative splicing serves as a cell type specific mechanism that provides isoform specific Adgrl2 for discerning functions controlling neural circuit assembly and cerebrovascular homeostasis.

neuroscience↗

bioRxiv2025

Relationship between SARC-F score and Peripheral Blood Lymphocytes in Juvenile Idiopathic Arthritis: An Observational Pilot Study

BackgroundGiven the relatively high prevalence of sarcopenia and immune profile abnormalities in inflammatory arthritis such as rheumatoid arthritis (RA), we investigated the relationship between exercise habits, SARC-F score and peripheral blood lymphocyte profiles in patients with Juvenile idiopathic arthritis (JIA). MethodsAll participants with JIA completed the SARC-F survey and self-reported exercise habits through online questionnaires. We defined two groups based on SARC-F scores as musculoskeletal function impaired (SARC-Fhi+) and musculoskeletal function not impaired (SARC-Fhi-). We used flow cytometry of peripheral blood mononuclear cells to define immune cell subpopulations. Statistical analyses were performed using GraphPad Prism software version10. ResultsOf the 18 participants with a median age of 24 years - five belonged to the SARC-Fhi+ group and 13 to the SARC-Fhi-group, of whom 80% and 38% were female, respectively. The SARC-Fhi + group had fewer CD45RA+CD27+ naive CD4+ T cells (26.60% vs. 45.30%, p=0.0264) and greater CD45RA-CD27-effector memory CD4+ T cells (11.90% vs. 7.00%, p=0.0350). The SARC-Fhi+ group also had fewer CD56-CD16+ NK cells compared to the SARC-Fhi-group (2.60% v. 4.28%, p = 0.0194). The moderate exercise group (n = 13) had increased numbers of total CD4+ T cells (54.06% vs. 37.30%, p=0.0140) and 3-fold fewer CD45RA+CD27-EMRA CD8+ T cells (3.17% vs. 10.40%, p=0.0350). There were no other significant differences for other immune cells / subpopulations including B cells. ConclusionsOur study findings suggest notable differences in immune profile relative to SARC-F score. Furthermore, the 3-fold lower frequency of CD8+ TEMRA subpopulation of T cells, reflective of immunosenescence, suggest a potential inverse relationship between moderate exercise and peripheral immune cell profile in JIA. Key messagesO_LISARC-F score was used as a clinically relevant tool to identify musculoskeletal function in JIA C_LIO_LISARC-Fhi+ group had fewer naive CD4+ T cells and greater effector memory CD4+ T cells C_LIO_LIModerate exercise group had 3-fold lower frequency of CD8+ TEMRA T cells C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=54 SRC="FIGDIR/small/681879v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1eb9d4org.highwire.dtl.DTLVardef@13a18a4org.highwire.dtl.DTLVardef@127d55corg.highwire.dtl.DTLVardef@28bddf_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Spike protein E2 of chikungunya virus: a plant-based vaccine exhibited potent immunogenicity in BALB/c mice

Over the last two decades, chikungunya virus (CHIKV) infections have surged worldwide, causing significant suffering. CHIKV E2 gene codes for spike protein E2, essential for virus-host interactions and thus serves as a potential vaccine candidate. We expressed a full-length E2 (S27 African prototype) in both E. coli and Nicotiana tabacum, which triggered an immune response in BALB/c mice. First, E2 was computationally analyzed for PTM patterns and prediction of B-cell and T-cell epitopes. Next, molecular docking of epitopes with MHCs (Class I and II) revealed high affinity, confirmed by Molecular Dynamics Simulation. Then, the chemically synthesized E2-6xHis tag was cloned and expressed in both E. coli and N. tabacum under T7 and CaMV promoters, respectively. E2 was cloned into the pUC57 vector (E. coli) and expressed using the pET28a(+) vector in BL21(DE3)pLysS cells, followed by cloning into the pCAMBIA1302 vector and transformation into Agrobacterium tumefaciens. RT-PCR and confocal visualization confirmed the formation of E2 transcripts. Recombinant E2 was purified on Ni-NTA columns and visualized as a protein of [~]49 kDa on SDS PAGE. Finally, E2 was injected into BALB/c mice; neutralizing antibodies, including IgG, were detected as positive in the indirect ELISA, with the highest levels observed at 3 days post-infiltration (3 dpi). Western blot also confirmed E2 expression in E coli and tobacco, and induction of E2-specific antibodies in BALB/c mice. This study presents a promising approach to developing a safe and effective vaccine against chikungunya fever in plants.

molecular biology↗

bioRxiv2025

Structural variants are enriched in deleterious visible phenotypes in Drosophila

Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore long reads. These assemblies enabled the creation of a pangenome graph containing comprehensive, nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncovered new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, we mapped the tarsal joint defect AblpeyD to an 8 kb Roo retrotransposon insertion into an intergenic enhancer, a finding validated via CRISPR-Cas9. The wing vein phenotype plexus (px1) was linked to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c1) wing phenotype was linked to a 7.5 kb DM412 retrotransposon inserted into the coding sequence of the muscle protein gene Strn-Mlck. We also unveiled 8 SV alleles of previously identified causal genes, including previously uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of the genes causing phenotypic changes harbored candidate SVs over 100 bp, whereas only 28% is expected based on euchromatic SVs. Our data, based on the 50 Drosophila phenotypes, 44 of which are strongly deleterious, suggests a disproportionately larger contribution of SVs to deleterious changes in visible phenotypes in Drosophila.

genomics↗

bioRxiv2025

Mechanistically explainable AI model for predicting synergistic cancer therapy combinations

This study introduces a Large Language Model (LLM)-based framework that combines drug combination data with a knowledge graph to predict synergistic oncology drug combinations with mechanistic insights. Using a retrieval-augmented generation (RAG) approach, over 50,000 in vitro drug pair assay results and 1,631 human clinical trial or preclinical test entries were integrated to enhance predictive accuracy and explainability. Validation achieved an F1 score of 0.80, demonstrating the frameworks potential to streamline drug discovery and improve translational strategies in cancer treatment.

cancer biology↗

bioRxiv2025

RAPID: Real-time Animal Pattern re-Identification on edge Devices

Automatic re-identification of animals has significant potential for addressing pressing challenges of our times via population monitoring, individual health assessment or detailed behavior analysis. Although numerous computer vision based solutions have been proposed and many achieve high accuracy, those still remain unsuitable for real-time analysis and deployment on edge devices. Here, we introduce RAPID, an open-source1 algorithm for re-identifying patterned animal images at a rate exceeding 40-60 queries per second on standard PC or Laptop and over 10 queries per second on an inexpensive off-the-shelf edge device. RAPID operates efficiently in computationally restricted environments, relying solely on CPU, leaving GPU resources available for other tasks, all while maintaining state-ofthe-art accuracy. Our approach leverages SIFT descriptors, which continue to demonstrate competitive robustness and accuracy against recent traditional and deep-learning based methods. To counterpoise SIFTs primary limitations its high-dimensional feature vectors and the associated computational costs - we incorporate recent advancements in vector similarity search and construct a database of feature vectors rather than database images, further accelerating the search process. We evaluate our method, RAPID, on public re-identification datasets; additionally propose a RAPID-based tool, FalseTagFinder, for cleaning benchmark dataset labels and as a demonstration, provide corrections for the StripeSpotter dataset.

ecology↗

bioRxiv2025

Integrative multi-omic analysis reveals oral microbiome-metabolome signatures of obesity

Obesity is a major global health challenge and a leading risk factor for cardiometabolic disorders. The global surge in obesity, driven by industrialization and the widespread consumption of low-fiber, ultra-processed food, highlights an urgent need for deeper biological insights. While the gut microbiome has been studied in the context of obesity, the contribution of the oral microbiome--the second largest microbial ecosystem in the human body-remains largely underexplored. Here, we report findings from a deeply-phenotyped prospective-cohort of 628 Emirati adults, leveraging amplicon sequencing of mouthwash samples and multi-omics profiling and functional and metabolic activity analysis of 97 obese individuals and 95 matched controls, making this the most comprehensive multi-omics analysis of the oral microbiome. We identified significant differences in oral microbial diversity, composition, functional pathways, and metabolic profiles between obese and non-obese groups. Integrated multi-omics analysis of the 192 matched metagenomes and metabolome samples uncovered significant metabolic reprogramming and altered energy regulation in obesity. Specifically, the oral microbiome of obese participants were enriched for the proinflammatory Streptococcus parasanguinis and Actinomyces oris, and the lactate-producing Oribacterium sinus. Many microbial pathways involved in dietary carbohydrate metabolism, histidine degradation, as well as the production of obesogenic biomolecules were also enriched in obese participants; however, B-vitamin and heme production pathways were depleted. Consequently, metabolites resulting from these pathways such as lactate, histidine derivatives, choline, uridine, and uracil were elevated in obesity. These consistent microbiome-metabolite shifts were strongly associated with prominent obesity-associated cardiometabolic markers, including serum triglycerides and alkaline phosphatases, establishing a robust link between oral microbiome and obesity. These findings provide the most comprehensive insights into how disrupted microbial-metabolic cross-talk in the oral cavity may contribute to obesity and related cardiometabolic disease risk, underscoring the potential of targeting of oral microbiome-host interactions as a novel avenue for obesity prevention and intervention.

microbiology↗

bioRxiv2025

Multi-locus phylogenetic network analysis of Ampelomyces mycoparasites isolated from diverse powdery mildews in Australia and the generation of two de novo genome assemblies

The interactions between powdery mildews (Ascomycota, Erysiphaceae), obligate biotrophic pathogens of many plants, and pycnidial fungi belonging to the genus Ampelomyces, are classic examples of specific mycoparasitic relationships. These interactions are common and finely tuned tritrophic relationships amongst host plants, powdery mildews, and Ampelomyces mycoparasites wherever these organisms co-occur in the field. Selected Ampelomyces strains have already been developed as biocontrol agents of powdery mildew infections of some crops. In Australia, their study has received little attention so far. Only a single Ampelomyces strain, included in a whole-genome sequencing (WGS) project, was known from this continent. Here, we report the isolation of 20 more Ampelomyces strains from eight powdery mildew species in Australia. Multi-locus phylogenetic network analyses of all the 21 Australian Ampelomyces strains carried out in combination with 32 reference strains from overseas revealed that the Australian strains belonged to four molecular taxonomic units (MOTUs). All those MOTUs were delimited earlier based on Ampelomyces strains isolated in Europe, North America, and elsewhere. Analyses indicated possible recombination events amongst phylogenetically different Ampelomyces strains. Based on the phylogenetic analyses, two Australian strains belonging to different MOTUs were selected for WGS. Long-read (minION) and short-read (Illumina) technologies were used to provide genome assemblies with high completeness. Both assemblies reported here had bipartite structure, i.e., consisted of AT-rich, gene-sparse regions interspersed with GC-balanced, gene-rich regions. These new high-quality assemblies and evidence-based annotations are important resources for future analyses of mycoparasitic interactions to disentangle molecular mechanisms underlying mycoparasitism, possible new biocontrol applications, and natural tritrophic relationships.

microbiology↗

bioRxiv2025

Melatonin Enhances Sleep via MT1-Driven Activation of Slo1 in Suprachiasmatic Nucleus Neurons

Melatonin promotes sleep through mechanisms that have remained elusive. Here, we identify a molecular pathway by which melatonin promotes sleep by activating BK channels (Slo1) via MT1 receptors in the suprachiasmatic nucleus (SCN), the brains master circadian clock. In melatonin-proficient CBA/CaJ mice, knockout of either MT1 or Slo1 reduces REM and NREM sleep during the rest phase (daytime), accompanied by prolonged action potentials and diminished afterhyperpolarization in SCN neurons. These electrophysiological and behavioral changes are minimal during the active phase (nighttime). Strikingly, Slo1 expression in the SCN peaks during the daytime, contrary to previous reports, but aligning with its sleep-promoting function. Slo1, but not MT1, deletion also triggers spontaneous seizures, highlighting broader functions beyond circadian control. Structural mapping identifies critical domains mediating MT1-Slo1 coupling. Together, these findings position the MT1-Slo1 signaling axis as a core circadian mechanism linking melatonin to sleep regulation and a potential therapeutic target for sleep disorders.

neuroscience↗

bioRxiv2024

Regulation of angiogenesis by signal sequence-derived peptides

BackgroundThe neuropilin-like, Discoidin, CUB and LCCL domain containing 2 (DCBLD2) is a transmembrane protein with an unusually long signal sequence (SS) composed of N-terminal (N) and C-terminal (C) subdomains, separated by a transition (tra) subdomain. DCBLD2 interacts with VEGFR-2 and regulates VEGF-induced endothelial cell signaling, proliferation and migration, as well as angiogenesis. The exact mechanisms by which DCBLD2 interacts with VEGFR2 to modulate VEGF signaling remain unclear. MethodsSearching for VEGFR2 interacting DCBLD2 domains, we generated various constructs containing different DCBLD2 domain combinations and conducted co-immunoprecipitation and signaling studies in HEK 293T and endothelial cells. Several peptides were synthesized based on the identified domain, and their effect on VEGF signaling was assessed in vitro in cell culture and in vivo using matrigel plug and corneal micropocket assays. The effect of the lead peptide was further evaluated using a murine hindlimb ischemia model. ResultsDCBLD2 SS interacted with VEGFR2 and promoted VEGF signaling. SS was not cleaved in the mature DCBLD2 and its hydrophobic transmembrane traC segment, but not the N subdomain, was involved in DCBLD2-VEGFR2 interaction. The smallest unit in DCBLD2 SS that interacts with VEGFR2 was the L5VL5 sequence. Even after the central valine was removed, the L10 sequence mimicked the DCBLD2 SS traCs effect on VEGF-signaling, while shorter or longer poly-leucine sequences were less effective. Finally, a synthetic traC peptide enhanced VEGF signaling in vitro, promoted VEGF-induced angiogenesis in vivo, and improved blood flow recovery following hindlimb ischemia. ConclusionDCBLD2 SS along with its derivative peptides can promote VEGFR2 signaling and angiogenesis. Synthetic peptides based on DCBLD2 SS hold promise as therapeutic agents for regulating angiogenesis. Importantly these findings refine the traditional view of signal sequences as mere targeting elements, revealing a role in cellular signaling. This opens new avenues for research and therapeutic strategies.

cell biology↗