Biology subjects

Zhao, Y.

Publications and source records attributed to Zhao, Y..

At least 271 records · Page 15Linked to original sources

bioRxiv2025

Distributed control circuits across a brain-and-cord connectome

Just as genomes revolutionized molecular genetics, connectomes (maps of neurons and synapses) are transforming neuroscience. To date, the only species with complete connectomes are worms1-3 and sea squirts4 (103-104 synapses). By contrast, the fruit fly is more complex (108 synaptic connections), with a brain that supports learning and spatial memory5,6 and an intricate ventral nerve cord analogous to the vertebrate spinal cord7-11. Here we report the first densely reconstructed adult fly connectome that unites the brain and ventral nerve cord, and we leverage this resource to investigate principles of neural control. We show that effector neurons (motor neurons, endocrine cells and efferent neurons targeting the viscera) are primarily influenced by sensory neurons in the same body part, forming local feedback loops. These local loops are linked by long-range circuits involving ascending and descending neurons organized into behavior-centric modules. Single ascending and descending neurons are often positioned to influence the voluntary movements of multiple body parts, together with the endocrine cells or visceral organs that support those movements. Brain regions involved in learning and navigation supervise these circuits. These results reveal an architecture that is distributed, parallelized and embodied, reminiscent of distributed control architectures in engineered systems12,13.

neuroscience↗

bioRxiv2025

DNAH14 deficiency impairs sperm motility by reducing flagellar beat amplitude

Male infertility affects approximately 15-20% of couples worldwide, with asthenozoospermia accounting for 19% of cases. Nevertheless, the genetic basis of many asthenozoospermia cases remains poorly understood. In this study, we generated Dnah14 knockout mice, which displayed subfertility due to impaired sperm motility despite normal sperm morphology. Comprehensive kinematic analysis revealed that Dnah14-deficient spermatozoa exhibited reduced flagellar beat amplitude but increased beat frequency, while other dynein components remained unaffected. Notably, increasing sperm concentration during in vitro fertilization (IVF) experiments partially rescued the fertilization defects caused by Dnah14 deletion, suggesting a compensatory mechanism for this specific form of asthenozoospermia. Our results establish DNAH14 as a critical regulator of sperm motility and propose a potential therapeutic strategy for affected individuals.

developmental biology↗

bioRxiv2025

Bidirectional Crosstalk Between Sleep and Pulmonary Arterial Hypertension

BackgroundPulmonary Arterial Hypertension (PAH) is a devastating cardiopulmonary disease characterized by pulmonary vascular remodeling due to vascular cells dysfunction. Among other clinical signs, emerging data suggest poor sleep quality in patients with PAH; however, how poor sleep impacts hemodynamic burden, symptom severity, and pulmonary vascular remodeling during PAH progression remains unknown. MethodsWe used two models of sleep disturbances (sleep fragmentation and chronic jet lag) and different mouse models of PAH to determine the effects of poor sleep on PAH. We carried out timepoint quantitative RT-PCR analyses to define the clock gene oscillations in human pulmonary artery smooth muscle cells (PASMCs) isolated from non-PAH and PAH patients. Bulk RNA-sequencing analysis, immunostaining, and proliferation assays were used to explore the mechanisms by which poor sleep impacts PAH. Electroencephalogram and Electromyogram recordings (EEG/EMG) were used to determine whether PAH affects sleep in mice. ResultsPoor sleep exacerbated right ventricular dysfunction, pulmonary vascular remodeling, and PAH. RNA-seq and immunostaining analyses showed that poor sleep induces lung inflammation. Inflammation affected the pulmonary vascular molecular clock to drive PASMC hyperproliferation and increased migration. SMC-specific deletion of Bmal1 protected mice from RV dysfunction, pulmonary vascular remodeling, and PAH. EEG/EMG measurements demonstrated that PAH causes poor sleep quality in mice. Lastly, we showed that improving sleep via melatonin delivery and blunting inflammation with clodronate inhibited pulmonary vascular remodeling and PAH. ConclusionsOur study demonstrates that PAH causes poor sleep which in turn induces inflammation, increases PASMC proliferation, and exacerbates PAH. This suggests that the relationship between PAH and poor sleep is a self-amplifying cycle, and that a combination of hypnotic and anti-inflammatory drugs may give PAH patients better clinical outcomes. Clinical PerspectiveO_ST_ABSWhat is New?C_ST_ABSO_LIPAH causes poor sleep quality which in turn induces lung inflammation, PASMC proliferation, and exacerbated PAH. C_LIO_LIBmal1 rhythmicity is disrupted, and its expression is increased in lungs of patients with PAH. C_LIO_LISMC-specific deletion of Bmal1 protects from PAH. C_LIO_LIImproving sleep quality and blunting inflammation attenuates PAH. C_LI What Are the Clinical Implications?O_LIBmal1 represents a promising disease-modifying agent with potential for clinical translation in the treatment of PAH. C_LIO_LIA combination of hypnotic and anti-inflammatory drugs has therapeutic potential to treat PAH. C_LI

pathology↗

bioRxiv2025

Off-target effects of PLX5622 revealed: mixing microglial function in anesthesia and addiction withdrawal

Microglia have gained increasing attention as important regulators in the brain. Acute microglial depletion using the colony-stimulating factor 1 receptor (CSF1R) inhibitor, PLX5622, has become a popular approach to uncover microglial function. PLX5622 treatment has been recently shown to significantly promote anesthetic emergence. In characterizing underlying mechanisms, we found that PLX5622 treatment did not change the global neuronal activity during anesthesia, but robustly enhanced anesthetic metabolism. Moreover, PLX5622 dramatically induced the expression of hepatic enzymes that extensively modify xenobiotic and endobiotic metabolism. Blocking increased enzymatic activity significantly reduced the arousal-promoting effects of PLX5622 in anesthesia, irrespective of microglial elimination. In addition, we demonstrate that enhanced drug metabolism also contributed to PLX5622-induced attenuation in nicotine-withdrawal anxiety. By revealing previously unrecognized effects of PLX5622, our findings raise caution in interpreting data generated from PLX5622 treatment and bring forward the need for designing more specific CSF1R inhibitors.

neuroscience↗

bioRxiv2025

Construction of a genome-wide pooled CRISPRi library as a resource for exploring the acid tolerance mechanism in Streptococcus mutans

Streptococcus mutans is recognized as the primary etiological agent of dental caries, one of the most prevalent infectious diseases globally. Its remarkable acid tolerance enables survival and proliferation in the low-pH biofilm microenvironment, establishing S. mutans as the dominant species in dental plaque and a key contributor to cariogenesis. Although numerous studies have identified genes linked to acid tolerance mechanisms, the full set of essential acid tolerance genes within its genome remains incompletely characterized, largely due to the lack of systematic, genome-scale investigations. To address this knowledge gap, we constructed a genome-wide pooled CRISPR interference (CRISPRi) library targeting 95% of the predicted S. mutans genes and employed next-generation sequencing to identify acid tolerance determinants systematically. Our screen revealed 95 acid tolerance-associated genes, a subset of which were functionally validated through gene knockout studies. Functional enrichment analysis demonstrated significant associations with metabolic pathways (including cofactor biosynthesis and amino/nucleotide sugar metabolism), tRNA modification, and transcriptional regulation. Protein-protein interaction (PPI) network analysis identified critical interactors (ComYC, SMU_1979c, DeoC, AcpP, NadD, and SMU_1988c) and two functionally cohesive modules. These findings provide novel mechanistic insights into the acid adaptation strategies of S. mutans and highlight potential therapeutic targets for caries prevention.

microbiology↗

bioRxiv2025

Characterization and Genome Insights of Two Novel Plastic-Degrading Acinetobacter Species

The ubiquitous presence of Acinetobacter species in the environment holds significant biotechnology potential, particularly in the degradation of various pollutants. In this study, we present two plastic-degrading bacteria, strains CAAS 2-6T and CAAS 2-13T, isolated from landfill leachate and a strawberry farmland, respectively. Strain CAAS 2-6T showed the highest 16S rRNA sequence similarity (97.7%) with Acinetobacter gerneri DSM 14967T, while strain CAAS 2-13T was most closely related (99.6%) to Acinetobacter gerneri PS-1T. Phylogenetic analysis of 16S rRNA and gyrB-rpoB genes placed both strains on distinct branches. Genomic comparisons revealed the highest digital DNA-DNA hybridization (dDDH) / average nucleotide identity (ANI) values for CAAS 2-6T with Acinetobacter indicus CIP 110367T (22.7%/77.0%) and for CAAS 2-13T with Acinetobacter gerneri PS-1T (66.5%/96.0%). Based on phenotypic and chemotaxonomic data, we propose strain CAAS 2-6T as the novel species Acinetobacter lentus sp. nov. (type strain CAAS 2-6T = GDMCC 1.3951T = JCM 36321T = KCTC 8156T), and strain CAAS 2-13T as the novel subspecies Acinetobacter kanungonis subsp. fragariae subsp. nov. (type strain CAAS 2-13T = GDMCC 1.3956T = JCM 36322T = KCTC 8157T). Both strains utilized PLA, PBSA, PBS, PBAT, and PBT as sole carbon sources, with CAAS 2-6T exhibiting superior growth on PBSA, PBS, and PBAT. Genomic annotation identified genes encoding plastic-degrading enzymes multicopper oxidase AbMCO and alkane hydroxylase AlkB. Enzymatic depolymerization assays confirmed in vitro production of plastic monomers. These findings expand the known metabolic capabilities of Acinetobacter and provide promising new candidates for plastic bioremediation. IMPORTANCEAcinetobacter spp. demonstrate significant potential for plastic bioremediation. We characterize two novel strains: CAAS 2-6T (A. lentus sp. nov.) and CAAS 2-13T (A. kanungonis subsp. fragariae subsp. nov.), capable of degrading five major polyesters (PLA, PBAT, PBT, PBS, PBSA) as sole carbon sources. Genomic and enzymatic analyses identified multicopper oxidase (AbMCO) and alkane hydroxylase (AlkB) as key depolymerase. This work: (i) Expands plastic-degrading Acinetobacter diversity; (ii) Provides novel biocatalysts and genomic resources; (iii) Delivers engineerable microbial chassis.

microbiology↗

bioRxiv2025

Cell-type-specific plasticity in synaptic, intrinsic, and sound response properties of deep-layer auditory cortical neurons after noise trauma

Peripheral trauma, such as noise-induced hearing loss (NIHL), triggers compensatory plasticity in the auditory cortex (ACtx) to maintain auditory function. While cortical plasticity in superficial cortical layers has been relatively well studied, the plasticity mechanisms governing deep-layer excitatory projection neurons remain less understood. Here, we investigated the plasticity of layer (L)5 extratelencephalic (ETs) and L6 corticothalamic neurons (CTs) following NIHL. Using a combination of in vitro slice electrophysiology, optogenetics, and in vivo two-photon imaging in a mouse model of NIHL, we characterized changes in evoked thalamocortical (TC) synaptic input strength, intrinsic excitability, and sound response properties. We found that TC input was initially equivalent between ETs and CTs, then shifted to CT-dominant one day after noise exposure. This shift renormalized to equivalent seven days after noise exposure and was associated with a transient increase in both the quantal size (q) in TC[->]CT synapses and intrinsic CT suprathreshold excitability. ETs maintained stable intrinsic properties and showed minor changes in their TC input. In vivo imaging revealed that CTs displayed a persistent elevation in sound intensity thresholds, whereas ETs transiently shifted their best frequency representation and reduced their responsiveness to high-frequency tones one day after NIHL, followed by recovery at seven days. Together, our findings highlight cell-type-specific plasticity mechanisms in deep-layer cortical neurons, enhance our understanding of cortical adaptation to peripheral damage, and highlight targets for developing therapeutic strategies to mitigate hearing loss and related disorders such as tinnitus and hyperacusis. Short AbstractPeripheral damage drives auditory cortex (ACtx) plasticity, but the underlying synaptic and cellular mechanisms remain poorly understood. We used a combination of in vitro slice electrophysiology, optogenetics, and in vivo two-photon imaging to investigate layer 5 extratelencephalic (ET) and layer 6 corticothalamic (CT) neuronal plasticity in mice, following noise-induced hearing loss (NIHL). Thalamocortical (TC) input was initially balanced between CTs and ETs but shifted to CT-dominant one day post-NIHL and then normalized by day seven. This transient shift was accompanied by increased quantal size and suprathreshold excitability in CTs, with minimal changes in ETs. In vivo, CTs exhibited persistent elevation in sound intensity thresholds, while ETs showed a transient shift in frequency tuning and reduced high-frequency responsiveness that recovered within a week. These findings reveal distinct, cell-type-specific plasticity mechanisms in deep-layer ACtx neurons following peripheral damage and highlight potential targets for treating hearing loss-related disorders such as tinnitus and hyperacusis.

neuroscience↗

bioRxiv2025

An increase of NPY1 expression leads to inhibitory phosphorylation of PIN-FORMED (PIN) proteins and suppression of pinoid (pid) null mutants

The PINOID (PID) protein kinase is required for flower initiation in Arabidopsis. The pid mutants fail to initiate flowers on inflorescences, a phenotype that is mimicked by disrupting either the NAKED PINS IN YUC MUTANTS (NPY) gene family or PIN FORMED 1 (PIN1). Both PID and NPY1 have been reported to positively modulate PIN-mediated polar auxin transport. Here, we show that overexpression of NPY1 (NPY1 OE) completely suppressed pid null mutants, demonstrating that NPY1 functions downstream of PID. NPY1 OE triggered phosphorylation of PIN proteins at multiple sites that are mostly different from the previously characterized phosphorylation sites regardless of the presence of PID. Phosphorylation of the newly identified PIN sites in NPY1 OE plants likely leads to the inhibition of PIN functions, as we previously showed that pid is suppressed by decreasing PIN1 gene dosage or decreasing PIN1 activity. Furthermore, we show that the Ser/Thr rich C-terminal motif in NPY1 is phosphorylated and is required for pid suppression by NPY1 OE. Overexpression of NPY1 that lacked the C-terminal motif (NPY1{Delta}C) failed to rescue pid, but overexpression of NPY1{Delta}C was still able to trigger phosphorylation of PIN proteins including PIN2, which is known to cause agravitropic roots when mutated. NPY1{Delta}C overexpression plants displayed a complete loss of root gravitropic response, likely caused by PIN2 phosphorylation. Our results suggest a pathway for auxin mediated-flower initiation, in which PID regulates NPY1 accumulation and/or activity, and subsequently, NPY1 triggers phosphorylation of PIN proteins and inhibition of PIN functions.

plant biology↗

bioRxiv2025

Gut microbiota and bile acids changes in MASLD mice model with hepatic PLD1 knockout

Hepatocyte phospholipase D1 (PLD1) knockout alleviated metabolic dysfunction-associated steatotic liver disease (MASLD) in mice, but the underlying mechanism is largely unknown. In this study, high-fat diet is fed to wild type (Con) and hepatocyte PLD1 knockout (Con_KO) mice to establish MASLD model (HFHC and HFHC_KO). Intestinal contents of mice are analyzed via metagenomics and metabolomics, the liver bile acids are assessed by mass spectrometry imaging. At phylum level, Bacillota in the intestines of MASLD model mice are significantly increased and Bacteroidota are significantly decreased. However, after the deletion of hepatocyte PLD1, Pseudomonadota and Candidatus Bathyarchaeota are significantly decreased in the MASLD model mice. Then at species level, compared with Con group, the Faecalibaculum rodentium is significantly increased in HFHC group, in which hepatocyte PLD1 knockout causes Desulfovibrionaceae bacterium LT0009 and Lachnospiraceae bacterium 10-1 to significantly decrease. As for intestinal bile acids, two bile acids (Hyodeoxycholic acid and Glycolithocholic acid) are found to be different between the HFHC_KO group and the HFHC group. Association analysis shows the Faecalibaculum co-occurs with DCA, {beta}MCA, {Omega}MCA and MCA, while probiotic Bacteroides uniformis is significantly correlated with UDCA, 12-KetoLCA, 7-KetoLCA. Finally, mass spectrometry imaging reveals that TCA and TDCA in liver are significantly decreased after hepatocyte PLD1 knockout. These findings demonstrate that hepatocyte PLD1 knockout alters gut microbiota and bile acids profiles, suggesting PLD1 deficiency may modulate MASLD progression by changing intestinal microbiota-bile acid homeostasis. HighlightsHere, we show that hepatocyte PLD1 knockout alters gut microbiota and bile acid profiles in metabolic fatty liver disease mouse by high-fat diet. O_LIWild type (Con) and hepatocyte PLD1 knockout (Con_KO) mice were used to establish HFHC and HFHC_KO models, respectively. C_LIO_LIIntestinal contents were collected for metagenomic and metabolomics analysis, and liver tissues were taken for mass spectrometry imaging to investigate gut microbiota-bile acid relationships. C_LIO_LIIn HFHC_KO mice, Desulfovibrionaceae bacterium LT0009 and Lachnospiraceae bacterium 10-1 were significantly reduced, accompanied by altered HDCA and GLCA. C_LIO_LIAssociation analysis revealed Faecalibaculum co-occurred with DCA, {beta}MCA, {Omega}MCA, and MCA, while Bacteroides uniformis was significantly associated with UDCA, 12-KetoLCA, and 7-KetoLCA. C_LIO_LIMass spectrometry imaging showed hepatocyte PLD1 knockout significantly decreased liver TCA and TDCA, suggesting PLD1 deficiency may modulates MASLD progression via microbiota-bile acid homeostasis. C_LI O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/663496v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1b5bfa8org.highwire.dtl.DTLVardef@139ed05org.highwire.dtl.DTLVardef@1f7e905org.highwire.dtl.DTLVardef@e34b59_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Pluripotent stem cell-derived siTNK cells attack tumors via a synthetic CD8-CD28 TCR complex

Tumor-associated antigen-specific T cell receptor (TCR)-engineered T cells offer a promising strategy for cancer therapy. Natural killer (NK) cells exhibit broad anti-tumor activity with low side effects but lack the capacity to recognize intracellular antigens. Here, we found that the human pluripotent stem cell (hPSC)-derived iNK cells, unlike tissue-isolated NK cells, expressed all four CD3 subunits at the transcriptome level. We introduced a synthetic gene-expressing complex (SCOTR), encoding a tumor antigen- specific TCR, CD8 coreceptor, and CD28 costimulatory molecule, into hPSCs to generate SCOTR-hPSCs. The SCOTR-hPSCs gave rise to abundant synthetic TCR complex-expressing iNK (siTNK) cells via an organoid induction method. These siTNK cells showed HLA-dependent, antigen-specific cytotoxicity against tumor cells and significantly suppressed tumor growth in tumor xenograft animal models, while also preserving universal non-specific tumor-killing activity. Collectively, siTNK cells, as hPSC-derived hybrid cells with dual features of adaptive T and inherent NK cells, offer an artificial cell source for human immunotherapies.

immunology↗

bioRxiv2025

Synaptic properties of layer 6 auditory corticothalamic inputs in normal hearing and noise-induced hearing loss

Layer 6 corticothalamic neurons (CTs) provide strong feedback input that is crucial to perception and cognition in normal and pathological states; however, the synaptic properties of this input remain largely unknown, especially in pathology. Here, we examined the synaptic properties of CT axon terminals in the medial geniculate body (MGB), the auditory thalamus, in normal hearing mice and in a mouse model of noise-induced hearing loss. In normal hearing mice, we found that the synaptic strength of CTs to the core-type ventral subdivision of the auditory thalamus (MGv), which mainly conveys rapid sensory information, is stronger than the synaptic strength of CTs to the matrix-type dorsal subdivision of the auditory thalamus (MGd), which likely conveys higher-order internal state information. This is due to increased functional release sites (n) in CT[->]MGv compared to CT[->]MGd synapses. After noise trauma, we observed enhanced short-term facilitation in CT[->]MGd but not CT[->]MGv synapses. Our findings reveal a previously unknown mechanism of short-term synaptic plasticity after noise-induced hearing loss via which CTs enhance the throughput of matrix-type thalamus, likely to improve perceptual recovery via higher-order contextual modulation.

neuroscience↗

bioRxiv2025

MuSHIN: A multi-way SMILES-based hypergraph inference network for metabolic model reconstruction

Genome-scale metabolic models (GEMs) are indispensable tools for probing cellular metabolism, enabling predictions of metabolic fluxes, guiding strain optimization, and advancing biomedical research. However, their predictive capacity is often compromised by incomplete reaction networks, stemming from gaps in biochemical knowledge, annotation inaccuracies, and insufficient experimental validations. Here we present MuSHIN (Multi-way SMILES-based Hypergraph Interface Network), a novel deep hypergraph learning method that integrates network topology with biochemical domain knowledge to predict missing reactions in GEMs. Evaluated on 926 high- and intermediate-quality GEMs with artificially removed reactions, MuSHIN significantly outperforms state-of-the-art methods, achieving up to a 17% improvement across multiple metrics and maintaining robust recovery even under severe network sparsity. Furthermore, MuSHIN substantially enhances phenotypic predictions in 24 draft GEMs associated with fermentation by resolving critical metabolic gaps, as validated against experimental measurements. Together, these findings highlight MuSHINs potential to advance GEM reconstruction and accelerate discoveries in systems biology, metabolic engineering, and precision medicine.

bioinformatics↗

bioRxiv2025

DREAM-GNN: Dual-route embedding-aware graph neural networks for drug repositioning

Drug repositioning presents a compelling strategy to accelerate therapeutic development by uncovering new indications for existing compounds. However, current computational methods are often limited in their ability to integrate heterogeneous biomedical data and model the intricate, multi-scale relationships underlying drug-disease associations, while large-scale experimental validation remains prohibitively resource-intensive. Here we present DREAM-GNN (Dual-Route Embedding-Aware Model for Graph Neural Networks), a multi-view deep graph learning framework that incorporates biomedical domain knowledge with two complementary graphs capturing both topological structure and feature similarity to enable accurate and biologically meaningful prediction of drug-disease associations. Extensive experiments on benchmark datasets demonstrate that DREAM-GNN significantly outperforms current state-of-the-art methods in recovering artificially removed repositioning candidates. These results establish DREAM-GNN as a robust and generalizable computational framework with broad potential to streamline drug discovery and advance precision medicine.

bioinformatics↗

bioRxiv2025

Endogenous Nitroalkene Exploits Dependence on Autophagy-Lysosome Pathway in PARPi-Resistant TNBC

Lack of DNA double-strand break repair efficiency exquisitely sensitizes cancers to poly-ADP ribose polymerase inhibitors (PARPi). Unfortunately, resistance to PARPi poses an insurmountable challenge for patients. Mechanisms that confer insensitivity to PARPi therapy include enhanced DNA damage repair and autophagy. Natural and non-natural unsaturated fatty acid nitroalkene derivatives (NFA) show anticancer actions that sensitize TNBC cells to PARPi and other DNA-damaging treatments. We reveal that nitro-oleic acid (OA-NO2) re-sensitizes PARPi-resistant TNBC cells to PARPi. RNA-seq analysis of clinically relevant mutBRCA1 PARPi-resistant TNBC cell lines exhibited upregulation in autophagy and lysosomal pathways. Bio-orthogonal analysis identified the autophagy regulator SQSTM1/p62 as a novel OA-NO2 target, alkylating two redox-sensitive Cys residues of p62 (Cys105 and Cys113). These Cys are essential for p62 regulation of autophagy and mimicked the effects of p62 Cys105 and Cys113Ala mutants and when alkylated by OA-NO2 showed impaired p62 oligomerization, degradation, and inhibition of autophagy. Combination treatment of PARPi-resistant TNBC with a PARPi and OA-NO2 synergistically inhibited p62-associated autophagy and lysosome function. These data emphasize the clinical potential of OA-NO2 for treating PARPi-resistant TNBC patients.

pharmacology and toxicology↗

bioRxiv2025

A Compact Two-Photon Module for Simultaneous Dual-Depth, Multi-Region in vivo Brain Imaging

Understanding how distributed brain regions interact across cortical depths is crucial for uncovering the neural basis of behavior and cognition. Two-photon microscopy (2PM) excels at imaging the superficial layer, while three-photon microscopy (3PM) penetrates deep tissues but lacks sufficient speed for capturing fast superficial dynamics. Here, we present a compact two-photon imaging module (2PIM) that seamlessly integrates with existing 3PM to achieve simultaneous, high-speed imaging of superficial and deep brain regions, while preserving the deep tissue penetration of 3PM. This dual-modality system allows for remote and independent control of imaging planes in both axial and lateral dimensions. Leveraging this technology, we discovered context-dependent modulation of hippocampal CA1 and visual cortex responses to identical tactile stimuli, layer-specific temporal dynamics in sensory cortex during air puff stimulation, and depth-divergent neuronal activity patterns in motor cortex across acute-to-chronic pain. These results highlight the systems potential for dissecting the spatiotemporal coordination of distributed brain circuits.

bioengineering↗

bioRxiv2025

SpatialMap: A Scalable Deep Learning Method for Cell Typing in Subcellular Spatial Transcriptomics

Subcellular imaging transcriptomics has offered unprecedented resolution of spatial mapping of gene expressions at subcellular level. However, accurate and robust cell type annotation at cellular level remains a challenge. Here we present SpatialMap, a deep weakly supervised cell typing framework that combines graph neural networks (GNN) with transfer learning to annotate cellular identities in subcellular spatial transcriptomics (ST). SpatialMap consistently outperforms state-of-the-art annotation methods on both simulated and real-world ST datasets. It demonstrates strong scalability across diverse tissue types and platforms, including NanoString CosMx, MERFISH and 10x Genomics Xenium. When applied to a mouse primary motor cortex dataset, SpatialMap successfully identified Micro, L4/5 IT, and L6 IT Car3 absent from the reference data, showcasing its capability to discover novel cell types. Furthermore, SpatialMap accurately annotated malignant cells in human liver cancer samples. Its design also enables seamless extension to cross-omics cell typing and cross-platform annotation within proteomics.

bioinformatics↗

bioRxiv2025

NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing

Nanopore long-read sequencing has expanded the capacity of long-range, single-base, and single-molecule DNA-methylation (DNAme) detection and haplotype-aware allele-specific epigenetic phasing. Previously, we benchmarked and ranked the robustness of seven computational tools for DNAme detection using nanopore sequencing. The top performers were Megalodon, Nanopolish, DeepSignal and Guppy. However, these algorithms exhibit lower performance at regions with discordant non-singleton DNAme patterns compared to genome-wide regions. Furthermore, long-read sequencing analysis of mammalian genomes requires higher computational resources than next-generation sequencing. To address these issues, we developed a NANOpore Methylation (NANOME) a consensus DNAme predictive model using XGBoost, which integrates the output of Megalodon, Nanopolish, and Deepsignal for analyzing data obtained using Oxford Nanopore Technologies (ONT). NANOME enhanced DNAme detection precision (mean square error) at single-base resolution by 11% and improved accuracy (F1-score) at single-molecule resolution by 2.4% for human B-lymphocyte European cell lines (NA12878). The consensus model also detected [~]200,000 more CpGs than all three tools. Combing variant calling and long-read phasing, NANOME can detect haplotype-aware allele-specific DNAme in known imprinting controls in resolved and previously unresolved regions. We conducted haplotype-aware methylation detection on the T2T genome for dataset NA12878, revealing significant variations in differentially methylated region (DMR) density between gap and non-gap regions. Overall, NANOME represents a significant step forward in DNAme detection and long-range epigenetic phasing, offering a robust and accessible tool for researchers studying the epigenome.

bioinformatics↗

bioRxiv2025

The time of the quantitative biology in cell level: Increasing stomatal density to an intermediate level through over-expressing FSTOMAGEN improved the biomass of plants

Stomata are the pores on plant surface, and these tiny pores are responsible for the flow of gas between plants and atmosphere. Currently, whether quantifying stomatal density to a moderately high level via genetical manipulation could improve Arabidopsis biomass remains unknown. The Arabidopsis transgenic lines with increased stomatal density were acquired through overexpressing a gene (the homologs of STOMAGEN, FSTOMAGEN, the homologs in Flaveria). The biomass of Arabidopsis transgenic lines with intermediate stomatal density increased. Compared with the other lines, the biomass of the transgenic lines with excessive stomatal density exhibited no difference or decrease. There was a positive and significant correlation between biomass and relative water content. During the earlier phase of growth, the leaf growth rate and leaf area of the lines with higher stomatal density was faster and larger respectively, and there was a significant linear relationship between stomatal density and leaf growth rate and a strong linear relationship between stomatal density and leaf area, which was in agreement with the notion that more stomata indicated faster CO2 assimilation and then faster accumulation of biomass, although it occurs in earlier phase. This suggested that the increased biomass was attributed to the earlier phase. Results indicated that finely tuning stomatal density could improve Arabidopsis biomass by genetically manipulating FSTOMAGEN. The functions of STOMAGEN homologs are extremely conserved in the evolution, thus it is promising that this genetically modified strategy could be applied in other species, which benefits the reduction of the concentration of atmosphere CO2 and the production.

cell biology↗