Biology subjects

Liu, S.

Publications and source records attributed to Liu, S..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

A BCG toxic effector induces mitochondrial DNA compaction to refrain protective immunity

Innate immune memory typically emphasizes nuclear chromatin remodeling that determines transcriptional memory in monocytes and macrophages. Here, we show that compaction of mitochondrial DNA (mtDNA), governed by mitochondrial transcription factor A (TFAM) abundance and mtATP-dependent remodeling, defines the transcriptional and functional state of trained macrophages. While typical pathogen-associated molecular pattern (PAMPs) triggered mtDNA accessibility, Bacillus Calmette-Guerin (BCG) effector PE18 directly interacted with and activated SLC25A5 to reduce mtATP levels, thereby inhibiting TFAM degradation by AFG3L2. Accumulated TFAM restricts mtDNA accessibility, suppressing the transcription of the mtNd1 and thereby reducing mtNd1-mediated mtROS production, which diminishes the trained capacity of macrophages against secondary infections. Notably, BCG{Delta}pe18 maintains macrophages cytokine transcriptional capacity independent of classical nuclear histone modifications. Moreover, BCG{Delta}pe18 provides robust and lifelong protective immunity against Mycobacterium tuberculosis (Mtb) infection. These findings reveal mitochondrial genome as a regulatory entity in trained immunity, and suggest a potential strategy for improving vaccine performance.

immunology↗

bioRxiv2025

OS2CR-Diff: A Self-Refining Diffusion Framework for CD8 Imputation from One-Step Inference to Conditional Representation

Stain imputation in multiplex immunofluorescence (mIF) imaging addresses the challenge of missing or damaged biomarker channels by reconstructing target biomarker images from a limited set of available stains. This approach offers a faster and more efficient alternative to full-panel staining, enabling detailed analysis of the tumour microenvironment. Existing One-Step Inference Models (OSIMs), primarily based on generative adversarial networks (GAN) or autoencoders, often generate suboptimal images with significant artifacts or reduced signal intensity. These limitations impair visual interpretability and reliability of the downstream immunotherapy response assessment. The challenge is further amplified when imputing cytoplasmic biomarkers such as CD8 from commonly used stains such as DAPI, due to the limited spatial correlation and the inherently complex structure of cytoplasmic signals. To address these limitations, we propose a self-refining diffusion model, OS2CR-Diff, which utilises the results from OSIMs as additional conditional representations. Unlike prior studies that rely on a single or limited conditional inputs, OS2CR-Diff incorporates three conditional inputs: the OSIM-imputed target biomarker image, OSIM-imputed complementary biomarker images, and non-antibody-stained images. Furthermore, we propose a feature fusion module that employs a cross-gated attention mechanism to effectively integrate these inputs, enabling context-aware feature refinement and improving the quality and reliability of imputed biomarker images. We evaluated OS2CR-Diff for CD8 biomarker imputation on mIF images of melanoma tissues. Our method out-performed state-of-the-art methods, achieving a 73.4% increase in the Structural Similarity Index Measure (SSIM), a 28.9% gain in the Peak Signal-to-Noise Ratio (PSNR), a 61.2% improvement in Mean Absolute Error (MAE), and significantly lower false positive rates compared to OSIM.

bioinformatics↗

bioRxiv2025

High-Concordance Validation of Droplet Digital PCR and Next-Generation Sequencing for EGFR Mutation Detection Across Diverse Biospecimens in a Large-scale NSCLC Cohort Study

BackgroundsNext-generation sequencing (NGS) and droplet digital PCR (ddPCR) are both established methods for detecting EGFR mutations in non-small cell lung cancer (NSCLC). However, comprehensive validation of their concordance in mutation detection and variant allele frequency (VAF) quantification across heterogeneous sample types remains limited. Inconsistent results from different sample types (e.g., cfDNA, FFPE) pose a significant challenge to clinical decisions. This is particularly critical for advanced NSCLC patients, who often rely on liquid biopsy, yet the concordance between liquid and tissue-based testing lacks validation in large-scale studies. Another issue in clinical practice is that many tumor samples are limited in quantity, making it difficult to meet testing requirements. Therefore, it is worth exploring whether pre-capture NGS libraries can serve as substitutes for original DNA. MethodsIn this study, we first developed three assays to detect EGFR L858R, exon 19 deletions (Ex19del) and T790M, respectively using ddPCR platform. Their Limit of Detection (LOD) could reach 0.01% at 100 ng of input DNA. Subsequently, we conducted a large retrospective clinical study to systematically compare the detection performance of ddPCR and NGS across three mutation types using approximately 1,000 EGFR-positive samples, including cell-free DNA (cfDNA), pre-capture NGS libraries of cfDNA (cfDNA-prePCR), FFPE-derived DNA (ffpeDNA), pre-capture NGS libraries of FFPE-derived DNA (ffpeDNA-prePCR), fresh tumor tissue DNA (ttDNA), pre-capture NGS libraries of ttDNA (ttDNA-prePCR), pleural effusion supernatants DNA (peDNA), and pre-capture NGS libraries of peDNA (peDNA-prePCR). They were analyzed for detection concordance and VAF correlation. Especially, we made comparisons of the tumor DNA, including ctDNA and tumor tissue DNA, with their paired pre-capture NGS library. ResultsKey findings demonstrated excellent overall agreement between NGS and ddPCR. The mutation detection concordance rates were 98.72% (overall), with subtype-specific rates of 98.93% (L858R), 99.23% (Ex19del), and 97.14% (T790M). VAF measurements between ddPCR and NGS showed exceptional correlation (Pearsons r = 0.975, P<0.001). Notably, pre-capture NGS libraries showed remarkable VAF concordance with their source materials (0.993 for cfDNA libraries vs cfDNA; 0.998 for tumor tissue libraries vs tumor DNA with EGFR L858R; 0.991 for tumor tissue libraries vs tumor DNA with EGFR Ex19del). ConclusionsNGS and ddPCR demonstrate high concordance in EGFR mutation detection and VAF quantification, supporting their complementary roles in clinical testing. Using pre-capture libraries as an alternative to source samples can avoid repeat biopsies and enables subsequent testing for patients with inadequate FFPE sample quantity. These findings establish an evidence base for integrated diagnostic paradigms leveraging NGSs multiplexing power and ddPCRs sensitivity.

cancer biology↗

bioRxiv2025

Effects of carbon dioxide enrichment and environmental factors on photosynthesis, growth and yield and their interaction in cucumber: a meta-analysis

Despite the ongoing increase in atmospheric carbon dioxide concentrations, these levels remain well below the optimal threshold for cucumber growth and development. In addressing the challenges posed by climate change to agricultural production, the use of carbon dioxide enrichment (eCO2) has become increasingly widespread in order to meet global demand for cucumbers. Nevertheless, the impact of eCO2 and environmental factors on cucumber growth remains to be elucidated. In this study, we conducted a meta-analysis of 73 research papers on eCO2 in cucumbers was conducted, and their photosynthesis, growth, and yield were analysed. In summary, under conditions of elevated CO2 levels, the net photosynthetic rate, biomass, and yield of cucumbers exhibited a marked increase of 56.31%, 27.75%, and 21.98%, respectively. Concurrently, stomatal conductance and transpiration rate exhibited a decline of 36.07% and 30.42%, respectively. In the context of the implementation of eCO2 at varying levels within a production environment, the prevailing recommendation pertains to the range of 800-1200 ppm. It is advised that this be integrated with elevated light intensity, augmented temperature, suitable humidity levels, and a sufficient supply of fertiliser to achieve a synergistic effect. The findings of this study contribute to enhancement of environmental control in the context of greenhouse cultivation of cucumber in response to climate change, as well as promoting the green and sustainable development of the cucumber industry.

plant biology↗

bioRxiv2025

Production of the anticancer drug intermediate strictosidinic acid in engineered yeast

Strictosidinic acid is a key intermediate in the biosynthetic pathway of camptothecin, a plant alkaloid that serves as a precursor for semisynthetic anticancer drugs. At the moment, camptothecin is mainly sourced from trees, causing limited supply and high costs. Improving access to strictosidinic acid would help to elucidate yet unknown biosynthetic steps and in the long term enable sustainable production of camptothecin in heterologous hosts. While structurally similar to the common monoterpene indole alkaloid precursor strictosidine, strictosidinic acid has not been the target of metabolic engineering efforts before. Here, we present a strategy to produce strictosidinic acid from glucose and tryptophan in engineered yeast. First, we create a basic strain that generates 75 mg/L strictosidine. We further optimise this strain by introducing a membrane steroid binding protein and a second copy of the farnesyl pyrophosphate synthase mutant gene ERG20WW, boosting strictosidine levels by 5.5-fold to 398 mg/L. At these higher titres, a previously overlooked shunt product, (2E,6E)-2,6-dimethylocta-2,6-dienedioic acid (DOA), was identified that diverts flux from the pathway. Lastly, we reprogrammed our strictosidine strain to strictosidinic acid production by four genomic modifications. Final fed-batch cultivation in shake flasks resulted in 843 mg/L strictosidine or 548 mg/L strictosidinic acid, respectively, after 168 hours. Taken together, our work now grants access to strictosidinic acid by metabolic engineering, while revealing strategies to further enhance the production of strictosidine and related monoterpene indole alkaloids. These findings will help to produce plant alkaloids in microbial cell factories in the future at scale.

bioengineering↗

bioRxiv2025

Midbrain microglia-integrated organoids as a next-generation tool for chronic morphine withdrawal research: A pilot study

In the midst of an opioid epidemic, opioid use disorder (OUD) can lead to significant clinical impairment or distress (such as opioid dependence and/or addiction) and overdose deaths. Therefore, it is significant to elucidate the exact molecular mechanisms of OUD and identify more effective therapies. Human induced pluripotent stem cell (hiPSC)-derived organoids are self-organized 3D tissues and mimic in vivo human organs. Increasingly, human-specific features of opioid abuse are being investigated using emerging brain organoids, which faithfully model the key functional, structural and biological complexities of neural tissues. However, a significant limitation of brain organoids is the absence of microglia which plays a fundamental role in OUD-related remodeling of neural circuits. In this pilot study, using hiPSC KOLF2.1J cell line, we developed our approach for generating both midbrain organoid and microglia and verified that our midbrain organoid was successfully integrated with microglia. We found that chronic exposure to morphine triggers key elements of immune responses including increased TNF signaling and downregulation of sirtuin3 (Sirt3, a mitochondrial protein, preventing oxidative stress) and manganese superoxide dismutase (MnSOD, located in the mitochondrial matrix) in microglia-organoid co-cultures. Our findings suggest that immunocompetent midbrain organoids provide excellent models with which to study human-specific mechanisms of neuroinflammation and neurodegeneration. By combining disease relevance with scalability, the model system can be utilized as an effective tool for drug screening and toxicity testing.

neuroscience↗

bioRxiv2025

Golden Promise-rapid, a fast-cycling barley genotype with high transformation efficiency

The spring barley cultivar Golden Promise (GP) is the major reference genotype for transformation due to its high transformability and availability of a reference genome. However, GP is characterized by a long generation cycle and stress susceptibility under non-optimal growth conditions because it carries a mutation at the floral inducer Photoperiod-H1 (Ppd-H1). Previously, we showed that a GP introgression line, Golden Promise-fast (GP-fast), generated by introducing the wild-type Ppd-H1 allele from the winter barley cultivar Igri, exhibits early flowering and improved stress resilience. In this study, we generated a fast-cycling genotype, Golden Promise-rapid (GP-rapid), isogenic to GP with high transformation efficiency. We conducted two backcrosses of GP-fast to reduce the residual Igri genome. The resulting genotype contains only a single introgression of approximately 0.6 Mbp at the Ppd-H1 locus on chromosome 2H. Under speed breeding conditions, its generation time was reduced to 63 days (25% shorter than GPs 84 days). Parallel transformation of GP, GP-fast, and GP-rapid using CRISPR/Cas9-mediated genome editing of Ppd-H1 revealed high regeneration and transformation efficiencies of GP-rapid, comparable to GP. Overall, we report on the development of a fast-cycling GP isogenic line as a research tool for efficient generation of transgenic and gene-edited barley plants. HighlightsA new fast-cycling barley genotype, GP-rapid, reduces generation time by 25% while retaining high transformation efficiency, advancing functional genomic studies in barley.

plant biology↗

bioRxiv2025

Characterization of Cancer-Reactive T Cells and Neoantigen-specific T Cell Receptors

Not all tumor-infiltrating T cells are cancer-reactive (CR). Several studies have reported gene expression signatures associated with CR-T cells. To integrate these findings, we developed a computational workflow, CAT (Cancer-Associated T cells), which harmonizes existing CR-T cell signatures and applies them to identify CR-T cells across an atlas of one million T cells. Our findings reveal that the abundance of CR-T cells varies across cancer types and that baseline levels of CR-T cells predict patients responses to immunotherapy. In parallel, we established a high-throughput computational platform, Neo-TCR, for systematic screening of neoantigen-specific TCRs and their cognate neoantigens. The efficacy of Neo-TCR is validated by cross-validation studies and replications in two independent datasets. Together, our findings suggest a new direction for developing biomarkers for cancer detection and monitoring: integrating CR gene expression signatures with neoantigen-specific TCRs.

cancer biology↗

bioRxiv2025

Identification and functional characterization of an AMD associated c-ABL binding SNP streak within the ARMS2 gene promoter region

BackgroundLarge-scale genome-wide association studies (GWAS) have identified the human 10q26 locus as a major genetic risk factor for age-related macular degeneration (AMD). The AMD-associated interval has been refined to a 5,196 bp segment flanking the ARMS2-HTRA1 region, excluding HTRA1 and the ARMS2 3' indel (443del54ins) variant by risk haplotype analysis. Although the missense SNP rs10490924 has been proposed as a functional variant, its role in AMD remains controversial, and the causative variants and underlying mechanisms within this region remain unresolved. MethodsAn unbiased bioinformatic screen identified a 5-SNP block within the 5,196 bp interval that potentially alters c-ABL protein binding. Protein-DNA interactions were validated using electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assays. Genetic association with AMD (dry and wet subtypes) was assessed in patient cohorts using blood genomic DNA. The regulatory effect of the 5-SNP block was further examined using luciferase reporter assays. FindingsWe identified a 5-SNP block located [~]556 bp upstream of the ARMS2 start codon, representing a cluster of predicted c-ABL tyrosine kinase binding sites. This block, in complete linkage disequilibrium with rs10490924 (A69S), showed a strong association with both wet and dry AMD (136 controls, 179 dry AMD, 251 wet AMD). EMSA and ChIP confirmed direct c-ABL binding, while luciferase reporter assays demonstrated reduced transcriptional activity mediated by the 5-SNP block in the presence of c-ABL. InterpretationOur results suggest that the c-ABL-responsive 5-SNP regulatory streak in the ARMS2 promoter region act as functional non-coding elements that may contribute to AMD pathogenesis through altered transcriptional regulation.

molecular biology↗

bioRxiv2025

Open Raman Microscopy (ORM): A Modular Hardware and Software Framework for Accessible Raman Imaging

Raman microscopy is a label-free, non-destructive imaging tool for spatially resolved chemical fingerprinting. Its powerful ability to reveal molecular information has driven rapid growth in applications across fields as varied as materials science, environmental analysis, and biomedical research. Despite its versatility, the accessibility of Raman microscopy is limited by expensive commercial setups and the technical barriers faced by researchers attempting to build custom systems. Here, we introduce an Open Raman Microscopy (ORM) framework based on a readily accessible modular microscopy platform. The ORM platform provides configurations for both high-throughput imaging and confocal imaging. We developed a dedicated python-based control and acquisition software, the ORM-Integrated Raman and Imaging Software (ORM-IRIS) designed to accommodate modular integration and control of components, including the laser source, spectrometer, and translational stages. Implemented across three institutions we demonstrate the ORM platform for high-throughput imaging of articular cartilage tissue, confocal three-dimensional imaging of a zebrafish embryo, and imaging of gold colloid decorated surfaces for surface enhanced Raman spectroscopy. Together, this open-source hardware and software framework enhances the accessibility of Raman microscopy across an expanding range of scientific applications.

biophysics↗

bioRxiv2025

The mechanical code of DNA impacts its interaction with DNA gyrase

DNA:protein interactions involving large structural deformations of DNA underpin essential biological processes. Although correlative evidence suggests that local, sequence-encoded, mechanical properties of DNA can modulate its interactions with large bent-DNA complexes like nucleosomes, direct high-throughput measurements of programmable mechanical modulation of DNA:protein interactions remain lacking. DNA gyrase is a type II topoisomerase that introduces negative supercoils in bacterial chromosomes via a process that involves extensive, nucleosome-scale, DNA wrapping around its two C-terminal domains (CTDs). Here we combine Systematic Evolution of Ligands by EXponential enrichment (SELEX), neural network predictions of DNA intrinsic cyclizability, and high-throughput DNA-compete binding assays to broadly reveal that sequence-encoded DNA mechanics tunes gyrase:DNA interactions by modulating wrapping of DNA around the CTDs. Further, we find that both genomic gyrase cleavage sites, and SELEX-enriched strong gyrase-binding sequences, display marked mechanical asymmetry: an extended region of flexible DNA facilitating wrapping around only one CTD exists on one half of the enzyme footprint. High throughput binding assays further reveal that strong binding to one CTD alone can compensate for weaker dual binding, suggesting that asymmetric attachment may have evolved to balance the need for stable anchoring with conformational flexibility required for catalytic remodelling. Additionally, we identify key GC-rich motifs that independently enhance gyrase:DNA interactions, also in an asymmetric fashion. Our findings establish sequence-encoded DNA mechanics as a tunable determinant of protein:DNA interactions and illustrate how functional asymmetry within a symmetric enzyme can couple stable substrate association with structural plasticity.

biophysics↗

bioRxiv2025

End-to-end automation of repeat-target cryo-EM structure determination in CryoSPARC

Single particle cryo-EM is a valuable and growing technique for life science and drug discovery. Currently, obtaining state-of-the-art results from cryo-EM data analysis requires a human in the loop to analyze intermediate results and make image processing decisions. This bottleneck limits the achievable throughput of structure determination, especially in high-throughput settings such as structure-based drug design. In this work, we develop an end-to-end automation strategy for repeat-target structure determination using new tools in CryoSPARC. We demonstrate completely hands-off processing of 21 challenging G protein-coupled receptor (GPCR) datasets. In 17 of 21 cases, automated processing meets or exceeds published resolution and map quality and, in several cases, provides significant improvement in receptor and ligand density that allows improved model building. Our results on both active and inactive state GPCRs show that our automation strategy generalizes easily to new target classes, and that complete automation of data processing is straightforward to achieve in CryoSPARC. We provide downloadable CryoSPARC Workflow files so that users can import, replicate, adapt and extend our automated workflow for their own targets, enabling cryo-EM to be applied at larger scales and to answer larger biological questions.

biophysics↗

bioRxiv2025

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems

Aquatic environments host immense RNA viral diversity, yet the extent to which waterborne viruses influence the virome of aquatic animals remains unclear. Here, we conducted a comprehensive longitudinal metatranscriptomic analysis of water, shrimp, and fish across multiple culture stages in aquaculture systems. We identified 3,211 RNA viruses spanning 21 viral supergroups, with 97.4% representing novel species. Water exhibited the greatest viral diversity (3,093 species), followed by shrimp (1,280) and fish (398), with most viruses detected in shrimp and fish also detected in water. Diversity analyses revealed increasing richness and significant compositional shifts in 92 high-abundance viruses (>1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture.

microbiology↗

bioRxiv2025

Rice Ethylene Receptors Function as Ca2+-Permeable Ion Channels to Orchestrate Calcium-Dependent Antagonism of Ethylene Responses in Roots

The gaseous phytohormone ethylene governs essential plant processes spanning development, productivity, and stress resistance. As an essential nutrient and second messenger, calcium (Ca2+) is widely implicated in diverse plant physiological activities; however, its role in the ethylene signal transduction pathway remains elusive. Here, we identified a calcium-dependent antagonism of ethylene response (CAER) specifically modulates root elongation in the model cereal rice (Oryza sativa). Interestingly, we demonstrate that the ethylene receptors OsERS1 and OsERS2 both function as Ca2+-permeable channels, with OsERS1 further acting as a non-selective cation channel capable of permeating both monovalent and divalent cations. Mutagenesis analysis reveals that OsERS1 channel activity relies on homomeric assembly sites (C4/C6) rather than its ethylene-binding site (C65), indicating a clear decoupling of the molecular modules governing receptor signaling and ion channel function. The loss-of-function mutant Osers1/2 does not exhibit the CAER phenotype of the wild type (WT), confirm that this calcium-dependent regulatory mechanism is dependent on both OsERS1 and OsERS2. These findings uncover an unexpected ion-channel function of ethylene receptors, redefining their molecular identity beyond canonical signaling proteins and establishing the novel "hormone receptor-type ion channel (HRIC)" paradigm--one that fundamentally expands our understanding of how plant hormones transduce signals at the membrane.

developmental biology↗

bioRxiv2025

Oncogenic EGFR rewires STING-TBK1 immune machinery to license DNA damage tolerance

EGFR hotspot mutations (mEGFR), including primary L858R, exon 19 deletion, and secondary T790M, are pivotal oncogenic drivers in human non-small cell lung cancer (NSCLC). Meanwhile, NSCLC resistance to third-generation tyrosine kinase inhibitors (TKIs) is a major clinical challenge and remains mechanistically unresolved. Here, we uncover a previously unrecognized immunological mechanism whereby mEGFR exploits cGAS-STING innate immune signaling, conventionally regarded as tumor-suppressive, to sustain oncogenic signaling and therapeutic resistance. Mechanistically, mutant EGFR kinase aberrantly incorporates into STING signalosomes, directly phosphorylating STING (Y245/Y314) and TBK1 (Y577/Y677), stabilizing and hyperactivating TBK1 proteins, and establishing an unexpected and kinase loop critical for DNA damage repair. Disruption of this mEGFR-STING-TBK1 axis, genetically or pharmacologically, profoundly sensitized resistant patient-derived NSCLC organoids to chemotherapy. Combining TBK1 inhibition with cisplatin notably eradicated mEGFR-driven tumors in spontaneous and immunocompetent NSCLC murine models and patient-derived organoids. Our findings suggest a new function of cGAS-STING in the DNA damage repair program, its paradoxical exploitation by oncogenic driver mutations, and an innate immune therapeutic vulnerability in NSCLC.

cancer biology↗

bioRxiv2025

LabOS: The AI Co-Scientist That Sees and Works With Humans

Modern science advances fastest when thought meets action. LabOS represents the first AI co-scientist that unites computational reasoning with physical experimentation through multimodal perception, self-evolving agents, and XR-enabled, embodied human-AI collaboration. To empower agentic AI with embodied intelligence, we built LabSuperVision, the first vision-language-model (VLM) benchmark spanning biomedical and materials science laboratories, designed to evaluate scientific perception and reasoning. This endowed LabOS with visual reasoning capabilities that surpass those of general-purpose models on laboratory-specific tasks. By connecting multi-model AI agents, smart glasses, and human-AI-robot collaboration, LabOS allows AI to see what scientists see, understand experimental context, and participate in real-time execution through immersive XR interaction and robotic autonomation. Across applications-from cancer immunotherapy target discovery to cell engineering-LabOS shows that AI can move beyond computational design to participation, turning the laboratory into an intelligent, collaborative environment where human and machine discovery evolve together.

bioengineering↗

bioRxiv2025

C. elegans astrocytes mature in two phases from lineally distinct progenitors through CEH-43/DLX-mediated convergent transcription

Mammalian radial glia can remodel to become astrocytes, which acquire common transcriptional states despite spatially and lineally distinct origins. To uncover molecular programs driving convergent radial-glia-to-astrocyte transformation, we investigated development of C. elegans CEPsh astrocytes, which also arise from distinct progenitors without cell division. Using lineage-restricted single-cell RNA sequencing, we delineate a two-phase program for CEPsh astrocyte formation. Transcriptionally disparate nascent CEPsh glia rapidly acquire a common radial-glia-like state, facilitating nerve ring (brain) assembly. Subsequently, convergent CEPsh glia upregulate astrocyte-specific gene expression. Both phases require the distal-less transcription factor CEH-43, expressed in CEPsh glia and their progenitors. CEH-43 binds conserved astrocyte-expressed genes, cell-autonomously activating both early and late CEPsh glia-specific gene expression. CEH-43 misexpression is sufficient to induce CEPsh astrocyte reporter expression. We demonstrate that CEH-43 homologs, DLX1/2, are expressed in mouse astrocytes, and comparative transcriptomics reveal additional parallels. Our findings provide a molecular foundation for understanding cell-division-independent radial-glia-to-astrocyte transformation.

neuroscience↗

bioRxiv2025

Presynaptic Release Probability Determines the Need for Sleep

Sleep is universal among animals with synapses, yet the synaptic functions determining the need for sleep remain elusive. By directly measuring synaptic transmission at anatomically defined synapses in Drosophila, we found that synaptic strength remained stable or declined after sleep deprivation in a circuit-specific manner. In contrast, presynaptic release probability (Pr) consistently decreased with sleep loss across circuits and species, stemming from reduced Ca2+ influx or weakened vesicle-channel coupling at presynaptic terminals, and recovered after sleep. Bidirectional manipulations of Pr altered sleep pressure, establishing a causal relationship between presynaptic function and sleep need. Non-synaptic sleep-regulatory signaling pathways consistently modulate Pr but not synaptic strength. Thus, our findings identify Pr, rather than synaptic strength, as the conserved synaptic substrate underlying sleep need.

neuroscience↗