Biology subjects

Yao, M.

Publications and source records attributed to Yao, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Stabilizing gas in aqueous liquids with metal-organic frameworks for persistent acoustic transduction

Gas is the most efficient mediator of acoustic energy owing to its high compressibility, yet its thermodynamic instability in aqueous environments makes it inherently transient, limiting sustained ultrasound-biological interfacing. Here, we show that gas can be stabilized, confined, and manipulated in the liquid phase to function as a persistent acoustic transducer. By trapping gas within designed microporous metal-organic framework (MOF) nanocrystals, interfacial forces establish a stable ternary-phase equilibrium that suppresses water intrusion and prevents gas collapse, enabling reversible, non-destructive oscillations under ultrasound stimulation and providing design principles for stabilizing gas in liquid environments. By leveraging high-resolution ultra-high-speed digital image correlation (DIC), we unveil the previously inaccessible spatiotemporal dynamics of confined gas oscillations within these nanotransducers under ultrasound stimulation, revealing localized amplification of the surrounding acoustic field and establishing a quantitative structure-function relationship for programmable acoustic transduction. These aqueous-phase gas nanotransducers exhibit sustained acoustic amplification over millions of excitation cycles and remain functional after prolonged storage (>2 years) under physiological conditions. In vitro and in vivo, this platform enables long-term ultrasound imaging and sustained, non-invasive neuromodulation by converting confined gas oscillations into persistent and amplified mechanical actuation. Our findings establish a generalizable design framework for stabilizing gas in liquid environments to achieve persistent and programmable acoustic transduction, thereby enabling sustained ultrasound-biological interfacing and opening opportunities for gas-based therapeutics.

bioengineering↗

bioRxiv2026

Human and Mouse Models of the Bipolar Disorder-Associated ANK3 p.W1989R Variant Display Altered Somatostatin Interneuron Connectivity and Function

Bipolar disorder (BD) is a debilitating neuropsychiatric disorder characterized by recurrent mood perturbations, cognitive and functional impairment, and increased risk of suicide. Genome-wide association studies (GWAS) have repeatedly identified the gene ANK3, which encodes the neuronal scaffolding protein ankyrin-G, as a risk locus for BD. Ankyrin-G interacts directly with the GABAA receptor-associated protein (GABARAP) to stabilize inhibitory synapses, providing a potential mechanistic link between ANK3 variation and GABAergic dysfunction observed in BD. Previously, we identified an ANK3 p.W1989R variant in a family with BD and demonstrated that this variant abolishes the ankyrin-G/GABARAP interaction, resulting in inhibitory signaling deficits in mice. Here, we investigated the effects of this variant in human induced pluripotent stem cell (hiPSC)-derived neurons generated from an affected individual heterozygous for the ANK3 p.W1989R variant. CRISPR correction of the variant increased inhibitory synapse density on both glutamatergic and GABAergic patient-derived neurons. Integrated spatial transcriptomics and calcium imaging identified cell-type-dependent changes in gene expression and calcium dynamics. ANK3 p.W1989R somatostatin (SST) positive interneurons displayed altered calcium dynamics and reduced SST expression. To determine whether the variant impacts SST interneuron-mediated inhibition of cortical circuits, we selectively stimulated prefrontal cortical SST interneurons in heterozygous Ank3 p.W1989R mice and recorded optically evoked inhibitory postsynaptic currents (oIPSCs) from cortical pyramidal neurons. SST interneuron-mediated oIPSC peak amplitude, charge transfer, and decay times were reduced in variant mice, without a significant change in the paired-pulse ratio. These findings, using complementary human and mouse models, identify novel roles for ankyrin-G in SST interneuron-mediated inhibitory signaling and demonstrate that altered inhibitory connectivity and SST interneuron function are associated with ANK3 p.W1989R. This work provides mechanistic insight into how disrupted ankyrin-G-dependent synaptic function may contribute to inhibitory signaling deficits relevant to BD.

neuroscience↗

bioRxiv2026

Engineering of CAR-less lentiviral vectors via ER retention-mediated CAR blockade

Chimeric antigen receptor (CAR)-T cell therapies have transformed the treatment of various tumor types by redirecting and activating T cells against tumor cells. However, CAR-T cell manufacturing approaches remain challenging and limit their widespread use in clinical settings. In vivo CAR-T therapy bypasses ex vivo cell manufacturing and patient preconditioning limitations; however, it faces a significant safety concern as CAR proteins on viral packaging cells are incorporated into budding virions, leading to off-target transduction of tumor cells. Here, we address this risk by developing the CAR-Less ER-Anchor Vector (CLEAN-V) system. By exploiting endoplasmic reticulum (ER) retention, CLEAN-V prevents the CAR protein from trafficking to the cell surface during viral packaging, thereby blocking its incorporation into the viral envelope. CLEAN-V particles exhibit near-complete loss of CAR-mediated tumor cell transduction. Furthermore, CLEAN-V integrates seamlessly into existing third-generation LVV workflows in four- or five-plasmid formats and generates CAR-T cells with preserved phenotypic and functional integrity. These results establish CLEAN-V as a robust platform for developing safe, targeted lentiviral vectors for in vivo CAR-T therapy.

bioengineering↗

bioRxiv2026

Energetically constrained turnover drives the emergence of aging

Aging is characterized by progressive functional decline, yet why such decline is observed broadly across living systems remains unclear. While molecular and cellular mechanisms describe how aging progresses, they do not explain why functional decline should arise as a natural consequence of living organization. Here, we show that aging naturally emerges from three general features of life: unavoidable damage, turnover-mediated maintenance, and the energetic constraint of turnover. We develop a hierarchical damage-turnover model in which component-level damage and energetically constrained turnover jointly determine whole-system performance. In the model, damage stochastically converts functional components into non-functional components, whereas turnover restores component performance at a rate coupled to whole-system performance. Analytical and Monte Carlo analyses reveal two regimes: a non-aging regime, in which performance remains finite, and an aging regime, in which performance progressively collapses toward zero. Performance-independent turnover always maintains a positive steady state, whereas performance-dependent turnover generates irreversible decline when reduced performance weakens maintenance capacity. Stochastic fluctuations further promote collapse near the transition boundary, even when deterministic analysis predicts a nonzero steady state. These results indicate that unavoidable damage and energetically constrained turnover are sufficient to generate aging-like decline, providing a minimal theoretical explanation for long-term irreversibility in biological systems.

biophysics↗

bioRxiv2026

Midazolam suppresses glioma progression by attenuating neuronal activity and downregulating IGF1 signaling

Glioma is the most common primary malignant tumor of the brain, and accumulating evidence indicates that neuronal activity plays a pivotal role in tumor progression. In this study, neuronal activity is modulated in vitro using potassium chloride (KCl)-induced depolarization and midazolam (MDZ)-mediated suppression. MDZ is a neuronal activity modulation medication, commonly used for sedation, anxiolysis, and amnesia in clinics. After treatment, conditioned media derived from these neuronal cultures are subsequently co-cultured with glioma cells. EdU incorporation assays demonstrate that MDZ significantly inhibits glioma cell proliferation in vitro. Furthermore, an orthotopic xenograft glioma model is established to assess the anti-tumor efficacy of MDZ in vivo, as evaluated by tumor volume and Ki-67 immunostaining. Mechanistically, insulin-like growth factor 1 (IGF1) is identified as the neuronal-activity-regulated factor that promotes glioma growth through activation of the PI3K/AKT signaling pathway. Moreover, transcriptomic profiling of brain tissues reveals that MDZ attenuates neuronal activity and downregulates neuron-derived growth factors in both glioma and non-tumor regions, thereby exerting anti-tumor effects in vivo. Collectively, these findings demonstrate that MDZ suppresses glioma progression by suppressing neuronal activity and inhibiting neuron-derived trophic factors, providing new insights into the development of therapeutic strategies for glioma.

neuroscience↗

bioRxiv2026

Colony morphogenesis regulates sporulation dynamics in bacterial biofilms

In multicellular systems, organized phenotypic heterogeneity emerges from the interplay of processes spanning scales from molecular to population-level. Using Bacillus subtilis, we investigated feedback between the collective process of colony expansion and the distribution of spore development among individual cells, a process triggered by starvation. Biofilms are commonly studied using a strain with inhibited sporulation. Intact regulation yielded high-frequency sporulation early in biofilm growth. Biofilm composition was organized by a wave of sporulation driving biofilms toward dormancy from within. However, expansion was also maintained by non-sporulating cells in a narrow front at the external edge. Along with mathematical modeling, we also used mutants with altered biofilm morphogenesis to probe the relationship between colony expansion and sporulation. Sporulation dynamics were patterned by radial expansion, but the faster biofilms spread, the greater the separation of growth and sporulation distributions. We demonstrate essential interplay between cell behavior and the physics of collective expansion that organizes differentiation among cells.

microbiology↗

bioRxiv2026

Detection of Somatic Point Mutations Directly from Spatial Transcriptomics Enables in vivo Spatiotemporal Lineage Tracing

Spatial transcriptomics reveals tissue organization but lacks in vivo lineage-tracing methods applicable to humans. We introduce SpaceTracer, a computational framework that accurately detects somatic single-nucleotide variants (SNVs) directly from spatial transcriptomics data. By leveraging naturally occurring somatic SNVs, SpaceTracer reconstructs cellular phylogenies within native tissue architecture, enabling the mapping of lineage spread, migration, lineage-coupled expression changes and lineage-aware local interactions. Applied to human cutaneous squamous cell carcinoma, it traced tumor initiation and progressions, uncovered widespread pre-invasive migration of dedifferentiated epithelial cells and characterized mutant B cells migrating from tertiary lymphoid structures (TLS) into the tumor boundary. The framework also reconstructed developmental lineages across multiple tissues and identified tissue-resident mutant immune cells. SpaceTracer thus provides a perturbation-free platform for high-resolution spatiotemporal lineage tracing, offering a transformative tool for elucidating complex biological systems--especially tumor-immune ecosystems--with direct implications for advancing cancer immunotherapy.

bioinformatics↗

bioRxiv2026

PhyloSOLID: Robust phylogeny reconstruction from single-cell data despite inherent error and sparsity

While lineage tracing based on somatic mutations in single-cell sequencing data offers a powerful approach to reconstructing cellular histories in vivo, its reliability is fundamentally limited by pervasive technical artifacts--specifically, high error rates and data sparsity. These issues introduce false phylogenetic signals that corrupt tree topology and lead to spurious evolutionary conclusions. To overcome these limitations, we present PhyloSOLID, a phylogenetic algorithm designed to be inherently robust to these data imperfections. PhyloSOLID employs a progressive scaffolding strategy that begins with graph-based construction of a low-resolution, high-confidence backbone tree from reliable and uniformly covered mutations. This scaffold is then refined through the iterative integration of remaining data, guided by a Bayesian statistical model that penalizes phylogenetic inconsistencies to effectively separate the true evolutionary signal from technical artifacts. Benchmarking on both simulated datasets and multiple ground-truth datasets demonstrates that PhyloSOLID achieves superior lineage reconstruction accuracy over existing methods, for both single-cell RNA-seq and DNA-seq data. Additionally, a user-friendly web interface enables customized quality assessment, artifact removal, and interpretation of lineage structures. PhyloSOLID provides a powerful solution for decoding cellular evolution in developmental and disease contexts.

bioinformatics↗

bioRxiv2026

Critical role of cell competition in gliomagenesis

ABSTRACTMalignant glioma is incurable. Using a mouse genetic mosaic system to generate sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null OPCs outcompete wildtype counterparts during their expansion. Blocking competition by mutating/strengthening wildtype OPCs impeded both pre-malignant progression and malignant expansion of glioma. "In-tissue" phosphoproteomic profiling revealed an enrichment of phosphopeptides related to RNA splicing and protein translation at the peak of cell competition, suggesting that competitiveness may stem from unique protein species. Among candidates was mTORC1, whose pharmacological inhibition or genetic disruption resulted in a loss of competitiveness in our mouse model. Finally, analysis of patient biopsies and interrogating the role of individual gliomagenic mutations in OPC competition supported its relevance in human gliomas. Together, these findings identified the driving role of competitive interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic strategies to target this process.

cancer biology↗

bioRxiv2025

Multicolored, Sonosensitizer-optimized Organic Mechanoluminescent Nanoparticles for Functional Sono-optogenetics

Light enables precise visualization and control of cellular processes, but its utility in deep tissues is fundamentally limited by poor optical penetration, particularly in the deep brain. Ultrasound-triggered mechanoluminescence offers a non-invasive strategy for remote light delivery, yet existing organic systems remain monochromatic and low-intensity, largely due to an incomplete understanding of ultrasound-induced emission. Here, we report a multicolor mechanoluminescence platform that couples reactive oxygen species-responsive chemiluminescent donors with fluorescent acceptors via Forster resonance energy transfer, generating tunable emission from blue (459 nm) to red (592 nm). Systematic screening potentially reveals that electronic energy gap-dependent reactive oxygen species generation serves as a predictive design principle for high-performance mechanoluminescent materials. The emitted spectrum and intensity are sufficient to activate ChR2 and ChRmine and inhibit eOPN3, enabling bidirectional, fiber-free neuromodulation under focused ultrasound. By integrating spatially precise ultrasound with programmable photon output, this platform establishes a non-invasive strategy for deep-tissue neural monitoring and provides a foundation for applications in bioimaging, gene editing, and precision therapeutics.

bioengineering↗

bioRxiv2025

Vascular smooth muscle cell loss, but not neuroinflammation, drives cerebrovascular reactivity impairment in Alzheimer disease

INTRODUCTIONCerebrovascular reactivity (CVR) impairment is a key feature of Alzheimers disease (AD), but its mechanistic basis remains unclear. This study examined whether vascular smooth muscle cell (VSMC) loss, rather than amyloidosis or neuroinflammation, underlies CVR deficits. METHODSNon-contrast MRI, including phase-contrast and pseudo-continuous arterial spin labeling, was performed in mouse models of amyloidosis (5xFAD), VSMC degeneration (CADASIL), and lipopolysaccharide-induced neuroinflammation. Characterization of vascular, amyloid-{beta}, and inflammatory markers were performed for pathological assessment. RESULTSCVR impairment emerged only when VSMC loss was present in CADASIL mice and at older ages in 5xFAD mice (9-12 months). Amyloid-{beta} deposition occurred earlier than VSMC loss or CVR decline. Neuroinflammation primarily altered baseline cerebral blood flow without affecting CVR or VSMC integrity. DISCUSSIONThese findings identify VSMC degeneration as an important driver of CVR impairment independent of cerebral amyloid angiopathy or inflammation, highlighting vascular integrity as a potential therapeutic target in AD. HighlightsO_LICerebrovascular reactivity (CVR) impairment occurred in 5xFAD mice only when vascular smooth muscle cell (VSMC) loss was present C_LIO_LI5xFAD mice exhibited prominent parenchymal but minimal vascular amyloid-{beta} deposition C_LIO_LIVSMC developmental deficiency resulted in CVR impairment in a small-vessel disease (SVD) model C_LIO_LINeuroinflammation primarily altered baseline cerebral blood flow (CBF) without affecting CVR C_LI

bioengineering↗

bioRxiv2025

Spatial transcriptomics reveals distinct inflammatory and adaptive immune properties of rheumatoid arthritis synovial fibroblasts

ObjectiveRheumatoid arthritis (RA) synovium displays cellular heterogeneity, with gene expression driving pathogenesis. Prior transcriptomic studies relied on disaggregated tissue, which causes cell loss and induction. We applied spatial transcriptomics to investigate synovial lining and sublining fibroblasts and macrophages from RA and osteoarthritis (OA) patients. MethodsFresh frozen synovial tissues from 7 RA and 8 OA patients were analyzed using the NanoString GeoMX DSP Whole Transcriptome Assay. Lining and sublining regions were segmented into fibroblasts and macrophages. Principal component analysis separated samples by cell type and disease. Differentially expressed genes (DEG) were analyzed by linear mixed models (p-value<0.05 and |log2 fold change|>0.5) and Reactome pathway (FDR<0.02) analysis. ResultsDEG analysis of RA compared to OA revealed distinct gene signatures across regions and cell types. RA lining fibroblasts exhibited a strong pro-inflammatory and matrix-destructive signature, while RA sublining fibroblasts showed an unexpected role in antigen presentation and adaptive immunity. RA lining macrophages exhibited enrichment for interleukin signaling, extracellular matrix organization, and translation-related pathways. In contrast, sublining macrophages showed minimal transcriptional differences between RA and OA, suggesting limited pathogenic involvement. Comparison between lining and sublining within RA showed that lining fibroblasts display a higher activated phenotype than sublining cells. ConclusionSpatial transcriptomic analysis uncovers distinct region- and cell-type-specific transcriptional profiles in RA synovium. Lining fibroblasts are highly activated and destructive, and sublining fibroblasts contribute surprisingly to adaptive immunity. This data provides clues to region-cell-type-specific functions that could be exploited to identify novel therapeutic targets.

immunology↗

bioRxiv2025

VISTA-FISH: Video Imaging with Spatial-Temporal Analysis by Fluorescent In Situ Hybridization

Performing live-cell microscopy and high-dimensional gene expression measurements on the same cells is crucial for unraveling the molecular mechanisms underlying complex temporal phenotypes, yet this remains challenging using traditional approaches. To address these limitations, we developed Video Imaging with Spatial-Temporal Analysis by FISH (VISTA-FISH), a technique that matches live-cell recordings of cultured cells with the expression of thousands of genes in the same cell at the end of the video. Moreover, VISTA-FISH can simultaneously detect CRISPR guide RNAs in pooled screens, enabling investigation into the fundamental underpinnings of cellular activity, organelle transport, and other pivotal cellular functions. Using VISTA-FISH, we measured gene expression and neuron activity in the same differentiating neurons. This combined single-cell transcriptomic and video data allowed us to link differentiation stage, subcellular transcript localization, and cell subtype with neuron activity. Using these measurements, we built a model to predict activity from expression. Finally, we performed a pooled CRISPR interference screen with live-cell lysosome imaging, identifying alterations in lysosome movement and morphology as well as gene expression in perturbed neurons. Collectively, these studies position VISTA-FISH as a powerful new tool for elucidating the molecular mechanisms underlying neuron activity, organelle trafficking, and other complex temporal phenotypes.

molecular biology↗

bioRxiv2025

Wearable Focused Ultrasound Neuromodulation and Electrophysiological Recording Patch for REM Sleep Enhancement

The rise in sleep disease affecting the general population globally in the past decade has been detrimental to individually and socioeconomically. As of now, approaches often are temporary through medication, permanently using invasive implants with surgical complications or neuromodulation therapy. However, non-invasive, state-dependent neuromodulation during sleep is technically challenging, especially with the lack of flexibility, comfortability and robustness for sleep conditions. Here, we introduce a Non-invasive Electrophysiological Recording and Ultrasound Neuromodulation Sleep Patch (NEUSLeeP) in delivering focused ultrasound stimulation to the subthalamic nucleus (STN) overnight with simultaneous stable polysomnography recording. Our sleep patch integrates a custom eight-channel concentric ring transducer array with real-time electroencephalography (EEG), electrooculography (EOG), electromyography (EMG) recording, and individualized line-of-sight targeting to sonicate deep brain areas while preserving mobility. Our platform operated safely and comfortably across the two-nights sleep study. Stimulation of the left STN was delivered every 90 minutes throughout the night and was associated with a 25% increase in REM (Rapid Eye Movement) sleep duration and a 43 minutes reduction in REM sleep latency compared to a sham night in a study of 26 subjects. Blood Oxygen Level Dependent (BOLD) signal attenuation in functional Magnetic Resonance Imaging (fMRI) was localized primarily to a left ipsilateral basal-ganglia-midbrain-temporal circuit, consistent with selective network modulation rather than global arousal changes. Overall, NEUSLeeP demonstrates feasibility by (i) a light weight and wearable ultrasound neuromodulation and sleep recording during natural sleep; (ii) establishing a potential mechanism relating targeted ultrasound stimulation of STN/sleep networks to REM enhancement.

bioengineering↗

bioRxiv2025

CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies

Causal mediation analysis investigates whether the effect of an exposure on an outcome operates through intermediate variables known as mediators. Although progress has been made in high-dimensional mediation analysis, current methods do not reliably control the false discovery rate (FDR) in finite samples, especially when mediators are moderately to highly correlated or follow non-Gaussian distributions. These challenges frequently arise in DNA methylation studies. We introduce CoxMDS, a multiple data splitting method that uses Cox proportional hazards models to identify putative causal mediators for survival outcomes. CoxMDS ensures finite-sample FDR control even in the presence of correlated or non-Gaussian mediators. Through simulations, CoxMDS is shown to maintain FDR control and achieve higher statistical power compared with existing approaches. In applications to DNA methylation data with survival outcomes, CoxMDS identified eight CpG sites in The Cancer Genome Atlas (TCGA) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on lung cancer survival, and two CpG sites in the Alzheimers Disease Neuroimaging Initiative (ADNI) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on time to Alzheimers disease conversion.

bioinformatics↗

bioRxiv2025

Qimai: a multi-agent framework for zero-shot DNA-protein interaction prediction

Accurate prediction of DNA-protein interactions, a fundamental task in genomics, is limited by the poor generalization of existing models to novel proteins not seen during training. To address this challenge, we introduce Qimai, a modular AI agent framework that integrates deep learning predictions with biological evidence using Large Language Model (LLM) as reasoning engine. Qimai combines direct motif evidence from the query protein, indirect motif evidence from its interactors, and quantitative prediction from a new transformer-based DPI model to produce explainable predictions with confidence scores. On a benchmark of 78 unseen proteins, Qimai consistently outperforms standalone deep learning models across all metrics, increasing the Area Under Curve of the Precision-Recall (AUC-PR), the Area Under Curve of the Receiver Operating Characteristic (AUC-ROC), and Matthews Correlation Coefficient (MCC) by 17.6%, 15.6%, and 244% respectively compared to the best standalone model. Ablation analyses reveal that this gain is driven by the LLMs ability to dynamically weigh diverse evidence, with indirect motif evidence of co-factors particularly critical for unseen proteins. Qimai establishes a generalizable and interpretable paradigm for integrating heterogeneous data in predictive genomics. This framework is accessible via the Qimai web portal (https://qimai.wanglab.ucsd.edu/).

bioinformatics↗

bioRxiv2025

Multiscale Hyperbolic Embedding for Cell Hierarchies in Large-Scale Bioinformatics Data

The rapid expansion of biological and computational datasets demands scalable methods that support both visualization and quantitative interpretation. Hyperbolic embeddings are well suited to represent hierarchical structure, but existing approaches are limited by fixed curvature assumptions or poor scalability to large datasets. We introduce MuH-MDS, a multiscale hyperbolic multidimensional scaling algorithm that employs an adi-abatic optimization strategy: local positions are iteratively refined while cluster centroids are temporarily fixed. This strategy accelerates computation by 103 and enables scaling to datasets with over 80,000 samples. Applied to diverse benchmarks, including C. elegans embryogenesis scRNA-seq data, MuH-MDS uncovers intrinsic hierarchical organization and improves both pseudotime inference and lineage reconstruction relative to UMAP and other standard methods. In contrast to UMAP and t-SNE, which prioritize local neighborhoods at the expense of global coherence and metric fidelity, MuH-MDS pre-serves both local detail and global hierarchy, providing a metrically faithful framework for multiscale analysis of complex biological systems.

biophysics↗

bioRxiv2025

The development of FEDUPP: Feeding Experimentation Device Users Processing Package to Assess Learning and Cognitive Flexibility

Cognitive flexibility, the ability to adapt behavior in response to changing contingencies, is a key component of adaptive decision-making and is impaired in multiple neuropsychiatric disorders. Traditional rodent assays of cognitive flexibility are conducted in experimenter-controlled sessions in restrictive environments, limiting ecological validity and temporal resolution. Here, we developed a fully automated, home-cage paradigm using the Feeding Experimentation Device 3 (FED3) and a companion open-source analysis pipeline, the Feeding Experimentation Device Users Processing Package (FEDUPP), to assess learning and cognitive flexibility with minimal experimenter intervention. The paradigm combines a single-day fixed-ratio 1 (FR1) task with a multi-day, reversal learning task in which active port assignment switches every 25 pellets collected. FEDUPP implements multi-scale learning metrics, including overall accuracy, an 80% accuracy milestone, and a machine learning-based classification of meal accuracy to capture motivated, goal-directed feeding. In wild-type mice, the paradigm detected rapid FR1 acquisition and progressive within-block adaptation during reversal. Application to mice with dorsal hippocampal knockdown of the scaffolding protein CASK revealed faster FR1 acquisition and higher accuracy than controls but a delayed onset of the first accurate meal after reversal, suggesting a selective deficit in updating goal-directed feeding behavior. These findings demonstrate that FEDUPP enables high-resolution, continuous assessment of learning and cognitive flexibility in ethologically relevant settings, and that meal-based accuracy provides a sensitive metric for detecting subtle flexibility impairments not captured by traditional measures.

animal behavior and cognition↗