Biology subjects

Wei, S.

Publications and source records attributed to Wei, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Direct electrochemical cortisol detection via transition-resolved interrogation at a defect-engineered graphene interface

Continuous tracking of cortisol is central to understanding human stress physiology, yet direct electrochemical detection without biological receptors remains challenging despite its promise for stable and dynamic sensing. Electrochemical reduction of cortisol typically occurs at highly negative potentials, where parasitic interfacial currents, hydrogen evolution, and substantial capacitive background overlap with the cortisol reduction signal, preventing accurate quantification. We overcome this barrier through an integrated material-measurement strategy combining a defect-engineered graphene interface with a transition-resolved interrogation (TRI) measurement strategy. First, we engineered polybenzimidazole-derived laser-induced graphene containing nitrogen-rich defects while suppressing oxygen-derived functionalities which reduced parasitic background currents within the same cathodic potential regime. Next, we designed TRI to leverage differences in the time-dependent evolution of overlapping cathodic processes to isolate a localized cortisol-associated electrochemical reduction transition. Derivative-domain projection coupled with background estimation enables its reliable quantification. This integrated sensing architecture enables sensitive, selective, and dynamic cortisol detection in both artificial and biological interstitial fluids at low nanomolar concentrations. The response remains reproducible across physiologically relevant variations in pH, ionic strength, temperature, and repeated cycling. Together, these capabilities provide a basis for continuous electrochemical cortisol monitoring for future study of stress physiology.

bioengineering↗

bioRxiv2026

3D printing and deep learning enable holistic and dynamic analyses of tens of thousands of parasites infecting hundreds of genotypes

Host-parasite interactions are dynamic systems, where parasites usually outnumber hosts by one or more orders of magnitude. However, our understanding is often limited by the assessment of parts of the host, at arbitrary time points, and/or aggregate parasite responses. Here we combined custom-built 3D-printed hardware and deep-learning-based algorithms to enable holistic (i.e. all infecting individuals on the whole plant), spatio-temporal, and parasite-centric analyses of plant-parasitism by nematodes from timelapse videos of infection over months. In so doing, we tracked the dynamic growth and development of all individual parasites, at the organismal level, for thousands of hosts across hundreds of genotypes of Arabidopsis thaliana. Categorising traits into the static (i.e. in an acquired image at a given time point) and dynamic (i.e. phenotypic changes over time), we revealed a greater extent of host-genetic control of parasite traits, and new physiological limits of the species under these conditions. Using this capability, we identify Quantitative Trait Loci (QTL) in the host plant associated with 18 phenotypic traits in the parasite as a resource for the community. Finally, we leverage the large and diverse dataset to understand fundamental features of the parasite, independent of host genotype, revealing aspects of the life cycle which are pseudo-deterministic as well as local, deleterious interactions between co-infecting parasites. Given that plant-parasitic nematodes cause an estimated $100 billion in agricultural damages per year, these insights are contextualised in a global challenge driven by plant-parasitic nematodes.

pathology↗

bioRxiv2026

Tirzepatide attenuates atherosclerosis through weight loss-independent anti-inflammatory mechanisms

BackgroundAtherosclerosis is a chronic inflammatory vascular disorder with persistent residual inflammation even after standard lipid-lowering therapy. Mounting evidence from bench to bedside suggests that diabetes and obesity accelerate atherosclerosis development. Tirzepatide (TZP), a dual Glucagon-Like Peptide-1 Receptor/Glucose-Dependent Insulinotropic Polypeptide Receptor (GLP-1R/GIPR) agonist approved for treating diabetes and obesity, has demonstrated proven cardiometabolic efficacy in large cardiovascular outcome trials. However, it remains largely uncertain whether TZP attenuates atherosclerosis independent of its anti-diabetic and anti-obese effects through direct actions on the vasculature. MethodsWe established atherosclerotic mouse models under diabetic, obese, and non-diabetic/non-obese conditions. Analysis of covariance (ANCOVA) and pair-feeding experiments were applied to experimentally decouple weight-dependent metabolic improvement from intrinsic vasculoprotection. Molecular and cell biological assays in human umbilical vein endothelial cells (HUVECs) and human aortic endothelial cells (HAECs) were performed to dissect the underlying signaling mechanisms. ResultsTZP markedly reduced aortic plaque burden and inflammation, restrained necrotic core enlargement, and improved plaque stability across all experimental mouse models. Both ANCOVA and pair-feeding experiments confirmed that these atheroprotective effects were independent of food intake and body weight loss. Furthermore, TZP attenuated systemic and vascular inflammation in Tumor Necrosis Factor- (TNF)-treated C57BL/6J mice, and this protection occurred without changes in body weight or blood glucose levels. Mechanistically, TZP directly targeted endothelial cells and activated the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA)/endothelial nitric oxide synthase (eNOS) pathway, increased eNOS phosphorylation and nitric oxide bioavailability, consequently downregulating the expression of the pro-inflammatory adhesion molecules Vascular Cell Adhesion Molecule-1 (VCAM-1) and Intercellular Adhesion Molecule-1 (ICAM-1). ConclusionsTZP arrests atherosclerosis progression through weight loss-independent anti-inflammatory mechanisms. These findings implicate TZP as a promising therapeutic drug for mitigating residual vascular inflammation in patients with atherosclerotic cardiovascular disease (ASCVD), irrespective of glycemic status or obesity. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LITirzepatide exerts direct anti-atherosclerotic effects in preclinical mouse models of atherosclerosis under diabetic, obese, and non-obese conditions. C_LIO_LITirzepatide directly targets endothelial GLP-1R/GIPR and downstream cAMP/PKA/eNOS signaling pathway to suppress NF-{kappa}B-driven vascular inflammation, thereby uncovering a previously unrecognized vasculoprotective mechanism underlying its cardiovascular benefits C_LI What Are the Clinical Implications?O_LITirzepatide exerts direct vascular protective effects independent of body weight reduction, suggesting that its cardiovascular benefits may extend beyond glycemic control and obesity management. C_LIO_LITirzepatide may represent a promising therapeutic drug for addressing residual vascular inflammation in ASCVD patients, including those without overt diabetes or obesity C_LI

physiology↗

bioRxiv2026

EEG-Neurofeedback Targeting Gamma Oscillations at the Parieto-Occipital Region Reduces Pain Perception

Pain is closely associated with both spontaneous and stimulus-evoked gamma oscillations, which differ in their phenomenology and their relationship to pain perception. These associations make gamma oscillations a promising target for pain interventions, such as closed-loop real-time neurofeedback (NFB). While modulating stimulus-evoked gamma oscillations is technically challenging due to their concurrent occurrence with pain perception, targeting spontaneous gamma oscillations is both feasible and practical, as it could influence subsequent cortical nociceptive processing and reduce pain. To test this mechanistic hypothesis, we developed a novel NFB training protocol aimed at increasing spontaneous gamma oscillations in the parieto-occipital region to alleviate pain. Eight-eight healthy, right-handed subjects were randomly assigned to either an active or sham NFB group and completed three sessions of NFB training. During each session, subjects underwent EEG recording and received randomized laser stimulation while watching a video. After three training sessions, approximately 52% of subjects in the active group successfully increased the spectral power of spontaneous gamma oscillations in the parieto-occipital region. Crucially, the spectral power of spontaneous gamma oscillations was significantly and negatively correlated with subjective pain intensity after the third NFB session. Additionally, subjects who responded successfully to active NFB showed significant reductions in pain intensity, unpleasantness, and laser-evoked potentials compared to the sham group. Together, these findings establish a causal relationship between spontaneous gamma oscillations in the parieto-occipital region and pain perception, potentially offering a novel NFB-based therapeutic strategy for pain management.

neuroscience↗

bioRxiv2026

Generation of Genetically Identical Mammalian Oocytes from Parthenogenetic Double-Haploid Embryonic Stem Cells

Generating genetically identical mammalian oocytes is challenging due to stochastic meiotic recombination. Here, we established parthenogenetic double-haploid embryonic stem cells (PG-DhESCs) possessing complete homozygosity. By employing blastocyst complementation in Prdm14-deficient embryos, we generated chimeric females that produced oocytes derived exclusively from these donor cells. Fertilization of these oocytes yielded viable, fertile, maternally semi-cloned (MSC) mice of both sexes. Although DNA methylation was largely restored during gametogenesis, subtle epigenetic defects correlated with increased body weight in MSC offspring. This study establishes a robust platform combining PG-DhESCs with blastocyst complementation to generate isogenic mammalian oocytes, overcoming traditional limitations in mammalian cloning.

developmental biology↗

bioRxiv2026

Extending island biogeography theory to biotic islands: Microbial communities in epiphytic bird's nest fern Asplenium nidus

1. Biotic insular systems differ from conventional islands because patch attributes change dynamically as patch-forming organisms develop. It therefore remains unclear whether the assembly mechanisms predicted by island biogeography theory (IBT) operate in such systems. Here, using epiphytic birds nest ferns (BNFs, Asplenium nidus) as a model biotic island system, we tested whether fungal and bacterial community diversity conform to species-area relationships predicted by IBT. With a stratified sampling scheme, we further evaluated the underlying mechanisms (passive sampling, disproportionate effects, and environmental heterogeneity) of species-area relationships, and assessed isolation effects using distance-decay patterns in community similarity. 2. We treated each BNF individual as a microbial island and categorized 24 BNFs into three size classes. Microbial and humus samples from multiple litter layers within each BNF individual were collected; microbial communities were characterized using next-generation sequencing, and humus chemical properties (pH and C:N ratio) were measured to characterize microhabitat conditions. To investigate mechanisms underlying species-area relationships, we applied a multi-scale rarefaction framework to partition diversity components. Spatial distances among BNFs were quantified to evaluate isolation effects. 3. Consistent with IBT predictions, both fungal and bacterial communities exhibited positive species-area relationships, indicating that larger BNFs harbored greater microbial richness. Diversity partitioning suggested that fungal richness increased through both disproportionate effects and environmental heterogeneity, whereas bacterial richness was primarily driven by environmental heterogeneity. Within larger ferns, greater heterogeneity in litter pH was associated with increased species turnover across litter layers, suggesting that decomposition-driven pH gradients create diverse microhabitats that promote microbial diversity. In addition, both microbial communities exhibited distance-decay patterns, indicating that isolation contributes to community assembly through dispersal limitation. 4. Synthesis. Our results demonstrate that BNFs function as a biotic insular system, in which both patch size and spatial isolation structure microbial diversity, consistent with predictions from IBT. Furthermore, we show that environmental heterogeneity generated by the growth of the habitatforming BNF mechanistically links island area to microbial diversity. Our study integrates both local habitat heterogeneity and regional spatial structure, highlighting the potential to extend IBT and metacommunity theory to organism-formed habitats.

ecology↗

bioRxiv2026

Efficient Reprogramming of the Epiblast Enables the Generation of Cloned Mice

Somatic cell nuclear transfer (SCNT) can generate viable mammals despite pervasive epigenetic abnormalities in cloned embryos, yet the mechanism underlying this paradox remains unclear. Here we show, using single-cell transcriptomics, that efficient reprogramming occurs exclusively in the epiblast (EPI), but the not primitive endoderm (PrE) of late mouse SCNT blastocysts. Integrating this with previous findings of trophectoderm (TE) aberration, we propose the EPI as the sole effectively reprogrammed lineage. By innovatively employing a Lego-like multi-lineage embryonic aggregation approach, where the extra-embryonic lineages were replaced with fertilization-derived counterparts, we demonstrated that SCNT-derived EPI inherently possesses full-term developmental potential nearly identical to that of fertilized EPI (20.5% vs. 21.8% birth rate), functionally confirming its effective reprogramming. Our study uncovers a lineage-specific asymmetric reprogramming mode where the EPI specifically achieves effective reprogramming, thereby constituting the deterministic basis for cloned animal generation. This work also provides a versatile strategy for investigating lineage potency and function.

developmental biology↗

bioRxiv2026

Efficient derivation and transcriptional characterization of mouse extra-embryonic endoderm stem cell lines generated by somatic cell nuclear transfer

Somatic cell nuclear transfer (SCNT) holds great promise for regenerative medicine and agriculture, but its application is severely hampered by low efficiency, primarily attributable to aberrant epigenetic reprogramming. Although embryonic stem cells (ESCs) and trophoblast stem cells (TSCs) have been successfully derived from cloned embryos, an in vitro counterpart of the primitive endoderm (PrE) lineage has remained unavailable. To address this gap, this study reports the first successful establishment of extra-embryonic endoderm stem cell lines (XENs) from mouse SCNT-derived blastocysts (NT-XENs). Under conventional culture conditions, NT-XENs were generated from hybrid B6D2F1 blastocysts at a high efficiency of 55%, comparable to that of fertilization-derived XEN lines (FD-XENs, 50%), whereas derivation from inbred C57BL/6J SCNT-derived blastocysts was markedly lower (12.5%). Immunofluorescence and NanoString multiplex gene expression profiling confirmed that NT-XENs robustly expressed specific marker genes for PrE/XENs (e.g., Gata4, Gata6, Sox17), while exhibiting negligible or absent expression of pluripotency and trophoblast markers. Based on NanoString assay data, NT-XENs and FD-XENs shared highly similar global gene expression patterns, yet also exhibited some nonnegligible differences, exemplified by the differentially expressed genes (DEGs) Pecam1, Gtl2, Thbd and Xlr3b, which may suggest that the NT-XENs resided in a more differentiated state (potentially biased toward parietal endoderm (PE)) and retained SCNT-specific epigenetic imprinting errors, including aberrant X-chromosome inactivation and dysregulation of imprinted domains. In summary, this study successfully establishes NT-XEN cell lines, providing a valuable in vitro model for investigating the reprogramming scenarios of PrE lineage in SCNT and offering novel insights into the mechanisms underlying developmental failure of cloned embryos.

developmental biology↗

bioRxiv2026

A druggable redox switch on SHP1 controls macrophage inflammation

Immunological proteins are major disease targets, yet most remain undrugged. Post-translational redox modification of cysteine residues has emerged as an important mode of immune cell regulation, particularly in macrophage cytokine responses. Here, we develop a strategy for systematic discovery and small-molecule functionalization of redox-regulated cysteines on immunological proteins. Using deep redox proteomics, we annotate 788 in vivo redox-regulated cysteines across diverse immune-relevant protein domains. We demonstrate how these sites enable cysteine-directed pharmacology through discovery of a novel cysteine activation site on the immune regulator SHP1. Targeting Cys102, we develop a highly selective covalent agonist, SCA, which binds the N-SH2 domain to relieve autoinhibition and activate SHP1. In mouse and human macrophages, SCA selectively engages SHP1 Cys102, antagonizing IRAK signaling and LPS-induced pro-inflammatory cytokine production. Together, this work identifies a druggable cysteine redox switch controlling macrophage cytokine responses and provides a compendium of redox-regulated sites for therapeutic development.

biochemistry↗

bioRxiv2026

Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome

The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains, to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6 likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa. IMPORTANCECattle serve as natural reservoirs of zoonotic strains of E. coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.

genomics↗

bioRxiv2026

A genetically encoded ionic-stress sensor reveals protons as a sleep driver

Dynamic ionic changes are hallmarks of physiological and behavioral state transitions, including sleep in animals. Although biosensors for specific cellular ions are widely available, real-time monitoring of overall ionic strength in living organisms remains challenging. Here, we present a genetically encoded nuclear translocation ionic sensor (GENTIS) that enables direct visualization of ionic stress in vivo. Using GENTIS in C. elegans, we uncover rhythmic elevations in ionic strength during larval molting transitions that coincide with the lethargus sleep. Cytosolic proton ionic increase through inhibition of v-ATPase is sufficient to induce GENTIS nuclear translocation and evoke behavioral quiescence, characterized by reduced feeding and activation of sleep-active neurons. Apical membrane v-ATPases undergo disassembly during lethargus and under sleep-inducing stress conditions, leading to proton accumulation. Notably, this proton-mediated sleep is suppressed by proton buffering with ammonium. Together, these findings establish GENTIS as a powerful tool for tracking ionic strength dynamics in living organisms and support protons as a physiological driver of sleep.

animal behavior and cognition↗

bioRxiv2026

Discovery of potent oligopeptides for various metabolic diseases using deep learning

Artificial intelligence (AI)-based methods are increasingly critical in peptide drug discovery, but their applications are limited in a narrow scope such as antimicrobial peptides. For indications where peptide therapy inherently excels, such as metabolism, endocrinology, and tissue regeneration, AI-based pipeline for therapeutic peptide discovery is long awaited but still unmet. Here, we propose a deep learning-based pipeline, Deepeptide, capable of identifying therapeutic oligopeptides for various metabolism-related indications. Leveraging the intrinsical relationship of disease indication -- biological processes -- molecular functions, Deepeptide discovers oligopeptides with indication-ameliorating-related molecular functions as lead candidates for indication of interest. Deepeptide was applied in five representative indications of metabolism, endocrinology, and tissue regeneration: angiogenesis, lipid metabolism, osteogenesis, glucose metabolism, and anti-angiogenesis. Overall, 62% of the identified oligopeptide candidates demonstrated significant bioactivity in vitro, with most of them showing comparable potency to the first-line drugs. Notably, the heptapeptide AP7 exhibited angiogenic potency comparable to VEGF in excisional wound splinting mouse model by promoting cell migration rather than proliferation, and hexapeptide TP6 showed significant dual-efficacy against hyperlipidemia and obesity in high-fat diet mice by inhibiting lipid synthesis and regulating gut microbiota. These findings highlight the potential and generalizability of Deepeptide in therapeutic oligopeptide discovery for metabolic diseases.

bioinformatics↗

bioRxiv2025

An in situ generated CAR-M with IFNg and negative dominance Sirpa isoform augments hepatocellular carcinoma immunotherapy

Background and AimsChimeric antigen receptor (CAR) T cells have shown strong efficacy in hematological cancers but limited success in solid tumors. Macrophages, with their natural ability to infiltrate tumors, modulate immunity, and phagocytose cancer cells, offer a promising alternative when engineered with CARs. While studies have demonstrated the feasibility and anti-tumor activity of CAR macrophages (CAR-M), enhancing their persistence and phagocytic capacity remains a key challenge. Methods and ResultsBuilding on first-generation CD3{zeta}-based CAR-M, we developed a novel CAR targeting human GPC3, incorporating IFN-{gamma} and the extracellular domain of SIRP (SIRPECD) to improve CAR-M persistence and block the CD47-SIRP immune checkpoint. Following delivery via lipid nanoparticle-encapsulated mRNA (LNP-mRNA), the self-secreted IFN-{gamma} sustained M1 polarization through phospho-STAT1 activation. Meanwhile, the ectopically expressed SIRPECD competitively bound to CD47 on tumor cells, thereby blocking the endogenous SIRP-SHP2 interaction in a dominant-negative manner. This design enhanced pro-inflammatory activity and anti-tumor efficacy compared to CD3{zeta}-only CAR-M. Single-cell RNA sequencing and cellular analysis showed that in situ programmed CAR-M reprogrammed the tumor microenvironment toward inflammation in a murine HCC model. Moreover, CAR-M derived from human peripheral blood mononuclear cells (PBMCs) effectively phagocytosed human HCC organoids while sparing healthy tissues, indicating clinical potential. ConclusionsCollectively, our work presents a novel CAR design that enhances phagocytic function and sustains anti-tumor activity, offering a promising strategy for human solid tumor immunotherapy.

cancer biology↗

bioRxiv2025

MS4MS: LLMs-driven Multi-agent System for Small-molecule Identification via LC-MS/MS

Small molecule identification is central to research fields such as drug discovery, but in complex systems like Traditional Chinese Medicine (TCM), traditional mass spectrometry analysis methods remain constrained by bottlenecks including insufficient database coverage, fragmented analysis workflows, and poor result interpretability. To address these limitations, we developed MS4MS, a large language model-driven multi-agent system that enables an end-to-end automated pipeline from raw data to small molecule identification. Validation on a public benchmark demonstrates that MS4MS achieves state-of-the-art performance in molecular formula prediction. Furthermore, its innovative small molecule identification agent enables efficient and interpretable compound elucidation. Verification using herbal extracts indicates MS4MSs outstanding performance regarding analytical coverage and the discrimination of isomers. Consequently, MS4MS offers a novel, accurate, interpretable, and high-throughput end-to-end automated strategy for small molecule identification, overcoming the analytical bottlenecks of traditional mass spectrometry in natural products and complex TCM systems.

bioinformatics↗

bioRxiv2025

Sensitive Hormone and Neurotransmitter Detection with Carbon Flower Electrodes

Carbon-based electrochemical sensors have attracted substantial attention for continuous health monitoring due to their high surface area, wide potential window, capability for repeated measurements, and compatibility with soft wearable electronics. However, they face challenges when detecting target biomarker concentrations in the low nanomolar range (sensitivity) and differentiating them in a mixture (selectivity), limiting their applicability in real scenarios. Herein, we present sensitive and selective carbon flower sensors, fabricated via a facile and patternable spray-coating process on soft, stretchable substrates. The carbon flowers--obtained through the synthesis of polyacrylonitrile and subsequent heat treatments--exhibit unique hierarchical morphologies, high surface area, and excellent conductivity, ideal for mass transport and electrochemical detection. We demonstrate the detection of estradiol, serotonin, melatonin, dopamine, uric acid, and ascorbic acid with detection limits as low as sub-nanomolar. The carbon flower sensors exhibit good repeatability across 100 cycles and over several weeks, robustness to pH and salt variations, and excellent performance in complex bio-fluids such as artificial saliva. In mixtures containing up to four analytes, they differentiate individual molecules, demonstrating the selectivity of the carbon flowers. This combination of sensitivity, selectivity, and mechanical compatibility makes carbon flower sensors well-suited for biomolecular sensing in soft, skin-conformable wearable electronic patches.

bioengineering↗

bioRxiv2025

KG-Bench: Benchmarking Graph Neural Network Algorithms for Drug Repurposing

MotivationDrug repurposing leverages existing drugs for new indications, accelerating drug development. Computational methods integrating diverse biological and chemical data can systematically prioritize repurposing candidates, but standardized benchmarks for deep learning evaluation are lacking. We present KG-Bench, a benchmarking framework for drug-disease association prediction using the Open Targets dataset. We constructed a knowledge graph (KG) of drugs, diseases, and targets, including annotations such as therapeutic area and molecular pathway, and ensured retrospective validation by leveraging regular dataset updates. To avoid data leakage, we removed redundant entities across splits. ResultsBenchmarking several graph neural network (GNN) architectures, TransformerConv achieved the highest performance (APR: 0.87). KG-Bench also assesses bias, node/feature importance, and uses GNNExplainer for interpretability. Our open-source framework enables fair, reproducible evaluation of graph-based drug repurposing algorithms. Availability and ImplementationData and codes are available at https://github.com/cmbi/Benchmark_GNN_OpenTargets.

bioinformatics↗

bioRxiv2025

Plant-soil feedback persists beyond host death to shape density-dependent plant competition

Background and AimsPlant-soil feedback (PSF) shapes plant competition, yet classic PSF experiments often overlook the density dependence and temporal complexities of PSFs, especially after host death. We ask whether microbial effects vary after host death and mediate density dependence in seedling competition. MethodsWe combined forest inventory data from a subtropical forest with a density-gradient greenhouse experiment to evaluate seedling competition among two tree species with different mycorrhizal associations (ectomycorrhizal versus arbuscular mycorrhizal). In 2023, we collected soil inocula from living and dead trees (died between 2014 and 2019) with unsterilized and sterilized treatments. We applied invasion analysis to infer seedling competitive outcomes and used bootstrapping to evaluate uncertainty. ResultsSoil microbial communities shaped seedling competition, favoring the ectomycorrhizal species. Using soils collected from living versus dead hosts as live inocula, we found similar plant competitive outcomes, indicating that PSF persists for over 4-9 years following host death. In contrast, when using sterilized inoculum, we found shifts in competition after host death, suggesting underlying abiotic changes which might masked by microbial effects. Moreover, we found significant evidence that soil microbes can mediate nonlinear density dependence in seedling competition. ConclusionWe provide experimental evidence of persistent microbial legacies that benefit ectomycorrhizal tree species in a subtropical forest. Our study demonstrates how integrating field-based census data with density-gradient experiments and explicit uncertainty estimation can better capture the temporal dimensions, complexities of density dependence, and uncertainties of PSF.

ecology↗

bioRxiv2025

A Cell Type-Specific Role for Tubb6 in Ciliogenesis of Xenopus Epidermal Multiciliated Cells

Cilia are microtubule-based organelles found on the surface of most eukaryotic cells. These microtubules are composed of - and {beta}-tubulin heterodimers, and different tubulin isotypes can confer distinct properties to microtubules. Despite their importance, the contribution of individual tubulin isotype to cilia formation and function remains largely unexplored in vertebrates. Here, we identify a critical role for the {beta}-tubulin isotype Tubb6 in the formation of motile cilia in Xenopus epidermal multiciliated cells (MCCs). Tubb6 mRNA is selectively expressed in MCCs, and its protein product localizes to ciliary axonemes. Loss of Tubb6 leads to a marked reduction in cilia number and length, resulting in defective MCC function. In contrast, mono-motile cilia in the gastrocoel roof plate are unaffected by Tubb6 depletion, suggesting a selective requirement for ciliogenesis in MCCs. Together, our findings uncover a cell type-specific role for Tubb6 in motile cilia formation and highlight the functional specialization of tubulin isotypes in vertebrate cilia assembly.

developmental biology↗