Biology subjects

Xu, K.

Publications and source records attributed to Xu, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Staurosporine drives non-canonical melanocyte maturation by coupling β-catenin signaling to actin-dependent dendrite remodeling

Skin pigmentation relies on the coordinated regulation of melanin production and dendritic morphology to ensure effective pigment distribution. While staurosporine is widely used as a proapoptotic agent in malignant cells, its effects on normal human melanocytes have not been fully characterized. Here, we investigated the impact of staurosporine on melanocyte biology and identify it as a potent inducer of non-canonical melanocyte maturation at sub-cytotoxic concentrations. In primary human neonatal melanocytes, staurosporine treatment enhances melanogenesis and promotes pronounced dendritic remodeling, leading to functional maturation distinct from its apoptotic effects in melanoma cells. Phenotypic analyses demonstrate increased pigment production and expanded dendritic networks that support efficient pigmentation. Molecular characterization indicates that these effects are associated with coordinated activation of {beta}-catenin signaling and actin-dependent cytoskeletal remodeling. The physiological relevance of these findings was further examined in vivo. Topical application of staurosporine to normal guinea pig skin increased baseline pigmentation without detectable inflammation. In addition, staurosporine accelerated repigmentation in a rhododendrol-induced leukoderma model by restoring functionally mature melanocyte populations and enhancing nuclear localization of {beta}-catenin. Together, these results identify staurosporine as a non-canonical modulator of melanocyte maturation and highlight the coordinated regulation of pigment production and dendritic remodeling as a key process supporting pigmentation in acquired hypopigmentary conditions. SummaryO_LIStaurosporine promotes non-canonical maturation of human melanocytes at sub-cytotoxic concentrations. C_LIO_LITreatment enhances both melanogenesis and dendritic remodeling, supporting functional pigmentation. C_LIO_LIStaurosporine increases baseline skin pigmentation in vivo without inducing inflammation. C_LIO_LIRepigmentation is accelerated in a rhododendrol-induced leukoderma model through restoration of mature melanocyte populations. C_LIO_LIThese findings highlight coordinated regulation of pigment production and dendritic morphology as a potential strategy to promote pigmentation in acquired hypopigmentary conditions. C_LI SignificanceLoss of melanocyte dendricity and functional maturation is a shared feature of multiple acquired hypopigmentary disorders, including vitiligo and chemical-induced leukoderma. This study demonstrates that staurosporine promotes dendritic remodeling and pigmentation in normal human melanocytes and enhances repigmentation in vivo. By identifying a melanocyte-intrinsic, ultraviolet-independent maturation program, our findings provide a biological framework for strategies aimed at restoring functional melanocytes in depigmented skin.

cell biology↗

bioRxiv2026

Targeting THOC2-Mediated mRNA Export Induces PARP Inhibitor Vulnerability in DNA Repair-Competent Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) remains a lethal malignancy with limited therapeutic options. While Poly (ADP-ribose) polymerase inhibitors (PARPi) exploit synthetic lethality in tumors with DNA repair defects, their clinical utility in HCC is hindered by the low prevalence of canonical repair gene mutations and the enhancing DNA repair capacity. Through proteomic analysis of two independent cohorts (n=260), we identified the THO complex component THOC2 as a master regulator of DNA damage response (DDR) via mRNA nuclear export control. Clinically, THOC2 overexpression predicted poor survival (HR=2.68-6.84, P<0.001) and correlated with enhanced DDR gene expression. Mechanistically, THOC2 chaperones mRNA nuclear export of DDR effectors (MDC1, PRKDC, MSH6) and proliferation drivers (TOP2A), thereby establishing a dual pro-repair/pro-growth program. Targeting this vulnerability, THOC2 knockdown induced synthetic lethality with PARPi, reducing Olaparib IC50 by up to 61% and suppressing tumor growth by 76% (P<0.001). Our study illuminates mRNA transport as a druggable DDR modulator and establishes THOC2 as both a prognostic biomarker and a therapeutic target to overcome PARPi resistance in HCC. This work pioneers a strategy to expand synthetic lethality beyond genetic defects by targeting post-transcriptional regulation.

cancer biology↗

bioRxiv2026

Somatic-to-germline transmission of horizontally acquired extrachromosomal circular DNA in Brassica graft chimeras

Whether somatically acquired traits can contribute to heritable variation has remained an open question in plant biology for over a century. Here, using graft-induced periclinal chimeras between Brassica juncea and Brassica oleracea, we identified extrachromosomal circular DNA (eccDNA) as mobile genetic elements capable of crossing histological boundaries and entering the germline. We demonstrated that grafting could promote the horizontal transfer of eccDNA between somatic cell layers, enabling its stable maintenance in recipient tissues and permitting transmission through sexual reproduction across multiple generations. We found that transmitted eccDNA is non-randomly distributed across the genome, preferentially originating from gene-dense regions, and enriched for features associated with molecular persistence, such as inverted repeats, hairpin-forming sequences, and autonomously replicating sequence (ARS) consensus motifs. These genetic regions conferred replication competence, as evidenced by autonomous propagation in an ARS-less heterologous yeast system. Sexual progeny carrying graft-acquired eccDNA exhibited reproducible and lineage-dependent alterations in leaf morphology and drought tolerance, accompanied by coordinated transcriptional reprogramming. Notably, a subset of inherited eccDNA remained transcriptionally active in progeny, producing transcripts absent from self-grafted controls. Our findings establish eccDNA as heritable extrachromosomal elements that link graft-mediated somatic genetic transfer with stable germline transmission, thereby expanding the molecular scope of heritable variation in plants and providing a conceptual framework for graft-based trait transmission.

plant biology↗

bioRxiv2026

Gut microbiota-derived indole-3-propionic acid preserves dorsal hippocampal catecholamines to prevent post-stroke cognitive impairment

BackgroundGut dysbiosis has been increasingly implicated in post-stroke cognitive impairment (PSCI), yet the causal contribution and therapeutic potential of gut microbiota-derived metabolites remain unclear. This study aimed to identify key microbiota-derived metabolites involved in PSCI and to elucidate their underlying mechanisms. ResultsWe found that both PSCI patients and middle cerebral artery occlusion (MCAO) mice exhibited distinct gut microbial alterations, characterized by a marked reduction in tryptophan-metabolizing bacteria and indole-3-propionic acid (IPA), a gut microbiota-derived tryptophan metabolite. Exogenous IPA administration alleviated PSCI-like phenotypes in MCAO mice. Mechanistically, IPA preserved tyrosine hydroxylase-positive (Th) fibers and catecholamine levels in the dorsal hippocampus. Further analyses showed that IPA binds to the adaptor protein Ywhab, promotes ERK activation, and enhances neuronal survival, thereby counteracting neuronal apoptosis-associated inflammation and subsequent Th fiber degeneration. ConclusionThese findings identify IPA as a gut microbiota-derived neuromodulator that mitigates PSCI by preserving dorsal hippocampal catecholaminergic transmission. IPA may therefore serve as a promising predictive biomarker and therapeutic candidate for PSCI.

neuroscience↗

bioRxiv2026

Enhanced GPP synthesis by Erg20p-peptide fusions and biomolecular condensates boosts monoterpene production in yeast

Monoterpenes are a diverse class of natural products with broad industrial and pharmaceutical applications. While there is great interest in transitioning their production from chemical synthesis and natural source extraction to yeast bioprocesses, this approach remains limited by the dual functionality of the endogenous farnesyl diphosphate synthase Erg20p, which produces the monoterpene precursor geranyl diphosphate (GPP) but favors its subsequent conversion to farnesyl diphosphate (FPP). To address this limitation, we recruited Erg20p and monoterpene synthases into synthetic membraneless organelles, improving production. In doing so, we found that short C-terminal peptide fusions used for recruitment also significantly enhance GPP synthase activity relative to FPP synthase activity. The combined effects of metabolic spatial organization and GPP synthase activity enhancement significantly boost production of different monoterpenes, including geraniol titers exceeding 4 g/L. The strategies presented here can be readily integrated with other traditional metabolic engineering approaches to build yeast strains with high levels of monoterpene production.

bioengineering↗

bioRxiv2026

Autophagy acts as a spatial organizer of cell-type-specific plant immunity

Effective plant immunity requires precise spatial coordination of immune responses across cell-types to restrict pathogens while preventing tissue damage, yet the intracellular pathways that organize this spatial architecture remain unknown. Here we show that autophagy serves as a spatial coordinator of immunity, partitioning and calibrating immune strategies across tissues during Pseudomonas syringae infection in Arabidopsis thaliana. Combining single-cell transcriptomics, cell-type-specific complementation, and live-cell imaging, we uncover distinct and opposing roles of autophagy across tissues. In guard cells, autophagy promotes pathogen-induced stomatal reopening by suppressing abscisic acid (ABA) signalling in part via autophagic turnover of the guard cell ABA receptor PYL4. In contrast, in mesophyll cells, autophagy restricts immune activation while simultaneously enabling effective immune execution: its loss enhances EDS1-PAD4-ADR1 pathway expression yet compromises PTI outputs. Mechanistically, bacterial infection triggers autophagic EDS1 turnover, supporting a model in which controlled EDS1 recycling facilitates HR elicitation. Cell-type-specific complementation reveals that PTI competence may involve coordinated autophagy across tissues, whereas mesophyll-autonomous autophagy is partially sufficient for HR execution. Together, these findings establish a framework in which spatial control of proteostasis orchestrates multicellular immune coordination, with broad implications for understanding how conserved degradation pathways regulate layered immunity across organisms.

plant biology↗

bioRxiv2026

Inactivation of the RB1 and PTPN14 tumor suppressors cooperatively enables the carcinogenic activity of the human papillomavirus E7 oncoprotein

High-risk human papillomavirus (HPV) E7 proteins bind and inactivate host cellular tumor suppressors and are essential for the immortalization of primary human keratinocytes. E7 proteins from high- and low-risk HPV genotypes bind directly to at least two tumor suppressors, RB1 and PTPN14, and inactivate both. We previously characterized mutations in high-risk HPV E7 proteins that selectively abrogate the ability of E7 to bind either RB1 or PTPN14. Here, we established a genetic complementation system using the E7 mutants defective for binding to RB1 or PTPN14. Neither mutant alone could extend the lifespan of primary keratinocytes. When expressed together, the mutants could, like wild-type high-risk HPV E7, extend keratinocyte lifespan. Both high- and low-risk E7 reduced PTPN14 protein levels and reduced expression of keratinocyte differentiation genes, whereas only high-risk E7 reduced steady-state RB1 levels and induced E2F-dependent genes. Depletion of either RB1 or PTPN14 could cooperate with low-risk HPV6 E7 to extend keratinocyte lifespan. Our findings advance the model that inactivation of at least two tumor suppressors is required for the lifespan extension activity of high-risk HPV E7. SignificanceInactivation of the retinoblastoma tumor suppressor (RB1) is necessary but insufficient for HPV E7-mediated immortalization of human cells. In addition to inactivating RB1, HPV E7 proteins also target for degradation PTPN14, a tumor suppressor and inhibitor of the YAP1 oncoprotein. We report genetic complementation experiments demonstrating that RB1 inactivation and PTPN14 inactivation are separate activities of E7. Either depletion of RB1 or PTPN14 can confer lifespan extension activity on a low-risk HPV E7. These findings redefine our understanding of E7 transforming activity. The predominant difference between high- and low-risk E7 is their ability to degrade RB1, but inactivation of both tumor suppressors is required for E7 activity. Targeting either E7/RB1 or E7/PTPN14 could be of therapeutic benefit.

microbiology↗

bioRxiv2026

PRMT5-Mediated Arginine Methylation of HSP90AA1 Drives Esophageal Squamous Cell Carcinoma Progression

Dysregulated HSP90AA1 chaperone activity is a hallmark of multiple human cancers, yet its post-translational modifications in esophageal squamous cell carcinoma (ESCC) are poorly defined. Here, we identify a PRMT5-driven modification of HSP90AA1, symmetric dimethylation at arginine 182 (R182), as a pivotal switch that fuels ESCC progression. HSP90AA1 physically associates with PRMT5, and genetic or pharmacologic PRMT5 blockade diminishes HSP90AA1-R182 methylation and downstream oncogenic signaling. Functionally, HSP90AA1 loss suppresses ESCC cell proliferation, migration, and invasion; enforces cell cycle arrest and reverses epithelial-mesenchymal transition (EMT). Re-expression of wild-type HSP90AA1 rescues cancer cell growth and EMT in vitro and in vivo, whereas the methylation-deficient R182A mutant does not. Furthermore, clinically oriented analysis shows HSP90AA1 overexpression in ESCC tissues and indicates moderate prognostic utility. Moreover, dual targeting of the PRMT5/HSP90AA1 axis is therapeutically attractive, and combined PRMT5/HSP90AA1 inhibition acts synergistically to exert anti-tumor activity, markedly reducing clonogenicity, invasion, and tumor burden in both cell-derived and patient-derived xenograft models. These findings demonstrate that PRMT5/HSP90AA1 serve as mechanistic drivers and actionable biomarkers in ESCC and provide a rationale for biomarker-guided co-inhibition of PRMT5/HSP90AA1 in translational studies.

cancer biology↗

bioRxiv2026

L-Lactate reprograms tumor-associated macrophages to drive pancreatic cancer progression via BCL3 lactylation

Metabolic reprogramming fuels pancreatic ductal adenocarcinoma (PDAC) malignancy, creating a nutrient-deprived and waste-rich microenvironment. How this extreme metabolic pressure dictates the phenotypic remodeling of infiltrating immune cells remains largely unclear. Metabolomic profiling of PDAC reveals that robust tumor glycolysis proceeds without a commensurate accumulation of extracellular lactate. Integrated single-cell profiling and tissue multiplex immunofluorescence demonstrate that tumor-associated macrophages (TAMs) act as the primary consumers of tumor-secreted lactate. The uptake of L-lactate directs macrophages toward a pro-tumorigenic state through site-specific L-lactylation of the transcriptional co-regulator BCL3 at lysine 21 (K21). Functioning as a molecular switch, K21 lactylation triggers BCL3 nuclear translocation and enhances its interaction with the NF-{kappa}B p50 subunit. The ensuing BCL3-p50 complex competitively displaces the pro-inflammatory p65 subunit, rewiring the transcriptional output to suppress inflammation and enforce tumor-supporting networks. In vivo, macrophage-specific expression of a lactylation-deficient BCL3 mutant (K21R) abolishes lactate-driven phenotypic shifts and restricts tumor growth. Clinically, a BCL3-lactylated macrophage signature spatially correlates with CD8+ T cell exclusion and predicts poor patient survival, providing a strong rationale for targeting the BCL3-lactylation axis to reverse TAM-driven PDAC progression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/710237v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@173159eorg.highwire.dtl.DTLVardef@9065f3org.highwire.dtl.DTLVardef@153e0aorg.highwire.dtl.DTLVardef@9c2678_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Streak-Aware Localization Microscopy Enables High-Throughput Brain Imaging Across Platforms

Optical, ultrasound, and optoacoustic localization microscopy based on microparticle tracking has enabled surpassing the resolution limits imposed by ultrasound diffraction and optical diffusion in tissues. However, its reliance on high-speed (kilohertz) data acquisition systems for precise emitter localization and tracking substantially increases methodological complexity and data storage demands, limiting scalability and applicability beyond specialized benchtop platforms. Here, we present streak-aware localization microscopy (SALM) that employs localization- and tracking-free deep learning model to convert motion-blurred streaks originating from low frame rate recordings of flowing emitters into super-resolved structural and functional readouts. In optical implementations, SALM exploits streaks captured by low-speed cameras to recover capillary-level cerebrovascular maps across a variety of benchtop, miniaturized, and second near-infrared preclinical imaging platforms, achieving over 30-fold reduction in the reconstruction time compared to conventional localization pipelines. We further introduce three coded excitation strategies that embed finer time-varying vectorial flow signatures into individual streaks, enabling single-frame velocimetry and video-rate hemodynamic imaging. Extending SALM to ultrasound imaging enables high-fidelity vascular imaging with centimeter-scale penetration in rhesus macaque and rat brains while reducing plane-wave compounding frame rates by up to one order of magnitude. By overcoming long-standing trade-offs between spatiotemporal resolution and hardware complexity, SALM offers a flexible and scalable framework for next-generation super-resolution microscopy.

neuroscience↗

bioRxiv2026

EnzySeek: Efficient Exploration of Enzyme Reaction Pathways Using AI Agents

With the rapid development of Large Language Models (LLMs) and Agent technologies, AI can assist in solving a variety of real-world problems across multiple domains, such as autonomous driving, drug discovery, and materials design. In this work, we present EnzySeek, an enzyme catalysis AI agent designed to assist researchers in enzyme catalysis simulations. First, we constructed a domain-specific knowledge base by curating thousands of papers related to enzyme catalysis. Second, we customized Model Context Protocol (MCP) interfaces for each step of the enzyme catalysis simulation workflow, enabling these functions to be invoked by LLMs. Finally, we configured an agent capable of simultaneously referencing past empirical studies on enzyme catalysis, autonomously executing tool calls, and analyzing as well as presenting the results. EnzySeeks capabilities cover multiple aspects, including protein structure prediction, molecular docking, system preparation and parameterization, molecular dynamics (MD) simulations, and QM/MM calculations. The conclusions drawn by EnzySeek are primarily based on the results of QM/MM calculations. We employed the semi-empirical quantum mechanical method GFN2-xTB to calculate the QM region of the system. Benchmark results indicate that the GFN2-xTB method can achieve high efficiency while maintaining accuracy. The EnzySeek agent is designed to continuously learn from newly published literature and past computational tasks. During its operation, every AI decision is manually verified and scored by human experts. This human-in-the-loop validation provides the AI with sufficient case-based support, ultimately contributing to the full automation of enzyme catalysis computations. All data generated during the simulations are compiled into a dataset, which is used to establish evaluation criteria specific to enzyme catalysis computational results.

biochemistry↗

bioRxiv2026

A single-nucleus multiome analysis of transcriptome and chromatin accessibility reveals cell-type-specific immune modulation for chronic cannabis use among people with HIV infection

As cannabis use continues to rise among people with HIV (PWH), understanding its impact on immune function in this population is becoming increasingly important. To provide new insights on how cannabis modulates immune function, we analyzed single-nucleus multi-omic profiles of peripheral blood mononuclear cells (PBMCs) from PWH to characterize the changes in gene expression and chromatin accessibility associated with chronic cannabis exposure. We identified numerous differentially expressed genes (DEGs) between cannabis users and non-users in each cell type, approximately half of which were unique to individual cell types. Changes in pro- and anti-inflammatory gene expression associated with cannabis use are dependent on cell lineage and type. We identified hundreds of differential chromatin accessibility regions in each cell type, including cis-regulatory elements correlated with cell-type-dependent DEGs (e.g. NFKBIA in CD4+ T cells and CCL3L1 in classical monocytes). Multiple cannabis-associated transcription factors (e.g., NFKB1, FOS, and TCF7) emerge as regulators of the differentially expressed inflammatory genes. Furthermore, cannabis altered the communication between classical monocytes and lymphocytes. These findings indicate that cannabis-induced immunomodulatory effects are profound, dynamic and complex among cell types and that transcriptional changes are regulated at least in part by epigenetic mechanisms.

genomics↗

bioRxiv2026

BARTsc identifies key transcriptional regulators from single-cell omics data

Inference of transcriptional regulatory mechanisms from single-cell (sc) omics data, such as scRNA-seq, scATAC-seq, and scMultiome, remains an important problem in single-cell biology and functional genomics. Most existing methods for predicting functional transcriptional regulators (TRs) from single-cell data rely on co-expression between regulator and target genes and/or sequence motif enrichment, holding inherent limitations. Here, we present BARTsc, a computational method that accurately predicts functional TRs from clustered single-cell omics data by leveraging a large collection of public ChIP-seq profiles. BARTsc implements a novel framework to infer a cis-regulatory profile from differential genomic features from either unimodal (RNA or ATAC) or bimodal (scMultiome) single-cell profiling data and identify TRs whose binding profiles most associate with the cis-regulatory profile. BARTsc can quantify TR activity across cell clusters and predict key regulators for each cell cluster. We demonstrate that BARTsc can successfully identify active TRs in each cell type and cell-type-defining key regulators across diverse biological systems, including mouse cortex, human peripheral blood mononuclear cells (PBMCs), and human pancreatic ductal adenocarcinoma (PDAC). Using a generative-AI-assisted, literature-supported collection of cell-type key regulators as benchmarks, we show that BARTsc consistently outperforms existing state-of-the-art methods. We apply BARTsc to identify critical regulators in PDAC, including NEFLA, a novel PDAC key regulator, and validate its function in pancreatic tumor proliferation by experiments. As a robust and versatile computational method, BARTsc provides deeper insights into cell-type-specific regulatory programs, facilitating the discovery of key regulators across diverse biological systems.

bioinformatics↗

bioRxiv2026

MolSpecFlow: Mass-Constrained Hybrid Flow Matching for Joint Molecular-Spectral Analysis

Identifying the "dark matter" of the chemical universe requires bridging the fundamental gap between molecules and mass spectra. Existing approaches struggle to accurately map between these distinct data formats, often yielding results that are either chemically implausible or inconsistent with the physical evidence. We introduce MolSpecFlow, a unified foundation model pretrained on 100 million molecules and 42 million spectra, which leverages a hybrid flow matching framework to orchestrate optimal transport paths for spectral peaks and discrete probability flows for molecular tokens. Furthermore, to guarantee the physicochemical validity of the generated structures, we incorporate explicit rule-based constraints into the generative process, utilizing a token-level mass control mechanism that strictly enforces alignment with the precursor molecular weight. MolSpecFlow establishes a new state-of-the-art on the MassSpecGym benchmark, surpassing diffusion and retrieval baselines in de novo generation (Top-1 accuracy +35%), spectral simulation, and molecular retrieval, demonstrating the power of physics-grounded unified modeling.

bioinformatics↗

bioRxiv2026

A high fermentable fiber Western diet reduces indole levels

Changes in gut microbiota composition due to diet impact health. Fiber-rich diets promote beneficial microbiota and reduce the risk of metabolic diseases, while low-fiber, calorie-dense diets are linked to dysbiosis and increased disease risk. This study examines the effects of a Western diet (WD) and explores dietary fiber supplements as potential modifiers of those effects. 10-week-old C57Bl/6J male mice were fed control (low-fat) or WD (high-fat, high-sucrose) containing 0% fermentable fiber (FF) or WD supplemented with 20% FF (fructooligosaccharides, FOS; guar gum, GG, or pectin, Pec). After 19 weeks, analysis of the cecal metagenome using whole-genome shotgun sequencing, metabolome by untargeted and targeted LC-MS/MS, and tissue RNA and protein expression by RT-PCR and immunoblotting was undertaken. WD-FF reduced metabolic derangements from WD while also improving GM diversity and altering cecal metabolites, particularly tryptophan metabolism. A profound increase in cecal indole levels (targeted metabolomics) was noted in WD vs WD-FF groups. As the primary indole-oxidizing enzyme, CYP2E1 generates indoxyl sulfate, which contributes to oxidative stress and a leaky gut. Mice on WD displayed higher expression of Cyp2e1 mRNA in the gut. In the liver, the levels of both CYP2E1 protein and mRNA were higher in the WD group compared to the WD-FOS group, with protein levels also higher than in the WD-Pec group and mRNA levels higher than in the WD-GG group. mRNA expression of markers of oxidative stress, inflammation, and leaky barrier was significantly higher in the liver and intestine of the WD vs the WD-FF groups. FFs reduced high plasma indoxyl sulfate levels (except in WD-GG), and boosted short-chain fatty acids and indole acetic acid. Our data suggest that WD disrupts GM tryptophan metabolism, possibly by altering the balance between indole-producing and utilizing gut bacteria. Dietary fiber supplementation exerts protective effects, in part, by mitigating this imbalance.

physiology↗

bioRxiv2026

Direct selection under resource allocation trade-offs enables the evolution of obligate and facultative sexuality

Sexual reproduction is considered to incur multiple costs relative to asexual reproduction. Although previous research has identified indirect selective advantages that help explain the widespread occurrence of sex, the emergence and maintenance of high rates of sexual reproduction remain a central puzzle in evolutionary biology, because indirect selection favoring sex becomes weak when the sexual rate is high. Using a modifier framework that allows the simultaneous evolution of sexual rate and sex allocation, I investigate the evolution of sex via direct selection by incorporating resource allocation trade-offs between sexual and asexual reproduction. The results show that such trade-offs can substantially facilitate the invasion of sex. Crucially, the evolutionarily stable sexual rate depends on the return exponents of female fertility and asexual fertility with respect to resource investment, as well as on the initial allocation to female function within sexual reproduction. Obligate sexuality is evolutionarily stable when asexual fertility exhibits linear or accelerating returns on investment and when both the initial sexual rate and female function allocation within sexual reproduction exceed certain levels. In contrast, facultative sexuality will be evolutionarily stable when female fertility within sexual reproduction and/or asexual fertility exhibit diminishing returns. Contrary to previous theoretical predictions, self-fertilization often inhibits the evolution of sex or reduces the evolutionarily stable sexual rate. This study provides insights into the prevalence of high sexual rates, as well as the continuous spectrum of sexual rates in some groups, highlighting the importance of key parameters in reproductive ecology in shaping the evolution of sex. Significance statementWhy sexual reproduction is so common despite its substantial costs remains a longstanding puzzle in evolutionary biology. Most previous explanations focus on indirect genetic benefits of sex, which generally become weaker as the rate of sexual reproduction increases, and therefore cannot explain the prevalence of intermediate to high sexual rates in nature. This study shows that with resource allocation trade-offs between sexual and asexual reproduction, obligate or facultative sexuality can evolve and be stably maintained via direct selection alone, depending on the marginal returns of asexual and female fertility, as well as the initial allocation to female function. These results highlight the underappreciated role of reproductive ecology in shaping the evolution of sex in nature.

evolutionary biology↗

bioRxiv2026

A Bear-Specific Coding Exon in TMEM41B Is Associated with Cold Adaptation

AbstractBears exhibit an unusual form of hibernation in which core body temperature remains relatively high despite profound suppression of whole-body metabolism. How such a warm yet hypometabolic state is achieved remains poorly understood. Here, through integrative analysis of 238 RNA-seq datasets spanning seven species, we identify transmembrane protein 41B (TMEM41B) as an evolutionarily conserved factor associated with thermogenic capacity. Loss of Tmem41b in mice and Drosophila results in severe cold intolerance, whereas its overexpression enhances thermogenic performance, supporting a conserved role in heat production. Comparative genomic analyses reveal a bear-specific 51-amino acid N-terminal extension in TMEM41B, arising from a 5' untranslated region mutation that converts a premature stop codon into coding sequence. Interactome profiling indicates that this bear-specific isoform differs from the canonical TMEM41B in its protein interaction landscape, including reduced association with components of mitochondria-associated endoplasmic reticulum membranes such as voltage-dependent anion-selective channel protein 1 (VDAC1). Consistent with this altered interaction profile, the extended isoform is associated with reduced mitochondrial oxidative activity. Functional analyses further suggest that the 51- amino acid extension modulates multiple cellular programs, including suppression of oxidative phosphorylation and myogenic differentiation alongside activation of osteogenic pathways, collectively biasing cells toward a hypometabolic state. Notably, expression of the polar bear TMEM41B isoform in mice induces a torpor-like phenotype under fasting conditions. Together, these findings identify TMEM41B as a conserved regulator of thermogenic capacity and suggest that evolutionary modification of its N terminus may contribute to metabolic suppression and energy conservation during bear hibernation.

evolutionary biology↗

bioRxiv2026

Identification of Novel Extracellular Vesicles Scaffold Proteins for Versatile Cargo Engineering

Extracellular vesicles (EVs) are promising drug delivery platforms that have been engineered to carry various drug modalities. Key strategies for generating those therapeutic EVs involve the direct fusion of protein of interest (POI) to EVs scaffold proteins with inherently high EVs-sorting ability. In this work, we identified raftlin (RFTN1) and poliovirus receptor (PVR) as novel EVs scaffold proteins for loading EVs lumen and surface cargos respectively. Truncation studies revealed that the N-terminus 15 residues from RFTN1 (RFTN1-N15) were sufficient for EVs engineering, as demonstrated by distinct cargos including gene editing tools, cytosolic enzymes as well as type II transmembrane proteins. On the other hand, PVR efficiently displayed secreted proteins including antibodies and serum albumins on EVs surface. Critically, RFTN1 and PVR-engineered EVs demonstrated consistent and efficient cargo delivery in vivo. In summary, the discovery of RFTN1 and PVR can potentially benefit EVs engineering for both fundamental research and clinical translation in the future.

bioengineering↗