Biology subjects

Cao, M.

Publications and source records attributed to Cao, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

How spatial genome architecture coordinates rhythmic gene transcription across scales in plants remains poorly understood. Here, we integrated bridge linker Hi-C (BL-Hi-C), H3K9ac ChIP-seq and RNA-seq at six time points across a 24-h circadian cycle in rice. While global higher-order structure was largely invariant, with 84.5% of A/B compartments and over 95% of topologically associating domains (TADs) conserved across all time points, we identified 557 dynamic compartment transitions coupled to changes in active chromatin marks. Within this stable structural scaffold, 35.8% of TADs containing clustered loci of multiple rhythmic genes with synchronized expression phases. In contrast, fine-scale intradomain contacts and chromatin loops exhibited pronounced temporal plasticity. Chromatin interactions connected rhythmic genes with diverse expression phases. Myb-binding motifs were enriched at chromatin interaction anchors at dawn and early day (ZT0 and ZT4). Together, our findings demonstrate that localized chromatin rewiring occurs within relatively stable architectural frameworks, providing a spatiotemporal context for circadian gene regulation in rice.

genomics↗

bioRxiv2026

Dysregulation of miR-103a-3p/AGFG1 axis links endocytic trafficking dysfunction to ER stress in Parkinson's disease

Background: Parkinson's disease is defined by progressive dopaminergic neurodegeneration and -synuclein pathology. Endoplasmic reticulum (ER) stress and clathrin-mediated endocytosis dysfunction are implicated in disease pathogenesis, but the molecular mechanisms connecting these processes remain poorly understood. Here, we investigate a miR-103a-3p/AGFG1 axis as a regulator link between endocytic trafficking and ER stress in Parkinson's disease. Methods: MiR-103a-3p and AGFG1 were examined in plasma and postmortem substantia nigra from patients with Parkinson's disease and controls. Gain- and loss-of-function studies, target validation and live-cell imaging were used to define the role of the miR-103a-3p/AGFG1 axis in ER stress and endocytic trafficking. The pathway was further investigated in SNCA A53T and LRRK2 G2019S hiPSC-derived neurons. Therapeutic targeting of AGFG1 was evaluated using antisense oligonucleotides (ASOs) in vitro and in a 6-hydroxydopamine mouse model. Results: MiR-103a-3p was significantly reduced in Parkinson's disease plasma and substantia nigra, whereas AGFG1 was increased in nigral tissue. MiR-103a-3p directly repressed AGFG1 and attenuated thapsigargin-induced ER stress, while miR-103a-3p inhibition or AGFG1 overexpression exacerbated stress signalling. AGFG1 knockdown reversed the effects of miR-103a-3p inhibition, establishing AGFG1 as a functional downstream effector. Mechanistically, AGFG1 associated and co-trafficked with clathrin-positive vesicles, whereas ER stress progressively disrupted AGFG1-clathrin vesicle dynamics, revealing an association between endocytic trafficking and stress signalling. In genetic Parkinson's disease models, SNCA A53T and LRRK2 G2019S neurons showed mutation-dependent differences in AGFG1 expression and stress regulation. eIF2 phosphorylation increased in both SNCA A53T and LRRK2 G2019S neurons, whereas AGFG1 and GADD34 upregulation was selective to SNCA A53T neurons. Importantly, ASO-mediated AGFG1 suppression attenuated ER stress in vitro and preserved nigral dopaminergic neurons with improved motor performance in vivo. Conclusion: Our findings identify the miR-103a-3p/AGFG1 axis as a previously unrecognised molecular link between endocytic trafficking dysfunction and ER stress in Parkinson's disease, and support AGFG1 as a mechanistically potential therapeutic target.

neuroscience↗

bioRxiv2026

Structural Basis for Activation of HRI by the DELE1 C-terminal domain

Haem-Regulated Inhibitor (HRI, aka EIF2AK1) is one of four stress-sensing kinases that phosphorylate eIF2 as part of the integrated stress response (ISR). HRI was first characterized as a haem-sensing kinase where it is inhibited when bound to haem. Recent studies have revealed another role for HRI in sensing mitochondrial stress via the mitochondrial protein DELE1. Upon stress, DELE1 is cleaved, and its C-terminal fragment (DELE1CTD) is released from the mitochondria to the cytoplasm, where it interacts with HRI, to trigger the ISR. This pathway is critical for mitochondrial quality control and neuronal health. Here, we perform biophysical analysis to demonstrate that purified recombinant DELE1CTD binds with high affinity to the N-terminal region of HRI, competing with and displacing haem to activate HRI and pointing to a shared binding site. Using Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS), we map the binding footprint of DELE1CTD on HRI and confirm that it overlaps with the haem-binding site. These findings support a simple activation mechanism: DELE1CTD activates HRI by excluding inhibitory haem from its binding site.

biochemistry↗

bioRxiv2026

An inflammation-associated five-gene expression signature stratifies survival and immune states in lung adenocarcinoma: an integrative public-cohort analysis

Background: Inflammation and the tumor immune microenvironment contribute to lung adenocarcinoma (LUAD) progression, but the relationship among inflammation-linked transcriptional heterogeneity, patient survival, and immune-state variation remains incompletely defined. Objective: We aimed to identify inflammation-associated LUAD subtypes, derive a parsimonious survival-stratification signature, and characterize its immune and pathway context across public transcriptomic cohorts. Methods: Expression profiles and clinical data were obtained from TCGA-LUAD, GTEx normal lung, and GEO datasets GSE11969, GSE30219, GSE31210, and GSE40791. A curated set of 596 inflammation-related genes was used for consensus clustering. Differential-expression analysis, functional enrichment, univariate Cox regression, and LASSO-Cox modeling were integrated to construct a gene-expression risk score. The prognostic dataset comprised 730 cases and was randomly divided into training (n=502) and internal-validation (n=228) sets; 85 GSE30219 cases formed an external-validation cohort. Immune-cell enrichment, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and pan-cancer analyses were used for biological contextualization. Results: The LUAD-versus-control comparison identified 1,305 differentially expressed genes, including 498 upregulated and 807 downregulated genes. Consensus clustering resolved two inflammation-associated subtypes and 67 subtype-associated genes, of which 64 were higher and 3 were lower in Cluster 1 relative to Cluster 2. Thirty-three genes overlapped between the tumor-control and subtype contrasts. LASSO-Cox regression selected CHRDL1, FDCSP, CXCL13, CYP4B1, and S100P. The 1-, 3-, and 5-year areas under the time-dependent receiver operating characteristic curve were 0.6625, 0.6581, and 0.6658 in the training set; 0.7422, 0.6537, and 0.6761 in internal validation; and 0.6560, 0.6387, and 0.6753 in external validation. Risk groups differed across multiple T-cell, B-cell, natural-killer-cell, myeloid, dendritic-cell, macrophage, and granulocyte signatures. Positive GSEA signals included cell cycle (normalized enrichment score [NES]=2.67; adjusted P=1.42 x 10-), DNA replication (NES=2.52; adjusted P=2.52 x 10-), and mismatch repair (NES=2.20; adjusted P=1.77 x 10-). Conclusions: The five-gene expression score separated LUAD survival groups and captured coordinated proliferative and immune transcriptional states. Its moderate discrimination supports further biological and clinical validation rather than immediate clinical application.

bioinformatics↗

bioRxiv2026

Leukocyte Immunoglobulin-Like Receptor B1 and its Interactions with Human Leukocyte Antigens

Interactions between Human Leukocyte Antigen (HLA) molecules and their cognate immunoreceptors are essential for regulating innate and adaptive immune cell functions. Leukocyte Immunoglobulin-like Receptors (LILRs) are key regulators of HLA-mediated immune responses, owing to their broad expression across immune cell populations and their ability to modulate both immune activation and tolerance. Among these, LILRB1-HLA interactions are increasingly recognised as important in transplantation, chronic infection and cancer therapies. Unlike other HLA-binding receptors, which recognise epitopes specific to HLA subsets, LILRB1 primarily engages the relatively conserved 3 and {beta}2-microglobulin components of HLA molecules, supporting its role as a broad regulator of pan-HLA class I-mediated functions. Nonetheless, there have been conflicting findings regarding the breadth of LILRB1-HLA-I interactions. While direct affinity studies on a limited subset of HLA-I molecules have revealed no significant differences in LILRB1 binding, broader analyses using single-antigen bead arrays suggest underlying variability. Here, we show through a broad binding assay that, while LILRB1 is a broad HLA-I-binding receptor, it exhibits differential preferences across HLA-I allotypes. Molecular dynamics analyses of the HLA-I-LILRB1 interface suggest that HLA-3 domain dynamism underlies these binding differences. We further determined the crystal structure of LILRB1 and used it to highlight intrinsic structural flexibility within its domains. Finally, these structural insights were leveraged to refine our understanding of the binding modalities of therapeutic monoclonal antibodies currently described. Together, our findings establish structural and mechanistic bases for differential HLA-I recognition by LILRB1 and provide insights into immunotherapeutic targeting of LILRB1.

immunology↗

bioRxiv2026

Fine tuning energy metabolism in skeletal muscle: Discovery of a novel autoinhibitory mechanism in the N-terminal extension of AMPKγ3

AMP-activated protein kinase (AMPK) regulates metabolism in response to metabolic stress that includes stimulating glucose uptake in skeletal muscle independently of the canonical insulin signalling pathway, positioning it as an attractive therapeutic target for insulin resistance and type 2 diabetes mellitus (T2DM). AMPK is an {beta}{gamma} heterotrimer, with multiple isoforms for each subunit enabling the formation of 12 different complexes with distinct tissue expression profiles. Among these, the 2{beta}2{gamma}3 complex is predominantly expressed in skeletal muscle, the major site of glucose disposal and a highly desirable therapeutic target for T2DM. Here, we characterise the functional role of a unique, 182 residue N-terminal extension (NTE) within {gamma}3 subunit. Deletion of the {gamma}3-NTE from 2{beta}2{gamma}3 complex increases basal AMPK activity without affecting activation by AMP or pharmacological AMPK activators, demonstrating the {gamma}3-NTE performs an autoinhibitory function. Using complementary biophysical techniques, including hydrogen-deuterium exchange-mass spectrometry, surface plasmon resonance, chemical crosslinking and co-pulldowns, we identified a 39-residue sequence in the {gamma}3-NTE (residues 129-168), that directly interacts with the C-helix of the AMPK kinase domain small lobe, a key regulatory element in many protein kinases. Using AlphaFold3, we probe the interaction predicted to take place between a {gamma}3-NTE -helix ({gamma}3-iHelix; [~]T142-E154) and the C-helix in the 2{beta}2{gamma}3 complex. These findings provide the groundwork for developing novel T2DM therapies that target AMPK activation selectively in skeletal muscle involving reversal of the {gamma}3 autoinhibition.

biochemistry↗

bioRxiv2026

Dystrophic changes of nigrostriatal axons harboring a Synj1 Parkinson mutation suggest catastrophic failure of endocytic mechanisms

Synaptojanin 1 is a brain enriched phosphoinositide phosphatase implicated in endocytosis at the synapse. A mutation (R258Q) that selectively impairs its Sac1 phosphatase domain causes early onset familial Parkinsonism. Neurons of mice with this mutation display synaptic vesicle traffic defects across the brain, but selective dystrophic changes in a subset of dopaminergic axons in the dorsolateral striatum. Using correlative light microscopy-FIB-SEM of mutant mouse striata to visualize in 3D these abnormal structures we show that they represent clusters of focal axonal dilations harboring massive, onion-like DAT enriched plasma membrane infoldings, generally localized next to cell bodies of neighboring cells, often engulfing evaginations of such cells. This dysmorphia was associated with a deficit in dopamine release in the same striatal region. Given the involvement of Synj1 in endocytic mechanisms, these structures may reflect an imbalance between exocytosis and endocytosis. Their occurrence only in a subset of axons suggest a vulnerability threshold of these axons beyond which the expansion of the plasma membrane is not counteracted by compensatory mechanisms.

neuroscience↗

bioRxiv2026

“Mapping of Gonadal Development in Cryptorchidism: UTF-1 and Germ Cell Dysgenesis”

Study questionHow does cryptorchidism affect germ cell development and UTF-1-mediated pluripotency potential at the time of orchiopexy? Summary answerCryptorchidism was associated with the following germ cell abnormalities: germ cell clustering with many cords/tubules lacking germ cells and reduced UTF-1 expression, suggesting limited germ cell differentiation into spermatogonia What is known alreadyCryptorchidism, affecting 1.6-9% of male newborns, is known to increase the risk of infertility and testicular cancer due to abnormal germ cell development. Germ cells and pluripotent stem cell gene, UTF-1, play critical roles in spermatogonia differentiation, self-renewal, and spermatogenesis. No prior study has evaluated the testicular development by immunohistochemically mapping of these cell populations, Study design, size, durationA cross-sectional study of 31 postnatal cryptorchid testis and 5 age-matched scrotal testicular biopsies obtained from UCSFs pathology department performed between 1993-2023. Participants/materials, setting, methodsSpecimens were grouped by age at surgery (6-18 months, 19 months-7 years, 8-12 years, and [≥]13 years) and testis location (palpable vs. non-palpable). Scrotal prepubertal testis biopsies were sourced through the Pedi-LIFE program, a fertility preservation research biobank, with at least one control per age group. Immunohistochemistry was performed to stain specimens for germ cell (DDX4, OCT4, TSPY), pluripotent cell marker (UTF-1), as well as other key testis cell markers (A-actin, AR, P450, Sox-9), with staining graded based on control expression levels. The number of germ cells per seminiferous tubule was quantified and compared across anatomical locations using appropriate statistical analyses. Main results and the role of chanceThis study included 36 specimens, comprising 31 cryptorchid testes (86%) and 5 scrotal control testes (16%). The cryptorchid group exhibited testicular dysgenesis and reduced germ cell expression, correlated with increased age and testis location. Qualitative assessment revealed reduced germ cell expression across all ages in cryptorchid testes. The number of germ cells per tubule was markedly reduced in cryptorchid compared with scrotal testes after 19 months of age for DDX4, TSPY, and UTF-1. Germ cell clusters were identified in 15 out of 31 cryptorchid specimens (48%) stained for DDX4 and TSPY. UTF-1 expression was lower in cryptorchid testes across all age groups. No significant differences were noted in other testicular cell markers. Large scale dataNA Limitations, reasons for cautionFirst, the power and generalizability of the study are limited by the availability of specimens within each age group, particularly for scrotal testes, as biopsies of these tissues are not routinely performed. Second, a cross-sectional study design limits a longitudinal comparison to evaluate changes in marker expression, delayed maturation, or irreversible germ cell loss. Third, immunohistochemistry data is semi-quantitative, and protein detection is affected by antibody sensitivity and tissue preservation and influenced by antibody sensitivity. Lastly, scrotal testis used as controls were obtained from cryopreserved tissue from patients with other unrelated pathology, which may influence histological profiles. Wider implications of the findingsCollectively, our findings support a model in which cryptorchidism involves both germ cell depletion and disrupted SSC lineage formation, with UTF-1 downregulation and germ cell clustering as early signatures of testicular dysgenesis. These features may help identify high-risk patients for worsening gonadal dysgenesis and infertility and can provide a rationale for earlier orchiopexy or SSC-preserving strategies. Study funding/competing interest(s)The authors declare no conflicts of interest and received no funding for this study. Data Availability StatementThe data underlying this article cannot be shared publicly due to ethical and legal restrictions related to the use of human tissue specimens, which may compromise donor privacy and confidentiality. Data are available from the corresponding author upon reasonable request and subject to institutional and ethical approvals.

Developmental Biology↗

bioRxiv2026

Structural basis of substrate recognition and allosteric inhibition in human B0AT2

The SLC6 family is a major target for neuropsychiatric therapeutics. Human B0AT2 (SLC6A15) regulates amino acid homeostasis and glutamatergic transmission and is linked to major depressive disorder, yet its transport and inhibition mechanisms remain unclear. Here we report cryo-EM structures of B0AT2 in apo state and in complex with substrates (proline, leucine, methionine) and inhibitors (loratadine, tiagabine), capturing outward-open, early substrate-bound intermediate, outward-occluded, and inward-open conformations along the transport cycle. These structures reveal an early substrate-sensing mechanism at the substrate-binding pocket (S1), where a substrate-dependent rotameric switch of Phe308 remodels pocket geometry to tune substrate accommodation and selectivity. Loratadine stabilizes an outward-occluded state via allosteric inhibition at the extracellular S2 pocket, whereas tiagabine stabilizes the inward-open state through cooperative multi-site inhibition involving S1 and two previously unrecognized intracellular cavities (S3 and S4). Together with functional assays, these data define the molecular basis of B0AT2 substrate selectivity and state-dependent inhibition. Notably, the two intracellular cavities are conserved across SLC6 transporters, reflecting a shared intracellular vestibular architecture and enabling rational design of conformation-selective modulators for neuropsychiatric disorders.

biophysics↗

bioRxiv2026

A highly versatile real-time quantitative RT-PCR method and sampling strategies for the accurate detection of citrus yellow vein clearing virus

Citrus yellow vein clearing virus (CYVCV) is the causal agent of an emerging disease representing a potentially high-impact threat for citrus production. Despite remaining outside Europe for decades, CYVCV has now expanded towards two important European citrus producers, Italy and, more recently, Spain. The presence of this virus in the EPPO region represents a current threat with unpredictable and potentially devastating consequences for European citriculture. Therefore, urgent protective measures need to be taken to prevent CYVCV spread and minimize its impact. Diagnostics is a key measure in the management of viral diseases, highlighting the need for harmonized methods suitable for reliable routine detection of the currently known CYVCV diversity. In this study, an inclusive, efficient and highly sensitive real-time RT-qPCR for the detection of CYVCV in plant material and transmission vectors has been developed and validated according to EPPO standards. Moreover, the validated method has been successfully adapted to both PCR digital platforms, that allow high-sensitive absolute quantitative detection, essential in the diagnostics at low viral concentrations; and PCR portable tools, that can be applied in a real diagnostic context for on-site detection. This versatility combines standard validated performance, absolute sensitive quantitation and real on-site detection. The study has also addressed sampling strategies to support reliable molecular diagnostic performance. Our results represent an improvement in the detection of CYVCV to be applied in epidemiological studies and different real diagnostic contexts for the containment of this important citrus pathogen.

molecular biology↗

bioRxiv2026

Molecular Logic of DNMT3A1 Recruitment: Resolving Multivalency at the Chromatin Interface

Histone modifications correlate with DNA methylation, but the underlying mechanisms remain unclear. The DNA methyltransferase DNMT3A1 engages nucleosomes through multivalent interactions with linker DNA, histone H3 tails, the acidic patch, and ubiquitinated H2A. Using binding assays, kinetic analyses, and nanopore sequencing of engineered nucleosomes, we show that DNMT3A1 binding reflects avidity, limiting the impact of individual contacts. Accordingly, disrupting single interactions minimally affects overall affinity, whereas isolated domains and truncations remain modification-sensitive. Although histone modifications have little effect on kcat/Km for linker methylation, disrupting ADD-H3K4me0 interactions redistributes methylation away from the nucleosome core particle. Nucleosome competition assays reveal that H3K4me0 and H3K36me2 promote selective linker methylation, whereas H3K27me3 and PRC2/EZH2 have no effect. Notably, despite strong UDR-dependent binding to H2AK119ub1-modified nucleosomes, this mark fails to enhance methylation over an unmodified competitor. We propose a model of commitment to catalysis to reconcile weak kinetic differences with strong substrate selectivity. These findings highlight avidity and commitment in governing DNMT3A1 nucleosome recognition and DNA methylation specificity.

molecular biology↗

bioRxiv2026

Environmental factors that impact the development of infective juveniles of entomopathogenic nematode Steinernema hermaphroditum

Animals sense and integrate complex external cues to make developmental decisions that help them better survive and adapt to their natural habitats. Under environmental adversity, nematodes can enter an alternative developmental pathway to form a diapautic and stress-resistant stage, termed the dauer larvae. While dauer formation has been well characterized in Caenorhabditis elegans, how environmental factors influence the development of analogous stages in parasitic nematode species remains largely unexplored. This study examines how symbiotic bacteria, temperature, and pheromones affect the formation of the infective juvenile (IJ), a dauer-like and infective stage, in the insect-parasitic nematode Steinernema hermaphroditum. In contrast to C. elegans, where dauer entry requires exogeneous pheromone and is promoted by heat, IJ development in S. hermaphroditum does not rely on exogeneous pheromone and is enhanced by reduced temperature. Moreover, the presence and absence of live symbiotic bacterium Xenorhabdus griffiniae functions as an ON-and-OFF switch that regulates IJ formation. Nutrient-rich liver-kidney media that mimics host insect environment showed IJ entry induction in a DAF-22 dependent manner, suggesting that short-chain ascarosides (pheromone) promote S. hermaphroditum IJ formation through a conserved pathways across nematode species. Together, these findings reveal that environmental cues, such as temperature, microbial diet, and pheromone, can be perceived differently or similarly by S. hermaphroditum compared with C. elegans, reflecting species-specific adaptations to distinct ecological niches and life history strategies. Summary StatementParasitic nematodes rely on infective stages for host invasion, yet their developmental triggers remain largely unexplored. This study reveals how environmental cues regulate IJ formation.

developmental biology↗

bioRxiv2026

A modular bacterial platform for tunable double-stranded RNA delivery and RNA interference in nematode Caenorhabditis elegans

RNA interference (RNAi), one of the major molecular tools in model nematode Ceanorhabditis elegans, relies on feeding engineered bacteria that express double-stranded RNA (dsRNA), which modulates animal host gene expression in a programmable manner. Currently no synthetic biology toolkit exits in C. elegans RNAi, while dsRNA circuits construction is restricted to one type of architecture. To facilitate systematic strategies for dsRNA circuit design and expression, here, we performed strain-specific screen of synthetic promoters, based on which we developed seventeen modular genetic parts compatible for rapid assembly of dsRNA expression constructs in Escherichia coli HT115(DE3). We validated dsRNA production in vitro and assessed RNAi efficiency in live animals by feeding. As a proof of concept, a constitutive dsRNA circuit achieved rapid and near-complete gene knockdown, whereas a Ptac-driven circuit enabled tunable, partial silencing while minimizing the leakiness commonly observed in standard feeding RNAi systems. Together, this work establishes a synthetic biology toolkit for programmable dsRNA delivery, enabling precise control of RNAi outcomes from partial to complete gene silencing in C. elegans.

bioengineering↗

bioRxiv2026

Statins and genetic inhibition of the mevalonate pathway activate an ATF3-STMN2 regenerative program

Loss of neuronal regenerative capacity is a common feature of neurodegenerative disease and axonal injury, yet the transcriptional programs governing this state remain poorly defined. Stathmin-2 (STMN2), a tubulin-binding protein essential for axon maintenance and repair, is profoundly depleted following loss of nuclear TDP-43 in neurodegenerative disease. Here, we identify statins as potent inducers of STMN2 expression. Pharmacological and genetic suppression of the mevalonate pathway, and subsequent prevention of protein geranylgeranylation, restored STMN2 levels in TDP-43 deficient cells and promoted neurite growth. STMN2 induction was abrogated when using a statin analogue unable to interact with HMG-CoA reductase, and through co-administration of mevalonate or geranylgeranyl diphosphate substrates. RNA-seq revealed that statins induce a coordinated pro-regenerative transcriptional response, including activation of the AP-1 transcription factor complex gene, ATF3. Loss of ATF3 attenuated STMN2 induction in vitro, and diminished injury-induced Stmn2 upregulation in spinal motor neurons in vivo. These results demonstrate statins as modulators of ATF3 and STMN2 expression and highlight their therapeutic potential in neurodegenerative disease.

neuroscience↗

bioRxiv2026

G3DCT: An Interpretable Spatial Grid-based Framework with Temporal Convolution-Transformer for EEG Artifact Identification

Electroencephalography (EEG) serves as a fundamental tool in modern neurology, cognitive neuroscience, and brain-computer interfaces, but its practical application is often compromised by artifacts. Physiological artifacts are particularly intractable due to overlapping spectral features with neural signals, hindering reliable EEG interpretation. In this work, we propose Grid-based 3D Convolution-Transformer (G3DCT), an interpretable deep learning framework for EEG artifact identification. The framework embeds multi-channel EEG signals into fixed grids to leverage electrode spatial topology, employs parallel multi-branch temporal convolutions and Transformers to handle complex artifacts, and incorporates an attention module to visualize scalp activation patterns, which enhances physiological interpretability. Our evaluation on three datasets demonstrates that G3DCT outperforms existing state-of-the-art models. For challenging combined artifacts, it secures a gain of 2.8% in F1-score over the second-best model. These results demonstrate that G3DCT provides an efficient and robust solution for EEG artifact identification, which has the potential to enhance the reliability of EEG-based applications in practice.

neuroscience↗

bioRxiv2026

Stimulated human cortical waves: spatiotemporal dynamics across development

Traveling waves of neural activity are fundamental to cortical function, yet their spatiotemporal dynamics and structural constraints remain less understood in human brain. Conventional analyses focus on network topology and spatial geometry of neural signals, with limited emphasis on wave dynamics at high spatiotemporal resolutions. Here, we applied a manifold-based optical flow algorithm to an open-access intracranial electroencephalography (iEEG) dataset from the single-pulse stimulation cortico-cortical evoked potentials (CCEPs) paradigm, enabling direct construction of high-temporal-resolution cortical neural activity velocity fields. Spatiotemporal mode decomposition revealed a hierarchical organization: large-scale plane waves (mediating global propagation) dominate, complemented by local patterns for local computation. Dominant plane wave directions correlate with underlying white matter fibre tract orientations, indicating anatomical guidance of cortical dynamics. Velocity field singularities (sources, sinks, spirals and saddles) are non-randomly distributed, associating with default mode network (DMN) hubs. We further identified a nonlinear relationship between cortical wave speed and age, with developmental phases paralleling white matter maturation and aging. Our findings link cortical wave dynamics to anatomy, functional networks, and neurodevelopment, establishing wave speed as a potential yet important biomarker for brain function and health.

neuroscience↗

bioRxiv2025

Evolutionarily Conserved T-tubule-Mitochondria Contacts in Striated Muscle

The intricate architecture of skeletal muscle is essential for its contractile function, with the spatial organization of organelles such as T-tubules and mitochondria playing a crucial role in maintaining muscle performance and health1,2. T-tubules propagate electrical signals deep into muscle fibers to ensure synchronous contraction, while mitochondria provide the necessary energy for muscle contraction3-5. Previous studies have extensively documented the interactions between T-tubules and the sarcoplasmic reticulum (SR), which are essential for excitation-contraction coupling6,7. However, the detailed spatial relationship between T-tubules and mitochondria has remained relatively unexplored. In this study, we utilized zebrafish and mice as model organisms to investigate the contacts between T-tubules and mitochondria. Using array tomography, deep learning-based analysis, and advanced microscopy techniques, we discovered extensive membrane contact sites, termed T-tubule-Mitochondria (TTM) contacts. These contacts are evolutionarily conserved across vertebrates, including skeletal and cardiac muscles. Our findings reveal a previously unrecognized, intimate spatial coupling between T-tubules and mitochondria, with significant implications for muscle physiology and pathology. Understanding these TTM contacts could provide new insights into the mechanisms underlying muscle function and the development of muscle-related diseases.

cell biology↗

bioRxiv2025

An EEG-based Multi-Scale Hybrid Attention and Squeeze Network for objective taste assessment

Taste perception is central to flavor experiences. Electroencephalography (EEG) signals carry rich information about taste perception. Because these neural data are independent of verbal reports and bypassing conscious filtering, EEG holds promise as a neural-sensing platform for objective taste representation. However, taste-evoked EEG signals exhibit complex spatiotemporal and spectral dynamics that require advanced computational approaches to decode effectively. This study developed an EEG-based Multi-Scale Hybrid Attention and Squeeze Network (MHASNet) for taste evaluation. EEG signals evoked by distinct taste stimuli were recorded, a dedicated taste-EEG dataset was compiled, and a novel deep learning architecture, MHASNet, was designed to classify these signals. MHASNet synergistically integrates multi-scale convolutions to capture temporal dynamics across different time scales, dual-attention mechanisms to localize discriminative brain regions and electrode positions, and a squeeze-and-excitation module to optimize frequency-band contributions-collectively enabling precise extraction of taste-specific neural signatures. Results showed that the proposed model achieved superior performance across five taste categories (sweet, sour, salty, bitter, and tasteless), with 94.33% accuracy, 91.37% F1-score, 91.89% precision, and 92.07% recall. These results surpass benchmark models while maintaining millisecond-level inference latency suitable for real-time applications. By complementing subjective evaluations and instrumental analyses, the model offers an objective, neurophysiology-based solution for taste evaluation.

neuroscience↗