Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 217 records · Page 12Linked to original sources

bioRxiv2026

A comprehensive analysis of flagellar mutations in Vibrio cholerae: Trade-off mechanisms between motility loss and host adaptability

IntroductionCholera, caused by Vibrio cholerae, is a severe diarrheal disease threatening global health. The flagellum of V. cholerae functions not only for motility but also as an environmental sensor regulating virulence. The trade-off mechanism between motility loss and enhanced host adaptation remains unclear. ObjectiveThis study aimed to elucidate how flagellar mutations, which lead to a loss of motility, affect host adaptability in V. cholerae and to uncover the underlying molecular basis. MethodsWe analyzed 3,135 cholera-related samples to identify mutation hotspots in flagellar genes. A relevant flagellar mutant library was constructed and assessed for host adaptability. Multiple approaches, including molecular, genetic, transcriptomic, and proteomic analyses, were applied to dissect the FlgM-mediated pathway, with key findings revalidated in an adult mouse model using a specifically constructed 6N-labeled mutant pool. ResultsBig data analysis reveals those flagellar mutations in V. cholerae cluster in key structural and regulatory genes, including flhB, fliA, fliF, fliD, and fliM. Flagellar mutations led to a scenario where the secretion level of the regulator FlgM was negatively correlated with host adaptability. Intracellular FlgM inactivates either the {sigma}28 factor FliA directly or acts through the VarS/VarA-CsrA/BCD system, ultimately leading to the derepression of the quorum-sensing master regulator named hapR. HapR can directly bind to the promoters of genes involving in methionine transportation to regulate adaptability of V. cholerae. The 6N-labeled mutants pool experiment reconfirmed that motility loss promotes host adaptability via the FlgM-FliA-HapR-methionine axis. ConclusionOur findings demonstrate that secretion levels of the flagellar regulator FlgM drive an adaptive shift in V. cholerae from motility to host adaptability, mediated through quorum sensing and methionine metabolic reprogramming. This reveals a novel mechanism underlying bacterial evolution and pathogenicity.

microbiology↗

bioRxiv2026

TRPV4 Inhibition by a Natural Product Mediates Analgesia

The transient receptor potential vanilloid 4 (TRPV4) channel, a polymodal calcium-permeable cation channel, is activated by diverse stimuli, including hyposmolarity, moderate heat, mechanical stress, and acidic pH. TRPV4 plays a critical role in the onset and progression of pain and is implicated in multiple pathological conditions, positioning it as an attractive therapeutic target. However, the development of TRPV4-targeted therapeutics has been hindered by limited mechanistic understanding of its inhibition. Here, the natural product (R)-1-(3-ethylphenyl)ethane-1,2-diol (AH001) is identified as a potent, subtype-selective TRPV4 inhibitor. A potential gating mechanism of TRPV4 inhibition is proposed through a combination of structural analyses and site-directed mutagenesis. Electrophysiological studies and cryo-electron microscopy (cryo-EM) further reveal that AH001s glucuronide metabolite, AHP, retains robust TRPV4 inhibitory activity, providing a critical structural basis for rational optimization of AH001 as a lead compound. Notably, AH001 demonstrated significant efficacy in reducing neuronal hyperexcitability in dorsal root ganglia (DRGs) and produced pronounced analgesic effects across multiple pain models, highlighting its therapeutic potential in pain relief. This study offers critical structural and mechanistic insights into TRPV4 inhibition and lays the groundwork for the structure-based design of TRPV4-targeted therapeutics.

biochemistry↗

bioRxiv2026

P-Rex2 exhibits unique structural features and regulatory mechanisms distinct from the closely related RhoGEF P-Rex1

Rho guanine-nucleotide exchange factors (RhoGEFs) activate small GTPases to drive cytoskeletal rearrangement, cell motility, and proliferation. The phosphatidylinositol-3,4,5-trisphosphate (PIP3)-dependent Rac exchanger (P-Rex) subfamily of RhoGEFs includes P-Rex1 and P-Rex2 which, when misregulated, contribute to cancer progression and metastasis. P-Rex activity is controlled by accessory domains that maintain the protein in a cytosolic, autoinhibited state until activated by the lipid PIP3 and G protein {beta}{gamma} subunits. While P-Rex1 autoinhibition has been structurally and biochemically characterized, P-Rex2 has remained largely unexplored. Furthermore, despite high sequence similarity and domain conservation, P-Rex homologs differ in substrate specificity and regulatory interactions, and the molecular basis for these divergences is unknown. Here, we have taken an integrative structural biology approach to investigate these gaps. Using cryo-EM, we determined the first structure of full-length P-Rex2 to moderate resolution, revealing that, while the overall structure closely resembles that of P-Rex1, there is a substantial repositioning of the N-terminal module relative to the C-terminal core. This may play a key role in precluding the intramolecular interactions between the N- and C-terminal domains that are observed in autoinhibited P-Rex1. Hydrogen-deuterium exchange mass spectrometry revealed that, unlike P-Rex1, P-Rex2 dynamics are unaffected by IP4, the headgroup of PIP3. SEC-SAXS data support that the N-terminal module itself is less dynamic, and biochemical assays show that P-Rex2 may be more tightly regulated by autoinhibition, likely through a mechanism different from P-Rex1. These findings uncover unique features in the molecular mechanisms of P-Rex2 regulation.

biochemistry↗

bioRxiv2026

Abalone genomics reveals an ancient asymmetry axis and the multifunctionality of the mantle

Gastropod diversification represents one of the most spectacular evolutionary radiations, underpinned by a fundamentally asymmetric body plan and diverse pigmentation patterns. To understand the genetic underpinnings of these cardinal traits, we constructed a chromosome-level genome assembly for the rainbow abalone, Haliotis iris. Integrating systematic genomics, histoembryology, and molecular assays, we uncover an ancient regulatory axis, conserved for over 544 million years, in which the long non-coding RNA lncRNA1 functions as a competing endogenous RNA to shield pitx transcripts from miRNA-mediated degradation, thereby driving the establishment of asymmetric body patterning, including the mantle. Furthermore, we identify a wnt-mitf-tyr cascade as the driver of melanogenesis and demonstrate that the mantle is the primary site of melanin synthesis. Concurrently, we reveal the mantle as a multifunctional organ possessing mechanosensory capabilities. These findings elucidate the ancient genetic toolkit governing trait evolution in gastropods. TeaserA deeply conserved RNA switch directs gastropod body plans and reveals the mantles hidden talents.

genomics↗

bioRxiv2026

Integrative analysis of papain-like cysteine proteases and cystatins reveals stress-dependent regulatory modules in Arabidopsis thaliana

Plant papain-like cysteine proteases (PLCPs) and cystatins constitute a major protease-inhibitor system that contributes to plant signaling and responses to biotic and abiotic stress. Although the Arabidopsis genome encodes 31 predicted PLCPs and 7 cystatins, their coordinated regulation has not been systematically evaluated across major stress conditions. Here, we reprocessed and integrated AtGenExpress microarray datasets to analyze the expression patterns of 28 PLCPs and seven cystatins in response to bacterial infection (virulent and avirulent Pseudomonas syringae), wounding, and drought stress. In parallel, we performed in vitro enzyme activity assays to assess inhibition specificity of seven Arabidopsis cystatins against five abundantly expressed PLCPs. Finally, we used the support vector machine (SVM) package e1071 in R to integrate co-expression and inhibition data and to generate a hypothesis-generating PLCP-cystatin interaction network. Together, these analyses suggest that Arabidopsis deploys distinct PLCP and cystatin gene subsets in response to virulent versus avirulent bacterial infection, and that transcriptional modules associated with bacterial infection and wounding are largely distinct. In contrast, several drought-associated PLCP-cystatin modules overlap with those associated with basal defense, suggesting partially shared regulatory programs across abiotic and biotic stress.

plant biology↗

bioRxiv2025

Template-based RNA structure prediction advanced through a blind code competition

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previously unreleased structures to tackle this challenge. The top three submitted algorithms achieved scores within statistical error of the winners of the recent CASP16 competition. Unexpectedly, the top Kaggle strategy involved a pipeline for discovering 3D templates, without the use of deep learning. We integrated this template-modeling pipeline and other Kaggle strategies to develop a single model RNAPro that retrospectively outperformed individual Kaggle models on the same test set. These results suggest a growing importance of template-based modeling in RNA structure prediction.

biophysics↗

bioRxiv2025

OmniCell: Unified Foundation Modeling of Single-Cell and Spatial Transcriptomics for Cellular and Molecular Insights

A cells transcriptional programme is not fully defined by gene expression alone, but by the tissue context in which that programme is enacted. Single-cell RNA sequencing resolves molecular identity after dissociation, whereas spatial transcriptomics preserves tissue architecture but remains constrained by assay-specific sparsity and gene coverage. Here we present OmniCell, a tissue-contextual transcriptomic foundation model pretrained on 67 million dissociated and spatially resolved profiles. By integrating gene identity, expression magnitude and tissue context, OmniCell links transcriptional programmes to the cellular neighbourhoods and anatomical contexts in which they operate. OmniCell organised transcriptomes across molecular, cellular and tissue scales. It recovered cell-type-specific programmes and tissue-aligned gene modules, preserved robust cell-state structure across batches, species and rare populations, and improved the reconstruction of spatial cell identity, anatomical domains and cell-type composition. In human liver cancer Stereo-seq data, OmniCell resolved a tumour-margin transition zone characterised by immune infiltration, acute-phase inflammation, coagulation/complement activity and metallothionein-linked metal-ion detoxification. Contextual gene-embedding similarity analysis showed that gene relationships differed across tumour core, transition-zone and paratumour/adjacent non-malignant niches, indicating that OmniCell captures tissue-dependent gene function rather than expression similarity alone. In mouse brain development and macaque cortex, spatial virtual perturbations mapped regulatory genes onto stage- and region-specific anatomical programmes. Together, these results establish tissue context as a primary axis of transcriptomic representation and provide a framework for studying how cellular programmes acquire context-dependent biological meaning in intact tissues.

bioinformatics↗

bioRxiv2025

Semi-rational Engineering of Terminal Deoxynucleotidyl Transferase for High-efficiency Enzymatic de Novo DNA Synthesis

The 21st century has witnessed rapid advancements in synthetic biology, with DNA synthesis emerging as a foundational technology. Conventional phosphoramidite-based methods face significant limitations, including short DNA elongation lengths (<300 nt), hazardous chemical waste, and low stepwise incorporation efficiency. Enzymatic DNA synthesis using terminal deoxynucleotidyl transferase (TdT) offers a promising alternative, enabling kilobase-scale assembly with greater efficiency and minimal environmental impact. Here, we identified Bos taurus TdT (BtTdT) through UniProt database mining as a catalytically active scaffold for natural and 3'-modified dNTPs. Comprehensive characterization of BtTdTs enzymatic properties--including pH, temperature, metal ion dependence, and substrate specificity--revealed its optimal conditions. Truncation of the BRCT domain generated variants with enhanced activity compared to wild-type BtTdT. Guided by AlphaFold3-predicted structural models, we engineered a quintuple mutant (M5: Bt15AAR336L/K338G/L397M/E456S/D395G) optimized for 3'-ONH2-dNTP incorporation. M5 exhibited 30-fold activity enhancement relative to the triple mutant M3 (Bt15AAR336L/K338G/L397M) and achieved stepwise incorporation efficiency exceeding 98% in de novo synthesis of 10-nt ssDNA, demonstrating its potential for scalable enzymatic DNA synthesis. This work establishes a rational framework for TdT engineering through rational domain truncation and computational design, showing potential toward industrial-scale enzymatic DNA manufacturing.

synthetic biology↗

bioRxiv2025

Deletion of the polarity protein Llgl1 impairs cardiomyocyte intercalated disc integrity and permits cell cycle activity into adulthood

BackgroundCell polarity orchestrates spatial organization within tissues influencing cellular processes such as adhesion, proliferation, and differentiation. While the role of polarity proteins is well-established in epithelial systems, their function in mammalian cardiomyocytes remains poorly understood. Global deletion of the polarity protein, Llgl1, has been shown to impair cardiac trabeculation and disrupt cardiomyocyte junctions in zebrafish. Here, we investigate the role of Llgl1 in mammalian cardiomyocyte function. MethodsWe developed a mouse model whereby Llgl1 is deleted from cardiomyocytes (Llgl1CKO) and assessed cardiomyocyte intercalated disc integrity, cell cycle activity, cardiac function, and electrophysiology. We subjected mice to myocardial infarction to test if permanent Llgl1 deletion, or inducible Llgl1 deletion in adult cardiomyocytes (Llgl1TamCKO), influences the cardiac injury response. We performed RNAsequencing and in vitro knockdown and viral overexpression experiments to delineate the mechanisms by which Llgl1 influences cardiomyocyte phenotypes. ResultsLlgl1CKO mice display disrupted intercalated disc integrity indicated by reduced protein density at cardiomyocyte junctions, associated with electrical conduction defects that manifest as ventricular arrhythmia. Furthermore, Llgl1CKO mice display enhanced cardiomyocyte cell cycle activity extending into adulthood. Llgl1CKO mice and mice whereby Llgl1 is deleted by tamoxifen induction in adulthood both show improved cardiac function and reduced scar size following myocardial infarction. Mechanistically, Llgl1 alters mechanotransduction and cell cycle pathways in the heart, and regulates proper localization of N-cadherin to the cell membrane, a process that is optimized by phosphorylation of five serine residues at the C-terminus of Llgl1. ConclusionsWe elucidate a key role for Llgl1 in establishing proper intercalated disc integrity in mammalian cardiomyocytes. Disruption of intercalated discs and mechanotransduction via Llgl1 knockout is associated with cardiac arrhythmia, elevated cell cycle activity and resistance to cardiac injury. These studies shed light on mechanisms underlying intercalated disc establishment and connect disrupted cardiomyocyte junctional integrity with enhanced cell cycle activity.

cell biology↗

bioRxiv2025

Efficient Generation of Humanized Cloned Cattle via Embryonic Stem Cell-Mediated Dual-Round Site-Specific Editing

Transgenic cloning allows genetic modification in cattle, yet its translational potential is constrained by low cloning efficiency and limited gene-editing capacity, due largely to the restricted proliferative ability of somatic donor cells. Pluripotent stem cells (PSCs), with their unlimited self-renewal ability, represent a promising alternative to overcome these bottlenecks. Here, we first established stable bovine epiblast stem cell lines (bEpiSCs) and achieved site-specific integration of the HCSN2-HLF-GFP cassette into the {beta}-casein locus, with high transfection (72.07%) and correct integration efficiency (80.48%). Following Cre LoxP mediated excision of the selectable marker, we obtained marker free HCSN2-HLF bEpiSCs that retained pluripotency markers, tri lineage differentiation potential, and supported target protein expression in immortalized bovine mammary epithelial cells. When used as nuclear donors, these cells produced blastocysts with quality comparable to in vitro fertilization (IVF) embryos. Notably, cloning with HCSN2-HLF bEpiSCs resulted in the birth of twelve calves, with significantly higher birth and survival rates (30.71% and 16.74%, respectively) than those obtained using fibroblasts. Both PCR-based genotyping of the edited loci and microsatellite kinship analysis confirmed that all cloned calves were genetically derived from the HCSN2-HLF bEpiSCs. Collectively, this study establishes an efficient embryonic stem cell based platform for targeted gene editing and rapid production of multigene edited cloned cattle, offering a scalable strategy with strong potential for industrial translation.

bioengineering↗

bioRxiv2025

Identifying High-Dimensional Genomic Factors Modulating Biological Networks Across Multi-Omics Data

Biological traits such as genes, metabolites, and microbial taxa interact within complex networks, yet how genomic factors shape these interactions remains poorly understood. Here, we introduce GFBioNet, a computationally efficient method for identifying factors that modulate direct associations between biological traits within network models. Our two-stage strategy first estimates a baseline network using Gaussian graphical models and then tests whether genomic factors modulate specific network edges (trait-trait relationships), enabling scalable analysis of high-dimensional multi-omics data while explicitly controlling the false discovery rate (FDR). Simulations demonstrate reliable FDR control and high statistical power across a broad range of settings. Applied to multiple datasets, GFBioNet reveals host genetic variants influencing oral microbiome relationships, gut microbial taxa modulating metabolite networks in colorectal cancer, and somatic mutations and copy-number alterations reshaping gene expression networks in lung adenocarcinoma. By expanding network analysis to evaluate modifiers of trait-trait relationships, GFBioNet offers a versatile tool for uncovering the genomic architecture of biological networks across multi-omics studies.

genomics↗

bioRxiv2025

tBid mediated genetic ablation of connective tissue cells reveal their key regulatory function during limb regeneration in axolotls

Limb regeneration in adulthood is a fascinating phenomenon unique to salamanders, requiring precise coordination and interaction of various cell types. Connective tissue (CT) constitutes a major component of the limb and serves as the primary reservoir of positional information during regeneration. However, the direct evidence and the extent of CT in positional contribution remain limited. Here we develop an inducible Cre-LoxP-mediated tBid cell ablation system in axolotls and demonstrate efficient elimination of targeted muscle tissue and muscle stem cells through transient electroporation or genetic approach. Ablation of CT cells at early stages of regeneration results in delayed regeneration and loss of proximal limb segments (e.g., upper and lower limb), with minimal impact on hand differentiation. CT ablation during development yields similar defects as observed during regeneration, indicating an essential role for CT cells in determining the positional identity of developing and regenerating limb structures. Further scRNA-seq reveal a progressive proximal-to-distal transition among CT cells and identify distinct CT subtypes that contribute to proximal and distal segments. CT ablation results in reduction of the differentiated CT1--a subpopulation that maintains proximal identity throughout regeneration, and a delay of distal transformation in the proliferative CT1--a major CT subtypes showing progenitor property. These cellular shifts likely lead to the observed morphological deficits in regenerating limbs after CT ablation. Moreover, differentiated CT1 cells enhanced their interactions with surrounding cell types after CT ablation, to modulate adaptive proliferation in other populations, e.g., muscle stem cells. Our work establishes a tBid-based ablation strategy for functional studies of CT and other cell types in axolotls, and provides direct evidence demonstrating pivotal roles of CT cells in guiding positional memory and segmental patterning during organ regeneration.

molecular biology↗

bioRxiv2025

A K27-linked Ubiquitin Checkpoint Controls NOTCH Homeostasis

Cell surface receptors such as NOTCH1 must be tightly regulated to ensure developmental fidelity and prevent pathological activation. Although the proteolytic steps culminating in nuclear NOTCH1 signaling are established, how cells prevent excessive or uncontrolled activation has remained unresolved. Here we identify the autophagy-related protein UVRAG as a negative regulator of NOTCH1. Upon receptor activation, UVRAG, acting independently of autophagy, recruits and activates the E3-ligase ITCH to catalyze K27-linked ubiquitination of membrane-tethered NOTCH1, thereby licensing ESCRT-dependent lysosomal degradation. Disruption of the UVRAG-ITCH-ESCRT axis stabilizes activated NOTCH1 intermediates and amplifies oncogenic signaling. In T-cell leukemia models driven by constitutive NOTCH1 activity, restoring UVRAG expression reinstates receptor turnover, suppresses disease progression, and improves therapeutic response. These findings define a ubiquitin-directed safeguard circuit that enforces NOTCH1 signaling homeostasis and reveals a tunable axis for intervention in NOTCH1-driven cancers.

molecular biology↗

bioRxiv2025

Versatile high-speed volumetric imaging from microscopic to macroscopic scale by self-adaptive oblique plane microscopy

There is an increasing need for large-scale high-speed volumetric recording in complex multi-cellular model systems to define dynamic processes. Oblique plane microscopy (OPM) provides a solution that features oblique illumination, rapid optical scanning, and remote focusing to achieve real-time 4D microscopy. OPM implements light sheet imaging via a single primary objective lens, making the entire space below the objective accessible for large specimens, such as living mouse brain. Yet it is challenging to adopt OPM beyond a microscopic scale (i.e. size < 1mm), limiting its broad applications. Here we present a self-adaptive OPM that leverages Abbes sine condition to unlock its flexibility across a range of field-of-views (FOVs) (up to 8 mm2) and resolutions (down to 2.2 {micro}m3). This versatility enables brain-wide single neuron volumetric calcium imaging in behaving larval zebrafish (1x0.4 mm2 FOV at 5 Hz) and capillary blood cell tracking in living mouse brain (>3x3 mm2 FOV) with a sweeping 0.32 mm wide volume section at 100 Hz. In optically cleared mouse brain, the flexibility allows a screen-and-zoom capability by sequentially imaging the whole brain at low-and-high magnifications to locate and resolve subcellular structures such as dendritic tress and spines. By offering a switchable imaging resolution, volume, and speed, the self-adaptive OPM achieves a versatile platform for studying a wide range of multi-cellular model system, whether in vivo or fixed and optically cleared.

bioengineering↗

bioRxiv2025

Gasdermin E couples mitochondrial damage to pyroptotic neurodegeneration in Parkinson disease

Parkinsons disease (PD) features progressive loss of nigrostriatal dopamine neurons, but how mitochondrial damage engages programmed cell death pathways remains unresolved. Here, we identify gasdermin E (GSDME), the caspase-3-activated executor of pyroptosis, as a critical mediator of neurodegeneration in toxin-based PD models. In primary neurons and SH-SY5Y cells, the mitochondrial complex I inhibitor MPTP/MPP triggered caspase-3 activation, GSDME cleavage, and lytic membrane rupture. Genetic silencing of Gsdme or its transcriptional regulator SP1 reduced neuronal death. In vivo, Gsdme deficiency preserved substantia nigra pars compacta dopaminergic neurons, improved motor performance, and mitigated anxiety- and depression-like behaviors after MPTP administration. Loss of Gsdme also dampened microglial and astrocytic activation and lowered proinflammatory cytokines in striatum and substantia nigra. Mechanistically, cleaved GSDME localized to mitochondria, disrupted membrane potential, increased reactive oxygen species, and precipitated organelle injury, thereby coupling mitochondrial dysfunction to pyroptotic cell death. These findings identify GSDME-mediated pyroptosis as a mechanistic link between mitochondrial toxicity and neuroinflammation in PD and nominate GSDME as a therapeutic entry point to slow disease progression. SignificanceHow mitochondrial injury kills dopamine neurons in Parkinsons disease is a central unresolved question. We show that the pyroptosis executor GSDME is required for neurodegeneration and neuroinflammation in MPTP models, mechanistically linking caspase-3 activation and mitochondrial damage to lytic cell death. Targeting GSDME may provide a strategy to protect vulnerable neurons in PD. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/694264v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@15364e7org.highwire.dtl.DTLVardef@57b65org.highwire.dtl.DTLVardef@1e85108org.highwire.dtl.DTLVardef@1200d34_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsGSDME drives PD-linked neuronal loss. Silencing GSDME (or its transcriptional factor Sp1) ameliorates MPTP-triggered neuronal cell death. Genetic ablation of Gsdme is protective in the MPTP-induced PD mouse model. Gsdme-/-mice retain nigrostriatal DA neurons, show improved motor and affective behaviors, and exhibit reduced microglial and astrocytic activation and cytokines release upon MPTP treatment. Cleaved GSDME accumulates on mitochondria, collapses {Delta}{Psi}m, raises ROS, and links mitochondrial toxicity to pyroptosis, thus positioning GSDME as a tractable target to slow PD progression.

neuroscience↗

bioRxiv2025

Automatic binding of basic sensory features requires consciousness

Conscious awareness requires establishing coherent percepts. Yet, whether consciousness is necessary for initiating the integration of basic sensory features remains unclear. Competing theories implicate distinct functional regimes of consciousness in the process of feature binding and creating conscious percepts. We used a novel multi-feature oddball paradigm with intracranial stereo-electroencephalography (sEEG) recordings in awake and anesthetized states to investigate the functional boundary of consciousness. In the awake state, the auditory attributes of loudness and tone, as well as the binding of the two features, were automatically encoded without attention to the stimuli in a functionally localized sensory cortical network. In the anesthetized state, the cortical registration of single attributes was preserved, whereas the binding was abolished. Moreover, anesthesia mostly influenced later cortical processes after stimuli offset. These results reveal the borderline of exertion of consciousness between the encoding and manipulation of basic sensory features in local cortical circuits - the functional boundary of consciousness constrains the feedforward binding and recurrent process directly at local rather than global level computations.

neuroscience↗

bioRxiv2025

Fast Loading and Transformation of Large-Volume Bioimaging Data Consistently Approaching the I/O Peak Speed

High-resolution large-volume biological imaging techniques are now widely used in biological research, but inefficiencies in data processing and visualization persist due to bottlenecks in loading/saving pipelines and limitations of conventional pyramid formats. To address these issues, we have decoupled data loading process into reading from disk and in-memory decompression, while data saving has been separated into in-memory compression and writing to disk. This approach allows us to dedicate more CPU cores to decompression and compression tasks, optimizing resource allocation and maximizing disk I/O throughput. As a result, both loading and saving processes operate near the disks peak data transfer capacity. Further, we integrated a video stream-inspired format into the pyramid structure, allowing direct access to regions of interest (ROIs) without loading extraneous data into RAM, reducing memory overhead. Compared to the latest methods, our approach improves pyramid data transformation efficiency by at least 6x and dramatically accelerates downstream tasks like visualization and deep learning inference. TeaserNovel bioimaging data processing pipeline achieves near-peak I/O throughput via decoupled architecture and video-formatting.

bioinformatics↗

bioRxiv2025

Age-specific Aβ-Tau interactions underlie spatial memory deficits in an APP/PS1 amyloidosis model

BackgroundAmyloid-{beta} (A{beta}) and tau pathology are key molecular hallmarks of Alzheimers disease (AD), yet how their interaction contributes to cognitive decline remains unclear. We investigated the relationship between A{beta} burden, tau pathology, presynaptic density, and spatial learning and memory in the APPswe/PSEN1{Delta}E9 (APP/PS1) transgenic (TG) mouse model of amyloidosis. MethodsSpatial learning and memory were assessed with the Barnes maze test in male TG and wild-type (WT) littermate mice, aged 6, 12, and 18 months. Gross visual function was assessed indirectly in 18-month-old animals using the light/dark exploration test. Brains were collected for autoradiography of tau pathology and presynaptic density with [18F]Flortaucipir and [3H]UCB-J, respectively, while A{beta} plaque load was measured by immunohistochemistry. Correlation and linear mixed-effects regression analyses were used to assess relationships between behavioral and pathological measures. ResultsAPP/PS1 mice showed normal cognitive performance at 6 months, a selective long-term memory deficit at 12 months, and severe impairments in learning and retention at 18 months, independent of visual confounds. Age-dependent increases in [18F]Flortaucipir binding and A{beta} plaque load were observed in all brain regions of TG compared to WT mice, whereas [3H]UCB-J binding was increased in a region-dependent manner in 18-month-old TG vs. WT animals. Barnes maze performance during the final day of testing correlated negatively with both A{beta} and tau pathology across all areas examined. Linear regression revealed a significant association between tau and age and between tau and A{beta} in the cortex, indicating that memory decline in ageing TG mice was driven by the combined effects of these pathologies. ConclusionsDeficits in memory retention precede impairments in task learning performance in APP/PS1 mice. Spontaneous tau accumulation contributes to the progressive cognitive decline, capturing key aspects of the A{beta}-tau interaction observed in human AD.

neuroscience↗