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Geng, Y.

Publications and source records attributed to Geng, Y..

At least 19 recordsLinked to original sources

zAcademy: an open-source programmable conditioning arena reveals sex- and genotype-dependent avoidance learning in adult zebrafish

Zebrafish are widely used to study learning and memory. Here, we describe zAcademy, a programmable conditioning arena released in full as open hardware and open software. zAcademy combines a 3D-printed dual-chamber arena, bottom-mounted LED matrices that generate visual patterns under software control, graphite rod electrodes gated by an Arduino-controlled relay, an overhead infrared camera, and a position-based analysis workflow. In one 180-min session, adult zebrafish were classically conditioned to associate a checkerboard light pattern beneath the arena (conditioned stimulus, CS) with a mild shock (unconditioned stimulus, US). Conditioned avoidance was assessed in six unreinforced CS-alone probes: one immediately after training to test learning, the remaining five at 30-min intervals to test memory. Spatial preference was quantified as a performance index (PI; occupancy of the dark zone). Wild-type fish shifted toward the dark zone immediately after training, whereas shank3 KO fish did not. The wild-type response was carried primarily by females rather than males. In addition, among initial responders, females sustained elevated PI at more later probes. zAcademy provides an inexpensive, fully documented, and readily modified platform for comparing experience-dependent behavioral change across genotypes and sexes.

animal behavior and cognition↗

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

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

ecology↗

A Comprehensive Computational Model of the Human head for Designing and Optimizing Visual Brain-Machine Interfaces

Brain-machine interfaces (BMIs) for vision restoration require models that accurately simulate the anatomy and electrical properties of visual pathways. However, current models focus only on isolated structures, such as the retina or brain, and overlook surrounding tissues. Here, we present a comprehensive computational model of the human head, incorporating the entire visual pathway--including the eye, optic nerve, and brain--along with critical neighboring tissues such as the orbit, paranasal sinuses, enabling precise simulations. Validation using human and large animal data demonstrated a strong correlation between the simulated and measured electrical potentials. Component elimination analysis revealed that the optimized comprehensive model outperformed simplified versions. The models utility was demonstrated through multiple applications: (1) comparative analysis of electrical neuromodulation technologies for optic neuropathy, revealing the filed intensity limitations of noninvasive approaches and the safety concerns of invasive intraorbital approach; (2) identification of optimal stimulation site, revealing that transnasal stimulation at the optic chiasm outperformed traditional approaches; and (3) in silico design of electrode arrays for optic nerve prosthetics, demonstrating theoretical advantages in invasiveness and visual field coverage compared to existing retinal and cortical prosthetics. This validated and versatile computational resource supports the development of neuromodulation strategies and visual BMI technologies.

bioengineering↗

Quercetin Promotes Adipose Thermogenesis and Metabolic Health

The activation of thermogenesis in brown adipose tissue (BAT) represents a pivotal target for ameliorating disorders of glucose and lipid metabolism. This study sought to elucidate the regulatory effects of quercetin on thermogenesis and glucose-lipid metabolism within brown adipocytes, alongside its underlying molecular mechanisms. The findings demonstrated that quercetin markedly upregulated the expression of uncoupling protein 1 (UCP1), a critical thermogenic protein in brown adipocytes, thereby enhancing cellular thermogenic capacity and effectively mitigating glucose and lipid metabolism disorders. Subsequent mechanistic investigations confirmed that quercetin activated the COX2-PGE2-EP4-UCP1 signaling axis by augmenting the stability of cyclooxygenase 2 (COX2) protein, thus mediating its thermogenic-promoting and metabolism-improving effects. This study identifies quercetin as a potential therapeutic agent for the improvement of glucose and lipid metabolism disorders, uncovers a novel molecular mechanism through which quercetin regulates brown adipocyte thermogenesis, and provides a theoretical and experimental foundation for the application of quercetin in the prevention and treatment of obesity and related metabolic diseases.

molecular biology↗

Top2a-dependent neuronal regulation of social behavior and persistent rescue of social deficit through PRC2-mediated epigenetic reprogramming

Disruption of social behavior is a core feature of autism spectrum disorder (ASD), yet the molecular and cellular mechanisms governing social behavior development are not well understood. We previously identified topoisomerase II (Top2a) as a critical regulator of social behavior and restricted and repetitive behavior through antagonism of polycomb repressive complex 2 (PRC2)-mediated H3K27 trimethylation (H3K27me3), based mainly on pharmacological perturbations during embryogenesis in zebrafish and mouse. However, whether neuronal Top2a is genetically required for social behavior in mammals, and whether PRC2 inhibition can rescue genetically induced social deficits, remain untested. Here, we establish a neuron-specific Top2a conditional knockout mouse model and demonstrate that neuronal Top2a haploinsufficiency selectively impairs social interaction without inducing restricted and repetitive behaviors or cognitive deficits. Pharmacological inhibition of PRC2 using the EZH2 inhibitor tazemetostat, combined with elacridar to facilitated blood-brain barrier penetration, robustly rescues social deficits in Top2a conditional knockout mice. Strikingly, a one-week oral dosing regimen produced a rescue effect that persisted for up to two months after treatment cessation, far exceeding the temporal window typically observed for neuromodulatory drugs targeting neurotransmitter systems. These results showcase the unique capability of epigenetic modulatory therapy to induce durable behavioral improvements and their therapeutic potential for treating social dysfunction in neuropsychiatric disorders. Together, our results provide direct genetic evidence that neuronal Top2a governs social behavior in mice and establish the neuronal Top2a-PRC2 axis as a conserved, targetable epigenetic pathway regulating social behavior.

neuroscience↗

High-Precision Pneumatic Induction of Traumatic Brain Injury in Larval Zebrafish

Zebrafish have recently emerged as a cost-effective vertebrate model for Traumatic brain injury (TBI) research. However, current injury paradigms, particularly the weight-drop method, suffer from poor reproducibility due to sensitivity to small variations in materials and setup. Here, we introduce a high-precision pneumatic piston system, the Zebrafish Pneumatic Injury Device (ZePID), which delivers controlled, repeatable pressure pulses to induce TBI in larval zebrafish. ZePID achieves 97% accuracy in applied force and substantially reduces variability compared with weight-drop approaches. Using 6-days-post-fertilization (dpf) larvae, we quantified injury severity by tracking seizure-like locomotor behaviors. Larvae exposed to 150 psi exhibited a significant increase in maximum swimming speed relative to uninjured controls, as well as increased total distance traveled, consistent with TBI-associated hyperactivity. Overall, ZePID provides a standardized, compact, and high-efficiency method for inducing TBI in larval zebrafish.

neuroscience↗

EpiBrain: the brain's epigenetic landscape in a snapshot

Epigenetics connect nature with nurture and can help explain how genes, experiences, and the environment influence gene expression to promote individual differences in behavior and mental health. However, how these perturbations induce epigenetic changes across various regions of the brain remains largely unknown. To visualize changes in brains epigenetic landscape at a glance, we develop EpiBrain, a method utilizing whole-brain imaging and registration to capture epigenetic changes in the entire zebrafish brain in a snapshot. Using this method, we uncovered brain-wide epigenetic changes induced by brain activity, chemical exposures, and genetic mutations. We found that gadd45b, an immediate early gene with epigenetic modulatory activity, mediates experience-induced epigenetic changes in the brain, and that these changes contribute to brain activity and behavioral alterations. EpiBrain enables rapid and unbiased assessment of whole-brain epigenetic changes following physiological and disease-relevant perturbations and facilitates mechanistic discoveries at the molecular level.

neuroscience↗

Spatial Flavonoid Accumulation in Soybean Pericycle Restricts Phytophthora sojae Invasion

Root immunity relies on coordinated defenses across distinct tissues, yet the underlying cellular mechanisms remain unclear. Here, we integrated single-cell transcriptomics, spatial metabolomics, and genetic manipulation to dissect soybean (Glycine max) interactions with Phytophthora sojae. In resistant Williams82 (Wm82) roots, P. sojae hyphae were excluded from the stele, exhibiting negative tropism toward the pericycle. scRNA-seq revealed that this resistance is mediated by infection-induced pericycle cells expressing high levels of flavonoid biosynthetic genes, including GmCHS7 and GmCHI4A. CRISPR-Cas9 knockout of these genes compromised resistance, whereas overexpression enhanced immunity in susceptible cultivars. Metabolomic and spatial metabolic analyses identified naringenin, a flavonoid phytoalexin, as a key antimicrobial compound that specifically accumulates in pericycle-adjacent tissues of Wm82 during infection. Naringenin directly inhibited hyphal growth in vitro and enhanced resistance when applied exogenously. These findings uncover a spatially targeted immune strategy where pericycle-localized activation of flavonoid synthesis forms a chemical barrier to safeguard vascular integrity, highlighting pericycle-centered metabolic immunity as a target for engineering durable resistance.

plant biology↗

Shared feedback control principles across standing and walking

Intrinsic mechanisms and feedback control act together to stabilize the body in upright tasks. In unperturbed standing and walking, their combined effects can be captured by lumped stabilization models, relating delayed center of mass position and velocity information to current ground reaction forces. If and how lumped stabilization parameters change across these tasks is unclear. We applied a stabilization model to estimate and compare stabilization between unperturbed standing and walking. Fifteen healthy young participants (21+/- 4 yrs, 63 +/- 9 kg, 1.70 +/-0.10 m, 13 females, 2 males) walked at 1.25 m/s for 5 minutes, and performed 3 different standing tasks: normal standing, unipedal standing, and step posture for 1 minute, repeated 5 times. Whole-body kinematics and ground reaction forces were collected and used to fit the stabilization model and estimate the effective delay and lumped gains. Only small differences were found between standing tasks. Model fits were significantly higher in standing than in walking. ML effective delays were significantly longer in walking than in standing, whereas AP delays were comparable. The stabilization gains varied significantly across tasks and directions. The lumped position gains in most tasks exceeded critical stiffness, except for the mean values in walking, which were lower than the critical stiffness. Lumped velocity gains were all at under-damped level. The ratio of lumped position to velocity gains in standing were consistently close to human body's eigenfrequency (sqrt(g/l)) as predicted by the extrapolated center of mass concept. In walking, the ratio was close to the eigenfrequency during phases in which stabilization was significant. Our findings suggest that stabilization is organized at the task level, with lumped effects of all stabilizing mechanisms acting to preserve a consistent weighting between position and velocity contributions across tasks, effectively regulating the CoM motion to follow a pendulum-like trajectory.

neuroscience↗

Butyrate rescues chlorpyrifos-induced social deficits through inhibition of class I histone deacetylases

Chlorpyrifos (CPF) is a widely used organophosphate pesticide effective through inhibiting acetylcholinesterase, which leads to the accumulation of acetylcholine and continuous nerve stimulation. In addition to its well-known acute toxicity, exposure to CPF has also been linked to chronic conditions such as an increasing risk of autism spectrum disorder (ASD) and adverse effects on gut health, including disturbances to the gut microbiome and metabolism. However, the underlying mechanism of CPFs contribution to ASD remains unclear, and the roles of the gut microbiome and gut metabolites in CPF-induced neurodevelopmental toxicity remain elusive. Using a high-throughput social behavior assay, we found that embryonic exposure to CPF induced lasting social deficits in zebrafish. Through a small-scale screen of common health beneficial gut microbiome metabolites, we discovered that butyrate effectively rescued CPF-induced social deficits. RNA sequencing of zebrafish brain tissues revealed that early exposure to CPF induced a lasting suppression of neuronal genes, including many ASD risk genes, and elevated expression of circadian genes. Butyrate partially reversed the suppression of key neuronal genes. Butyrate is a non-selective inhibitor of histone deacetylases (HDACs). Through a series of loss-of-function experiments utilizing CRISPR-Cas9-induced knockouts and selective chemical inhibitors, we found that the class I HDAC, HDAC1, most likely mediates butyrates rescue effect. Metabolomics analysis detected changes in several nitrogen metabolism-related pathways in the zebrafish gut following CPF exposure. Metagenomics analysis revealed an increase in abundance of the denitrifying bacteria Pseudomonas and a reduction in the nitric oxide-sensitive bacteria Aeromonas in the CPF-exposed zebrafish gut microbiome. Our results connect CPF-exposure with changes in the gut microbiome, metabolome, epigenetics, gene expression, and behavior, inspiring a novel hypothesis for the underlying molecular mechanisms of CPF-induced neurodevelopmental toxicity. In the long run, our findings may help elucidate how CPF exposure contributes to autism risk and inspire therapeutic developments.

neuroscience↗

Cytoplasmic localization of the mRNA encoding actin regulator, Serendipity-α, promotes adherens junction assembly and nuclear repositioning

The subcellular localization of mRNAs is conserved from prokaryotes to humans. In Drosophila embryos [~]70% of mRNAs localize to specific sites in the cytoplasm, but the functional significance of this mRNA localization is largely unknown. During the process of embryo cellularization, mRNA encoding Serendipity- (Sry-), an actin filament (F-actin) binding protein, moves apically, concentrating near centrosomes. Transport is mediated by the Egl/BicD/Dynein complex and requires two stem loops in the 3UTR of the mRNA, which serve as localization signals. mRNA localization is dispensable for Sry- function at cleavage furrows in early cellularization but is necessary for repositioning nuclei in late cellularization. Sry- protein promotes assembly of cortical F-actin and apical spot adherens junctions (AJs) in late cellularization, and these AJs contribute to nuclear repositioning. We suggest that mRNA localization restricts cytoskeletal functions in late cellularization to regulate nuclear repositioning in preparation for the tissue morphogenesis events that immediately follow.

cell biology↗

Advancing Inter-brain Synchrony Measurement: A Comparative Hyperscanning Study of High-Density Diffuse Optical Tomography and Functional Near-infrared Spectroscopy

Inter-brain synchrony (IBS), measured by hyperscanning, refers to the synchronization of multiple individuals brain activities during social interactions. Traditional fNIRS-based hyperscanning suffers shortcomings like low spatial resolution and high susceptibility to superficial interference, causing imprecise estimation of IBS in complex social tasks. This study aims to fill the knowledge gap by comprehensively assessing how high-density diffuse optical tomography (HD-DOT), an enhanced alternative to fNIRS, can benefit hyperscanning studies of complex social interactions. Sixteen dyads were engaged in both collaborative and individual tangram puzzle tasks, and their brain activities were recorded simultaneously using HD-DOT and fNIRS. We found that HD-DOT demonstrated significantly stronger IBS and identified more brain regions with significant IBS compared to fNIRS during the collaborative task. Specifically, while fNIRS detected IBS only in the dorsolateral prefrontal cortex (DLPFC) and supramarginal gyrus (SMG), HD-DOT revealed additional IBS in the superior temporal gyrus (STG). Additionally, compared to the individual task, the collaborative task showed increased IBS in HD-DOT, not only in the DLPFC but also in the SMG, frontal eye fields (FEF), and inferior frontal gyrus (IFG). By highlighting the superior spatial resolution and sensitivity of HD-DOT in capturing detailed and extensive neural activity during complex social interactions, our findings for the first time clarified the potential strengths of HD-DOT in measuring IBS over traditional fNIRS. These advances provide a stronger empirical foundation for investigating the neural basis of social interaction, paving the way for future research on real-world, dynamic group behaviors. HighlightsO_LIFirst application of HD-DOT for inter-brain synchrony measurement. C_LIO_LIFirst demonstration of HD-DOTs superiority over fNIRS in IBS measurement. C_LIO_LIHD-DOT detects stronger IBS and more brain regions than fNIRS. C_LI

neuroscience↗

Modular Inter-brain Synchrony Network Associated with Social Difficulty in Autism Spectrum Disorder: a Graph Neural Network-Driven Hyperscanning Study

Understanding social difficulties in Autism Spectrum Disorder (ASD) remains challenging due to its neurobiological heterogeneity and the limited ecological validity of conventional neuroimaging methods in capturing dynamic social interactions. Hyperscanning analysis based on functional near-infrared spectroscopy (fNIRS), which measures inter-brain synchrony (IBS) during dyadic interaction, offers a novel avenue to address these challenges. However, prior studies on ASD have reported inconsistent findings, primarily focusing on intra-regional synchronization while overlooking cross-regional network dynamics. To bridge this gap, we proposed an interpretable graph neural network (GNN) model to systematically identify ASD-specific IBS modular network between child-caregiver dyads during naturalistic cooperative puzzle-solving and free-talking tasks. We identified distinctive key IBS sub-networks for the cooperative puzzle-solving task and free-talking task, with the frontal eye field (FEF) of caregivers, the dorsal lateral prefrontal cortex (DLPFC) and the motor region of children highlighted. Furthermore, the key IBS sub-networks were found to be able to predict multiple domains of the core ASD symptoms. By integrating hyperscanning with GNN-driven analysis, this work uncovers task-dependent inter-brain neural mechanisms underlying social difficulties in ASD. These findings advance the field by proposing a data-driven framework to identify IBS biomarkers tied to clinical profiles, paving the way for personalized interventions that integrate computational neuroscience with clinical practice.

neuroscience↗

Homodimerized Arpins: Binding to Arp2/3 Complexes with Positive Synergy to Inhibit Lamellipodia-Dependent Tumor Metastasis

The Arp2/3 complex is a central regulator of actin polymerization dynamics and cancer cell motility, with its dysregulation implicated in metastasis and therapeutic resistance. Despite its therapeutic potential, targeting Arp2/3 remains challenging due to the lack of precise molecular insights into endogenous inhibitors. Arpin, a lamellipodia-localized Arp2/3 inhibitor, has emerged as a critical modulator of cancer migration; however, the structural and mechanistic basis of its inhibitory function remains unresolved. Here, we report the 1.65-[A] crystal structure of Arpins N-terminal globular domain, revealing a unique structural fold distinct from all known Arp2/3-binding factors. Structural and biophysical analyses demonstrate that Arpin forms homodimers via a conserved interface, which is essential for cooperative inhibition of Arp2/3-dependent actin polymerization. Functional studies in cancer models reveal that Arpin homodimerization potently suppresses lamellipodia-driven migration and invasion, effects further enhanced by engineered dimeric constructs or artificially designed dual-tailed peptides. These findings elucidate a structural basis for Arpin-mediated suppression of cancer cell motility and identify homodimeric cooperativity as a druggable mechanism for targeting metastatic progression. Our work provides a molecular framework for designing Arpin-inspired inhibitors to counteract therapeutic resistance and metastasis in cancers reliant on Arp2/3-driven actin dynamics.

cancer biology↗

Cold-activated hepatocyte derived exosomes promote BAT thermogenesis through miR-293-5p

The liver-adipose axis serves as a fundamental regulatory network governing systemic lipid homeostasis, with hepatic-derived signals orchestrating adipose tissue plasticity through multimodal mechanisms. Comprehensive elucidation of these bidirectional crosstalk mechanisms may reveal novel therapeutic strategies for metabolic disorders. Our investigation demonstrates that cold exposure induces hepatic secretion of exosomes that potentiate adipose thermogenic activation in both in vitro and in vivo models. This thermogenic potentiation is mechanistically linked to cold-induced upregulation of hepatocyte-derived exosomal miR-293-5p. Notably, pharmacological administration of miR-293-5p agomir significantly attenuates diet- induced obesity and associated metabolic dysregulation in murine models. Through mechanistic interrogation, we identified Tet1 as a direct downstream target of miR- 293-5p, where ectopic Tet1 expression disrupts brown adipose tissue (BAT) thermogenic programming independently of miR-293-5p modulation. Our findings establish cold-activated hepatocyte exosomes as endocrine signaling mediators containing thermogenic microRNA cargos, with miR-293-5p emerging as a regulatory nexus coordinating mitochondrial bioenergetics and systemic energy equilibrium through liver-adipose cross-talk.

genetics↗

Vacuum and sonication treatment enables efficient transient gene expression in various monocot and eudicot plant seedlings

Transient gene expression in intact plants is essential for rapidly addressing biological questions, where the current toolkit can be improved for higher efficiencies and broader plant species range. Here, we introduce VAST (Vacuum and Sonication-Assisted Transient expression): a transient transformation method that substantially enhances gene expression efficiency, reproducibility, and versatility across diverse monocot and eudicot intact seedlings. By systematically optimizing plant growth conditions and incorporating vacuum infiltration and sonication pre-treatments prior to seedling co-culture with Agrobacterium tumefaciens, we significantly improved transient gene expression efficiency while minimizing tissue damage compared to existing methods in Arabidopsis thaliana. We further demonstrated the broad applicability of VAST by successfully transforming key model and crop species, including tomato, Brassica rapa, Medicago sativa, Setaria italica (foxtail millet), switchgrass, and wheat. We also demonstrated a case study using the VAST-mediated transient transformation, where a cross-species analyses of nitrate-responsive gene expression highlighted both the conserved and diverged biological responses between the two model crops, A. thaliana and S. italica. VASTs simplicity, versatility, and efficiency provide a powerful tool for functional genomics, synthetic biology, and biotechnology research, opening new avenues for the rapid exploration of gene function, regulation, and editing in diverse plant systems.

plant biology↗

Upright stance is controlled close to critical stability across different postures

Withdrawal StatementThe authors have withdrawn version 4 of this manuscript because it erroneously contains the PDF intended for a different preprint (10.1101/2025.01.09.632072). Therefore, the authors do not wish this version to be cited. Versions 1-3 are not affected by this withdrawal, and the work described in those versions has been published in doi:10.1016/j.humov.2026.103470. If you have any questions, please contact the corresponding author.

neuroscience↗

Proteome-wide reverse molecular docking reveals folic acid receptor as a mediator of PFAS-induced neurodevelopmental toxicity

Per- and polyfluoroalkyl substances (PFAS) are a class of long-lasting chemicals with widespread use and environmental persistence that have been increasingly studied for their detrimental impacts to human and animal health. Several major PFAS species are linked to neurodevelopmental toxicity. For example, epidemiological studies have associated prenatal exposure to perfluorooctanoate (PFOA) and perfluorononanoate (PFNA) with autism risk. However, the neurodevelopmental toxicities of major PFAS species have not been systematically evaluated in an animal model, and the molecular mechanisms underlying these toxicities have remained elusive. Using a high-throughput zebrafish social behavioral model, we screened six major PFAS species currently under regulation by the Environmental Protection Agency (EPA), including PFOA, PFNA, perfluorooctane sulfonate (PFOS), perfluorohexanesulfonic acid (PFHxS), perfluorobutane sulfonate (PFBS), and hexafluoropropylene oxide dimer acid ammonium salt (GenX). We found that embryonic exposure to PFNA, PFOA, and PFOS induced social deficits in zebrafish, recapitulating one of the hallmark behavioral deficits in autistic individuals. To uncover protein targets of the six EPA-regulated PFAS, we screened a virtual library containing predicted binding pockets of over 80% of the 3D human proteome through reverse molecular docking. The screen predicts that folate receptor beta (FR-{beta}, encoded by the gene FOLR2) interacts strongly with PFNA, PFOA, and PFOS but to a lesser degree with PFHxS, PFBS, and GenX, correlating positively with their in vivo toxicity. These predictions were validated through in silico molecular docking, in vitro protein binding analysis, and in vivo loss-of-function verification. Furthermore, embryonic co-exposure to folic acid effectively rescued social deficits induced by PFAS. The folate pathway has been implicated in autism, indicating a novel molecular mechanism for PFAS in autism etiology.

pharmacology and toxicology↗