Biology subjects

Yu, X.

Publications and source records attributed to Yu, X..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Comparison and Dynamic interaction between Auditory Cortex and Prefrontal Cortex of Behaving Monkeys during Novelty Detection

The ability to detect deviations from expected sensory input is fundamental for adaptive behavior. We recorded electrocorticographic activity from the auditory (AC) and prefrontal (PFC) cortices of behaving macaques during an auditory oddball task to probe the cortical dynamics of predictive processing. Repetition of standard stimuli evoked suppression and facilitation in AC and strong low-frequency (2 Hz) enhancement in PFC, accompanied by bidirectional delta-band coupling indicative of a shared predictive state. Deviant stimuli triggered early AC responses followed by PFC activation and increased feedforward and feedback connectivity across delta, theta, and gamma bands. Behavioral engagement amplified both prediction and prediction error signals, strengthening cortical network coordination. Together, these findings reveal a hierarchical predictive network in which the AC encodes sensory regularities and violations, while the PFC integrates predictive context in a behaviorally dependent manner.

neuroscience↗

bioRxiv2025

GT61 β-1,2-xylosyltransferases define a conserved xylan modification in gymnosperm and Arabidopsis primary cell walls

Plant primary and secondary cell walls differ in molecular composition, structure, and mechanical properties. While secondary wall xylan has been extensively characterised, the structure of xylan in primary walls remains less well understood, particularly in gymnosperms. Here, we identify a previously uncharacterised {beta}-1,2-linked xylosyl side chain in conifer and Arabidopsis thaliana xylan. Using enzymatic fingerprinting, NMR, and mass spectrometry, we show that this structure is positioned two xylose residues away from glucuronic acid substitutions, forming an evenly patterned substituted xylan. This spacing pattern is consistent with xylan-cellulose interaction, suggesting a structural role in primary wall architecture. This modification, found in primary wall-rich tissues of diverse conifer species, including needles and pro-embryogenic mass (PEM), is also present in Arabidopsis callus. We demonstrate that conifer Group III GT61 glycosyltransferases introduce this modification with consistent positional specificity. In Arabidopsis, three closely related GT61 enzymes act redundantly to generate the same structure, and their combined loss results in its complete absence. These findings uncover a conserved primary wall xylan modification in seed plants and define the GT61 enzymes responsible for its biosynthesis, opening new avenues to explore how xylan structure contributes to primary wall function. Significance StatementXylan structure is well characterised in secondary walls, but its primary wall counterpart remains poorly understood. We identified a conserved {beta}-1,2-xylosyl modification on xylan in the primary walls of conifers and Arabidopsis. This side chain is positioned at a defined position from a glucuronic acid substitution and is introduced by GT61 glycosyltransferases that cluster in one phylogenetic subclade. Our findings revealed a previously unrecognised xylan structural pattern and the biosynthetic enzymes responsible for its addition. This work expands the current understanding of primary wall architecture across seed plants.

plant biology↗

bioRxiv2025

Walking Selectively Modulates Behaviorally Relevant Auditory Responses According to Stride Cycle Phase

Perception in natural environments unfolds while the body is in motion, yet how locomotion shapes cortical computations for fine-grained and dynamic scene analysis remains unclear. Here, we combined over-ground walking with mobile EEG and a transitional click-train paradigm to test how natural locomotion influences auditory processing in humans. Participants listened to two-segment click trains in which a subtle inter-click-interval (ICI) change signaled a pitch shift and performed a task-engaged change-detection task while either sitting or walking; an independent cohort also completed a passive-listening version. Walking elevated behavioral detection thresholds and slowed responses, indicating reduced sensitivity to fine temporal changes. Neurally, locomotion produced a response-component-specific attenuation: activity time-locked to the ICI transition--the change response previously linked to temporally integrative updating of an ongoing auditory object--was strongly reduced, whereas the offset response was largely preserved and onset responses were only modestly affected. Critically, this modulation persisted during passive listening and was selectively amplified near the perceptual threshold during task-engaged detection, revealing an interaction between motor state and cognitive demand. Thus, natural locomotion does not uniformly degrade hearing; instead, it preferentially down-weights a behaviorally critical, temporally demanding stage of auditory processing, offering a framework for understanding how motor-cognitive state shapes auditory scene analysis in the moving brain.

neuroscience↗

bioRxiv2025

Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica x Zoysia matrella F2 and F1 populations

Anthocyanins play diverse roles in plants, including attracting pollinators and protecting cells from oxidative damage. In zoysiagrass, a warm season turfgrass, their accumulation in seed heads and stolons can decrease the aesthetic appeal. In this study, a high-density genetic map with [~]8000 single nucleotide polymorphism (SNP) markers organized into 20 linkage groups was generated in a Zoysia japonica acc. Meyer x Zoysia matrella acc. PI 231146 F2 population. Using this genetic map, a large-effect quantitative trait locus (QTL) for anthocyanin variation in stolons and seed heads was mapped to chromosome 12 (PP locus). Variant analysis of a candidate gene for PP, Zjn_sc00004.1.g07010.1.sm.mk, which encodes a MYC-bHLH transcription factor that regulates anthocyanin biosynthesis, revealed a SNP at an exon-intron boundary in Meyer that led to intron retention. Interestingly, an F1 population derived from the same parents segregated for seed head color but uniformly displayed purple stolons. Seed head color in the F1 population co-mapped with the PP locus which, combined with genotypic and yeast two-hybrid analyses, revealed that a SNP in PI 231146 leading to an Ala163Ser substitution in the MYB-interacting N-terminal domain of the same MYC-bHLH transcription factor was likely causal. The Ala163Ser substitution affected interaction of MYC-bHLH with MYB in a MYB-dependent manner. The identified mutations can be exploited to develop cultivars with green seed heads and stolons. The high-marker-density interspecific Z. japonica x Z. matrella F2 genetic map also provides a robust tool for identifying genomic regions and genes of agronomic interest that differentiate the two species.

genetics↗

bioRxiv2025

Retrograde Optogenetics Reveals Functional Convergence within a Corticotectal Pathway of Non-Human Primates

Understanding how the cerebral cortex communicates with subcortical areas to drive behavior remains a central question in system neuroscience. One key unresolved issue is whether prefrontal cortical outputs to motor-related subcortical regions carry predominantly motor commands or mixed sensory-motor signals. Retrograde optogenetics offers a powerful way to interrogate such projection-defined circuits, but its use in non-human primates has been limited. Here, we applied retrograde optogenetics in awake macaques to directly test the functional organization of the corticotectal projection from the frontal eye field (FEF) to the superior colliculus (SC). We asked whether the FEF output signals to SC are motor-dominant or broadly sensory-motor. Optical activation of this pathway evoked robust, contralateral saccades and selectively modulated reaction times, demonstrating its causal role in saccade generation. Optogenetically tagging FEF neurons projecting to SC revealed a heterogeneous population of visual, visuomotor, and motor neurons. This diverse output converged predominantly onto motor-related neurons in the SC. These findings support a visuomotor convergence model, in which diverse FEF outputs drive motor-selective SC neurons with activity sufficient for saccade generation, and thus resolve long-standing questions over the composition of FEF outputs. Additionally, our results establish retrograde optogenetics as a tool for dissecting projection-defined circuits in primates and for precisely probing the neural pathways that link perception to action. HighlightsRetrograde optogenetics enabled pronounced and selective modulation of behavior in macaques. Selective optical stimulation of the FEF-SC pathway evoked contralateral saccades and modulated reaction times. Opto-tagging revealed diverse visual, visuomotor, and motor FEF outputs converging onto motor-related SC neurons. Findings support a visuomotor convergence model and demonstrate the power of projection-specific optogenetic tools in primates.

neuroscience↗

bioRxiv2025

Approaching an Error-Free Diploid Human Genome

Complete human genomes now resolve regions long inaccessible to genetic analysis, yet repetitive and structurally complex sequences remain prone to assembly errors because of limitations in current assembly algorithms. We introduce a support-based framework founded on the principle that each sequencing read provides independent evidence for the underlying genome sequence. Implemented through Sufficient Alignment Support (SAS), the framework identifies regions lacking concordant read support, localizes residual errors, and guides correction. Applying SAS to T2T-YAO, a haplotype-resolved Han Chinese genome, produced a support-validated assembly in which nearly all sequences outside unresolved rDNA arrays and long homopolymer tracts are supported by independent sequencing evidence. This work establishes a scalable framework for genome validation and provides a support-validated East Asian diploid reference for investigating human genomic diversity.

genomics↗

bioRxiv2025

A Deep Learning-based Method for Drug Molecule Representation and Property Prediction

Accurately and robustly representing drug molecule features, prediction of drug-target biomacromolecule interactions, and determining drug molecule physicochemical properties are crucial in drug development. However, due to issues such as insufficient generalization ability of single-modal representation, lack of multi-task prediction frameworks, and weak adaptability in cold-start scenarios, these tasks remain challenging. Here, we introduce DrugDL, a framework designed for drug molecule representation and the prediction of multiple downstream tasks, including drug-target interactions, binding affinities, binding sites, physicochemical properties, toxicity, and drug-drug interactions. DrugDL achieves joint representation learning of the drug chemical space and the target protein biological space and analyzes the multi-scale interaction mechanisms between drug molecules and target proteins by introducing cross-modal contrastive learning and single-modal feature enhancement algorithms. It employs a multi-task prediction framework to predict multiple properties of drug molecules. In practical applications, DrugDL outperforms state-of-the-art methods, especially in cold-start tasks. Its successfully applied to high-throughput screening, identifying inhibitors for SARS-CoV-2 and metabolic enzymes, and aids in predicting cancer-targeted drugs. Validations for EGFR and ALK targets confirm its efficiency as a precise drug discovery tool. Leveraging accurate molecular representation and multi-property prediction, DrugDL provides full-chain technical support for drug development, significantly accelerating the drug discovery process.

bioinformatics↗

bioRxiv2025

Granulin+ macrophages promote lineage plasticity in prostate cancer through paracrine signaling loops

The role of tumor-infiltrating immune cells in driving phenotype switching remains unclear, despite the well-established association between lineage transition and drug resistance in prostate cancer. This study employed an integrated analysis of single-cell multiomics to investigate the dynamics of immune infiltration, transcriptional programs, and cell-cell communication in prostate cancer. Our results demonstrated that granulin (GRN) positive macrophages facilitated the transition from adenocarcinoma to a multilineage state with mesenchymal and stem-like traits by activating intra-tumoral NF-{kappa}B signaling. Subsequently, the multilineage clones induced macrophages to highly express granulin through the secretion of CSF1, forming a positive feedback cell communication loop. Next, we validated the biological function of granulin in mediating epithelial-mesenchymal transition in vitro. Additionally, organoids drug resistance assay demonstrated that granulin drove resistance to androgen receptor (AR)-targeted drug (enzalutamide). Moreover, pharmacologic blockade of the CSF-1/CSF-1R axis in TRAMP mouse models reduced the expression of GRN in macrophages and suppressed the formation of multilineage subclones in prostate malignant cells. Furthermore, multiplex immunofluorescence staining of tumor samples from TRAMP mouse models revealed the VIM lineages were spatially in close contact with macrophages. Meanwhile, Cytometry by Time-Of-Flight (CyTOF) analysis validated our findings at single-cell protein level in patients with castration-resistant prostate cancer. Besides, three distinct tumor-infiltrating subsets associated with disease relapse were identified, including DCN+ endothelial cells, CCL7+ fibroblasts, and IFIT1+ neutrophils. These results offer potential therapeutic targets to address lineage plasticity-driven resistance to AR-targeted therapy.

cancer biology↗

bioRxiv2025

Features fade, pointers persist: dissociable parietal mechanisms in visual working memory formation and maintenance

An emerging body of work has adopted the theoretical construct of pointers: an object is mentally represented by a content-free pointer binding the corresponding features together. Indeed, fMRI studies have highlighted dissociable parietal regions sensitive to pointer and feature load respectively. Specifically, while the superior IPS (intraparietal sulcus) is sensitive to feature load, inferior IPS is only sensitive to the number of pointers - i.e., the number of objects. However, the spatiotemporal dynamics remain unclear, and therefore it is unknown whether these effects reflect visual working memory (VWM) formation, maintenance, or both, especially given limited temporal resolution of fMRI. In our current MEG (magnetoencephalography) study, participants memorized visual arrays with different numbers of objects (object/pointer load: two, four), as well as different features and feature-per-object (color, orientation, bifeatural) in a VWM task. We observed a dissociation between inferior and superior IPS in the temporal dynamics of feature-sensitive and pointer-sensitive responses. While pointer-sensitive signals persisted across VWM formation and maintenance in inferior IPS, feature-sensitivity was only transiently manifested during VWM formation in superior IPS. This spatiotemporal dissociation may reflect a representational architecture optimized for efficiency, reducing the need for sustained neural activity to maintain features once they are bound to pointers. In revealing the spatiotemporal profile of pointer and feature representations, our results provide novel evidence on how pointers underlie energy-efficient neural representations in VWM.

neuroscience↗

bioRxiv2025

Spectral disruption of inter-hemispheric resting-state BOLD coherence at vasomotor frequency (~0.1 Hz) links vascular dysfunction to functional connectivity loss in carotid artery stenosis

In the brain, vasomotor dynamics at infra-slow frequencies ([~]0.1 Hz), driven by synchronized oscillations of smooth muscle cells in vessel walls, are thought to play a crucial role in regulating cerebral perfusion and underlie resting-state functional connectivity (FC), typically measured by correlated time courses of functional signals. In particular, rodent studies have demonstrated that vasomotor activity contributes to the coherence of blood oxygenation level dependent (BOLD) signal fluctuations. However, in humans, detecting this contribution non-invasively remains challenging due to the limited spatiotemporal sensitivity of functional magnetic resonance imaging (fMRI) to vasomotion. Given that prior studies have identified internal carotid artery stenosis (ICAS) as an informative conditional lesion model of vasomotor and hemodynamic impairments in humans, we investigated whether ICAS affects interhemispheric BOLD coherence at [~]0.1 Hz. Using a multi-modal fMRI framework integrating resting-state fMRI with quantitative mapping of cerebral blood volume, blood flow, oxygen metabolism, and BOLD time lag, we compared BOLD coherence between patients with asymptomatic unilateral ICAS and healthy controls. Frequency-specific analysis revealed significantly diminished interhemispheric BOLD coherence at [~]0.1 Hz across canonical resting-state networks in ICAS patients, while ultra-slow (<0.05 Hz) coherence remained largely preserved. This reduction was spatially widespread and particularly pronounced in watershed areas, i.e., border zones between major vascular territories, associated with significantly increased lateralization of cerebral blood volume (p < 0.01). Notably, coherence-based FC patterns at [~]0.1 Hz were heterogeneous within watershed areas but homogeneous outside, suggesting an interplay between compensatory mechanisms and cerebrovascular impairment. Taken together, our findings demonstrate that ICAS induces subtle, frequency-and region-specific alterations in interhemispheric FC, consistent with a model in which impaired vasomotor activity impacts on resting-state FC in the human brain.

neuroscience↗

bioRxiv2025

DCPS modulates TDP-43 mediated neurodegeneration through P-body regulation

The proteinopathy of the RNA-binding protein TDP-43, characterized by nuclear clearance and cytoplasmic inclusion, is a hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimers disease (AD). Through CRISPR interference (CRISPRi) screening in human neurons, we identified the decapping enzyme scavenger (DCPS) as a novel genetic modifier of TDP-43 loss-of-function (LOF)-mediated neurotoxicity. Our findings reveal that TDP-43 LOF leads to aberrant mRNA degradation, via disrupting the properties and function of processing bodies (P-bodies). TDP-43 interacts with P-body component proteins, potentially influencing their dynamic equilibrium and assembly into ribonucleoprotein (RNP) granules. Reducing DCPS restores P-body integrity and RNA turnover, ultimately improving neuronal survival. Overall, this study highlights a novel role of TDP-43 in RNA processing through P-body regulation and identifies DCPS as a potential therapeutic target for TDP-43 proteinopathy-related neurodegenerative diseases.

neuroscience↗

bioRxiv2025

FRA1 drives melanoma metastasis through an actionable transcriptional network

Transcriptional dysregulation has emerged as a critical driver of melanoma progression, yet the molecular mechanisms governing this process and their potential as therapeutic targets remain inadequately characterized. Here, we identify FRA1 as a potent and actionable driver of melanoma metastasis. FRA1 enhanced both the initial seeding and subsequent outgrowth of metastatic lesions. Comprehensive multi-omics integration revealed transcriptional target genes of FRA1, with AXL, CDK6, and FSCN1 exhibiting increased expression in melanoma metastasis and a significant correlation with poor patient outcomes. Silencing AXL, CDK6, or FSCN1 abrogated FRA1-mediated invasion in vitro and reduced metastatic colonization. Furthermore, pharmacological inhibition of CDK6 and FSCN1, and to a lesser extent AXL, suppressed melanoma metastasis and prolonged overall survival. The expression of FRA1 and its target genes correlates with shortened survival across multiple cancer types, highlighting the broader clinical relevance of this pathway. This study unveils an actionable FRA1-mediated transcriptional network that drives cancer progression and metastasis, offering potential avenues for therapeutic interventions. SIGNIFICANCEFRA1 promotes melanoma metastasis by enhancing the expression of AXL, CDK6, and FSCN1 and this transcriptional network is associated with poor survival across several cancer types. Targeting these FRA1 effectors suppresses metastasis and extends survival, offering a therapeutic strategy for metastatic melanoma and potentially other aggressive cancers.

cancer biology↗

bioRxiv2025

Beyond the G-Loop: CRBN Molecular Glues Potently Target VAV1 via a Novel SH3 RT-Loop Degron

This study reports the discovery and characterization of novel CRBN molecular glues that selectively induce the proteasomal degradation of the hematopoietic-specific signaling protein VAV1, a key target in hematological malignancies and autoimmune diseases. Utilizing unbiased global proteomics, we identified phenyl-glutarimide derivatives NGT-201-12, as effective VAV1 degraders, with its C-terminal SH3 domain (SH3-2) being crucial for this interaction. A significant finding is the elucidation of a non-canonical RT-loop degron (RDxS motif, residues 796-799) within VAV1 SH3-2, distinct from previously characterized G-loop degrons. This discovery, supported by advanced computational modeling using the physics- and AI-driven GluePlex workflow and validated by site-directed mutagenesis, highlights versatility of CRBN in recognizing diverse neosubstrate motifs. Furthermore, we demonstrate that applying Free Energy Perturbation (FEP+) calculations to these predicted ternary structures yields cooperativity metrics that correlate with experimental degradation potency, overcoming the limitations of standard molecular docking. This establishes a robust workflow where, once a ternary complex is predicted, even with initial weak binders, FEP+ can be utilized to prospectively rank analogs and optimize molecular glue potency. Additionally, we demonstrate that strategic chemical modifications, particularly conformational restriction via halogen substitution (e.g., NGT-201-18), markedly potentiate VAV1 degradation, a principle supported by density functional theory (DFT) calculations. Comprehensive structure-activity relationship (SAR) studies provided a roadmap for designing next-generation VAV1 degraders. Importantly, dose-response proteomics not only confirmed VAV1 as the primary target but also revealed LIMD1, possessing a canonical G-loop, as an off-target for some analogs, indicating a single molecular glue can engage disparate degron motifs. The identification of the VAV1 RT-loop degron prompted a proteome-wide search, revealing other SH3-containing proteins as potential targets or off-targets. In conclusion, this research unveils a novel non-canonical RT-loop degron in VAV1, demonstrates the utility of conformational restriction in enhancing degrader potency, and underscores the critical role of integrating global proteomics with advanced structural modeling and FEP calculations for understanding degrader potency and selectivity. These findings offer a promising therapeutic strategy for targeting VAV1 and significantly expand the landscape of CRBN neosubstrate recognition and the rational design of molecular glue degraders.

biochemistry↗

bioRxiv2025

A multi-step immune-competent genetic mouse model reveals phenotypic plasticity in uveal melanoma

Uveal melanoma (UM) is a highly aggressive intraocular malignancy with limited therapeutic options for metastatic disease. Existing transgenic UM mouse models inadequately recapitulate human disease progression, while transplant models lack immune competence for studying the tumor immune microenvironment and therapeutic interventions. To address these limitations, we developed a genetically engineered mouse model incorporating stepwise genetic alterations implicated in human UM progression. Spatiotemporally controlled expression of mutant GNAQQ209L from the endogenous locus induced choroidal nevi with limited penetrance. Concomitant BAP1 deletion enhanced nevus formation, while further MYC activation led to fully penetrant intraocular tumors with metastatic potential. Single-cell RNA sequencing revealed malignant cells segregated into Melanocytic and Neural Crest-like subpopulations characterized by distinct transcriptional and biosynthetic programs. Trajectory analyses inferred dedifferentiation from the Melanocytic toward the Neural Crest-like state during tumor progression. Comparison to human UM revealed commonalities with highly aggressive Class 2 UM, including gene expression signatures and copy number gains affecting genes that map to human chromosome 8q beyond the activated MYC allele, suggesting cooperative effects of multiple drivers in this chromosomal region. The tumor microenvironment featured immunosuppressive macrophage populations and exhausted T cells, closely resembling human UM. This physiologically relevant, immune-competent model provides a platform for investigating UM biology, functionally characterizing candidate driver genes, and developing immune-based therapeutic strategies. SIGNIFICANCE STATEMENTWe developed a mouse model that resembles the genetic progression and phenotypic plasticity of human UM. This spatially controlled model confirms the critical role of driver mutations in GNAQ and BAP1, proposes MYC as a promoter of malignant transformation in coordination with other chromosome 8q genes, and reveals UM progression through distinct cellular states. This model offers an urgently needed preclinical platform for understanding the immunogenomics of UM and for testing immune and targeted treatments for this lethal cancer.

cancer biology↗

bioRxiv2025

Structural and temporal dynamics analysis on PANoptosis in sepsis: a bibliometric analysis

PANoptosis, as a new type of programmed cell death, is characterized by pyroptosis, apoptosis and necroptosis, and is a key mechanism causing a variety of inflammatory diseases. Despite the growing number of studies indicating the crucial role of PANoptosis in sepsis, there has been no bibliometric analysis of the research hotspots and trends in this field. Therefore, this study aims to explore the history, research hotspots and emerging trends of PANoptosis in sepsis related research in the past 20 years from the perspective of structure and temporal dynamics. The articles related to PANoptosis in sepsis were retrieved from the Web of Science Core Collection (WoSCC) database from 2000 to 2024. CiteSpace and HistCite were used to analyse the historical features, the evolution of active topics, and emerging trends about PANoptosis in sepsis. 6165 original articles and reviews on PANoptosis in sepsis were included in the bibliometric analysis. In the last 20 years, the number of published documents is increasing year by year and reaches a peak in 2022. At the same time, many activation themes have emerged at different times, as evidenced by a total of 96 categories, 865 keywords and 629 reference bursts. Keyword clustering anchored eight emerging research subfields, namely 0# oxidative stress, 1#pyroptosis, 2#sepsis-associated encephalopathy, 3#acute kidney injury, 4#immunosuppression, 5#necroptosis, 7#lung injury and 8#extracellular vesicles. The keyword alluvial map shows that the most persistent research concepts in this field are phosphatase. And the emerging keywords are toll_like_receptors, regulatory T cells, recognition, etc. In a timeline visualization based on the time span of the citations, we find five relevant emerging topics, namely 1# immunosuppression, 2# sepsis-induced cardiomyopathy, 3# pyroptosis, 4# acute kidney injury, and 13# COVID-19. Our study provides a comprehensive bibliometric analysis and summary about the current status and trends on PANoptosis in sepsis, which will aid researchers in conducting further scientific research in this field.

bioinformatics↗

bioRxiv2025

Subtype-Specific Freezing of Gait Detection Strategies via Feature-Masked-Based CNN

ObjectiveFreezing of gait (FOG), a disabling symptom of Parkinsons disease, varies in manifestations and motion contexts. Its heterogeneity motivates subtype categorization such as manifestation-specific subtypes (akinesia, trembling or shuffling) or motion-specific subtypes (gait-initiation, walking or turning). Despite numerous promising deep learning FOG detection studies, few consider FOG heterogeneity. It remains unclear whether different subtypes require distinct detection strategies, and whether tailoring subtype-specific models could enhance detection generalizability across subtypes. Methods: To address these questions, we categorize FOG data into manifestation- or motion-specific subtypes and derive their corresponding detection strategies as interpretable feature masks. We then propose a feature-mask-based CNN that explicitly embeds the identified strategies. Using waist-mounted 3D accelerometer data, a general CNN and subtype-specific CNNs are trained. Results: According to feature-mask analysis, motion-specific subtypes share a common detection strategy, whereas manifestation-specific subtypes require distinct strategies. Manifestation models exhibit enhanced generalizability across subtypes compared to the general model, boosting the overall average FOG detection sensitivity by 24.95%{+/-}9.80% and specificity by 18.29%{+/-}8.71%. Conversely, motion models reduce the overall FOG sensitivity by 1.89%{+/-}8.74% and specificity by 5.17%{+/-}10.76%. Conclusions: The detection strategy is mainly driven by manifestation composition of the data. The general model favors the dominant manifestation-specific subtype group(s), a bias corrected by tailored manifestation-specific strategies. No comparable benefit arises from motion models due to their similar manifestation compositions. Significance: This study interpretably reveals the detection strategies required by different FOG subtypes and demonstrates the effectiveness of subtype-specific tailoring in improving FOG detection generalizability.

bioengineering↗

bioRxiv2025

A domestication change at PvMYB26 in common bean sheds light on the origins of Middle American agriculture

Domestication imposed radically different selection pressures on plants, eventually transforming them into the cultivated forms that support global populations today. Here, we investigate the loss of seed dispersal via pod shattering during common bean (Phaseolus vulgaris L.) domestication. We identified an eight-kb deletion eliminating the transcription start site and promoter of the candidate gene PvMYB26. Mutants express PvMYB26 at < 1% of the level of wild types and produce 44% less pod lignin. Whole-genome sequencing revealed that the mutation is nearly diagnostic for domestication status among Middle American common bean, indicating its importance in domestication. We also identified a high-frequency PvMYB26 frameshift/premature stop mutation unique to Andean domesticates. Wild haplotypes most like Middle American domesticates are found in eastern Jalisco, Mexico. Our results suggest that West-Central Mexico was the site of common bean domestication and suggest that this region may have been important in the rise of Middle American agriculture.

evolutionary biology↗

bioRxiv2025

CLONEID: A Framework for Monitoring and Steering Subclonal Dynamics

Molecular assays can resolve clonal structure, but they are expensive and typically sparse in time, whereas phenotypic observations such as imaging can be collected frequently but often are not preserved in the context needed for later interpretation. We present CLONEID, an event-based framework for organizing clone-resolved phenotypic, molecular, and specimen-context records so that genotype-to-phenotype interpretation can be maintained across time. CLONEID links time-stamped Events, assay-specific Perspectives, and reconciled Identities through structured ingestion, provenance-aware retrieval, and reproducible export, complementing upstream clone-calling methods. In a long-term gastric cancer density-selection experiment, CLONEID linked repeated culture events, growth measurements, and late karyotypic profiling within a shared record, supporting longitudinal interpretation of phenotypic adaptation together with underlying chromosomal state.

bioinformatics↗