Biology subjects

Sun, L.

Publications and source records attributed to Sun, L..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗

bioRxiv2025

Bringing the Genetically Minimal Cell to Life on a Computer in 4D

We present a whole-cell spatial and kinetic model for the 100 minute cell cycle of the genetically minimal bacterium, JCVI-syn3A. This is the first simulation of a complete cell cycle in 4D including all genetic information processes, metabolic networks, growth, and cell division. Integrating hybrid computational methods, dynamics of the morphological transformations were achieved. Growth is driven by synthesis of lipids and membrane proteins and constrained by new fluorescence imaging data. Chromosome replication and segregation is controlled by essential SMC and topoisomerase proteins in Brownian dynamics simulations with replication rates responding to dNTP pools from metabolism. The model captures the origin to terminus ratio measured in our DNA sequencing and recovers other experimental measurements like doubling time, mRNA half-lives, protein distributions, and ribosome counts. Because of stochasticity, each replicate cell is unique. Not only do we predict average behavior for partitioning to daughter cells, we predict the heterogeneity among them.

biophysics↗

bioRxiv2025

Multiple-level organizational logic of the locus coeruleus-norepinephrine system in structure and function

The locus coeruleus (LC) regulates various neural processes through a limited number of norepinephrine (NE)-releasing neurons with widespread axon projections. However, how the LC is organized to exert brain-wide regulatory functions remain elusive. Utilizing larval zebrafish as a whole-brain-scale model, we reveal that morphologically heterogenous but physiologically comparable LC-NE neurons assemble complementarily to implement region-specific regulation of brain-wide neural dynamics. Individual LC-NE neurons exhibit diverse axon projections with ipsilateral bias and region preference, but share comparable electrophysiological properties, sensory responses and neural function-related genes expression. Moreover, population LC-NE neurons display bilaterally symmetrical yet regionally different axon projections and fire synchronously, causing regionally patterned NE release. Along with the regional comparability of NE receptor expression, these enable the LC to tune brain-wide neural dynamics in an inverted-U manner with region difference. Thus, our study provides a comprehensive understanding of the organizational logic of the LC system.

neuroscience↗

bioRxiv2025

eSPred: Explainable scRNA-seq Prediction via Customized Foundation Models and Pathway-Aware Fine-tuning

Single-cell RNA sequencing (scRNA-seq) has been widely used for studying cellular heterogeneity, but its use for subject-level prediction and clinical applications is still limited. We introduce eSPred, a customized foundation model designed for predictive analysis of scRNA-seq. It integrates cell-type information through a grouping strategy during pre-training and leverages pathway information to guide network flow during fine-tuning. Across multiple datasets, eSPred improves prediction accuracy and highlights pathways linked to disease mechanisms. These results suggest that eSPred can help bridge the gap between single-cell data and subject-level clinical insights, supporting more precise diagnosis and better-informed treatment decisions.

bioinformatics↗

bioRxiv2025

cytoGPNet: Enhancing Clinical Outcome Prediction Accuracy Using Longitudinal Cytometry Data in Small Cohort Studies

Cytometry data, including flow cytometry and mass cytometry, are now standard in numerous immunological studies, such as cancer immunotherapy and vaccine trials. These data enable the monitoring of an individuals peripheral immune status over time, providing detailed insights into immune cells and their role in clinical outcomes. However, traditional analyses relying on summary statistics, such as cell subset proportions and mean fluorescence intensity, may overlook critical single-cell information. To address this limitation, we introduce cytoGPNet, a novel approach that harnesses extensive cytometry data to predict individual-level outcomes. cytoGPNet is designed to address four key challenges: (1) accommodating varying numbers of cells per sample; (2) analyzing the longitudinal cytometry data to understand temporal relationships; (3) maintaining robustness under the constraints of limited individual samples in immunological studies; and (4) ensuring interpretability to facilitate biomarker identification. We apply cytoGPNet to data from multiple diverse studies, each with unique characteristics. Despite these differences, cytoGPNet consistently outperforms other popular methods in terms of prediction accuracy. Moreover, cytoGPNet provides interpretable results at multiple levels, offering valuable insights. Our findings underscore the effectiveness and versatility of cytoGPNet in enhancing the analysis of cytometry data and its potential to advance immunological research.

bioinformatics↗

bioRxiv2025

PhysDock: A Physics-Guided All-Atom Diffusion Model for Protein-Ligand Complex Prediction

Accurate prediction of protein-ligand complexes remains a central challenge in structural biology. Traditional methods are computationally inefficient and prone to local minima, whereas deep learning approaches struggle to capture structural flexibility and physical plausibility. We introduce PhysDock, a physics-guided diffusion model that uniquely integrates (i) all-atom diffusion to model ligand flexibility and protein precision-flexibility (i.e., subtle conformational adjustments); (ii) physical priors as diffusion conditioning, alongside two-phase physics guidance during the denoising diffusion to ensure physical plausibility. PhysDock demonstrates state-of-the-art performance in redocking benchmarks and excels in the more challenging cross-docking assessments. For practical utility, PhysDock (i) resolves cannabinoid receptor selectivity across diverse molecules, achieving accuracy comparable to experiments; (ii) distinguishes most drug candidates from weak binders in virtual screening of NTRK3 kinase, while uncovering novel candidates with structural insights. PhysDock serves as a versatile tool for protein-ligand complex prediction, with substantial potential to accelerate structure-based drug discovery.

bioinformatics↗

bioRxiv2025

The China Brain Multi-omics Atlas Project (CBMAP)

The China Brain Multi-omics Atlas Project (CBMAP) aims to generate a comprehensive molecular reference map of over 1,000 human brains (Phase I), spanning a broad age range and multiple regions in China, to address the underrepresentation of East Asian populations in brain research. By integrating genome, epigenome, transcriptome, proteome (including multiple post-translational modifications), and metabolome data, CBMAP is set to provide a rich and invaluable resource for investigating the molecular underpinnings of aging-related brain phenotypes and neuropsychiatric disorders. Leveraging high-throughput omics data and advanced technologies, such as spatial transcriptomics, proteomics, and single-nucleus 3D chromatin structure analysis, this atlas will serve as a crucial resource for the brain science community, illuminating disease mechanisms and enhancing the utility of data from genome-wide association studies (GWAS). CBMAP is also poised to accelerate drug discovery and precision medicine for brain disorders.

neuroscience↗

bioRxiv2025

SNX-2112 inhibits the ERBB3high tumor population in Plexiform Neurofibromas

Plexiform neurofibroma (PN) is a monogenic disorder affecting the Schwann cell lineage in approximately half of Neurofibromatosis type 1 patients. It often manifests in early childhood and carries a risk of malignant transformation at puberty. While MEK inhibitors have recently been approved for pediatric and adult patients, their long-term clinical benefits remain uncertain due to adverse effects, particularly in pediatrics. The ERBB3high stem-like tumor cell subpopulation reflects the intrinsic PN heterogeneity and can serve as alternative druggable targets. Characterization using molecular signatures also reveals the heterogeneity within the PN cell lines, and the PN drug screen analysis proposes that SNX-2112, an HSP90 inhibitor, can inhibit PN cell viability by targeting ERBB3-associated signaling. Our in vitro results demonstrated a significant viability reduction in ERBB3high PN cells compared to the controls. Treatment with SNX-2112 led to a decrease in total ERBB3, p-ERBB3 (Tyr1289), and the downstream total AKT and p-AKT (Ser473) levels. Furthermore, the significant in vivo inhibitory efficacy of SNX-2112 was revealed using a transplantation model from mouse PN with DhhCreNF1f/f;Luc configuration. These findings support the efficacy of SNX-2112 as a potential alternative therapeutic strategy, highlighting its possible application in PN patients.

cancer biology↗

bioRxiv2025

Miniaturized and accessible functional ultrasound imaging system for freely moving mice

Functional ultrasound (fUS) imaging provides brain-wide activity maps with high spatiotemporal resolution and deep penetration, positioning it as a key technology for future non-invasive brain-computer interfaces (BCIs). Realizing this potential, particularly for chronic BCI applications requiring long-term monitoring in naturalistic settings, critically depends on significant system miniaturization to overcome the cost and complexity limitations of current platforms. Addressing this challenge, we present mini-fUS, a miniaturized, cost-effective fUS platform engineered for accessibility without compromising core performance for demanding neuroscience research. The system features a compact transmit-receiver, low-noise power supply, and high-speed data transfer, achieving pulse repetition frequencies up to 5 kHz with negligible jitter. Real-time GPU-accelerated beamforming and singular value decomposition (SVD) enable whole-brain activity mapping, demonstrated here in freely moving mice at up to 3.57 Hz with [~]100 {micro}m spatial resolution and 15 mm penetration depth. Validated through recordings of brain activity during sensory stimulation, anesthesia, and behavior, this design defines a practical hardware-software framework for fUS. By significantly improving accessibility and enabling robust monitoring in mobile subjects, this work advances the development of fUS for both fundamental research and future BCI technologies, while clarifying essential fUS operational principles.

neuroscience↗

bioRxiv2025

Nucleosome context regulates chromatin reader preference

Chromatin is more than a simple genome packaging system, and instead locally distinguished by histone post-translational modifications (PTMs) that can directly change nucleosome structure and / or be "read" by chromatin-associated proteins to mediate downstream events. An accurate understanding of histone PTM binding preference is vital to explain normal function and pathogenesis, and has revealed multiple therapeutic opportunities. Such studies most often use histone peptides, even though these cannot represent the full regulatory potential of nucleosome context. Here we apply a range of complementary and easily adoptable biochemical and genomic approaches to interrogate fully defined peptide and nucleosome targets with a diversity of mono or multivalent chromatin readers. In the resulting data, nucleosome context consistently refined reader binding, and multivalent engagement was more often regulatory than simply additive. This included abrogating the binding of the Polycomb group L3MBTL1 MBT to histone tails with lower methyl states (me1 or me2 at H3K4, H3K9, H3K27, H3K36 or H4K20); and confirmation that the CBX7 chromodomain and AT-hook-like motif (CD-ATL) tandem act as a functional unit to confer specificity for H3K27me3. Further, in vitro nucleosome preferences were confirmed by in vivo reader-CUT&RUN genomic mapping. Such data confirms that more representative chromatin substrates provide greater insight to biological mechanism and its disorder in human disease.

biochemistry↗

bioRxiv2025

TUCL-Seq for miRNA single molecule sequencing

MicroRNAs (miRNAs) are pivotal regulatory molecules in gene expression, and their precise quantification is essential for elucidating their roles in diverse biological processes. This research paper introduces a pioneering workflow for the single molecule sequencing (SMS) of miRNA, integrating advanced miRNA sample preparation with SMS sequencing. Central to our approach is TUCL-Seq, which is an automated, on-chip miRNA library preparation method designed to streamline the sequencing process. This innovative approach incorporates the addition of sequencing adaptor to RNA samples in solution, and converts it to cDNA on a sequencing flow cell for sequencing. Coupled with single molecule sequencing instrument and base-call software, our workflow significantly reduces sample-to-result time, and decreases the need for manual interventions compared to traditional SMS and next-generation sequencing methods. We demonstrate the efficacy of TUCL-Seq by accurately quantifying synthetic miRNA samples with a 24-hour workflow, showcasing its potential for high-throughput miRNA profiling. Our findings highlight the promise of this integrated workflow for advancing miRNA research and applications in diagnostics and therapeutics.

biochemistry↗

bioRxiv2025

Dentification of the Sorghum TMCO Gene Family and Differential Expression Analysis Under Aphid Infestation

The three-domain multicopper oxidase (TMCO) family, the largest subfamily of multicopper oxidases, plays a crucial role in plant growth, development, and responses to biotic stresses. To investigate the expression characteristics of the SbTMCO gene family under aphid infestation, a genome-wide identification and analysis of TMCO family members in sorghum were conducted using bioinformatics methods. Transcriptome data and qRT-PCR were utilized to preliminarily examine sorghums responses to aphid stress. The results revealed 42 TMCO genes in the sorghum genome, distributed across 10 chromosomes and classified into five subgroups. Members within the same subgroup displayed similar physicochemical properties, gene structures, and conserved motifs. Collinearity analysis suggested that tandem duplication and segmental duplication were the primary drivers of TMCO gene expansion in sorghum. Cis-acting element analysis identified multiple jasmonic acid (MeJA) and abscisic acid (ABA) responsive elements among SbTMCO genes. Gene expression analysis, based on RNA-seq and qRT-PCR, confirmed the relative expression levels of TMCO genes under aphid stress. This study establishes a foundation for exploring the anti-aphid functions of SbTMCO genes and provides recommendations and directions for further research on this gene family.

molecular biology↗

bioRxiv2025

Emergence of a New ST617 Hypervirulent Klebsiella pneumoniaewith ESBL+ and Strong Biofilm Forming Ability in China

The increasing infections caused by hypervirulent Klebsiella pneumoniae (hvKP) resistant to carbapenem, broad-spectrum {beta}-lactam and colistin has posed great challenges to global public health. However, the typing and detailed molecular features of the multi-drug resistant hvKP remain to be improved. Here, we characterized a broad-spectrum {beta}-lactam-resistant K. pneumoniae ST617 isolate that has not been previously reported to cause severe disease in China. We obtained the whole-genome sequence of one K. pneumoniae ST617 isolate--HZ7--from a patient with bile duct infection. Phylogenetic reconstruction was performed to investigate the possible host evolutionary origin of HZ7, and the virulence property was studied in comparison with the nearest ST617 neighbours--YZ strains isolated from patient blood infections. Our studies indicated that the HZ7 is an ESBL+ Kp that is likely evolved from environmental or animal-derived sources. Importantly, the virulence assay showed that HZ7 was highly virulent and compared with the well known hvKP strain--NTUH-K2044 and the highly virulent clinical strain ST11-K64--HZ54--isolated from a patient with severe pneumonia. In addition, HZ7 showed strong biofilm formation ability. Whole-genome sequencing analysis identified seven potential virulence genes in HZ7: kp7_000748, kp7_002156, kp7_002157, kp7_002158, kp7_002159, kp7_003103, kp7_003104, which are absent in K. pneumoniae patient isolates from Yangzhou and the environmental samples. Finally, transcriptomic analysis of HZ7 identified six genes--wcaJ, fimA, mrkH, pgaA, ugd, and gndA that are associated with biofilm formation. Given its high virulence likely associated with the seven unique genes acquired via horizontal transfer and strong biofilm forming ability, this strain should be closely monitored to prevent wider spread in the clinic.

microbiology↗

bioRxiv2025

Functional redundancy in chicken ANP32A mediates species-specific support of avian influenza virus polymerase

Host restriction of avian influenza virus (AIV) polymerase in human cells is driven by species-specific differences in ANP32A/B proteins. While AIV polymerase relies on ANP32A/B containing a 33-amino-acid insert unique to avian species, the structural and/or mechanistic basis for this requirement remains poorly characterized. Here, we demonstrate that chicken ANP32A (chANP32A) displays three functional determinants enabling its species-specific support of AIV polymerase: (1) a SUMO-interacting motif (SIM), (2) SUMOylation at residues K68/K153, and (3) a 28-amino-acid segment within the avian-specific insertion. These determinants function synergistically and redundantly, requiring at least two for optimal activity, to enhance interactions between AIV viral ribonucleoprotein (vRNP) and chANP32A, thereby promoting AIV vRNP assembly. In contrast, human ANP32A/B--which lack the other two determinants and rely solely on SUMOylation--exhibit a limited capacity to support AIV polymerase activity. Our findings unveil a cooperative mechanism where SUMO-dependent processes and structural motifs in chANP32A enforce species-specific adaptation of AIV polymerase, shedding light on how ANP32A/B governs host restriction of AIV polymerase.

microbiology↗

bioRxiv2025

Red Light-Activated Reversible Inhibition of Protein Functions by Assembled Trap

Red light offers strong tissue penetration and low phototoxicity, making it an attractive option for optogenetic applications. However, the available red light-inducible optogenetic tools are rather limited. Here, we present a novel red light-induced protein clustering system, namely R-LARIAT (Red Light-Activated Reversible Inhibition by Assembled Trap), that controls protein functions in a spatiotemporal manner. Our system capitalizes on the rapid and reversible binding of LDBs (nanobodies-based dimerization binders) to a bacterial phytochrome DrBphP, which uses a mammalian endogenous biliverdin chromophore to absorb red light. An anti-GFP nanobody fused with LDBs allows this method to quickly trap a wide variety of GFP-tagged proteins into light-induced protein clusters. Strikingly, our system exhibits an excellent performance in clustering efficiency with high light sensitivity and stability, it can function even when shielded by multiple glass plates. By utilizing the R-LARIAT system to trap and sequester tubulin, cell cycle progression can be blocked in HeLa cells. Therefore, the R-LARIAT system takes advantage of red light with greater tissue penetration and holds the potential to precisely control protein functions in living organisms.

cell biology↗

bioRxiv2025

RamEx: An R package for high-throughput microbial ramanome analyses with accurate quality assessment

Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped. Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets--including pathogenic bacteria, probiotic strains, and yeast fermentation populations--demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++ acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour. By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx.

bioinformatics↗

bioRxiv2025

Functional interaction of hybrid extracellular vesicle-liposome nanoparticles with target cells: absence of toxicity

Building on the success of COVID-19 vaccine development, lipid nanoparticles (LNPs) have emerged as leading vehicles for mRNA delivery in a range of therapeutic applications. Naturally-occurring extracellular vesicles (EVs), which share similar physical properties with LNPs, present a promising alternative platform because of their relative stability and lower immunogenicity. A key challenge common to both EVs and LNPs is enabling efficient vesicle - cell interactions and establishing a polarized permeability pathway required for effective cargo transfer. Membrane recognition and intercalation are essential for the function and delivery capacity of both systems, regardless of their complexity. In this study, we leveraged recent advances to create hybrid extracellular vesicles (HEVs) by using LNPs to load mRNA into EVs. We characterized HEV formation using Forster resonance energy transfer (FRET), cryo-electron microscopy (Cryo-EM), and super-resolution microscopy, and demonstrated their ability to deliver mRNA to recipient cells. In both, in vitro and in vivo models, HEVs exhibited superior transfection efficiency compared to conventional LNPs composed of synthetic lipids, while significantly reducing LNPs cytotoxicity - a not-well-recognized limitation of synthetic lipid-based systems. These results highlight HEVs as a safer and more effective alternative for mRNA and small molecule delivery. Future therapeutic strategies could involve isolating EVs from patients, hybridizing them with synthetic lipid carriers loaded with therapeutic cargo, and reintroducing them for personalized treatment.

cell biology↗

bioRxiv2025

Ultrasound Directly Activates Sparse Neurons and Modulates Visual Circuits in Deafened Mice

Focused ultrasound neuromodulation (FUN) is widely regarded as a next-generation technology for neural modulation, with applications spanning rodents, non-human primates, and humans. While mechanistic studies are advancing, a persistent confound--auditory interference--casts doubt on whether ultrasound exerts direct mechanical effects or merely indirect auditory responses. To resolve this, we engineered a circular ultrasound transducer compatible with two-photon calcium imaging and examined its effects on the primary visual cortex (V1) of surgically deafened mice, eliminating auditory contributions. Our results reveal that ultrasound directly activates a sparse subset of ultrasound-sensitive neurons (USSN) (response rate >30%) in V1, comprising only a small fraction of the total population and exhibiting a spatially sparse distribution. The proportion of USSN scale with ultrasound pressure, confirming a direct neuromodulatory effect independent of audition. Intriguingly, despite this sparse activation, ultrasound significantly modulates V1 circuitry: it alters the dynamics of light-sensitive neurons (LSN), with subsets showing excitation, inhibition, or no change in response to visual stimuli. These findings provide the first rigorous in-vivo evidence that FUN induces direct mechanical effects on neural activity, disentangling them from auditory confounds. By demonstrating both the specificity and broader circuit-level impact of ultrasound in deafened mice, this study reframes our understanding of FUNs mechanisms and strengthens its potential as a precise neuromodulatory tool. HighlightsO_LIUltrasound directly activates sparse neurons in deafened mice, demonstrating auditory-independent effects. C_LIO_LISparse ultrasound-sensitive neurons in V1 show pressure-dependent responses. C_LIO_LIUltrasound modulates visual circuitry, with diverse excitatory and inhibitory effects. C_LI

neuroscience↗