Biology subjects

Li, J.

Publications and source records attributed to Li, J..

At least 181 records · Page 10Linked to original sources

bioRxiv2026

Balancing of immune activation and suppression during phage infection

Signaling-based anti-bacteriophage systems such as CBASS and Thoeris synthesize infection-triggered nucleotide signals that activate anti-phage effectors1,2. However, the phage features sensed by these systems and the mechanisms phages use to evade signaling immunity remain poorly understood. Here, studying clinically relevant Pseudomonas aeruginosa phages from the Migulavirinae family3, we show that closely related phages encode subtle allelic variation in side tail fiber proteins that determine sensitivity to type II Thoeris. In parallel, these same phages encode an "anti-defense hotspot" that contains three adjacent genes that are each sufficient to facilitate phage evasion of both CBASS and Thoeris defenses, counter-balancing the activating proteins. Comparative analysis of this anti-signaling hotspot across the broader family of related N4-like phages uncovered a new Thoeris anti-defense (Tad) protein that sponges NAD-derived molecules (e.g. gcADPR) and exhibits sequence and structural similarity to a poorly characterized nucleotide-binding region of the human ryanodine receptor. Together, these findings reveal how the balance between immune activation and antagonism shifts phage outcomes and reveals a surprising similarity between a phage molecular sponge and an important human protein.

microbiology↗

bioRxiv2026

Differences in microbial community structure and soil nutrients between healthy and diseased soils of Zingiber officinale

To investigate the differences in soil nutrients and microbial community structure in the rhizosphere between healthy and diseased Zingiber officinale plants, soil samples were collected from healthy root-zone soil (ZSH), healthy rhizosphere soil (RSH), diseased root-zone soil (ZSD), and diseased rhizosphere soil (RSD). Diseased soils had significantly higher pH values, whereas RSH showed the strongest acidity. Moreover, pH, AN, and AK contents in diseased soils were significantly higher than those in healthy soils, while SOM and AP were significantly lower. The -diversity of microbial communities in diseased soils was significantly reduced, and the community structure was distinctly differentiated from that of healthy soils. In diseased soils, the abundance of potential pathogenic taxa such as Ralstonia solanacearum increased significantly, while beneficial genera such as Bradyrhizobium decreased. Redundancy analysis and correlation analysis indicated that soil pH, AN, SOM, and AP were the major environmental factors driving changes in microbial community structure. The occurrence of soil-borne diseases in Zingiber officinale is closely associated with soil nutrient imbalance and disruption of microbial community structure. The study identified candidate microbial taxa (e.g., beneficial Sphingomonas, Streptomyces) and key soil properties (pH, available nitrogen) that differentiate healthy from diseased ginger soils. Together, these findings provide a theoretical basis for improving diseased soils through microecological regulation strategies, and also serve as a foundation for generating testable hypotheses in future hypothesis-driven research on ginger soil-borne disease suppression.

microbiology↗

bioRxiv2026

An open-source stereotaxic container with an integrated cutting guide for human brain fixation during magnetic resonance imaging and sectioning for histology

IntroductionPostmortem imaging at ultrahigh field strengths, such as 7 Tesla (7T) magnetic resonance imaging (MRI), enables unprecedented visualization of fine brain structures and pathology. However, precise registration between MRI and histology is often compromised by tissue deformation and lack of standardized tools for preserving anatomical orientation. A reliable, high-resolution MRI-to-histology workflow is essential for MRI-guided sampling to investigate neurodegenerative diseases. MethodsWe developed a human postmortem brain container composed of stereotaxic enclosure and cutting guide system using iterative 3D printing. The final design is constructed from Victrex AM 200, a polyaryletherketone material engineered with MRI compatibility, high mechanical strength, and high resistance to fixatives. Human brains were embedded in an agar/sucrose mixture within the container and scanned at 7T using high-contrast and high-resolution imaging sequences. The cutting guide enables reproducible sectioning at defined tissue coronal slab thicknesses (9.2 {+/-} 0.6 mm). Block face photographs of each coronal slab were then co-registered with MRI for targeted tissue sampling. ResultsTo date, 215 human postmortem brains have been imaged ex vivo using this container. The container maintains consistent spatial orientation from imaging through sectioning, supporting correlation between MR-visible features and histological findings. Imaging-visible abnormalities, such as white matter hyperintensities and cerebral microbleeds, were localized and sampled with minimal deformation. The container enables single-scan workflows, avoiding custom cutting templates or repeat imaging. It supports deep learning-based lesion segmentation and MRI-guided histology registration, facilitating large-scale neuropathological investigations. ConclusionThe stereotaxic cutting guide system addresses a critical gap in postmortem imaging by integrating MRI-compatible materials, precision-guided sectioning, and high-throughput imaging. It has enabled multimodal studies of aging and neurodegeneration and is being adopted in neuropathological workflows. This platform provides a reproducible, scalable, and anatomically precise solution for aligning ultrahigh field MRI with histology, enhancing both clinical research and digital pathology efforts.

bioengineering↗

bioRxiv2026

Plant growth forms shaping biodiversity patterns can guide conservation planning on the Qinghai-Tibet Plateau

Plant growth forms effectively reflect profound evolutionary adaptations that underpin ecosystem functioning; however, how their biogeographic disparities influence conservation prioritization remains poorly understood. We here integrate a comprehensive phylogeny with high-resolution distribution data for 14,468 vascular plant species across the Qinghai-Tibet Plateau, showing that growth-form identity decouples the spatial patterns of taxonomic and phylogenetic diversity, with distinct forms exhibiting marked differences in geographic range sizes and elevational optima (2,200-3,300 m). Although herbs dominate plant assemblages across spatial scales, their proportional abundance decreases along a northwest-to-southeast aridity gradient, yielding to structurally complex, non-herbaceous forms in humid, species-rich regions. Consequently, priority conservation areas derived for individual growth forms exhibit low spatial similarity. Despite this divergence, we identify trees and climbers as highly effective umbrella growth forms: prioritizing these functional groups captures [≥]75% of the multidimensional diversity of all other growth forms within a minimal spatial footprint. Our findings demonstrate that accounting for growth-form-based functional identity is essential for maximizing conservation efficacy, providing a scalable framework for biodiversity hotspots worldwide.

ecology↗

bioRxiv2026

Phage-encoded single-guide RNAs subvert CRISPR-Cas9 immunity

Central to CRISPR technologies is the single-guide RNA (sgRNA), an engineered fusion of a processed CRISPR RNA and tracrRNA that directs Cas9 and many Cas12 nucleases to bind and cleave target DNA1-4. Here, we report the discovery of similarly compact viral sgRNAs (vsgRNAs) encoded by bacteriophages that counteract bacterial CRISPR-Cas9 immunity. vsgRNAs inhibit Cas9 function via two complementary routes: by sequestering the Cas9 apoenzyme, and by re-directing the Cas9 nuclease to transcriptionally silence its own promoter. vsgRNAs also can cooperate with co-encoded anti-CRISPR proteins (Acrs), including AcrIIA25.1 that blocks DNA binding by Cas9 complexed with a standard sgRNA but not with the vsgRNA. We predict that phages evolved vsgRNAs by co-opting and repurposing host-encoded long-form tracrRNAs (tracr-L) responsible for Cas9 auto-repression and a countermeasure to Acrs5,6. Our search also uncovered Cas9-regulating small CRISPR-associated RNAs (scaRNAs), which we predict were inserted upstream of tracrRNAs to form tracr-L but were also co-opted by phages as viral scaRNAs to suppress Cas9 immunity. Finally, we found that vsgRNAs can enable genome editing in mammalian cells, offering a natural guide RNA template for CRISPR technologies. Overall, these findings reveal that bacteriophages devised their own compact sgRNAs tailored to subvert Cas9 immunity, long preceding their rational design to program RNA-guided nucleases2.

microbiology↗

bioRxiv2026

Assessing and Optimizing Low-Frequency Somatic Mutation Detection: A Multi-Platform High-Throughput Sequencing Perspective

The availability of multiple commercial short-read sequencing platforms necessitates systematic cross-platform performance comparisons, particularly for challenging applications such as low-frequency somatic mutation detection. Here, a large-scale targeted sequencing dataset from five Genome in a Bottle (GIAB) human genomic DNA reference standards, HG001 to HG005, alongside Twist Biosciences cfDNA reference standards featuring 1% variant allele frequency (VAF), was generated by six platforms (NovaSeq 6000, NovaSeq X, FASTASeq 300, GenoLab M, SURFSeq 5000, and MGISEQ-T7). To build a realistic benchmark while keeping authentic sequencing backgrounds, we developed PosMix, a simulating tool that generates position-specific VAFs. To overcome the limitations of conventional variant callers (high recall with poor precision for VarScan2, higher precision with lower recall for Strelka2/Mutect2), we developed SomaticXGB, a machine learning-based caller. In this study, SURFSeq 5000 consistently exhibited the lowest error rates and achieved superior accuracy for VAFs as low as 0.5%, outperforming all other sequencing platforms. On the other hand, SomaticXGB attained F1 scores of approximately 0.92 on simulated datasets with VAFs ranging from 0.5% to 1.5% and 0.89 on Twist 1% standards, substantially outperforming conventional methods. This work delivers a valuable rich multi-platform data resource, offering a standardized pipeline for performance benchmarking and a machine learning-based strategy for optimized somatic mutation detection.

bioinformatics↗

bioRxiv2026

Hepatic Acetate is an Essential Fuel for the Heart during Energy-Deprived States

Energy supply is fundamental to cardiac performance, yet the mechanisms by which the heart adapts to nutrient scarcity remain incompletely understood. Here, we identify acetate as a pivotal metabolic substrate that sustains cardiac contractile function during fasting-induced energy deficiency. Fasted mice reveal significant elevation of circulating acetate derived from hepatic fatty acid catabolism. Physiological concentrations of acetate alone can maintain ex vivo beating and electrical stability in Langendorff-perfused hearts. Primary mouse cardiomyocytes preferentially utilize acetate under energy-restricted conditions, which is abolished by knockdown of mitochondrial Acss1, the enzyme responsible for converting acetate to acetyl-CoA. Isotopic tracing with 13C-acetate demonstrated selective cardiac uptake during fasting. In vivo, acetate supplementation preserved heart rate and systolic function in fasted wild-type mice but not in Acss1-deficient hearts. These findings reveal an Acss1-dependent metabolic pathway enabling the heart to harness hepatic acetate as an endogenous fuel, representing a nutrient stress-responsive adaptation based on inter-organ crosstalk and implying therapeutic potential of acetate to energy-deficient heart diseases.

biochemistry↗

bioRxiv2026

Gut Microbiota Dysbiosis Drives Myocardial Hypertrophy Through GBP2b/GBP1-Mediated Immune Reprogramming and Exosomal Signaling in Chronic Colitis

BACKGROUNDPatients with inflammatory bowel disease (IBD) are at increased risk of cardiovascular disease, yet the mechanisms linking chronic intestinal inflammation to cardiac dysfunction remain poorly understood. IBD is characterized by profound gut microbiota dysbiosis, which we hypothesize drives systemic immune dysregulation and contributes to cardiac dysfunction. METHODSA chronic colitis mouse model was used to assess gut microbiota dysbiosis, systemic immune cell metabolism, and cardiac remodeling. Cardiac outcomes were evaluated by echocardiography, histology, and molecular analyses. Mechanisms were examined using fecal microbiota transplantation, immune cell depletion, exosome transfer, bone marrow chimeras, RNA-seq, co-immunoprecipitation, confocal microscopy, and siRNA-mediated gene silencing. RESULTSChronic DSS colitis induced cardiac dysfunction, hypertrophy, and fibrosis in mice. These changes were accompanied by sustained gut microbiota dysbiosis, metabolic reprogramming, and mitochondrial dysfunction in circulating immune cells. Fecal microbiota transfer experiments demonstrated that colitis-associated microbiota were sufficient to reprogram systemic immune cells and promote cardiac dysfunction. Immune cell depletion studies identified macrophages as key mediators of colitis-associated cardiac injury. Colitis increased systemic lipopolysaccharide (LPS) translocation, bone marrow chimera experiments demonstrated that hematopoietic TLR4 signaling was required for immune cell metabolic remodeling and cardiac dysfunction during chronic colitis. Transcriptomic analysis identified guanylate-binding protein 2b (GBP2b/GBP1, hereafter referred to as GBP1) as a key downstream effector of LPS-TLR4 signaling. Upon LPS stimulation, GBP1 localized to mitochondria, where it interacted with DRP1 and FIS1 to promote mitochondrial fission, oxidative stress, and enhanced immune cell migration into the heart. In addition, GBP1 was secreted via exosomes, which were taken up by cardiomyocytes and contributed to hypertrophic remodeling, and cardiac dysfunction. CONCLUSIONSThese findings establish the LPS-TLR4-GBP1 axis as a key driver of colitis-associated cardiovascular dysfunction and highlight this pathway as a promising therapeutic target for reducing cardiovascular risk in patients with IBD. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIPatients with inflammatory bowel disease have an increased risk of cardiovascular dysfunction that cannot be fully explained by traditional cardiovascular risk factors. C_LIO_LIGut microbiota dysbiosis and chronic innate immune activation are hallmarks of inflammatory bowel disease, but their direct contribution to cardiac remodeling remains unclear. C_LI What New Information Does This Article Contribute?O_LIChronic colitis-associated gut microbiota dysbiosis induces systemic immune cell metabolic and mitochondrial reprogramming that is sufficient to drive cardiomyocyte hypertrophy and cardiac dysfunction. C_LIO_LIHematopoietic Toll-like receptor 4 signaling links colitis associated gut microbiota to immune metabolic dysfunction and cardiac impairment, establishing a causal gut-immune-heart axis. C_LIO_LIGuanylate-binding protein 2b (GBP2b/GBP1) is identified as a critical downstream effector that promotes mitochondrial fission, oxidative stress, immune cell cardiac infiltration, and exosome-mediated cardiac remodeling. C_LI

pathology↗

bioRxiv2026

Trichome acylsugar defenses are equally effective against leaf-mining and free-living insects

Trichomes are epidermal projections, crucial components of plant defense systems. Whether these epidermal defenses are effective against leafminers, which infest the internal mesophyll layers, remains unclear. Using the devasting invasive tomato pest, Phthorimaea absoluta (tomato leafminer), and the trichome-rich wild tomato, Solanum pennellii, we demonstrate that trichome produced acylsugars effectively inhibit the growth of endophagous P. absoluta larvae feeding inside leaves. High spatial resolution leaf- and frass-metabolite analysis by MALDI-MSI and Stimulated Raman Scattering microscopy revealed that trichome-synthesized acylsugars are translocated into the mesophyll tissues when larvae infest leaves. We identified an ATP-binding cassette (ABC) transporter, SpABCB5, as the mediator of this translocation and as an essential component of defense against leafminers. These data reveal that epidermal trichomes not only defend against free-living (ectophagous) herbivores through direct contact or rapid deposition of chemical defenses onto leaf surfaces, but also defend against endophagous leafminers by rapidly depositing chemical defenses into internal tissues. By delivering mines against leaf miners, trichomes offer new avenues for breeding crops with resistance to leafminers.

plant biology↗

bioRxiv2026

A Novel Drug Candidate that Selectively Targets the Critical Androgen Receptor-ELK1 Growth Axis in Advanced and Drug-Resistant Prostate Cancer

Androgen receptor (AR)-dependent prostate cancer (PCa) cells require co-activation of ELK1 by AR to activate a critical set of cell cycle and mitosis genes, regardless of hormone - sensitivity. A small molecule antagonist (KCI807) that inhibits AR-dependent growth by selectively binding to AR and blocking its association with ELK1 is limited as a drug by auto-induced metabolism. Using structure-activity data, consistent with modeling a physically mapped KCI807 binding pocket, we developed a new class of compounds with a different core structure comprising 5-Hydroxy-2-(3-hydroxyphenyl)-1-methylquinolin-4(1H)-one (KCI830), with variable N- substituents. The compound with a N-2,2,2-trifluoroethyl substitution (KCI838) was the fastest acting and most potent inhibitor of AR-dependent cell growth and colony formation in PCa model cells, including exclusively AR splice variant-dependent and other enzalutamide-resistant cells, without affecting growth of AR-negative cell lines. Critical tests were conducted to establish that KCI838 recapitulates the previously elucidated mode of action of KCI807. KCI838 selectively inhibited ELK1-dependent vs. androgen response element (ARE)-driven promoter and gene activation by AR. KCI838 blocked AR binding to ELK1 in situ tested by BRET assay. Increasing the total cellular AR by [~]2-fold using ectopic AR expression caused the predicted change in drug dose-response profile for growth, implicating AR as the exclusive target for the activity of KCI838. KCI838s molecular scaffold conferred reduced enzyme induction in primary human hepatocytes and weakened interactions with human UGT1A1 and CYP1A2. In mice bearing an aggressive, enzalutamide-resistant patient-derived PCa tumor xenograft characteristically overexpressing prostatic acid phosphatase, daily bolus injections of a soluble 3phosphate monoester prodrug of KCI838 (KCI838PME) progressively inhibited tumor growth, concomitant with tumor accumulation of active hydrophobic drug, without significant toxicity. Additionally, ALZET osmotic pumps were used to establish proof-of-concept for reversible in vivo anti-tumor activity of KCI838PME administered in a low dose, controlled release mode. The results warrant investigation of KCI838PME in a controlled-release formulation, to treat PCa that is resistant to current AR-targeted therapies while obviating the need for testosterone suppression.

cancer biology↗

bioRxiv2026

Oral exposure to Perfluorooctanoic acid disrupts the microbiota-gut-liver axis and enhances the severity of chemically induced colitis in mice.

Inflammatory bowel diseases (IBD) affect millions of patients worldwide and impair quality of life. Although genetic and environmental factors are known to disrupt the gastrointestinal (GI) epithelial barrier and increase susceptibility to IBD, the precise contribution of specific environmental exposures remains unclear. Per- and polyfluoroalkyl substances (PFAS), or "forever chemicals," are widely used in consumer products and contaminate food and water sources, resulting in chronic oral exposure worldwide. Perfluorooctanoic acid (PFOA), a common PFAS, has been epidemiologically associated with the development of IBD, particularly in older adults. Here, we assessed the effects of oral PFOA exposure on the GI tract, liver, and susceptibility to colitis. C57BL/6 mice were exposed to PFOA (0.1 mg/kg or 1.0 mg/kg) beginning at weaning (post-natal day [P]21) for a time course of 4 or 8 weeks. GI physiology/pathology (Ussing chambers; histology), expression of pro-inflammatory cytokines (qPCR), microbiota composition (16S sequencing), bile acids production (qPCR; LC/MS), and liver pathology (histology) were assessed. Colitis susceptibility was evaluated in genetically predisposed (IL10 knockout) mice, and in induced (dextran sodium sulfate [DSS]) mouse models following PFOA exposure (8 weeks at 1.0 mg/kg). Oral PFOA exposure increased intestinal permeability, mildly increased cytokine expression, altered gut microbiota composition, disrupted liver and serum bile acids, and caused hepatic hypertrophy at higher doses and longer exposure. Although PFOA did not increase disease susceptibility in genetically predisposed Il10 KO mice, it significantly worsened DSS-induced colitis, but only in male mice. Together, these findings demonstrate that early-life PFOA exposure disrupts the gut-liver axis and may contribute to colitis development in a sex dependent manner.

pharmacology and toxicology↗

bioRxiv2026

Vagus nerve stimulation limits colonic inflammation through distinct neuroimmune circuitry shaped by inflammatory history

Bidirectional communication between the nervous and immune systems has been demonstrated to limit or enhance immune cell function across organ systems and conditions. Although these neuroimmune circuits can become activated as an anti-inflammatory reflex, vagus nerve stimulation (VNS) reduces inflammation in models of endotoxemia, rheumatoid arthritis, and intestinal inflammation. In the spleen during endotoxemia, VNS activates a "cholinergic anti-inflammatory pathway" (CAIP), whereby choline acetyltransferase (ChAT)-expressing T cells release acetylcholine to reduce macrophage activation. VNS can also drive CAIP-independent pathways to reduce inflammation in the spleen and intestinal tract, although the circuitry modulating colonic inflammation remains underexplored. Here, we demonstrate that left cervical VNS reduces acute LPS-induced inflammation, evidenced by reduced Tnfa expression in colon and spleen and decreased circulating TNF. In the colon, these protective effects required efferent but not afferent VNS and were independent of ChAT+ T cells, IL10, {beta}-adrenergic signaling, and colonic sympathetic innervation. Critically, the ability of VNS to modulate colonic inflammation depended on prior tissue-specific inflammation. Mice recovering from DSS colitis, despite near-complete histological recovery, were refractory to the protective effects of VNS in the colon. This lack of efficacy in the colon was not reflected in measures of inflammation in the spleen or serum, highlighting the need for target-organ-specific monitoring. This loss of efficacy after colonic inflammation was transient, with restoration occurring upon complete recovery. These findings demonstrate that VNS efficacy in colonic inflammation depends on circuitry distinct from canonical systemic anti-inflammatory pathways, and that tissue responsiveness is shaped by anatomical site and inflammatory history. Key PointsO_LIElectrical stimulation of the left cervical vagus nerve reduces LPS-induced inflammation in the mouse colon. C_LIO_LIThis colonic anti-inflammatory effect requires vagal efferents but not afferent signaling. C_LIO_LIUnlike canonical splenic anti-inflammatory pathways, the colonic response does not require ChAT+ T cells, IL-10, {beta}-adrenergic signaling, or local sympathetic innervation. C_LIO_LIRecent DSS colitis abolishes colonic responsiveness to VNS despite preserved splenic and systemic anti-inflammatory effects. C_LIO_LIRecovery of VNS anti-inflammatory efficacy after colitis shows that neuroimmune responsiveness in the colon is dynamically shaped by inflammatory history. C_LI

immunology↗

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

An oncolytic adenovirus armed with anticancer prodrug-activating enzyme offers enhanced tumor killing and antitumor immunity.

Oncolytic viruses are most commonly administered via intratumoral injection; however, their clinical efficacy in achieving tumor eradication remains limited by several challenges, including insufficient penetration into all tumor cells and the inability to elicit robust systemic antitumor immune responses capable of eliminating metastatic microtumors. Here, we report an oncolytic adenovirus, OAd-2B6, with an engineered adenoviral E1 region for tumor selectivity and carrying the prodrug- activating enzyme cytochrome P450 2B6 (CYP2B6) to activate the anticancer prodrug cyclophosphamide (Cytoxan, CTX). OAd-2B6 alone induced dose-dependent tumor cell killing across multiple human tumor cell lines and exhibited strong synergistic antitumor effects when combined with CTX. Importantly, OAd-2B6-mediated local activation of CTX resulted in a potent bystander killing effect that eliminated tumor cells not directly infected by the virus. In a H1299 lung cancer xenograft nude mouse model, intratumoral injection of OAd-2B6 combined with CTX significantly inhibited tumor growth and even achieved complete tumor regression, with markedly superior efficacy compared with monotherapy. In immunocompetent mice bearing 4T1 breast cancer xenografts, OAd-2B6 alone inhibited tumor growth and was accompanied by upregulation of IFN-{gamma} and GzmB expression in the tumor-infiltrated T cells. CTX combination therapy further enhances this anti-tumor immune response, promoting the activation of T cells to suppress non-injected tumors at a distal site. Collectively, this study demonstrates that OAd-2B6 exerts potent antitumor effects through multiple mechanisms, including direct oncolysis, intratumoral prodrug activation leading to bystander killing, and enhancement of systemic antitumor immunity. These findings provide a promising strategy for improving the therapeutic efficacy of oncolytic therapy.

cancer biology↗

bioRxiv2026

Genos-m: a foundation model for human-associated microbial genomes

Human-associated microbial genomes encode extensive strain-level diversity and niche-specific gene repertoires that are critical to host health. However, these complex sequence features remain difficult to capture using general-purpose DNA foundation models, highlighting the need for dedicated representation learning tailored to the human microbiome. Here, we introduce Genos-m, an open-source foundation model for human-associated microbial genome representation. Genos-m was pretrained on approximately 1.2 trillion nucleotide tokens from a curated microbial genome corpus, including human-associated prokaryotic isolates, high-quality metagenome-assembled genomes (MAGs) and bacteriophages, supplemented with GTDB species-level representative genomes to broaden prokaryotic taxonomic breadth. The model uses a sparsely activated Mixture-of-Experts (MoE) Transformer architecture, with 4.7 billion total parameters, approximately 330 million activated parameters per forward pass and a maximum context length of one million base pairs. We evaluated frozen Genos-m representations across short-sequence and gene-level tasks, biosynthetic gene cluster (BGC)-based regional sequence tasks, whole-genome strain phenotype prediction, and zero-shot transfer on prokaryote-related RNAfitness assays. Across these benchmarks, Genos-m consistently ranked among the leading comparison models, with the best performance in five of eight gene-fitness regression tasks and in BGC type classification. Using sparse autoencoders, we identified sparse features in Genos-m hidden activations that aligned with annotated ORFs, intergenic regions, and tRNA and rRNA loci. In downstream applications, Genos-m-derived genome-informed species representations in-corporated into a human microbiome self-supervised learning model improved colorectal cancer (CRC)-control classification over conventional species-abundance random forest models. Genos-m also generated stable sample-level embeddings from as few as 10,000 metagenomic reads, retaining gut microbial community structure that distinguished geographic origin and aligned with enterotypes defined from full-depth taxonomic profiles. Together, these results support Genos-m as a reusable representation model for microbial genomes and metagenomes, with conclusions bounded by the reported datasets, task definitions and evaluation protocols. Genos-m model weights, inference code, and usage documentation are publicly available on GitHub (https://github.com/BGI-HangzhouAI/Genos-m) and Hugging-Face (https://huggingface.co/BGI-HangzhouAI/Genos-m).

bioinformatics↗

bioRxiv2026

The origin and evolution of archaeal Borg extrachromosomal elements

Borgs are giant linear extrachromosomal elements (ECEs) of methane-oxidizing Methanoperedens archaea whose evolutionary origin and ecosystem distribution remain unknown. Here we detected 240 Borgs in diverse saline, soil, and freshwater ecosystems. 27 encode methyl-coenzyme M reductases central to methane metabolism, eight have full rRNA operons related to those of Methanoperedens, and some contain up to four ribosomal proteins. We also identified 323 mini-Borgs whose proteome content and gene phylogenies classify as a distinct ECE type. Based on 105 complete and near-complete genomes, Borgs and mini-Borgs share core genes in conserved order, indicating common ancestry. Phylogenetic and diversity analyses suggest that Borgs evolved via gene acquisition into a backbone inherited from mini-Borgs. This evolutionary trajectory mirrors those proposed for giant viruses of both eukaryotes and bacteria.

microbiology↗

bioRxiv2026

Energy Expenditure During Walking With a Novel Treadmill Controller That Induces Gait Asymmetry

Gait asymmetry is a common manifestation of walking impairment among clinical populations. We recently developed a novel treadmill walking approach called dynamic treadmill walking that can provide asymmetric gait training by changing the treadmill speed between fast and slow speeds within a single stride. Here, we studied the energy expenditure associated with a variety of dynamic treadmill walking conditions. We hypothesized that the metabolic power required for dynamic treadmill walking in all conditions would approximate the metabolic power associated with conventional walking at the mean of the fast and slow speeds employed in the task. Eleven young adults without gait impairment walked on an instrumented treadmill and breathed into a metabolic measurement system. During dynamic treadmill walking, the treadmill fluctuated between 0.75m/s and 1.50m/s, each for 50% of an individual's stride time. We used a metronome to synchronize participants' right heel-strikes with four different timing conditions. Net metabolic power during dynamic treadmill walking was significantly greater than normal walking at the mean speed of the task (1.125m/s) and generally lower than walking at the fast speed (1.5m/s). We did not observe any significant associations between net metabolic power and several measures of gait asymmetry during dynamic treadmill walking. These findings establish dynamic treadmill walking as a promising technique for improving gait symmetry in individuals who cannot tolerate fast treadmill walking, a common gait rehabilitation approach. Future work will assess the feasibility, metabolic demands, and clinical efficacy of using dynamic treadmill walking to improve gait symmetry in clinical populations.

physiology↗

bioRxiv2026

Insights into Genome Ejection by a Therapeutic phiKMV-like Bacteriophage

Ar-KM is a phiKMV-like therapeutic bacteriophage used in clinical candidate phage therapy cocktails to treat lung infections caused by Pseudomonas aeruginosa. Here, we present an integrative structural atlas of Ar-KM proteins using cryo-EM, proteomics, and bioinformatics. From a single purified Ar-KM preparation, we identified three distinct populations: mature DNA-filled virions, open-nozzle particles with ejection proteins extending from the tail, and closed-nozzle empty particles. Near-atomic-resolution reconstructions of all three states enabled us to build atomic models for eleven structural proteins. The mature virion revealed the pre-ejection conformation of three ejection proteins, gp41, gp42, and gp43, homologous to coliphage T7s gp14, gp15, and gp16, respectively. Unlike T7, peptidoglycan hydrolase activity associated with the ejectosome resides in the gp15-like periplasmic tunnel protein gp42, whereas in T7 the lysozyme-like domain is located at the N-terminus of gp16, underscoring the structural plasticity and evolutionary mosaicity of ejection proteins. We further identified a short -helical factor, gp34, present in eight copies at the mismatched interface between the portal barrel and gp41. Gp34 forms a cage within the nozzle, acting as a molecular wedge that stabilizes the open conformation and permits gp41 to assemble into a hexameric channel during ejection. Evolutionarily, gp34 appears to be an ortholog of the essential gene gp7.3 in phage T7 and is conserved across sequenced phiKMV-like phages. We propose that this protein functions as an ejection protein assembly factor, stabilizing the open nozzle during infection and allowing the coordinated exit of ejection proteins and their assembly into a DNA-ejectosome. HighlightsO_LIStructural polymorphism of phage Ar-KM defines open and closed nozzle states C_LIO_LIEjection proteins gp43, gp42, and gp41 assemble in a 4:8:8 stoichiometry C_LIO_LILysozyme domain shows modular positioning within the ejectosome C_LIO_LIPortal protein acts as the primary barrier to genome leakage C_LIO_LIWedge protein gp34 (T7 gp7.3 ortholog) bridges portal and gp41 C_LI

biophysics↗