Biology subjects

Ding, Y.

Publications and source records attributed to Ding, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Discovery of the rosalexin pathway expands the modular network of maize diterpenoid chemical defenses.

The evolutionary expansion of specialized metabolism has shaped the ability of plants to adapt to combined pathogen, pest, and other environmental pressures. For instance, the duplication and divergence of ancestral gibberellin pathway genes have given rise to specialized kauralexin and dolabralexin diterpenoids in maize (Zea mays) that serve as core components of disease resistance and stress adaptation. Here, we describe the biosynthesis and elicited production of rosalexins as a previously unrecognized component of the maize chemical defense network. By integrating genomics-enabled gene discovery, combinatorial enzyme assays, and AI-assisted enzyme mechanistic studies we show that maize rosalexin biosynthesis proceeds via a distinct 5-rosanol scaffold formed by the pairwise activity of two diterpene synthases, ZmTPS38/CPS2/AN2 and ZmTPS42/KSL1, recruited from gibberellin metabolism. Further oxygenation by the promiscuous P450 enzyme, ZmCYP71Z18, yields epoxyrosanol that, in turn, can undergo epoxide ring opening to form trihydroxyrosanol. Epoxyrosanol, but not 5-rosanol or trihydroxyrosanol, display strong inhibitory activity on fungal pathogen growth in vitro, highlighting the contribution of the epoxide group to antibiotic efficacy. Large variation in rosalexin presence and abundance exists across maize genotypes due to expansive ZmTPS42/KSL1 gene sequence variation and pseudogenization. Transcriptomics and targeted metabolomics demonstrated the pathogen-elicited accumulation of rosalexins in maize lines featuring functional ZmTPS42/KSL1 genes. However, no dominant pathogen resistance phenotype was observed in association with rosalexin abundance. These collective findings expand our knowledge of how multiple interconnected diterpenoid pathways arose in maize via duplication of hormone-metabolic genes and enable the utilization of a common precursor to form modular chemical defense layers. Significance StatementPlant diterpenoids play critical roles in crop development, stress defense and ecological adaptation. In maize, diterpenoids serve as key components of chemical defenses against pests and diseases with direct impact on crop immunity and vigor. Enzymes of the diterpene synthase and cytochrome P450 families largely drive diterpenoid chemical diversity. This study reports the discovery and characterization of the pathway forming rosalexin diterpenoids in maize. Pathogen-elicited accumulation and in vitro antifungal activity of rosalexin metabolites supports a physiological function in maize chemical defense.

plant biology↗

bioRxiv2026

CNS diseases cerebrospinal fluid single-cell atlas reveals immune characteristics of neuropsychiatric systemic lupus erythematosus

Neuropsychiatric systemic lupus erythematosus (NPSLE) is a potentially severe complication of systemic lupus erythematosus (SLE), yet its pathogenesis remains largely elusive. By jointly probing the immune dynamics of subjects cerebrospinal fluid (CSF) and peripheral blood, we showed that both innate and adaptive immune responses jointly contribute to the pathogenesis of NPSLE. In particular, we found the remarkable enrichment of BAM-CCL3, a subtype of border-associated macrophages with strong recruitment capacity, implicating its potential role in central nervous system (CNS) inflammation. We also observed pronounced activation of memory B cells and CD4+ regulatory T cells in NPSLE CSF, along with the preferential blood-to-CSF migration and subsequent within-CSF clonal expansion of CD8+ effector memory T cells in NPSLE patients, suggesting a persistent CNS-localized adaptive immune dysregulation. Finally, we developed the single-cell CNS disease CSF-Blood Atlas (scCDCB), a comprehensive collection for CSF and peripheral blood of multiple CNS diseases, which is publicly available at (https://sccdcb.gao-lab.org) to serve as a reference for future research on CNS diseases.

genomics↗

bioRxiv2026

Decoding of arousal and valence from fMRI data obtained during emotion inductions

Arousal and valence are fundamental dimensions of affective experience signifying levels of activation and pleasantness, respectively. These dimensions play a crucial role in shaping emotional responses and behaviors, with significant implications for psychopathology. Previous machine learning studies had some success decoding these states from brain activation patterns observed during task-based functional magnetic resonance imaging (fMRI), but the results have varied across studies. Moreover, prior studies have often been limited by small sample sizes, weak decoding performance, and non-whole-brain analyses, leaving the neural representations of arousal and valence largely unresolved. Here we successfully decoded arousal and valence from whole-brain task-fMRI data collected from 132 participants during exposure to 300 unique emotional stimuli, including 150 movie clips and 150 text scenarios that reliably induced a wide range of arousal and valence states. Mass univariate general linear models identified block-level activation (emotion stimuli > washout) from all gray matter voxels. Multivariate regression analysis predicted arousal and valence ratings based on these gray matter activations. Patterns in the fMRI data underlying arousal and valence were robust, as they were successfully decoded across both induction modalities using five different linear multivariate regression models. Although significant, decoding from scenarios was less successful than from movies, likely due to their more imaginative nature. In particular, decoding arousal from scenarios only showed low predictive utility. Representations of arousal and valence were widespread throughout the brain, and we reveal cerebellar and brainstem contributions that have largely been absent in past fMRI decoding studies. These findings clarify the distributed neural basis of arousal and valence and provide a foundation for future clinical research on the role of these constructs in affective dysregulation.

neuroscience↗

bioRxiv2026

EEG Foundation Model Improves Online Directional Motor Imagery Brain-computer Interface Control

Brain-Computer interfaces (BCIs) offer a link between neural signals and external computation, enabling control of devices for the purposes of restoring function to motor-affected individuals and enhancing capabilities of a wider set of populations. Electroencephalography (EEG) offers a high temporal resolution for dynamic and potential real-time feedback for non-invasive systems. However, its practical efficacy remains limited due to low spatial resolution and poor signal-to-noise ratio, leading to insufficient decoding accuracy and unintuitive control paradigms that hinder reliable user interaction. In this study, we present a framework for an online EEG foundation model by creating a custom foundation model through spectrogram reconstruction of compact temporal windows and online constraints during pretraining. We evaluate the performance of the model in a challenging control paradigm of single-arm, directional motor imagery with dynamic movements for guided and free movement cursor control tasks. Our foundation model approach achieved a final average accuracy of 51.3% during a goal-oriented guided control task. This represents a 15.8% increase over a conventional deep learning framework and a 26.3% increase above chance level, evaluated in a cohort of 11 human participants. During the free movement task, the foundation model invoked a higher rate of completion and lower completion times. Furthermore, the custom EEG foundation model demonstrated superior adaptability from same-session finetuning and indicated an enhanced capability to assist subject learning. These findings highlight the potential of EEG foundation models to support more robust and intuitive non-invasive BCI systems, providing a promising modelling framework for future BCI development.

bioengineering↗

bioRxiv2026

Blautia wexlerae Transforms Dietary Fatty Acids to Activate Enteroendocrine Signaling and Improve Metabolic Health in Mice and Humans

Metabolites produced by the gut microbiome influence host metabolic health, but how this occurs remains incompletely defined. Here, we report that a common human gut commensal, Blautia wexlerae, converts dietary fats into bioactive metabolites that induce gut hormone production to affect glucose metabolism and suppress appetite. We found that colonization with Blautia wexlerae correlated with healthier eating behaviors in humans. Blautia wexlerae encodes a unique acyl transferase and is capable of producing acyl amines from nutrient substrates. These Blautia acyl amines stimulated human enteroendocrine cells to secrete GLP-1 and other gut peptide hormones more potently than endogenously produced acyl amines. When fed to mice, acyl amines improved glycemic control and decreased appetite. In humans, higher stool levels of Blautia DNA encoding acyl amine synthesis genes correlated with leanness and decreased dietary fat intake. These results define a mechanism of action for how Blautia wexlerae affects host metabolic control.

microbiology↗

bioRxiv2026

Organization and evolution of sex-biased gene expression in Drosophila adult sexual circuits

Sexually dimorphic behaviors are widespread across animals. A key open question is how the underlying sexual circuits, which encode these behaviors, evolve to meet sex-specific fitness needs despite being built from largely shared developmental blueprints. Here, we use single-cell transcriptomics, leveraging the sex determination gene fruitless (fru) as a molecular handle, to examine the transcriptomic landscape and evolution of adult Drosophila sexual circuits at cellular resolution. We find that sex-biased gene expression is limited, highly cell-type-specific, and largely species-specific. Species divergence in gene expression is widespread and predominantly coupled between sexes, with sex-specific changes constrained by pleiotropic gene expression across cell types. Furthermore, a strong overlap of differentially expressed genes across sexes, species, and fru status points to a common set of genes, particularly neural signaling genes, whose expressions are highly labile across multiple contexts. Finally, transcriptomic divergence between sexes decreases from mid-pupae to adulthood, underscoring the developmentally dynamic nature of sex-biased gene expression. Our results provide fundamental insights into the organization and evolutionary mode of sex-biased gene expression, suggesting that sex-specific adaptation via selective gene programs at localized circuit nodes is a key mechanism that preserves circuit evolvability despite pervasive transcriptomic coupling between sexes.

evolutionary biology↗

bioRxiv2026

Direct effector recognition by a tandem kinase triggers non-canonical immunity in wheat

Tandem kinase proteins (TKPs) are an important class of disease resistance genes in cereal crops alongside nucleotide-binding (NB-ARC) leucine-rich repeat (LRR) (NLR) receptors. Here, we cloned the wheat (Triticum aestivum) resistance gene Lr41, which encodes a TKP with a C-terminal fusion, and its paired effector gene AvrLr41 from the rust pathogen Puccinia triticina. AvrLr41 is unusually large and highly divergent from most fungal effectors and is directly recognized by Lr41 through its pseudokinase domain. Immune activation mediated by Lr41 require auxiliary helper proteins, including either a minimal coiled-coil (CC) helper protein or its full-length NLR ortholog. These findings reveal a non-canonical immune system in which a kinase-type receptor directly recognizes an effector and recruits either CC or NLR helpers, demonstrating that full-length NLRs are not strictly required for NLR-linked immune execution and expanding the functional repertoire of disease resistance proteins in crops.

plant biology↗

bioRxiv2026

Network Modulation Enables 3D-Printed Citrate-Based Polymer Scaffolds with Broadly Tunable Mechanical Performance for Regenerative Engineering

Biomaterials with highly tunable mechanical properties and tissue-mimetic structural features are critical for diverse biomedical applications. Photopolymerizable citrate-based polymers (CBP), such as methacrylate polydiolcitrate (mPDC), enable high-resolution fabrication of biodegradable scaffolds via light-based 3D printing for regenerative engineering. However, mPDC scaffolds typically exhibits substantial brittleness due to the formation of highly crosslinked and heterogeneous polymer network, an intrinsic limitation of many acrylate-based polymers, thereby restricting their use across a broad range of tissue types. Herein, we report facile network-engineering strategies to modulate crosslinking density and network topology of CBPs through the incorporation of acrylate-based reactive diluents and/or a thiol-based chain transfer agent, 3,6-dioxa-1,8-octanedithiol (DOD). These approaches enabled significantly improved and broadly tunable mechanical properties, with Youngs modulus spanning 6.8-134 MPa, ultimate tensile strength ranging from 1.8 MPa to 18 MPa, and strain at break varying from 14% to 61%. Notably, incorporation of isobornyl acrylate (IBOA) alone significantly enhanced toughness, yielding a 3.6-fold increase in Youngs modulus (50 MPa vs. 14 MPa) and a 2.8-fold increase in strain at break (39% vs. 14%). Moreover, combined incorporation of IBOA and DOD remarkably improved ductility, achieving a 4-fold increase in strain at break to 61% while maintaining comparable stiffness. All mPDC composites exhibited tunable biodegradability, good cytocompatibility, and excellent 3D printability. Using these composite inks, 3D-printed meniscus scaffolds supported the human chondrocyte growth and fibrochondrogenic matrix deposition, while 3D-printed vascular stents supported endothelial monolayer formation. Collectively, this study establishes a versatile photopolymerizable citrate-based biomaterial platform with broadly tunable mechanical performance, controllable biodegradability, good cytocompatibility, and high printability, offering strong potential for customized biomedical applications ranging from load-bearing to soft tissue engineering.

bioengineering↗

bioRxiv2026

Forward Programming Identifies Inducers of Blood-Brain Barrier Properties in Human Pluripotent Stem Cell-Derived Endothelial Cells

Brain microvascular endothelial cells (BMECs) forming the blood-brain barrier (BBB) maintain brain homeostasis through specialized properties such as tight junctions, efflux transporters, and low levels of transcytosis. However, mechanisms governing induction of BBB properties during development remain poorly understood. We mined single-cell RNA sequencing datasets to identify transcription factors (TFs) critical for BBB development. Forty-four TFs were overexpressed in human pluripotent stem cell-derived endothelial cells cultured in the presence of the Wnt pathway agonist CHIR99021 to identify TFs capable of directing acquisition of BBB properties via forward programming. Individual TFs, including KLF2, KLF4, FOXF1, FOXF2, ZIC2, ZIC3, NR4A1, NR4A2, FOXC1, and FOXQ1, induced distinct BBB-like gene expression patterns. Combinations of these TFs induced many canonical BBB genes, yielding ECs with reduced endocytosis, increased efflux activity, and improved barrier function. The resultant forward programmed CNS-like ECs (fpCECs) offer promising tools for modeling human BBB development and neurovascular disease and for drug screening.

cell biology↗

bioRxiv2025

Metabolic dysfunction related to specific genetic variant sites of methylmalonic acidemia

Methylmalonic acidemia (MMA) is a genetic metabolic disease, with mut (mut-MMA, caused by MMUT gene variation) and cblC (cblC-MMA, caused by MMACHC gene variation) being the predominant subtypes. MMA patients carrying c.729_730insTT and c.609G>A exhibit severe clinical manifestations and have poorer outcomes. Little information is known on the potential mechanism. The metabotypes of MMA patients carrying c.729_730insTT and c.609G>A were profiled. The potential effect of genetic variation sites on the metabolism were explored. Leveraging the gene variation spectrum and the targeted metabolomics, propionic acid, indolelactic acid, myristoleic acid, tetradecenoic acid, tridecanoic acid, and oxoadipic acid showed strong enrichment in c.729_730insTT carrying mut-MMA patients. Whereas mutation c.609G>A caused adipic acid, pimelic acid, fructose, AMP, hexanylcarnitine, and methionine significnatly altered in cblC-MMA patients. Furthermore, the metabolomic profiles were obviously different in c.729_730insTT and non-c.729_730insTT carrying mut-MMA patients after treatment. Different metabolic alterations in cblC-MMA patients carrying c.609G > A and non-c.609G > A under treatment were also observed. Our findings provide unique insights into the metabolic basis of MMA specific subtypes and its implications across different variants.

molecular biology↗

bioRxiv2025

Computer-assisted dissection of the DNA mismatch recognition mechanism of the MutS protein

By sensing local conformational strains in DNA, TaqMutS utilizes a push-pull mechanism via the synergy of residues S57 and D472 to modulate {pi}-stacking interactions between the key recognition residue F39 and DNA, thereby achieving specific mismatch-site recognition. Meanwhile, residues K61 and R473 fine-tune non-specific binding of TaqMutS through electrostatic synergy.

synthetic biology↗

bioRxiv2025

Dopamine biosynthesis in plants

Dopamine, an essential human neurotransmitter, also plays important roles in plant-microbe interactions and abiotic stress tolerance. While dopamine biosynthesis is well-characterized in mammals, it remains largely unclear in plants. Through metabolite-based genome-wide association studies, we identified two putative polyphenol oxidase genes for dopamine biosynthesis in Brachypodium distachyon, located in the same chromosomal region as two tyrosine decarboxylase genes. Biochemical and knockout mutant analyses demonstrated that dopamine biosynthesis proceeds primarily via tyramine as an intermediate and contributes to plant tissue browning. Homology searches and functional assays indicate that this dopamine biosynthetic pathway is conserved across diverse plant species. This discovery provides valuable insights into plant dopamine biosynthesis with potential applications in reducing food browning, improving stress resilience, and bioengineering valuable compounds.

plant biology↗

bioRxiv2025

Transcranial focused ultrasound induces source localizable cortical activation in resting state humans when applied concurrently with transcranial electric stimulation

The effects of transcranial focused ultrasound (tFUS) on the human brain are poorly understood. Currently, the field is at odds with whether tFUS is subthreshold modulating the brains excitability towards other stimuli, producing suprathreshold neural stimulation on its own, or if it even has a spatially specific non-auditory induced affect. Herein, we investigated the ability of tFUS, transcranial direct current stimulation (tDCS) and a novel combination of the two (transcranial electro-acoustic stimulation; tEAS) to evoke cortical target-location specific activity in 27 resting state humans with whole brain electroencephalography recordings. In none of the exogenous event related potentials did tFUS or tDCS result in location-specific activations. However, the co-modulatory combination of tEAS did, providing evidence that tFUS has a location-specific subthreshold modulatory effect. We propose a minimally modified Hodgkin Huxley model that explains our results and provides a unifying framework for the field-wide observed effects (or lack thereof) of tFUS.

neuroscience↗

bioRxiv2025

Proteomic Analysis in Alzheimer's Disease with Psychosis Reveals Separate Molecular Signatures for Core AD Proteinopathy and Postsynaptic Density Disruption

Background and Hypothesis: Alzheimers disease with psychosis (AD+P) is a subgroup of AD patients with more rapid cognitive deterioration. While our previous study showed that AD+P is associated with loss of prefrontal cortex postsynaptic density (PSD) proteins, identifying proteins in the broader cellular environment that influence PSD loss addresses a critical knowledge gap about synaptic dysfunction mechanisms in early disease stages. Study Design: We conducted a proteomic analysis comparing prefrontal grey matter cortex tissue homogenates from elderly normal controls (n=18), individuals with AD+P (n=61), and individuals with AD-P (n=48), all with Braak stages 3-5. Study Results: AD+P showed the most pronounced alterations relative to controls (178 proteins with q<0.05), although alterations in AD-P and AD+P relative to controls were highly similar (R{superscript 2}=0.965, p<0.001). Weighted-gene correlation network analysis (WGCNA) identified four modules significantly associated with disease status comparing AD subjects to controls, but none differed significantly between AD+P and AD-P. We identified 15 proteins significantly correlated with PSD yield across all samples, including ENPP6, linked to AD+P by GWAS. Additionally, PSD yield-associated proteins showed minimal overlap with altered AD proteins (1 of 137). WGCNA revealed one module significantly correlated with PSD yield across all samples, enriched for inflammatory terms. Conclusions: Our findings suggest a model in which AD+P arises from the combination of quantitative alterations within a shared AD proteome profile and a superimposed set of protein alterations correlated with PSD yield that are largely independent of the shared AD proteome, conferring distinct mechanisms of synaptic vulnerability and psychosis risk.

neuroscience↗

bioRxiv2025

PlantScience.ai: An LLM-Powered Virtual Scientist for Plant Science

The accelerating growth of plant science literature presents a major challenge for researchers seeking to extract accurate, up-to-date knowledge from an increasingly fragmented and domain-specific corpus. General-purpose large language models (LLMs), while powerful, often misinterpret plant science terminology and lack mechanisms for source traceability. We created PlantScience.ai, a virtual plant biology scientist powered by our automated scientific knowledge graph construction pipeline (AutoSKG). PlantScience.ai exhibits expert-level reasoning in plant biology and maintains scholarly rigour in its citations. Through continuous learning, it integrates the latest research, ensuring that its knowledge base remains current and scientifically robust. Apart from providing the answers to the scientific questions, PlantScience.ai can interact with human scientists, follow instructions, and retrieve information with citation awareness, grounding each response in primary sources to ensure accuracy and verifiability. PlantScience.ai marks a pivotal advance toward a collaborative scientific paradigm in which virtual and human plant scientists work synergistically to accelerate discovery while preserving the unique value of human insight. PlantScience.ai is available at https://plantscience.ai.

plant biology↗

bioRxiv2025

Decoding the Glycan Signature: Unraveling N-Glycosylation Alterations in Glycogen Storage Disease Ia and Ib

Glycogen storage disease (GSD) types Ia and Ib are rare inherited metabolic disorders caused by pathogenic variants in G6PC or SLC37A4, respectively. These defects disrupt glucose homeostasis and may affect protein glycosylation. We systematically profiled sera N-glycomes from retrospectively collected GSD Ia (n=17), GSD Ib (n=8), and control (n=21) samples. Derived traits analyses revealed distinct, subtype-specific, and shared glycomic alterations, including shifts from 2,3-to 2,6-sialylation in both subtypes. GSD Ia showed enhanced branching and reduced fucosylation, whereas GSD Ib displayed elevated fucosylation, bisection, and reduced branching. In GSD Ia patients with hepatocellular adenoma/carcinoma (HCA/HCC), further enrichment of oligomannosidic and 2,3-sialylation was observed. Several individual N-glycans showed strong discriminatory performance, supporting their potential as biomarkers for GSD I subtyping and HCA/HCC surveillance. This study provides the first comprehensive characterization of systemic N-glycans in GSD Ia and Ib, revealing glycomic remodeling as a potential biomarker of disease subtypes and tumor progression. Take-home message (synopsis) of the articleSerum/plasma N-glycomic profiling reveals distinct glycosylation signatures in GSD Ia and GSD Ib, including tumor-associated shifts in GSD Ia, highlighting novel biomarkers for disease subtyping and surveillance of hepatic complications.

biochemistry↗

bioRxiv2025

Representational Similarity and Pattern Classification of Fifteen Emotional States Induced by Movie Clips and Text Scenarios

How do different emotional states relate to each other and how are they represented in the human brain? These are important questions in the field of affective neuroscience, with profound scientific and vast clinical implications. Different theories of emotion tend to emphasize the relative importance of distinct psychological constructs, for example categorical labels (e.g., fear, joy, or sadness) versus dimensional ratings (e.g., valence and arousal), for understanding human emotions. To investigate whether categorical or dimensional constructs correspond better to patterns of brain activity associated with human affective experiences, we experimentally induced 15 emotions (spanning positive, negative, and neutral valence) in 136 participants using 150 short movie clips and 150 one- or two-sentence text scenarios, while their blood oxygenation-level dependent activity was recorded in a magnetic resonance imaging scanner. Results from our representational similarity analyses suggest participants brain activity significantly correlated with their categorical labeling of, but not their dimensional rating of, the movie clips and text scenarios. Subsequently, we were also able to decode the categorical labels of these emotional stimuli using whole-brain multi-voxel pattern classification, with important voxels found in many cortical, limbic, subcortical, cerebellar, and brainstem regions. Finally, we found similar clusters of emotions through exploratory hierarchical clustering analyses of participants categorical labeling of and brain responses to these stimuli. Taken together, these findings greatly advance our understanding of how a large set of human emotions are related to each other both in terms of the participants self-report and their brain activity. Significance StatementWe successfully decoded fifteen emotional states induced by movie clips and text scenarios based on participants brain responses (blood oxygenation-level dependent signals) to these stimuli using multi-voxel pattern classification (a supervised machine learning approach). We also found that participants brain responses correlated with their self-reported emotional experience, i.e. which emotion they felt while they were presented with these stimuli, using representative similarity analysis (an unsupervised approach). Finally, we found that these emotions are organized in very similar ways both in terms of participants categorical labeling and their brain responses to these stimuli. Together, these data-driven and computational modeling-based findings greatly advance our understanding of how a large set of emotions are organized and represented in the human brain.

neuroscience↗

bioRxiv2025

Axially swept dithered light-sheet microscope to reveal cardiac morphology

Understanding cardiac microstructure and vascular networks in their entirety is critical for assessing cardiovascular development, disease progression, and therapeutic interventions. Light-sheet microscopy combined with tissue clearing enables high-resolution volumetric imaging of intact organs but faces limitations in trabeculated myocardium due to trade-offs among light-sheet thickness, effective range, and frame rate. We exploit temporal dynamics that govern illumination-detection interplay to maintain uniform resolution across specimens. Building on this, we implemented high-speed dithered light-sheet (DiLS) illumination, extending the confocal region by over 40% and enhancing the space-bandwidth product while preserving optical sectioning. Integration of DiLS with a sweeping approach establishes the axially swept dithered light-sheet (AS-DiLS), which enhances imaging throughput while preserving axial resolution and enables uniform illumination up to 12.5-millimeter range. AS-DiLS delivers near-isotropic resolution (~2.5 m) for investigating intricate ventricular trabeculae, vasculature, and extracellular matrix, providing a scalable platform for comprehensive cardiovascular morphology and topology assessment from embryos to adults. TeaserVolumetric imaging reveals microstructure and vascular networks in their entirety with near-isotropic resolution.

bioengineering↗