Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 325 records · Page 18Linked to original sources

bioRxiv2025

Deveolopment of patient-derived neuroprogenitor cells (hNPCs), neurons, and astrocytes to explore the etiology of Guam Parkinsonism-dementia complex (PDC)

Parkinsonism-Dementia Complex (PDC) is one phenotype of a disappearing neurodegenerative disease (Guam ALS-PDC) that shows clinical and neuropathological relationships with amyotrophic lateral sclerosis (ALS), atypical parkinsonism and Alzheimers disease. ALS-PDC has been linked with exposure to environmental factors (notably cycad plant neurotoxins), but evidence from human and animal studies is inconclusive. Patient-derived induced pluripotent stem cells (iPSCs) provide a powerful in vitro system to explore the underlying cause of PDC. iPSC lines were derived from lymphocytes of a PDC-affected Guamanian Chamorro female patient and an age- and gender-matched healthy Chamorro resident of PDC-unaffected Saipan using non-integrating episomal plasmids. iPSCs derived from both patients expressed pluripotency markers (Oct4, SSEA-4, TRA-1-60, Sox2) prior to the generation of neuroprogenitor cells (hNPCs), neurons and astrocytes. An embryoid body protocol was used to derive hNPCs from both iPSC lines while a differentiation media was used to generate neurons from hNPCs. hNPCs derived from both iPSC patients lines displayed established neuroprogenitor markers (nestin, Sox2), while the differentiated hNPCs exhibited both neuronal (beta-tubulin III, Map2, doublecortin) and synaptic (synaptophysin, PSD-95) markers. Expression of these protein markers in hNPCs and neurons by dot blotting was also observed for both lines. Astrocyte progenitor cells and mature astrocytes with appropriate markers were also developed from the hNPCs of both lines using commercial kits. Development of these patient-derived iPSCs provides a human model for evaluating the role of environmental (e.g., cycad toxins) and genetic factors in ALS-PDC and possibly other related neurodegenerative diseases.

neuroscience↗

bioRxiv2025

IGP receptors act as redox sensors to mediate broad-spectrum disease resistance induced by cellooligomers

Cys-oxidation is a well-established post-translational regulator of intracellular protein function, yet its role in extracellular receptor-mediated signaling remains poorly understood. Here, we investigate the LRR-Malectin receptor-like kinase IGP1, a key receptor for plant cell wall damage-associated molecular patterns (DAMPs). We demonstrate that IGP1 directly recognizes cellooligomers with a degree of polymerization [≥] 3 via a conserved binding groove in its LRR domain, not the malectin domain as anticipated. Strikingly, a pair of cysteines within the malectin domain functions as a redox sensor, undergoing hydrogen peroxide-induced oxidation that sterically reduces ligand binding affinity and attenuates immune signaling. Phylogenetic analyses reveal that IGP originated after the terrestrialization of plants, and is an evolutionarily conserved redox sensor in land plants. Functional studies in Arabidopsis (Arabidopsis thaliana), wheat (Triticum aestivum), and soybean (Glycine max) confirm that the IGP-cellooligomer module confers broad-spectrum disease resistance. Our work uncovers a unique mechanism where ligand perception and redox sensing are integrated into a single receptor to regulate DAMP-triggered immunity.

plant biology↗

bioRxiv2025

Degeneration and Impaired Resilience of Skull Bone and Hematopoietic Bone Marrow

Bone marrow health is central to transplantations, blood formation, and cancer progression. However, the bone marrow niche deteriorates with age, impairing haematopoietic stem cell function. Contrary to a recent report1 suggesting skull marrow resists ageing, our multi-laboratory investigation reveals the opposite: the skull marrow is among the vulnerable sites of age-related decline. Ageing skull niches consistently show loss of mesenchymal and osteoprogenitors, suppression of angiogenic and lymphatic programs, adipocyte accumulation, vascular senescence, DNA replication stress, mitochondrial dysfunction, cellular senescence, and heightened inflammation. Proteomic profiling further highlights this vulnerability, demonstrating that vertebral niches--unlike the skull--are relatively spared from these ageing hallmarks. Together, these convergent datasets overturn the notion of skull-specific resilience and instead establish the skull marrow as a fragile, degenerating environment. These findings redefine marrow ageing and highlight the skull as a critical, clinically relevant target for sustaining blood and immune health and reducing vulnerability to haematological disease.

cell biology↗

bioRxiv2025

Vaccine Elicitation of HIV-1 Neutralizing Antibodies Against Both V2 Apex and Fusion Peptide in Rhesus Macaques

Broadly neutralizing antibodies targeting multiple sites of HIV-1 Env vulnerability can be induced by infection, but simultaneous elicitation of neutralizing antibodies (NAbs) against multiple epitopes has not yet been achieved by vaccination. In this study, we designed a dual-epitope vaccine targeting both fusion peptide (FP) and V2 apex and evaluated its capacity to induce NAbs against both epitopes in rhesus macaques. This vaccine combined an FP conjugate with a cocktail of engineered Env trimers with enhanced V2 apex recognition and increased antigen retention in lymph nodes. Immunization of macaques with the dual-epitope vaccine elicited >1000-fold higher autologous tier 2-neutralization titers than the wildtype Env trimer and enhanced heterologous NAb breadth. Both FP and V2-apex monoclonal antibodies (mAb) were isolated from immunized macaques and showed heterologous neutralization with genetic and structural signatures that were similar to well-characterized FP and V2 apex bNAbs, although the V2 apex mAbs showed incomplete maturation. These results demonstrate proof-of-concept for simultaneous vaccine elicitation of NAbs against multiple sites of Env vulnerability, which will likely be critical for an effective HIV-1 vaccine. HIGHLIGHTSO_LIDesigned a dual-epitope vaccine targeting both fusion peptide (FP) and V2 apex C_LIO_LIV2-SET Env trimer conferred higher binding of V2 apex bNAbs, longer retention in draining lymph nodes, and >1000-fold higher induction of autologous neutralization titers compared with wildtype Env trimer C_LIO_LIDual-epitope vaccine enhanced serum tier 2 neutralization breadth C_LIO_LIDual-epitope vaccine elicited FP- and V2 apex-specific neutralizing mAbs with genetic signatures similar to well-characterized FP and V2 apex bNAbs C_LI

immunology↗

bioRxiv2025

Multi-Scale Kinetics Modeling and Advanced Assay for mRNA-Lipid Nanoparticle Potency Assessment

mRNA lipid nanoparticle (mRNA-LNP) technology has attracted global attention, especially in vaccine development, due to its superior delivery efficiency, molecular stability, and safety profile. However, evaluating mRNA-LNP potency--defined as the quantifiable biological response elicited by the product--remains costly and time-consuming when relying solely on in vitro experiments. Rapid and reliable potency assessment is hindered by limited mechanistic understanding of delivery processes and sparse experimental data. To address these challenges, we present a mechanism-informed, multi-scale kinetic modeling framework that quantitatively captures the coupled dynamics across particle-level, cellular, and macroscopic scales. This model incorporates variability in LNP-cell interactions and accounts for critical factors such as dosage, LNP and cell size distributions, and cell proliferation dynamics--all of which influence delivery efficiency and response variability. By integrating advanced multi-omics assays--such as single-molecule fluorescent in situ hybridization (smFISH), which enables single-cell resolution of mRNA and protein expression--our framework leverages heterogeneous, multi-scale data to support mechanistically grounded modeling of mRNA delivery and enable robust predictions of therapeutic potency. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/679406v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1f3ec2borg.highwire.dtl.DTLVardef@1163893org.highwire.dtl.DTLVardef@1dc530borg.highwire.dtl.DTLVardef@1d0264a_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

scRGP: Prediction of Single-cell Genetic Perturbation Transcriptional Responses based on Rank in Multiple Scenarios

Single-cell perturbation sequencing technologies (e.g., Perturb-seq, CROP-seq), which integrate CRISPR-based gene editing with single-cell transcriptome profiling, have revolutionized the analysis of transcriptomic changes induced by genetic perturbations at single-cell resolution. These technologies serve as a powerful tool for identifying key genes that inhibit tumor growth or reverse cancer cell phenotypes. However, they face two major challenges: data explosion with high experimental costs, and data complexity characterized by high dimensionality, noise, sparsity, and heterogeneity. To address these challenges, we developed the single-cell Rank-based Genetic Perturbation predictor (scRGP), the first deep learning framework leveraging gene expression rank-order information for this task. scRGP demonstrates superior performance in terms of robustness, cross-cell-line perturbation prediction, and high-throughput screening. Specifically, scRGP achieves an approximately 10-16 percentage points improvement in Pearson correlation coefficient (PCC) over state-of-the-art methods (e.g., GEARS and scFoundation) for single- and double-gene perturbation predictions, while also extending prediction capability to triple-gene perturbations. Furthermore, it outperforms these methods by approximately 5-9 percentage points in cross-cell-line predictions. These advancements promise to shift the paradigm of single-cell perturbation studies from experiment-driven to computation-driven approaches, providing new support for functional genomics and precision medicine.

bioinformatics↗

bioRxiv2025

The regulatory effect of Ca2+/calmodulin dependent protein kinase II mediated by receptor interacting protein kinase 3 on necroptosis of hypertrophic cardiomyocytes

Receptor interacting protein kinase 3 (RIPK3) plays a crucial role in the signaling pathway of necroptosis and calcium/calmodulin dependent protein kinase II (CaMKII) is a novel substrate for RIPK3 induced necroptosis. The aim of this study is to investigate the regulation and mechanism of RIPK3 on AngII induced cardiomyocyte hypertrophy.AngII was used to stimulate myocardial cells for 72 hours, inducingcardiomyocytehypertrophy; Use RIPK3 inhibitor GSK872 to reduce RIPK3 expression.Detect indicators related to myocardial hypertrophy, cell damage, necroptosis,CaMKII activation and gene expression, oxidative stress, mitochondrial membrane potential, etc. After AngII stimulation of cardiomyocytes, the expression of hypertrophy markers ANP and BNP increased, LDH release increased, ATP levels decreased, splicing factors ASF and SC35 expression increased, CaMKII oxidation and phosphorylation levels increased, and CaMKII{delta} alternative splicing was disrupted. However, treatment with GSK872 can alleviate myocardial dysfunction, inhibit CaMKII activation, correct CaMKII{delta} variant splicing disorder and ultimately alleviating myocardial hypertrophy. In addition, pretreatment with RIPK3 can reduce the accumulation of reactive oxygen species (ROS) induced by AngII, decrease the activity of ASF and SC35, and restore mitochondrial membrane potential. RIPK3 inhibitor GSK872 can inhibit the activation of CaMKII, alleviate necroptosis and oxidative stress to alleviate myocardial hypertrophy. It has a protective effect on myocardial hypertrophy and is expected to become a new targeted drug for clinical treatment of dilated cardiomyopathy and heart failure.

cell biology↗

bioRxiv2025

Crosstalk between Immune Microenvironment and Hair Follicle Cells Underlies Sexual Dimorphism in Androgenetic Alopecia

Androgenetic alopecia (AGA), also known as female pattern hair loss (FPHL) in women, is the most prevalent form of hair loss. It is characterized by progressive miniaturization of hair follicles and shortening of the anagen phase. The condition is widely attributed to genetic predisposition and androgen-mediated activation of androgen receptors. Other factors, such as the immune microenvironment, could also contribute to the pathogenesis. However, the specific mechanisms involved are still poorly understood. This study aimed to investigate the potential role of skin-resident myeloid cells in interacting with hair follicle cells under androgen stimulation, and to elucidate the sex-specific differences in dihydrotestosterone (DHT)-induced hair loss. Both female and male mice received DHT treatment, and histological examination was performed to assess DHT-induced alterations in skin morphology. Single-cell RNA sequencing (scRNA-seq) was utilized to profile skin cell populations and explore underlying mechanisms. Our results demonstrated that DHT inhibited hair regrowth in both sexes, altered skin thickness, and induced hair follicle miniaturization. scRNA-seq analysis revealed enhanced interactions between myeloid and fibroblast subpopulations, with more robust crosstalk observed in female mice. An in vitro experiment demonstrated that DHT promoted apoptosis of dermal papilla cells (DPCs) in the presence of macrophages. Treatment with polypeptides Y001 and Y002 effectively promoted hair regrowth by suppressing apoptosis signaling pathways. Our findings underscore the interactions between immune cells and hair follicular cells, particularly mediated by skin-resident myeloid cells, in the sexual dimorphism of androgenetic alopecia. The polypeptides Y001 and Y002 exhibit promising therapeutic potential by targeting apoptotic pathways, offering novel avenues for AGA treatment.

cell biology↗

bioRxiv2025

De Novo Design, Directed Evolution and Computational Study of Heme-Binding Helical Bundle Protein Catalysts for Biocatalytic Enantioselective Ge-H Insertion

De novo designed proteins offer a malleable platform for the development of stereoselective transformations not found in biochemistry. Here, we report the de novo design and directed evolution of helical bundle protein catalysts for enantioselective germylation through Ge-H insertion, a transformation not previously achieved by enzymatic catalysis. Comparative computational analysis revealed that, relative to Si-H insertion, the Ge-H insertion reaction proceeds through an earlier and more flexible transition state, introducing distinct challenges for stereocontrol. Using a fully de novo designed truncated four-helix bundle scaffold as the starting point, directed evolution afforded a quadruple mutant that catalyzes Ge-H insertion with high efficiency, enantioselectivity, and broad substrate scope. Molecular dynamics simulations indicated that beneficial mutations introduced from directed evolution enhanced active-site preorganization and modulated local back-bone flexibility, contributing to improved transition-state complementarity with fine-tuned binding pocket size and more stable cofactor positioning regulated by hydrogen bonding interactions. These findings showcase the excellent potential for de novo proteins to achieve stereoselective transformations previously unknown to biocatalysts and underscore the importance of active-site remodeling of de novo protein scaffolds via directed evolution in achieving selective catalysis involving flexible transition states. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/679279v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@11d5beaorg.highwire.dtl.DTLVardef@7d6559org.highwire.dtl.DTLVardef@88d0fborg.highwire.dtl.DTLVardef@501945_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Mechanism of Sanliangsan Lipid-Lowering in treating hyperlipidemia: insights from network pharmacology and molecular docking

Background and ObjectiveThis study aimed to identify the active ingredients, key targets, and signaling pathways of Sanliangsan Lipid-Lowering (SLL) in the treatment of hyperlipidemia (HLP) using network pharmacology, and to further clarify the material basis and mechanism responsible for its lipid-lowering efficacy. MethodsAll active ingredients of SLL were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), followed by the identification of target proteins corresponding to each active ingredient. Target genes associated with these target proteins were obtained from the Uniprot database, with duplicate genes excluded to generate the predicted targets of the active ingredients.Cytoscape was utilized to construct the "Herb-Active Ingredient-Predicted Target" network for SLL. Targets related to hyperlipidemia (HLP) were retrieved from the GeneCards, OMIM, and DrugBank databases using "hyperlipidemia" as the keyword. The intersection of the predicted targets of SLL active ingredients and HLP-related targets was defined as the potential therapeutic targets of SLL for HLP. Utilizing Cytoscape 3.9.1 software, the top 20 targets with the highest Degree values were selected to construct the "Herb-Active Ingredient-Target-Disease" network, (esignated as the "Herb-Active Ingredient-Target Network of SLL against HLP." The STRING database was employed to build a protein-protein interaction (PPI) network of the potential therapeutic targets, which was subsequently analyzed using the Network Analysis, CytoNCA, and CytoHubba plugins in Cytoscape to identify the top 10 key targets. The Metascape platform was used for Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the key targets, and the Bioinformatics online tool was applied to visualize the analytical results. Furthermore, AutoDock Tools 1.5 software was utilized to perform molecular docking between the active ingredients and key targets, thereby validating the results of the network pharmacology analysis. ResultsA total of 115 active ingredients and 255 corresponding predicted targets of SLL were screened from the TCMSP database. Additionally, 2106 HLP-related targets were retrieved from the aforementioned databases, and 140 common targets (potential therapeutic targets) were identified through intersection analysis. From these common targets, the top 20 with the highest Degree values were selected for the construction of the "Active Ingredient-Potential Target-Disease" network. Network analysis revealed that kaempferol, quercetin, and formononetin were the top three active ingredients in terms of content, while tumor necrosis factor (TNF), interleukin-6 (IL6), protein kinase B1 (AKT1), interleukin-1{beta} (IL1B), prostaglandin-endoperoxide synthase 2 (PTGS2), peroxisome proliferator-activated receptor {gamma} (PPARG), caspase 3 (CASP3), and hypoxia-inducible factor 1 (HIF1A) were the targets associated with the largest number of active ingredients. The PPI network consisted of 140 nodes and 3,207 edges. By using the CytoHubba plugin for analysis, six key targets were identified: AKT1, TNF-, IL-1 {beta}, IL6, PPARG and PTGS2. The GO functional enrichment analysis revealed 30 entries, which encompassed 10 biological processes (such as positive regulation of transcription by RNA polymerase II), 10 cellular components (such as extracellular space), and 10 molecular functions (such as transcription coactivator binding). Additionally, 10 KEGG signaling pathways were identified, including Lipid and atherosclerosis, the AGE-RAGE signaling pathway in diabetic complications, and Fluid shear stress and atherosclerosis. The findings indicated that SLL exerts a therapeutic effect on HLP by regulating multiple signaling pathways. Molecular docking results demonstrated that the binding energies of the three core ingredients--kaempferol, quercetin, and formononetin--with all key targets were less than -5.0 kJ/mol, with the lowest binding energy (-10.1 kJ/mol) observed between formononetin and PTGS2, indicating a strong binding affinity between these two molecules. ConclusionThis study identified the potential active ingredients, key targets, and core signaling pathways of SLL in treating HLP, confirming that SLL exerts its lipid-lowering effect through a synergistic "multi-component, multi-target, multi-pathway" mechanism. It provides a theoretical basis for further experimental validation and clinical application of SLL in managing HLP.

molecular biology↗

bioRxiv2025

Hepatitis E ORF2 blocks trophoblast autophagy to induce miscarriage via LC3B binding rather than PI3K/Akt/mTOR pathway suppression

Hepatitis E virus (HEV) is a zoonotic pathogen that can infect pregnant women and cause adverse pregnancy outcomes, including miscarriage and preterm delivery. The previous study demonstrated that HEV genotype 3 (HEV-3) inhibits complete autophagic flux in both mouse placental tissue and human trophoblast cells (JEG-3), evidenced by reduced expression of ATG proteins (including LC3, Beclin1, ATG4B, ATG5, and ATG9A) and accumulation of p62. However, the specific regulatory pathway involved remains unclear. Thus, eukaryotic expression vectors for HEV open reading frames (ORFs) were constructed, and ORF2 and ORF3 proteins were transiently overexpressed in JEG-3 cells via liposome transfection.. While both ORF2 and ORF3 significantly reduced LC3B protein levels (p < 0.01), only ORF2 induced p62 accumulation (p < 0.01), indicative of autophagic inhibition, which indicates that ORF2 was the key viral protein mediating autophagy suppression in JEG-3. The results of WB and RT-qPCR show that ORF2 suppressed the PI3K/Akt/mTOR pathway while enhancing nuclear translocation of TFEB (p < 0.01) and AMPK phosphorylation (p < 0.01), suggesting paradoxical activation of upstream autophagy regulators. Through co-transfection of mCherry-LC3 with ORF2, co-localization studies, and AlphaFold 3-based intermolecular interaction predictions, we proposed that ORF2 directly binds LC3B to block autophagosome formation. Finally, co-immunoprecipitation confirmed physical interaction between HEV ORF2 and LC3B, elucidating the molecular mechanism of HEV-induced autophagy suppression in trophoblasts. These findings reveal the molecular mechanism by which HEV inhibits autophagy leading to miscarriage in mice, providing new insights into HEV-induced reproductive damage.

pathology↗

bioRxiv2025

Structural and Functional Characterization of Encapsulin-Targeted Double Ferritin Fold Ferroxidases

Ferritins are a widespread family of proteins involved in iron homeostasis. While classic ferritins consist of four -helices and form 24-meric nanocages, related ferritin-like proteins display other types of assemblies and sometimes lack any iron storage capacity. Here, by analyzing the available genomic data, we identify a family of double ferritin-like proteins (DFLPs) composed of two four-helical domains, which arose by duplication of a ferritin fold protein. We characterize representative DFLPs from Thermocrinis minervae and Caldanaerovirga acetigignens, TmDFLP and CaDFLP, and show that they form homodimers and bind heme. We determine the X-ray structure of TmDFLP and demonstrate its ferroxidase activity. Furthermore, we show that some DFLPs, including TmDFLP and CaDFLP, are highly likely to be targeted into encapsulin shells. Our work expands the range of known iron metabolism systems and highlights the power of genome mining for discovery of new proteins. Graphical Abstract for Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/676036v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@72e6b0org.highwire.dtl.DTLVardef@18752fforg.highwire.dtl.DTLVardef@15a02e7org.highwire.dtl.DTLVardef@74cd02_HPS_FORMAT_FIGEXP M_FIG C_FIG A family of double ferritin-like proteins (DFLPs) composed of two four-helical domains is described and investigated. DFLPs are shown to form homodimers, bind heme, possess diiron sites and display ferroxidase activity. Some DFLPs are shown to be targeted to encapsulin shells as core or secondary cargo, thus representing a new type of iron metabolism systems.

biochemistry↗

bioRxiv2025

Sleep deprivation exhibits age-dependent effect on infra-slow global brain activity

Infra-slow (< 0.1 Hz) global brain activity, quantified by the global mean BOLD (gBOLD) signal in resting-state fMRI, is elevated during sleep and closely associated with cerebrospinal fluid (CSF) dynamics, a key mechanism for the brain waste clearance implicated in neurodegenerative disorders such as Alzheimers disease (AD). However, the effect of sleep deprivation on gBOLD activity and its interaction with aging remain poorly understood. Using a rigorously controlled in-laboratory total sleep deprivation (TSD) protocol, we demonstrate that TSD significantly increases both the amplitude of the gBOLD signal and its coupling with CSF flow, suggesting a compensatory mechanism that may enhance glymphatic clearance following acute sleep loss. Notably, these TSD-induced enhancements exhibit robust age dependency, with diminished responses in individuals at midlife (40-50 yrs). The absence of this compensatory mechanism in these midlife participants may exacerbate age-related impairments in neurotoxic clearance and increase dementia susceptibility, thereby offering mechanistic insights into the nexus between sleep disruption, aging, and neurodegeneration.

neuroscience↗

bioRxiv2025

Single-nucleus transcriptomics reveal disrupted pathways in the prefrontal cortex of Scn2a-deficient mice

Truncating variants in SCN2A, which encodes the NaV1.2 sodium channel critical for action potential initiation and propagation, are associated with autism spectrum disorder (ASD) and epilepsy. To investigate SCN2A deficiency-related phenotypes, we developed a preclinical mouse model with under 50% NaV1.2 expression, exhibiting neuronal hyperexcitability and social deficits. However, the neuronal populations and molecular alterations underlying these phenotypes at single-cell resolution have not been investigated. In this study, we conducted single-nucleus RNA sequencing (snRNA-seq) of wild-type (WT), homozygous Scn2a-deficient (HOM) mice, and HOM mice with Scn2a restoration (HOM-FlpO) to examine the effects of Scn2a level on gene expression in the medial prefrontal cortex (mPFC), a critical brain region related to ASD development. Differential expression analysis in GABAergic and glutamatergic neurons between genotypes revealed gene expression enriched in neurotransmitter activity regulation and synapse organization. Lastly, snRNA-seq results in HOM-FlpO identified genes that were rescued after Scn2a restoration. These results reveal that reduced Scn2a expression disrupts RNA transcriptomes in multiple neuronal subtypes, providing insight into cell type-specific mechanisms underlying SCN2A-related disorders.

neuroscience↗

bioRxiv2025

Digit-Tracking Reveals Curiosity-Driven Visual Attention in Macaque Monkeys

We used digit-tracking, a touch-based method for assessing visual attention, to investigate spontaneous exploration in macaque monkeys. By engaging with degraded images on a touch-sensitive display, monkeys could uncover high-resolution portions through finger movements, allowing for natural and unrestricted interaction. Monkeys received juice rewards after touching a predetermined number of pixels, but no specific regions were targeted. Attention maps were generated from their interactions, along with data from human digit-tracking and monkey eye-tracking experiments. We applied a saliency model and a Convolutional Neural Network (CNN) model to predict the empirical explorations. The correlation between model prediction maps and empirical attention maps indicated that monkeys focused non-randomly on information-rich regions, with the CNN model providing the most accurate predictions. These findings suggest that exploration was driven by intrinsic curiosity, beyond the extrinsic rewards for interaction. Digit-tracking offers a minimally invasive, portable alternative to eye-tracking, expanding research opportunities in visual cognition within ecologically valid settings.

animal behavior and cognition↗

bioRxiv2025

Prostate-specific EV capture with sufficient RNA yield to enable transcriptomic profiling

Prostate-specific antigen (PSA) screening has reduced prostate cancer (PCa) mortality but suffers from limited specificity, contributing to unnecessary biopsies and overdiagnosis of indolent disease. There is a critical need for biofluid-based biomarkers that improve the precision of PCa detection. Extracellular vesicles (EVs) offer a promising platform for noninvasive diagnostics, as they carry molecular cargo reflective of their tissue of origin. The ExoDx Prostate IntelliScore (EPI) test, a urine-based EV assay, is currently the only commercial EV diagnostic for clinically significant (cs)PCa, but its performance may be constrained by contamination from renal and bladder-derived EVs. To address this, we developed Exosome Diagnostics Depletion and Enrichment (EDDE), a novel immunocapture-based method for isolating prostate-derived EVs with high specificity. By targeting Prostate Specific Membrane Antigen (PSMA), we optimized EDDE to selectively enrich prostate EVs from post-DRE urine and recover sufficient RNA for transcriptomic analysis. Throughout development, we implemented a quantitative framework to track EV stoichiometry and assess depletion efficiency and yield, enabling rigorous optimization of the workflow. Our findings demonstrate that PSMA EDDE enriches prostate-specific EVs and yields RNA quantities compatible with sequencing. This platform enhances the specificity of EV-based biomarker discovery and holds promise for determining if tissue-specific EV biomarkers contribute advantages over bulk EVs.

cancer biology↗

bioRxiv2025

Total variation of quantitative phase map reveals cellular Young's modulus

Collective cell migration is a fundamental physiological process involved in wound healing, development, and tissue regeneration. Though the role of the environmental stiffness in collective cell migration has been extensively investigated, the effects of cellular stiffness have been less studied due to the lack of high-throughput in situ methods for characterizing cellular stiffness. Here, we characterize the cellular Youngs modulus in situ with a large field of view and in real time using use quantitative phase microscopy. We found that standard deviation and total variation of the phase are inversely related to the cellular Youngs modulus, while the total variation of phase has finer mechanical resolution. Integrating the total variation of phase with cell segmentation algorithms, we efficiently analyzed the cellular Youngs modulus for cells in a monolayer. Using this system, we found the cells at the wound frontier are much softer than that of the cells in the inner region of monolayer in in vitro wound healing assay. At single cellular level, the Youngs modulus of leader cells, boundary cells, and inner cells are significantly distinct from each other. To conclude, our method would help elucidate the essential role of cellular stiffness in collective cell migration and has the potential to further benefit the progress of mechanobiology.

biophysics↗

bioRxiv2025

Complete telomere-to-telomere genomes of cowpea reveal insights into centromere evolution in Phaseoleae

Cowpea (Vigna unguiculata) is a versatile legume crop providing a critical source of grain, vegetable and forage globally. Cultivated cowpea is classified into two main subspecies, subsp. sesquipedalis for fresh-pod vegetable and subsp. unguiculata for grain production. Here, we present two complete telomere-to-telomere (T2T) assemblies for the grain-type inbred lines HJD and vegetable-type FC6 through integrating PacBio HiFi reads, Oxford Nanopore ultra-long reads, and Hi-C data. The T2T genomes demonstrated improved contiguity, completeness, and accuracy compared to existing genomes, revealing clear telomeric and centromeric features. Comparative analysis of the T2T genomes highlighted inversions underlying subspecies divergence in cowpea. Evolutionary analysis uncovered contraction of gene families related to symbiosis in HJD, consist with its reduced root nodules compared to FC6. Distribution and composition of tandem repeat arrays and transposable elements in centromeric regions were largely conserved in cowpea, but displayed pronounced variation among Phaseoleae. Furthermore, frequent shifts of centromeric locations coincided with inversions found in Phaseoleae. Overall, this study provides a set of fundamental resources for cowpea improvement and enhances our understanding of cowpea subspecies divergence and genome evolution in Phaseoleae.

genomics↗