Biology subjects

Liang, C.

Publications and source records attributed to Liang, C..

At least 19 recordsLinked to original sources

bioRxiv2026

CAR-macrophage immunotherapy targeting fibroblast-like synoviocytes ameliorates inflammatory and degenerative arthritis

Rheumatoid arthritis (RA) is an inflammatory arthritis, whereas osteoarthritis (OA) is a degenerative joint disease. Despite their distinct etiologies, both are characterized by the pathogenic activation of fibroblast-like synoviocytes (FLS), which contribute to synovial hyperplasia, persistent inflammation, and cartilage destruction. Accordingly, pathogenic FLS represent an attractive therapeutic target for both RA and OA. Macrophages exhibit remarkable phenotypic plasticity, and interleukin-4 (IL-4) promotes an anti-inflammatory, tissue-reparative M2-like phenotype. Fibroblast activation protein (FAP) and nucleolin (NCL) are highly expressed on the surface of pathological FLS while exhibiting limited accessibility in normal tissues. Here, we developed two IL-4-armored, FLS-targeted chimeric antigen receptor macrophage (CAR-M) platforms directed against FAP or NCL, termed CAR-M2-FAP and CAR-M2-NCL, respectively. In vitro, both platforms enhanced FLS phagocytosis and promoted an M2-like transcriptional profile. Transcriptomic analysis further revealed enrichment of phagocytic, anti-inflammatory, and tissue-reparative programs. In a mouse model of RA, both CAR-M2 platforms attenuated arthritis severity, synovial hyperplasia, cartilage loss, and bone erosion. Similarly, in a mouse model of OA, they reduced synovitis, cartilage degeneration, and osteophyte formation. No overt acute toxicity was observed in either RA or OA mice following treatment with CAR-M2-FAP or CAR-M2-NCL. Collectively, the concordant therapeutic effects of CAR-M2-FAP and CAR-M2-NCL across RA and OA models provide preclinical proof of concept for FLS-targeted CAR-M2 as a potential therapeutic strategy for inflammatory and degenerative arthritis.

bioengineering↗

bioRxiv2026

PigGPA: A Domain-Constrained Agent for Porcine Genomic Breeding with Verifiable Tool Execution

Large language model agents can plan and execute scientific analyses, but successful task completion does not establish whether analytical decisions remain consistent across independent sessions or whether computations follow the parameters specified beforehand. We investigated these limitations using four genomic analysis tasks. General-purpose agents showed limited consistency in analytical decisions across repeated sessions (57.5-58.8%). Incorporating domain knowledge improved analytical performance, with reusable skills increasing mean evaluation scores from 73.44 to 89.06/100 , but did not resolve decision variability or ensure agreement between specified and executed parameters. To address these limitations, we developed an approach combining domain-constrained analytical skills with call-level execution contracts. Each tool invocation is linked to a pre-execution parameter declaration through SHA-256 hashing, with actual command-line arguments and execution records subsequently checked against the declared parameters. We implemented this approach in PigGPA, an autonomous agent for porcine genomic breeding that integrates statistical genetics, sequence-based functional prediction and multi-omics annotation. PigGPA completed all benchmark tasks with full agreement between declared and executed parameters, while its core quantitative-genetic results closely matched established software (r = 0.999-1.000). An application to loin muscle depth further demonstrated an integrated workflow from genetic association analysis to functional interpretation. These findings show that domain knowledge improves analytical performance, while direct verification of tool execution provides an additional basis for reproducible scientific computation.

bioinformatics↗

bioRxiv2026

A Novel Computational Framework to Investigate the Biomechanics of Burrowing

Head-first burrowing likely imposes strong mechanical demands on the skull of fossorial vertebrates, but how cranial tissues respond to these loads remains obscure. Here, we developed a computational framework integrating the discrete element method (DEM) with finite element analysis (FEA) to investigate cranial biomechanics during burrowing. We used Blanus cinereus, a round-headed amphisbaenian, as a model to establish DEM predictions that were validated and calibrated against in vitro experiments across three substrates and compared with in vivo push forces. DEM-calibrated particle contact forces were then transferred to an anatomically detailed finite element model to quantify cranial loading. The analyses suggested that soft tissues accommodated substantial deformation, while the skull transmitted burrowing loads from the premaxilla towards the occipital region. Cranial sutures further redistributed stresses and strains within the skull. This validated DEM-FEA framework links particle-scale substrate interactions with internal cranial biomechanics and provides a quantitative approach for investigating the mechanics of head-first burrowing across fossorial vertebrates.

bioengineering↗

bioRxiv2026

Down syndrome postmortem brains exhibit reduction in nifene binding to α4β2* nicotinic acetylcholinergic receptors

Alzheimer's disease (AD) pathology including amyloid beta (A{beta}) plaques and tau tangles accumulate with age in Down Syndrome (DS). Cholinergic abnormalities such as expression of nicotinic acetylcholine receptors (nAChRs) adversely contribute to cognitive decline and neurodegeneration in AD with similar features possible in DSAD. As a radiotracer for 4{beta}2* nAChRs, [18F]nifene was quantitatively evaluated in the frontal cortex (FCX) and temporal cortex (TCX) of DSAD, AD, and cognitively normal (CN) brain tissue using autoradiography. Anti-tau and anti-A{beta} immunostaining in adjacent sections confirmed the presence of tau tangles and A{beta} plaques. [18F]Nifene binding in brain sections demonstrated significantly more binding in gray matter (GM) than white matter (WM), with FCX exhibiting more binding than TCX (OptiQuant). Nicotine substantially displaced [18F]nifene binding in adjacent sections, resulting in average GM/nicotine ratios (DSAD=9.74, AD=10.5, CN=17; suggesting a 38% decrease in AD and a 43% decrease in DSAD) and WM/nicotine ratios (DSAD=2.73, AD=3.31, CN=5.62; suggesting a 41% decrease in AD and a 51% decrease in DSAD). [18F]Nifene was correlated with [125I]IBETA (A{beta}), showing a strong positive relationship between 4{beta}2* nAChRs and A{beta} in DSAD. [18F]Nifene GM/nicotine and WM/nicotine ratios were positively correlated with age in TCX and FCX. The findings of this study suggest that [18F]nifene has potential use in diagnostic investigations of the cholinergic system in DSAD using positron emission tomography. The study also points to a possible need for earlier therapeutic interventions to address the 4{beta}2* nAChRs deficit in DSAD.

neuroscience↗

bioRxiv2026

Application of the Bradley-Terry model to quantify components of sperm competition

In many species with female sperm storage, ejaculates from multiple males overlap in the female reproductive tract, making sperm competitive ability a key component of male reproductive fitness and a target of rapid evolutionary change in the underlying genes. Here, we used controlled laboratory assays of Drosophila melanogaster sperm competition, with doubly-mated females and paternity assignment of offspring, to ask whether a Bradley-Terry framework can effectively summarize and predict competitive outcomes. The Bradley-Terry model is a probabilistic approach that estimates a latent "ability" score for each contestant based on outcomes of pairwise contests, and thus is naturally suited to data from sperm competition, which are intrinsically pairwise. We selected five distinct male genotypes: four carried strongly expressed RFP or GFP markers that allowed us to distinguish their heterozygous offspring under UV illumination, and the fifth was Canton-S, a standard wild-type genotype that served as our reference. Using Canton-S females, we assayed all 20 ordered pairwise combinations of first and second male, recorded successful double matings, and quantified the offspring sired by each male. We then extended the Bradley-Terry model to estimate genotype-specific competitive success separately for first-male "defense" (fertilization success following initial mating, also called "P1") and second-male "offense" (fertilization success following a remating, also called "P2"). This framework provides a flexible and efficient way to integrate results across large arrays of pairwise mating tests and to derive predictive scores for sperm competitive performance.

evolutionary biology↗

bioRxiv2026

Effects of Mechanical Loading on Cranial Joint Mesenchymal Stem Cell Proliferation

Sutures are the primary sites of cranial bone growth, allowing the skull to accommodate the growing brain. External mechanical stimulus has been shown to delay suture fusion and induce tissue remodelling. Recent studies suggest that in vivo cyclic bone loading increased proliferation of mesenchymal stem cells (MSC) in the coronal suture. The overall aim of this study was to understand how many loading sessions (exposure-response) and how long after loading (time-course) did MSC proliferation increase in the coronal suture. In the exposure-response analysis, mice underwent 1, 3, or 5 loading sessions between Postnatal day 7 (P7) and P11, and in the time-course analysis, treated mice underwent 10 loading sessions between P7 and P21. Loading sessions were 10 minutes at a frequency of 1 Hz and a force of 10 g (0.1 N). The loading tip was positioned on the posterior aspect of the left frontal bone, dorsal to the coronal suture. The EdU marker shows a statistically significant increase in proliferation after one loading session and a decrease after three loading sessions. The PCNA marker shows a statistically significant increase after three and five loading sessions. The exposure-response analysis showed that when the results of both markers are combined, levels of proliferation cannot be interpreted until at least five loading sessions have been completed, after which a clear increase in proliferation was observed. In the time-course analysis, proliferation was highest immediately after the final treatment session and 24 hours after the final loading session the effects of mechanical bone loading gradually returned to baseline.

Developmental Biology↗

bioRxiv2026

Upregulation of ATP-purinergic P2x2 receptors in the cochlea over-amplifies hearing sensitivity leading to hyperacusis and attenuation by antagonists

Hearing hypersensitivity (hyperacusis) is a common hearing stress and can cause many psychological diseases, e.g., anxiety, learning disabilities, and attention-deficit/hyperactivity disorder (ADHD). Here, we report an unexpected finding that the upregulation of P2x2 ATP-purinergic receptors in the cochlea links to hyperacusis generation. We found that P2x2 expression in the cochlea but not in auditory centers was upregulated in the hyperacusis generated by Cx26 deficiency. Overexpression of P2x2 in the cochlea also caused hyperacusis. Conversely, downregulation of P2x2 expression or administration of P2x2 antagonists attenuated hyperacusis. We further found that upregulation of P2x2 receptors in the cochlea increased outer hair cell (OHC) electromotility through the post-transcription functional modulation to potentiate active cochlear amplification leading to hearing hypersensitivity. Such enhancements in OHC electromotility and active cochlear amplification were also suppressed by P2x2 receptor antagonists. Overall, these findings demonstrate that P2x2-mediated ATP-purinergic signaling in the cochlea plays a critical role in hyperacusis generation; targeting P2x2 receptors can attenuate hyperacusis stress, which may also offer a therapeutic strategy for other related psychological comorbidities. Significance statementHearing hypersensitivity is a common hearing stress and can cause many other psychological disorders. However, little is known about the underlying genetic and cellular mechanisms. Also, it lacks efficient drugs for their treatments in the clinic. In this study, we found that upregulation of P2x2 ATP-purinergic receptors in the cochlea can potentiate outer hair cell electromotility, which is an active cochlear amplifier in mammals and can increase hearing sensitivity and frequency selectivity, through post-transcription functional modulation to enhance active cochlear amplification leading to hearing hypersensitivity. These enhancements can be inhibited by administrations of P2x2 receptor antagonists both in vitro and in vivo. These findings revealed a new genetic and cellular mechanism underlying hyperacusis generation and opened a new avenue to develop an efficient therapy for this common hearing stress and other associated psychological comorbidities.

physiology↗

bioRxiv2026

Enterococcus faecalis biofilm rewires neutrophil metabolism to suppress antimicrobial functions

Enterococcus faecalis is an opportunistic pathogen that persists in biofilm-associated infections despite robust neutrophil recruitment. How E. faecalis evades neutrophils remains poorly understood. Here, we investigated how E. faecalis biofilms alter effector functions in human neutrophils and a murine wound infection model. We found that E. faecalis biofilm suppresses neutrophil extracellular trap (NET) formation, bacterial engulfment, and neutrophil-mediated control of biofilm growth. This suppression is partly driven by production of lactic acid through the lactate dehydrogenases (LDH) of E. faecalis, which acidifies the extracellular environment, lowers neutrophil intracellular pH, and disrupts glycolysis, the tricarboxylic acid cycle, and the oxidative pentose phosphate pathway. In a murine wound infection model, loss of LDH increased neutrophil recruitment and NETosis. We also found that high bacterial density, a defining feature of biofilms, suppresses NETosis through a lactic acid-independent mechanism. Collectively, these findings identify biofilm immune evasion strategies mediated by bacterial metabolism and the high-density structural organization of biofilm-associated bacteria. TeaserEnterococcus faecalis biofilms suppress neutrophil defenses through lactic acid and high bacterial density.

microbiology↗

bioRxiv2026

Circadian misalignment underlies immune escape in breast cancer

Circadian regulation shapes tissue physiology, yet how it organizes cellular and molecular dynamics within the tumor microenvironment (TME) and influences tumor immunity remains unclear. Using temporal single-nucleus multiomic profiling of mouse breast tumors, we uncovered extensive circadian programs that are both cell-type-specific and shared across the TME, governing proliferation and immune responses. Notably, cancer epithelial cells exhibited global acrophase misalignment relative to immune populations. This intercellular desynchrony manifests as temporal decoupling between tumor proliferation and immune activation, discordant antigen presentation and T cell recognition with intrinsic activation-exhaustion overlap in T cells, and asynchronous PD-1/PD-L1 oscillations that sustain checkpoint-mediated suppression. Similar patterns were observed in human triple-negative breast cancer (TNBC). Together, these findings establish intercellular circadian misalignment as a mechanism of tumor immune evasion and position the circadian architecture of the tumor-immune ecosystem as a previously underappreciated determinant of tumor development and therapeutic response. HIGHLIGHTSO_LISingle-cell multiomics maps circadian regulation of tumor-immune programs. C_LIO_LICircadian regulation in cancer epithelial cells is misaligned with immune cell populations. C_LIO_LITumor-immune temporal misalignment undermines antitumor immunity. C_LIO_LICircadian misalignment in human TNBC suggests relevance for immunotherapy timing. C_LI

cancer biology↗

bioRxiv2026

IFITM1 inhibits Henipavirus membrane fusion by trapping ephrinB2 receptors in fusion-unfavorable membrane nanodomains.

Nipah (NiV) and Hendra (HeV) viruses are prototype henipaviruses (HNV) within the family of Paramyxoviridae. They are highly pathogenic zoonotic paramyxoviruses that cause fatal encephalitis in humans, with case fatality rates of 40-70%. These viruses use the receptor-binding protein (G) to engage host receptors ephrinB2 and/or ephrinB3, while the fusion protein (F) drives membrane fusion leading to virus entry and cell-cell fusion. Interferon-inducible transmembrane (IFITM) proteins restrict the infection of many unrelated viruses at virus entry. We show that the knockdown of IFITM1 enhances HNV entry and cell-cell fusion in both human epithelial and endothelial cells, while overexpression of IFITM1 inhibits both. Using single-molecule localization microscopy, we observed that IFITM1 forms nanoclusters on the plasma membrane that are enhanced upon interferon stimulation. IFITM1 clusters spatially co-occur with GM1-enriched, raft-like membrane domains. Notably, IFITM1 interacts with ephrinB2, and redistributes ephrinB2 into larger and denser clusters, potentially within GM1-enriched regions. Using single-particle tracking, we further show that ephrinB2s lateral diffusion on the plasma membrane is confined by IFITM1, and this confinement is not reversed by amphotericin B, a membrane-permeabilizing agent that increases membrane fluidity. Our data suggest that IFITM1 sequesters ephrinB2 in fusion-unfavorable membrane domains, thereby enhancing the energy barrier for virus-cell membrane fusion and decreasing the virus-receptor encounters. SignificanceNipah (NiV) and Hendra (HeV) viruses are zoonotic paramyxoviruses that cause fatal encephalitis in humans. Here, we show that IFITM1 inhibits NiV and HeV entry at the surface of epithelial and endothelial cells. We report that IFITM1 restricts NiV entry by sequestering the host receptor ephrinB2 in membrane domains that are energetically unfavorable for virus-cell membrane fusion. IFITM1 also restricts ephrinB2 lateral diffusion on the plasma membrane, thereby reducing productive virus-receptor encounters. Notably, amphotericin B treatment, which increases membrane fluidity, did not rescue IFITM1-mediated confinement of ephrinB2 or restore NiV entry. Our data reveal a new mechanism by which IFITM1 restricts NiV infection, suggesting that its antiviral activity extends beyond simply altering membrane fluidity.

microbiology↗

bioRxiv2026

OneGenomeRice (OGR): A Genomic Foundation Model for Rice

The transition of genomics to a predictive intelligence discipline is driven by the advent of genomic foundation models. While substantial progress has been observed in all-life and human-centric models, plant species, particularly for the staple crops, remains hindered by a lack of models. Here we introduce OneGenome-Rice (OGR), a rice (Oryza sativa) genomic foundation model pre-trained on a genomic dataset comprising 422 high-quality genomes of cultivated and wild rice. OGR is engineered upon a Mixture of Experts (MoE) transformer architecture with 1.25-billion parameters and supports an ultra-long context window of up to 1 million base (Mb) pairs at single-nucleotide resolution. A comprehensive benchmark demonstrated that OGR significantly outperforms existing state-of-the-art multi-plant or all-life genome models in 11 categories (e.g. motif identification, sweep detection, etc). We further demonstrated the utility of OGR in several downstream applications, such as indica-japonica subspecies introgression analysis, identification of agronomy trait-associated functional loci and prediction of gene expression from DNA sequences. These results establish OGR as a promising foundational computational infrastructure for rice functional genomics and precision breeding. The OGR and its fine-tuned models, including pretrained weights, training code and the rice genomic benchmark suit, have been fully opened.

genomics↗

bioRxiv2026

Increased Binding of Nifene, a PET Imaging Probe for α4β2* Nicotinic Acetylcholinergic Receptors in Hippocampus-Subiculum of Postmortem Human Parkinsons Disease Brain

Non-motor symptoms in Parkinsons disease (PD) may be influenced by the 4{beta}2* subtype of nicotinic acetylcholine receptors (nAChR) present in the hippocampus and subiculum. To continue efforts in PET diagnostics for PD, autoradiographic [18F]nifene binding to 4{beta}2* nAChR was quantitively assessed in the hippocampus-subiculum (HP-SUB) of PD (n = 27; 14 males, 13 females) and cognitively normal (CN) (n = 32; 16 males, 16 females) cases. Anti-ubiquitin for Lewy body and anti--synuclein immunostaining on adjacent slices were analyzed in QuPath and [18F]nifene binding was quantified in OptiQuant. Subiculum had greater [18F]nifene binding (51% to 85%) compared to HP in all subjects. Significantly higher [18F]nifene binding (>250%) was seen in PD SUB and PD HP compared to CN in both males and females. The grey matter (GM) to white matter (WM) ratio in PD=3.53 while CN=1.33, a >150% increase in PD. Binding of [18F]nifene to GM and WM individually was >250% greater in PD compared to CN. Male CN exhibited an increase while and male PD exhibited a significant decrease in [18F]nifene binding with aging, while females did not exhibit significant differences. In summary, 4{beta}2* nAChR measured by [18F]nifene is significantly upregulated in the PD HP and SUB. This increased [18F]nifene binding may be of diagnostic value using PET imaging.

neuroscience↗

bioRxiv2026

Imaging FDG PET/CT Study of Nicotinic Acetylcholinergic Receptor α2 Knock-Out Mice and α2 Hypersensitive Mice Compared to Control Mice: Male-Female Differences and Nicotine Effects

ObjectiveNicotinic acetylcholinergic receptors (nAChRs), comprising of and {beta} subunits are present in the brain and whole body. The less abundant 2-subunit is a fast-acting receptor subtype and plays an important role in cognition and learning. To understand cellular functional consequences, this study evaluated glucose metabolism using [18F]FDG PET/CT in 2 knockout (2KO) and 2 hypersensitive (2HS) mice. MethodsControl (CN; 4M, 4F), 2 knockout (2KO; 4M, 4F) and 2 hypersensitive (2HS; 4M,4F), 12-16 month old mice were used. Mice were fasted and injected with [18F]FDG (3-5 MBq) while awake. After 40 minutes they underwent whole body PET/CT. On a separate day, nicotine challenge [18F]FDG studies were done. Reconstructed images were analyzed to obtain standard uptake values (SUV) of [18F]FDG in brain and interscapular brown adipose tissue (IBAT). Statistical analysis was performed. ResultsThe 2HS male mice exhibited the largest brain increase in [18F]FDG compared to 2KO male mice. The rank order of brain [18F]FDG uptake in the 3 groups: 2HS[male]> CN[male]> 2KO[male]> CN[female]= 2KO[female][≥] 2HS[female]. Nicotine treatment reduced brain [18F]FDG uptake in all mice. Females had lower [18F]FDG uptake compared to males and were less sensitive to 2 nAChR. In the case of IBAT, 2KO mice had significantly higher baseline [18F]FDG uptake compared to the other two groups: 2KO[male]> 2KO[female]> 2HS[female]> 2HS[male]> CN[female]> CN[male]. Nicotine decreased IBAT in 2KO mice rather than increase as observed in CN and 2HS mice. Conclusions2 nAChRs plays a significant role in brain activation as exhibited by the increase in [18F]FDG in 2HS mice. In the absence of regulatory control by the 2 nAChR, the 2KO mice IBAT exhibited higher [18F]FDG IBAT compared to controls and 2HS mice. Female mice were less affected by nicotine compared to the male mice. Overall, 2 nAChRs played a significant role in glucose metabolism in the brain and IBAT.

neuroscience↗

bioRxiv2026

MESSI: Multimodal Experiments with SyStematic Interrogation using nextflow

BackgroundMultimodal biomedical studies increasingly profile multiple molecular and clinical modalities from the same samples, creating new opportunities for disease prediction and biological discovery. However, benchmarking multimodal integration methods remains difficult because studies often use inconsistent preprocessing, unequal tuning strategies, and non-comparable evaluation schemes, limiting fair assessment across methods. ResultsWe developed MESSI (Multimodal Experiments with SyStematic Interrogation), a reproducible Nextflow-based benchmarking framework for multimodal outcome prediction that standardizes data preparation, supports interoperable R and Python workflows, and enforces leakage-free nested cross-validation for model selection and model assessment. MESSI currently implements representative intermediate- and late-integration methods and supports bulk multiomics, bulk multimodal, and single-cell multiomics datasets. In simulation studies with known ground truth, most methods were well calibrated in the absence of signal and achieved high performance under strong signal, whereas differences emerged under weaker signal and in feature recovery. We then applied MESSI to 19 real datasets spanning cancer, neurodevelopmental, neurodegenerative, infectious, renal, transplant, and metastatic disease settings, with diverse modality combinations including transcriptomic, epigenomic, proteomic, imaging, electrical, clinical, and single-cell-derived features. Across bulk multimodal datasets, classification differences were generally modest, although DIABLO and multiview cooperative learning tended to rank highest, while MOFA+glmnet and MOGONET were weaker overall. Biological enrichment analyses revealed clearer differences: DIABLO, RGCCA, MOFA, and IntegrAO more consistently recovered significant Reactome, oncogenic, and tissue-relevant gene signatures. In single-cell multiomics benchmarks, method rankings were more dataset dependent, but DIABLO performed consistently well across all case studies, while RGCCA also showed strong performance in specific settings. Computational analyses further showed that DIABLO and MOFA had the most favorable runtime and memory profiles, whereas multiview was the most time-intensive and IntegrAO the most memory-demanding. ConclusionsMESSI provides a reproducible, extensible, and equitable framework for benchmarking multimodal integration methods under a common model assessment strategy. Our results indicate that no single method is uniformly optimal across datasets and objectives; instead, method choice should balance predictive performance, biological interpretability, and computational efficiency. MESSI establishes a foundation for transparent benchmarking and future extensions to broader multimodal learning tasks.

bioinformatics↗

bioRxiv2026

Mysm1 mutations in meander tail mice cause anterior-selective cerebellum malformation

Mouse meander tail (mea) mutations produce kinked tails and selective malformation of the cerebellum anterior compartment. The anterior cerebellum defects are cell autonomous with respect to granule cell precursors, but the molecular basis has not been known. Myb-like, SWIRM, and MPN domain containing protein 1 (MYSM1) is a chromatin-associated deubiquitinase that promotes gene expression by removing monoubiquitin from histone H2A, among other targets. Loss of MYSM1 function in mice or humans results in bone marrow failure with defective maturation of B cell lineages. Here we show that extant mea alleles have mutations in Mysm1 and cause both neurological and hematological phenotypes, as do new non-complementing endonuclease-mediated mutations. Multimodal single-nucleus assays show Mysm1 effects on gene expression in several lineages and on the proportion of granule cell precursors by E14.5. Intriguingly, Mysm1 orthologs have been independently lost in several animal and fungal lineages, including yeast, flies, and nematodes. These results unite previously disconnected literature and demonstrate a requirement for MYSM1 activity in compartment-specific development of the cerebellum and suggest potential for compensatory pathways. Significance StatementPerturbations to core regulatory machinery often produce pleiotropic effects and even intensively studied systems can have significant phenotypic effects that were not assessed in models developed for a different purpose. Here we show that classical meander tail mice, characterized by ankylosing spondylitis in tail vertebrae and a cerebellum malformation that defined the anterior-posterior compartment boundary, have mutations in Mysm1, encoding a histone 2A deubiquitinase. We show pigmentation defects and hematopoietic abnormalities that model human disease. While Mysm1 mutations change gene expression patterns in many cerebellar cell types, they selectively decrease the proportion of granule cell lineages. Recurrent loss of Mysm1 orthologs across fungal and animal phylogenies suggests the potential for bypass mechanisms.

genetics↗

bioRxiv2026

Protocol for rapid allelic discrimination qPCR genotyping of the Winnie mouse model

Winnie mice are a widely used in vivo model of inflammatory bowel disease carrying a missense mutation in the Muc2 gene. Here, we present a protocol for genotyping Winnie mice using TaqMan allelic discrimination quantitative PCR. We describe tissue collection, rapid crude DNA extraction, probe-based amplification with dual-labeled fluorophores, and fluorescence-based genotype calling in a single reaction. This protocol enables qualitative SNP genotyping without post-amplification processing and can be readily adapted to other defined point mutations. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/704640v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1f5d985org.highwire.dtl.DTLVardef@19bbd34org.highwire.dtl.DTLVardef@1a2d2fcorg.highwire.dtl.DTLVardef@c9baed_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAllelic discrimination qPCR protocol for genotyping the Muc2 p.Cys52Tyr mutation using dual-labeled hydrolysis probes C_LIO_LIEnables rapid discrimination of wild-type, heterozygous, and mutant alleles in a single reaction C_LIO_LICompatible with standard real-time PCR instruments and requires no post-PCR processing C_LIO_LISupports high-throughput genotyping from crude DNA with minimal hands-on time C_LI

molecular biology↗

bioRxiv2026

BOLE: A Knowledge-Enhanced Multi-Agent Framework for Intelligent Genomic Breeding

Genomic breeding has become increasingly data-intensive, yet the practical integration of heterogeneous bioinformatics tools into coherent analytical workflows remains a major bottleneck. To address this, we present BOLE, a knowledge-enhanced multi-agent AI framework for autonomous genomic breeding analysis. By integrating a structured script knowledge base with constrained large language model reasoning, BOLE translates high-level analytical intent into validated and executable workflows. Specialized agents collaboratively perform intent interpretation, task decomposition, dependency reasoning, workflow synthesis, and controlled code generation to assemble validated, executable workflows without predefined pipelines. BOLE supports core genomic breeding tasks, including genome-wide association studies, heritability estimation, germplasm evaluation, and genomic selection while preserving artifact-level provenance to ensure reproducibility. Implemented as a web service, BOLE enables end-to-end genomic breeding analysis from raw data to actionable results for non-expert users. This work establishes a generalizable paradigm in which knowledge-driven multi-agent AI bridges the gap between mature analytical methods and their real-world application in genomic breeding.

genomics↗

bioRxiv2026

RSAD2/VIPERIN and CMPK2 Coordinate an Immunometabolic Response to Epstein-Barr Virus

Epstein-Barr Virus (EBV) infection and reactivation in B-lymphocytes is tightly regulated by host antiviral response genes. In the present study, we identify interferon stimulated genes RSAD2 (radical S-adenosyl methionine domain-containing 2) and CMPK2 (Cytidine/Uridine Monophosphate Kinase 2) as key modulators of EBV expression and cellular response during EBV infection and reactivation. EBV primary infection and reactivation lead to a coordinated up-regulation of RSAD2 and CMPK2. Depletion of RSAD2 reduced cell viability and limited EBV reactivation, while depletion of CMPK2 led to reactivation of EBV lytic gene expression during latency. Transcriptomic analysis revealed that RSAD2 and CMPK2 have overlapping functions in regulating IFN-signaling pathways, as well as oxidative phosphorylation, protein translation, and unfolded protein response during reactivation. Despite distinct subcellular localizations, RSAD2 at the Endoplasmic Reticulum (ER), and CMPK2 in mitochondria, both genes converge on shared immunometabolic pathways, including control of Gasdermin D (GSDMD) associated pyroptosis and ATF-4 associated unfolded protein response (UPR). EBV reactivation induced formation of antiviral ribonucleotide ddhCTP during lytic EBV reactivation which was strictly dependent on RSAD2. Knockdown of RSAD2 and CMPK2 had significant effects on global metabolites consistent with a remodeling of glycolysis, fatty acid biosynthesis and degradation of superoxides. These observations demonstrate that RSAD2-CMPK2 function in a coordinated ER-mitochondria stress-Interferon signaling axis that shapes EBV reactivation and host immune control, including a novel layer of immunometabolic regulation modulating viral latency and reactivation. Authors SummaryUnderstanding how Epstein-Barr virus (EBV) regulates host factors to control infection, latency and reactivation is critical for developing targeted therapies against EBV-associated diseases. This study identifies Interferon Stimulated Genes RSAD2 (Viperin) and CMPK2 as key regulators of EBV reactivation and host interferon responses in B-cells. Despite distinct organelle localizations, both genes converge on a shared immunometabolic pathways, revealing a coordinated ER-mitochondria axis that shapes viral expression and immune signaling. These findings provide new insights into the roles of host antiviral effectors and uncover potential targets for modulating EBV activity in inflammatory and oncogenic contexts.

microbiology↗