Biology subjects

He, H.

Publications and source records attributed to He, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Asymmetric listening conditions perturb verbal and nonverbal coordination dynamics during conversation

Human conversation depends on continuous coordination across verbal and nonverbal behaviour. Yet this coordination may become perturbed when one person experiences greater listening difficulty. Previous nonverbal joint action studies show that unequal task demands between partners can lead to complementary leader-follower dynamics, but whether similar patterns emerge during natural conversation remains unclear. We investigated how unequal listening conditions affect verbal and nonverbal coordination in 40 same-gender stranger dyads during three 10-minute face-to-face conversations. Each dyad participated in noise-free and asymmetric noise conditions, with one person exposed to speech-shaped noise at a time. Asymmetric noise reduced conversational flow and enjoyment, and shifted the balance of verbal contributions: noise-exposed participants took longer turns and contributed more speaking time, while their noise-free partners produced more backchannels. Interpersonal head-movement coordination became temporally asymmetric under noise, with movements of the noise-exposed participant more often preceding those of their partner. In contrast, interpersonal hand-movement coordination did not differ between conditions. Within individuals, hand coordination was stronger when participants themselves experienced noise than when their partner experienced noise. These findings demonstrate that perturbing one partner's auditory access affects coordination within and between individuals, revealing how unequal interaction demands produce different coordination patterns across verbal and nonverbal behaviour.

physiology↗

bioRxiv2026

A closed-loop language-model agent for target-specific multi-objective hit-to-lead optimization

Hit-to-lead optimization is a multi-objective molecular-design problem in which binding-related scores must be considered together with drug-likeness and synthetic accessibility. We developed a closed-loop language-model medicinal-chemistry agent that combines target and starting-hit context, PubMed retrieval, molecular-property tools, docking, and feedback from previously scored analogues. In a matched computational benchmark comprising six kinase targets, six methods, a 40-candidate budget, and six independent campaigns per method, the agent achieved the highest mean aggregate score under a pre-specified composite objective on four targets. Re-analysis of the same candidate sets with drug-likeness-gated docking and docking-drug-likeness hypervolume produced different target-level winners, showing that evaluation rules can change the comparative interpretation of an optimization campaign. Candidate distributions and component ablations indicated that the agent's advantage was associated primarily with retention of scored-candidate feedback and higher-QED regions rather than with docking alone. An EGFR case study illustrates a scaffold-preserving in-silico optimization trajectory from erlotinib. The study is a computational benchmark and evaluation framework; the prioritized molecules are hypotheses for subsequent experimental testing, not experimentally validated leads.

bioinformatics↗

bioRxiv2026

Calmodulin mutation N54I causes autosomal dominant CPVT in mice

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited arrhythmia syndrome characterized by stress- or catecholamine-induced ventricular arrhythmias in the absence of overt structural heart disease. Mutations in RYR2 and CASQ2 account for most genetically defined cases, although pathogenic variants in the three genes encoding calmodulin (CALM1-3) have also been linked to CPVT. Because all three CALM genes encode an identical calmodulin protein, pathogenic calmodulin variants are expected to be expressed in only a small fraction of total cellular calmodulin, raising the question of whether this limited abundance is sufficient to produce an arrhythmogenic phenotype in vivo. We generated a heterozygous mouse model carrying the human disease-associated N54I-equivalent mutation, N54I, in Calm1. Mutant calmodulin accounted for 13.7% of total cardiac calmodulin, consistent with expression from one of six Calm alleles. Under basal conditions, N54I/+ mice exhibited normal growth, survival, cardiac morphology, and surface electrocardiogram parameters. However, cardiomyocytes isolated from N54I/+ mice had increased rates of RyR2-mediated spontaneous calcium release. Following catecholaminergic challenge with isoproterenol and caffeine, N54I/+ mice exhibited significantly more premature ventricular contractions and arrhythmias than wild-type littermates. Exercise challenge in conscious mice similarly provoked ventricular ectopy and ventricular tachycardia. In addition, N54I/+ mice exhibited abnormalities of atrial and sinoatrial electrical activity, including premature atrial contractions, ectopic P waves, atrioventricular conduction slowing, and beat-to-beat variability. These findings demonstrate that expression of the N54I calmodulin variant from a single Calm1 allele is sufficient to produce a CPVT phenotype in vivo. This model provides experimental evidence linking a human disease-associated calmodulin variant to arrhythmogenesis and demonstrates the functional dominance of mutant calmodulin in the heart.

physiology↗

bioRxiv2026

Distinct RNA-RNA spatial interaction sub-networks of transcription factors in hepatic cells

We applied the latest RIC-seq technology to study the RNA-RNA interactions in human liver HepG2 cells. Integrating ChIP-seq data with the RIC-seq data, we clas-sified vari ous transcription factors (TFs) into two distinct clusters based on the in-teraction enrichment scores of the uaRNA (RNA transcribed in promoter regions) and eRNA (RNA tran scribed in enhancer regions) potentially transcribed by the TF binding sites. We went on to compare the genomic features and clinical significance across different clusters, by further integrating Hi-C, ATAC-seq, and clinical data from liver cancer patients. Our results showed that Cluster 1 exhibited low spatial interaction (RIC-seq derived RNA-RNA interactions between regulatory RNA ele-ments) and high tissue specificity (high proportion of binding sites covered by shared peaks between two different cell lines for each histone modification marker), showed higher associations with the B compartments and nucleoli, contained less densely clustered TF binding sites, and is more correlated with clinical outcomes. In contrast, Cluster 2 has higher spatial interaction, is more likely to be found in the A compartments and nuclear speckles, contained more densely clustered TF binding sites, and is more prone to form loops. These findings suggested that these transcrip-tion factors might play critical roles in regulating gene expression and serve as po-tential biomarkers and therapeutic targets with significant implications for cancer prognosis and treatment. In summary, groups of TFs could occur as distinct sub-networks based on spatial proximity of non-coding RNAs transcribed by the TF binding sites. These sub-networks appear to be related to regulatory differences for the TF groups and may partially explain the chromosome compartments/domains.

genomics↗

bioRxiv2026

CellMAGE: cell-type deconvolution for multi-parent population analysis of gene expression

Single-cell RNA-sequencing remains prohibitively expensive for multiparental population (MPP) studies. Existing deconvolution methods treat bulk RNA-seq as genetically anonymous mixtures, but in MPPs, the proportional contribution of each parental strain to each progeny's transcriptome is already known. CellMAGE (Cell-type deconvolution for Multi-parent Analysis of Gene Expression) weights parental cell-type profiles by each progeny's known genetic composition, requiring no model training and no minimum sample size. Validated in 16 Diversity Outbred mice across 12 prefrontal cortex cell types and 23,116 genes, predicted and measured gene expression were statistically equivalent (0.05) in all cell types (pooled Spearman = 0.923, 95% CI: 0.910, 0.934). CIBERSORTx required 96 additional samples to resolve at most 12.4% of genes and only 3 cell types; CellMAGE outperformed it even within this restricted comparison (per-cell-type median : 0.908-0.974 vs. 0.353-0.641). CellMAGE is applicable to any MPP with parental single-cell data, including diploid crop MAGIC populations.

genomics↗

bioRxiv2026

Range expansion of the invasive barnacle Balanus glandula into the Wadden Sea, its habitat and parasite fauna compared to established barnacle species

The impact of invasive species on marine ecosystems is rapidly increasing, where they often outcompete native species in the absence of natural enemies. The parasite release hypothesis states that the success of invasive species relates partly to the loss of natural parasites during introduction and lower susceptibility to native parasites. Barnacles are highly successful invaders due to broad environmental tolerance and dispersal via shipping, but whether parasite release also participates in this success remains unknown. In this study, we analyse parasite infection patterns in native and invasive barnacles in the Wadden Sea by surveying communities across tidal zones. Additionally, year-round molecular monitoring of larval stages and a literature review were used to track the distribution of the invasive Pacific barnacle Balanus glandula in Europe and document its appearance in the Wadden Sea. The long-established invasive Austrominius modestus dominated the high and middle intertidal zone, whereas native species (Balanus crenatus and Amphibalanus improvisus) prevailed in lower zones. Native and invasive barnacles differed in parasite infection frequency (mostly cestodes and trematodes). The native Semibalanus balanoides had the highest prevalence (27%), followed by the invasive A. modestus (11%), and no infections were found in B. glandula. Lower parasite prevalence in invasive barnacles is consistent with the hypothesis that parasite release supports invasion success. In the absence of competent parasites, B. glandula could impact native barnacles through competition. Continued monitoring of B. glandula is recommended to track its distribution, interactions with native species, and parasite acquisition, providing further insight into the parasite release hypothesis.

ecology↗

bioRxiv2026

Unbiased and Epicardial-Specific Lineage Tracing Reveal Epicardial Contribution to Vascular Endothelial Cells in Heart Development

Controversy surrounds the lineage potential of cardiac cells, particularly epicardial cells, during heart development, largely due to the non-specific expression of epicardial marker genes and the resulting non-specific labeling in Cre-loxP mouse models. Using DARLIN mice, a CRISPR/Cas9-based lineage-tracing system independent of the Cre-loxP system, we analyzed the lineage development of embryonic cardiac cells in an unbiased manner and identified lineages shared among different cell types, such as epicardial cells and vascular endothelial cells (Vas_ECs). To further confirm the lineage potential of epicardial cells, we identified an epicardial cell-specific marker gene, Lrrn4, through analysis of a multi-staged single-cell mRNA-sequencing (scRNA-seq) dataset, and generated a corresponding Lrrn4-CreER mouse line. We then bred this line with a reporter mouse to confirm its specificity for labeling epicardial cells, and subsequently performed prolonged lineage tracing, which revealed specification of the labeled epicardial cells into Vas_ECs. Finally, Using this mouse line, we investigated epicardial cell function by selectively ablating these cells and by expressing TGF{beta} in epicardial cells to convert their lineage from Vas_ECs to fibroblasts. Both approaches resulted in significant developmental defects in embryonic hearts. Together, these results indicate that epicardial cells can give rise to Vas_ECs, and that the Lrrn4-CreER mouse model is a valuable tool for elucidating the role of the epicardium in heart development.

developmental biology↗

bioRxiv2026

2-Hydroxyglutarate Redirects Fatty Acid Partitioning to Mitigate Lipotoxic Stress and Preserve Metabolic Fuel

The role of 2-hydroxyglutarate in lipid metabolism is currently unknown. Here we show that 2HG redistributes the partitioning of fatty acids into triglyceride storage and away from membrane phospholipid synthesis, mitochondrial oxidation, and lipotoxic intermediates. In primary human cardiac and vascular cells, both enantiomers, D2HG and L2HG, expanded triglyceride stores and lipid droplets while selectively depleting phosphatidylethanolamine, with L2HG acting more potently than D2HG despite lower intracellular accumulation. Mechanistically, L2HG increases DGAT-dependent triglyceride synthesis, slows triglyceride turnover, and constrains the ethanolamine branch of the Kennedy pathway. This response limits fatty acid oxidation, long-chain acylcarnitine accumulation, and lipid peroxidation independently of pseudohypoxic transcription or canonical lipid storage regulators, while also remodeling the phosphoproteome and redox proteome. L2HG accumulation induces hypertriglyceridemia in mice, redistributes the acyl chain composition of cardiac triglycerides, and limits ischemia-induced acylcarnitine accumulation in the heart, mirroring a positive association between circulating 2HG and triglycerides in humans. Thus, 2HG expands metabolic flexibility from whether fatty acids are used as fuel to how that fuel is allocated among storage, membrane synthesis, and oxidation.

cell biology↗

bioRxiv2026

Characterizing Functional Clusters of V4 Neurons in Digital Twins

Neurons in primate visual cortical area V4 display tuning for multiple visual features, including color, shape, texture, and depth. Whether and how these neurons are organized into functional architectures remains largely unknown. Using two-photon calcium imaging in anesthetized macaques, we recorded responses of hundreds of V4 neurons to natural images and used these data to train deep convolutional neural network models (digital twins), obtaining synthetic images (SI) that maximized neuronal responses. Based on their SIs, these neurons clustered into classes that spatially matched the orientation, color, and curvature maps from intrinsic signal imaging. Furthermore, lesion study in digital twins revealed different integration rules for different neuron classes. Thus, digital twins of V4 neurons can be applied as a promising tool to characterize neurons fundamental features, which underlie the functional clustering in this area. HighlightsO_LINeurons in V4 are examined with two-photon calcium imaging and DCNN modeling (digital twins) C_LIO_LISynthetic images derived from neurons digital twins reveal distinct neuron groups C_LIO_LIThese groups match functional types defined by intrinsic signal optical imaging C_LIO_LILesion study in digital twins demonstrates neural mechanisms underlying feature tuning C_LI

neuroscience↗

bioRxiv2026

Conserved and species-specific STIM autoinhibition revealed by AlphaFold3-guided dissection

Store-operated Calcium (Ca2+) entry (SOCE), mediated by dynamic STIM-Orai coupling, is crucial for cellular signaling, yet the molecular architecture of STIM autoinhibition remains poorly defined. Using an AlphaFold3-guided functional validation strategy combining FRET-based biosensors, mutagenesis, and Ca2+ imaging, we systematically dissected the CC1-SOAR autoinhibitory interface in both human STIM1 and C. elegans STIM (cSTIM). Our results reveal a conserved hydrophobic core essential for maintaining the resting state in both species. Interestingly, cSTIM possesses an extended polar interaction network that strengthens autoinhibition and correlates with slower activation kinetics. Species-specific polar networks differentially modulate interface stability, providing an additional layer of regulatory tuning. This integrated approach not only validates AlphaFold3 as a powerful tool for studying dynamic regulatory interfaces but also establishes a structural framework for understanding STIM activation and disease-associated mutations, offering mechanistic insights with therapeutic implications for SOCE-related disorders.

developmental biology↗

bioRxiv2026

New genes play a prominent role in evolution of new sperm classes of Drosophila

The widespread and regulated production of infertile parasperm assisting fertilization of eusperm provides a compelling model for elucidating the mechanisms of cellular innovation and altruism. Here we identify two specific parasperm lineages in Drosophila pseudoobscura that are segregated in development from the eusperm lineage by their single-cell transcriptomes. Most X-linked genes, except for species-specific new genes, show testis-specific repressive epigenetic modifications and become downregulated upon meiotic entry, supporting meiotic X chromosome inactivation. Between sperm classes, nearly half of the known meiotic arrest genes and their downstream targets are differentially transcribed, with over 200 genes displaying a gradient of transcription levels correlated with that of tail lengths. New genes are overrepresented throughout the hierarchical regulatory network of sperm divergence and over 60% of them exhibit a new cell-level expression compared to their parental copies. These results together indicate that new genes play a prominent role in the emergence of low-cost parasperm that shield the eusperm until fertilization.

evolutionary biology↗

bioRxiv2026

Cardiac Myosin Activation Enhances Contractility While Preserving Myocardial Energetics Compared With β-Adrenergic Stimulation

Impaired contractility and reduced myocardial energetic reserve underlie heart failure with reduced ejection fraction. Catecholaminergic inotropes such as dobutamine are used to augment cardiac output. However, dobutamine increases Ca{superscript 2} cycling, raising ATP demand and worsening energetic stress. The myotrope CK-138 increases contractility by directly activating myosin, sparing the added energetic cost of Ca{superscript 2} handling. This study compares CK-138 and dobutamine with respect to the relationship between contractile performance and myocardial energetic state, including high-energy phosphate balance, energetic efficiency, and substrate-specific metabolic fluxes. Isolated rat hearts were perfused with escalating concentrations of CK-138 or dobutamine. Contractility was assessed by measuring left ventricular pressure and rate-pressure product. Myocardial energetics were analyzed using 31P-NMR, and metabolic fluxes by 13C NMR and mass spectrometry. Unlike dobutamine, CK-138 increased LV contractility without increasing heart rate or LV end-diastolic pressure. CK-138 preserved ATP and phosphocreatine levels, maintaining a stable phosphocreatine-to-ATP ratio and free energy of ATP hydrolysis, whereas dobutamine progressively depleted both. At comparable workload, dobutamine exhibited higher glycolytic flux and lactate production, indicating greater reliance on glycolysis relative to mitochondrial oxidative metabolism, whereas CK-138 exhibited a 13% higher rate of ATP synthesis and [~]50% lower anaplerotic flux, consistent with preserved mitochondrial efficiency. In conclusion, CK-138 enhances cardiac contractility while preserving myocardial energetic state and substrate utilization. Unlike dobutamine, which depletes ATP reserves and shifts metabolism toward glycolysis, CK-138 maintains ATP homeostasis and supports oxidative metabolism. These findings support cardiac myosin activators, including CK-138 and omecamtiv mecarbil, as a mechanistically distinct class of energy-efficient inotropes.

physiology↗

bioRxiv2026

The emergent mental operation of the learning brain

How does the learning brain give rise to emergent mental operations that enable skill internalization and generalization? Using five-year longitudinal tracking of children acquiring abacus-based mental calculation, we reveal how sustained practice progressively reconfigures whole-brain states. Learning induces nonlinear transitions from stable baseline configurations through a transient exploratory phase toward restabilized associative brain networks. This hierarchical remodeling cascades from perceptual systems to action and default networks, mediated by adaptive neural variability and selective connectivity reweighting, with the salience-parietal memory network acting as a dynamic relay. These brain-state transitions accompany an ordered cognitive transfer cascade, emerging within arithmetic and extending to visuospatial and executive functions. Our findings are reproducible and provide a systems-level account of how ecological learning sculpts large-scale networks to enable complex skill acquisition.

neuroscience↗

bioRxiv2026

Divergent signaling profiles in mTOR gain-of-function Smith-Kingsmore syndrome (SKS) and TSC2 deficiency

Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder caused by gain-of-function mutations in MTOR, yet whether these mutations phenocopy TSC2 loss or establish a distinct signaling state remains unclear. Using quantitative proteomics, phosphoproteomics, and transcriptomics in isogenic cell models of SKS (MTOR{Delta}4aa), TSC2 loss (TSC2-/-), and wild-type controls under glucose depletion and refeeding, we find that MTOR{Delta}4aa and TSC2-/- cells occupy fundamentally distinct regulatory states. TSC2-/- cells exhibit broad anabolic remodeling and a transcriptional program dominated by NF-{kappa}B- and STAT-driven inflammatory responses. MTOR{Delta}4aa cells instead display enrichment of nuclear and RNA processing programs, E2F/MYC-driven transcription, and a constrained proteomic dynamic range across nutrient states. Phosphoproteomic analysis of MTOR{Delta}4aa reveals rerouting of nutrient-responsive signaling toward MAPK/ERK- and Ca2+/CaMK-dependent pathways with limited canonical mTORC1/S6K1 engagement. These findings establish SKS as a signaling rewiring disorder distinct from classical mTORC1 hyperactivation, with implications for therapeutic targeting.

molecular biology↗

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

Individualized Functional Connectivity-Guided TMS Targeting Theory of Mind Network for Autism Spectrum Disorder

Transcranial magnetic stimulation (TMS) shows promise in autism spectrum disorder (ASD), but variable outcomes may reflect suboptimal targeting. We developed a functional-connectivity (FC)-guided individualized TMS approach by identifying an ASD-relevant effective region and selecting superficial targets. In a multi-site mega-analysis of Autism Brain Imaging Data Exchange I data (298 ASD, 348 controls), the region with the greatest regional homogeneity (ReHo) abnormality was defined as the effective region. Individualized dorsolateral prefrontal cortex (DLPFC) and inferior parietal lobule (IPL) targets were localized as sites with strongest FC to this region. Group differences, symptom associations, and a six-patient case series were examined. The posterior cingulate cortex (PCC) showed the greatest ReHo abnormality and was implicated in theory-of-mind (ToM) circuitry. PCC-guided targets showed weaker FC in ASD in the right IPL, correlating with Autism Diagnostic Interview social scores; left DLPFC FC differences lacked symptom associations. In the case series, individualized PCC-IPL-guided TMS reduced ToM-related symptoms and Childhood Autism Rating Scale scores. PCC-IPL FC-guided TMS is a biologically informed intervention for modulating ToM circuitry in ASD.

neuroscience↗

bioRxiv2026

Evolutionarily informed gene sets reveal conserved and lineage-modified transcriptional programs during vertebrate forebrain evolution

The vertebrate forebrain exhibits striking diversity in anatomical architecture, yet is built from deeply conserved gene regulatory programs and cell types that underlie shared neural functions and behaviors. Understanding how these conserved cellular programs are maintained and modified across [~]500 million years of vertebrate evolution requires systematic cross-species single-cell comparisons, a challenge compounded by complex gene evolutionary histories that constrain joint analyses to shared one-to-one orthologs. Here we derive evolutionarily informed gene sets from a global homology graph and represent cells in a shared, interpretable gene-set feature space. Applying this framework to forebrain profiles from eleven vertebrate species, from sea lamprey to human, we construct a unified cross-vertebrate cell atlas. We find that conserved transcriptional programs define stable cell-type identities across vertebrates, with evolutionary divergence occurring predominantly within, rather than between, cell types. Gene-set conservation scales with evolutionary age, whereas lineage-modified programs reflect coordinated clade-level remodeling. Radial glia exhibit a conserved fate bifurcation into neurogenic and gliogenic trajectories with lineage-dependent modulation of transcriptional dynamics. Finally, human neuropsychiatric GWAS signals map onto conserved neural substrates across vertebrates. Together, our results demonstrate that vertebrate forebrain evolution proceeds through lineage-specific tuning of deeply conserved transcriptional programs embedded within stable cellular architectures.

evolutionary biology↗

bioRxiv2026

Chromosome-scale genome of the woody oilseed crop sacha inchi elucidates the molecular basis of alpha-linolenic acid biosynthesis and triacylglycerol accumulation in seeds

Sacha inchi (Plukenetia volubilis L.) is an emerging woody oilseed crop prized for its high alpha-linolenic acid (ALA) content. Despite its nutritional and economic value, the lack of high-quality genomic resources has hindered genetic improvement and the elucidation of its unique polyunsaturated fatty acid and lipid biosynthetic pathways. In this study, we report a high-quality, chromosome-scale genome assembly of sacha inchi with a total length of 710.62 Mb, integrated from Illumina, PacBio, and chromosome conformation capture (Hi-C) technology. The genome harbors 37,570 protein-coding genes, and 379.86 Mb (53.45%) of repetitive sequences. Phylogenomic analysis reveals that sacha inchi diverged from its closest relative Ricinus communis, [~] approximately 36.2 million years ago. Comparative genomics indicates that sacha inchi experienced only ancient whole genome duplication events. To elucidate the mechanisms governing ALA biosynthesis and triacylglycerol (TAG) accumulation in sacha inchi seeds, we performed temporal transcriptome profiling across six seed development stages. Our findings demonstrate that high TAG content is primarily driven by the sustained expression of biosynthetic genes and low activity of degradation genes during mid-to-late seed development. Notably, while genes encoding stearoyl-ACP desaturases (SADs) maintain the precursor pool, the expression of genes encoding fatty-acid desaturase 2 (FAD2) and fatty-acid desaturase 3 (FAD3) is positively correlated with the final accumulation of C18:2 and C18:3 fatty acids. We also identified lncRNAs as potential epigenetic regulators of these key pathways. This high-quality genome provides a critical foundation for elucidating the molecular mechanisms of seed growth and development in sacha inchi.

genomics↗