Biology subjects

Liu, W.

Publications and source records attributed to Liu, W..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Metabolomics-Guided Machine Learning Reveals Diagnostic and Mechanistic Biomarkers in CHB with MASLD

BackgroundMetabolic dysfunction-associated steatotic liver disease (MASLD) often coexists with chronic hepatitis B (CHB), yet early diagnosis remains challenging, particularly in non-obese patients or those with subclinical features. This study aimed to identify metabolic signatures of CHB-related MASLD and construct a predictive model using untargeted metabolomics integrated with machine learning. MethodsSerum metabolomics was performed on 160 subjects (80 CHB + MASLD and 80 healthy controls). Differential metabolites were identified and analyzed using KEGG enrichment and 4 machine learning algorithms (Random Forest, XGBoost, SVM, and LASSO). Metabolite-clinical correlations and diagnostic model performance were evaluated. ResultsA total of 924 differential metabolites were identified, with significant enrichment in pathways related to the TCA cycle, sphingolipid metabolism, and amino acid turnover. Machine learning prioritized six robust and biologically relevant metabolites: L-aspartic acid, succinic acid, caproic acid, sebacic acid, monomenthyl succinate, and glycolaldehyde, which consistently distinguished CHB + MASLD patients from controls (AUC > 0.75). These metabolites reflect key disruptions in mitochondrial function, lipid oxidation, and redox homeostasis. Integrated models combining metabolomics with clinical indices achieved perfect classification (AUC = 1.000). ConclusionCHB-associated MASLD is driven by systemic metabolic remodeling centered on mitochondrial overload, oxidative stress, and impaired amino acid metabolism. The identified metabolites provide mechanistic insights and hold promise for non-invasive MASLD screening in CHB patients. This study underscores the potential of multi-algorithmic metabolomics in advancing early diagnosis and personalized management of complex liver comorbidities.

bioinformatics↗

bioRxiv2025

Biomolecular tracking by FIRESCAPE reveals distinct modes of clearance, damage induction and cellular uptake for extracellular histone H3

In attempting to observe the behaviour of a protein of interest in vivo, akin to other observer effects, current techniques require modifications or interventions that inherently alter the protein or its host, leaving one uncertain as to whether natural behaviour remains unperturbed. The study of chromatin has mostly been restricted to defining its function in the nucleus, where histone proteins fulfil vital roles in packaging genomic DNA and regulating transcription. However, chromatin components can be released into the extracellular space, either intentionally via cellular secretion or during disease-induced cell death. These extracellular chromatin components, depending on the context, can consist of: free histones, free DNA, intact nucleosomes (histone octamers wrapped by DNA), or heterogeneous, higher order structures such as neutrophil extracellular traps (NETs). They have been associated with diverse pathologies such as inflammation, cancer, and sepsis, and distinct toxic effects. However, there is a widely acknowledged lack of methods that distinguish between them and between their unique functions. Here, we now address protein observer effects to explore the fate and function of extracellular free histones by utilizing FIRESCAPE ([18F]-Fluorine Isotopic Radiolabeling Enabling Scanning of Clearance After Proteolytic Events), a novel radiolabeling concept that leverages the unique, high-sensitivity properties of the radioisotope fluorine-18, 18F, and residue-specific protein editing chemistry. By installing close and then true 18F-containing protein sidechain mimics site-specifically, FIRESCAPE enables the hierarchical in vivo scanning of the half-lives, proteolytic susceptibility and clearance of single residues in a protein of interest, and at microdoses far below toxic levels (low nanomole). These radioequivalent proteins bearing near-zero-size, zero-background labels now precisely reveal the strikingly distinct distribution, half-lives, damage-inducing abilities and accumulation of free extracellular histones in cellulo and in vivo compared to intact nucleosomes. Free extracellular histone H3 is rapidly cleared from circulation, mediated first by proteolysis of the histone tail. By contrast, direct injection of free histones vs nucleosomes into tissue that is unprotected by such proteolysis (brain), provokes a starkly different response; free histones exhibited limited diffusion and swiftly promoted damage both in cell culture and in vivo, whilst intact nucleosomes were essentially passive and benign. Remarkably, synthetic extracellular histone H3 was observed to enter cells and integrate into chromatin, indistinguishable from native H3 in both localization and post-translational modification (PTM) accumulation, yet paired with cellular and tissue damage. The exploratory studies described here now provide much needed clarity to the distinct fates and effects of extracellular histones vs nucleosomes, in particular the strongly damaging effects of free histones, their rapid uptake into cells, and an associated histone-specific proteolysis pathway via the removal of the histone tail.

biochemistry↗

bioRxiv2025

Integral Synthesis and Clearance Analysis via DIA (ISDia) Reveals Coordinated Protein Dynamics Regulation during Endoplasmic Reticulum Stress

Endoplasmic Reticulum (ER) stress disrupts protein homeostasis, driving cellular responses critical for survival, development and disease. However, systematic proteome-wide analyses of protein synthesis and clearance during ER stress remain limited. In this study, we developed Integral Synthesis and clearance analysis via DIA (ISDia), a robust mass spectrometry (MS)-based workflow that integrates multiple pulsed-SILAC labeling timepoints under one condition into a single sample and utilize data-independent acquisition (DIA) to quantify heavy and light peptide changes across conditions. It enables proteome-wide tracking of protein synthesis and clearance with high coverage by directly comparing light and heavy peptides in pSILAC-DIA experiments across multiple conditions. Using ISDia, we uncover diverse regulatory mechanisms by which protein synthesis and clearance are modulated to regulate protein abundances during ER stress, revealing PERK dependent and independent regulatory mechanisms across subcellular compartments, complexes and isoforms. These findings highlight the potential of ISDia as a powerful and widely applicable workflow for revealing protein abundance regulatory mechanisms.

systems biology↗

bioRxiv2025

A scalable computational framework for predicting gene expression from candidate cis-regulatory elements

Deciphering the relationships between cis-regulatory elements (CREs) and target gene expression has been a long-standing unsolved problem in molecular biology, and the dynamics of CREs in different cell types make this problem more challenging. To address this challenge, we propose a scalable computational framework for predicting gene expression (ScPGE) from discrete candidate CREs (cCREs). ScPGE assembles DNA sequences, transcription factor (TF) binding scores, and epigenomic tracks from discrete cCREs into 3-dimensional tensors, and then models the relationships between cCREs and genes by combining convolutional neural network with transformer. Compared with current state-of-the-art models, ScPGE exhibits superior performance in predicting gene expression and yields higher accuracy in identifying active enhancer-gene interactions through attention mechanisms. By comprehensively analyzing ScPGEs predictions, we find a pattern in true positives (TPs) that the regulatory effect of cCREs on genes decreases with distance. Inspired by the pattern, we design two methods to enhance the ability to capture distal cCRE-gene interactions by incorporating chromatin loops into the ScPGE model. Furthermore, ScPGE accurately discovers some crucial TF motifs within prioritized cCREs and reveals the different regulatory types of these cCREs.

bioinformatics↗

bioRxiv2025

The Winners Take It All? Evolutionary Success ofH5Nx Reassortants in the 2020-2024 Panzootic

Avian influenza viruses undergo frequent genetic reassortment, which can coincide with phenotypic changes in transmission, pathogenicity, and host species niche. Since 2020, clade 2.3.4.4b H5 high pathogenicity avian influenza viruses (HPAIVs) have driven a global panzootic, causing mass mortality in wild birds, poultry, and, for the first time, repeated spillover infections in a variety of mammalian species. This worldwide resurgence of H5 HPAIV has coincided with a dramatic increase in the number of circulating reassortant strains; however, the scale, impact and drivers of these reassortants remain unclear. Here, we combined statistical and phylodynamic modelling to reconstruct the global evolutionary dynamics of H5Nx viruses across four epizootic seasons (2020-2024). We identified 209 genetically distinct reassortants, stratified into three transmission categories based on their phylogenetic and epidemiological profiles. Accounting for sampling depth and HPAIV incidence, we estimated that reassortants emerged most frequently from Asia, but major reassortants associated with increased host range, inter-seasonal persistence, and long-range dissemination, more frequently emerged from Europe. Altogether, reassortant emergence followed an episodic pattern in which most reassortants were transient, but 2% seeded large clusters of secondary reassortants soon after their own emergence. Statistical modelling revealed that reassortant success was strongly shaped by ecological factors, including sustained circulation in specific wild bird orders and detection across a wider range of host niches. Collectively, our findings uncover global reassortment dynamics in H5 HPAIVs and identify key virological and ecological drivers underpinning the emergence and spread of successful reassortants. These insights support the importance of enhanced surveillance to track evolution of H5 HPAIV and identify traits relevant for consideration in pandemic risk assessment.

evolutionary biology↗

bioRxiv2025

Modeling Post-Gastrula Development via Bidirectional Pluripotent Stem Cells

The absence of stem cells capable of efficiently generating both trophoblast and epiblast lineages has hindered precise recapitulation of embryonic development. Through high-content chemical screening, we established an AL medium to generate mouse and human bidirectional pluripotent stem cells (BPSCs) characterized by concurrent OCT4/CDX2 expression. Mouse BPSCs demonstrated high plastic differentiation into trophoblast, epiblast and primitive endoderm lineages in vitro within 48 hours without exogenous induction factors and efficiently contributed to the embryo and extraembryonic tissues in vivo. Mechanistically, hyperactivation of the Wnt signaling pathway breaks the early lineage differentiation barrier by initiating a Lef1-dependent bypass. Remarkably, BPSCs can efficiently generated E8.5 embryoids that completed gastrulation and displayed advanced features such as brain development, a closed neural tube, a beating heart, somite formation, and primordial germ cells. These findings highlight BPSCs as a powerful tool for investigating early lineage specification and post-gastrulation embryonic development, with potential applications across multiple species.

developmental biology↗

bioRxiv2025

EVscope: A Comprehensive Bioinformatics Pipeline for Accurate and Robust Analysis of Total RNA Sequencing from Extracellular Vesicles

MotivationExtracellular vesicle (EV) RNA sequencing has emerged as a powerful approach for studying RNA biomarkers and intercellular communication. Nevertheless, the extremely low abundance, fragmented nature and ubiquitous tissue origin of EV RNAs, alongside potential contamination from co-isolated materials, such as free DNA and bacterial RNA, pose substantial analytical challenges. These complexities highlight a pressing need for a standardized, computational workflow that ensures robust quality control and EV RNA characterization. ResultsHere, we present EVscope, an open-source bioinformatics pipeline designed specifically for processing EV RNA-seq datasets. EVscope employs an optimized genome-wide expectation-maximization (EM) algorithm that significantly improves multi-mapping read assignment at single-base resolution by effectively leveraging alignment scores (AS) and local read coverage, specifically tailored for fragmented and low-abundance EV RNAs. Notably, EVscope uniquely generates EM-based BigWig files for downstream analysis, a capability currently unavailable in existing EM-based BigWig quantification tools. The pipeline systematically integrates 27 major steps, including quality control, analysis of library structure, contamination assessment, read alignment, read strandedness detection, UMI-based deduplication, RNA quantification, genomic DNA (gDNA) contamination correction, cellular and tissue source inference and visualization with a comprehensive HTML report. EVscope incorporates a comprehensive, updated annotation covering 19 distinct RNA biotypes, encompassing protein-coding genes, lncRNAs, miRNAs, piRNAs, retrotransposons (LINEs, SINEs, ERVs), and additional non-coding RNAs (tRNAs, rRNAs, snoRNAs). Furthermore, it leverages two highly balanced circRNA detection algorithms for robust circular RNA identification. Notably, a downstream module enables the inference of the tissue/cellular origins of EV RNAs using bulk and single-cell RNA-seq reference datasets. EVscope is implemented as a convenient, single-command Bash pipeline leveraging Conda-managed standard software packages and custom scripts, ensuring reproducibility and straightforward deployment. Availability and implementationCode, documentation, and tutorials are available at GitHub (https://github.com/TheDongLab/EVscope) and archived on Zenodo (https://zenodo.org/records/15577789).

bioinformatics↗

bioRxiv2025

Giant viruses specific to deep oceans show persistent presence and activity

Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate deep-sea GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To investigate the global deep-sea-specific GV distribution, we compiled GV reference genomic data from the OceanDNA MAG project and other resources, and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included one GV identified in our Muroto sampling, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat. IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the deep-sea water. Using a global marine dataset, we further uncovered the widespread existence of deep-sea-specific giant viruses and characterized their unique gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.

genomics↗

bioRxiv2025

Human myelocyte and metamyelocyte-stage neutrophils suppress tumor immunity and promote cancer progression

Tumor-infiltrating neutrophils (TINs) are highly heterogeneous and mostly immunosuppressive in the tumor immune microenvironment (TIME). Current biomarkers of TINs and treatment strategies targeting TINs have not yielded optimal responses in patients across cancer types. Here, we separated human and mouse neutrophils into three developmental stages, including promyelocyte (PM), myelocyte & metamyelocyte (MC & MM), and banded & segmented (BD & SC) neutrophils. Based on this separation, we observed the predominance of human but not mouse MC & MM-stage neutrophils in bone marrow (BM), which exhibit potent immunosuppressive and tumor-promoting properties. MCs & MMs also occupy the majority of TINs among patients with 17 cancer types. Moreover, through the creation of a NCG-Gfi1-/- human immune system (HIS) mouse model, which supports efficient reconstitution of human TIN, we found a significant increase of BM MCs & MMs in tumor-bearing mice. By comparing the scRNA-seq analysis results of human neutrophils from both BM and tumors, we found CD63 and Galectin-3 distinguish MC & MM from neutrophil populations in cancer patients. Furthermore, we proposed a strategy with Flt3L to specifically induce the trans-differentiation of MCs & MMs into monocytic cells, and trigger tumor control in NCG-Gfi1-/- HIS mice. Thus, our findings establish an essential role of human MC & MM-stage neutrophils in promoting cancer progression, and suggest their potential as targets for developing potential biomarkers and immunotherapies for cancer.

immunology↗

bioRxiv2025

Membrane phosphoinositides allosterically tune β-arrestin dynamics to facilitate GPCR core engagement

Arrestin proteins bind active G protein-coupled receptors (GPCRs) through coordinated protein-protein, protein-phosphate, and protein-lipid interactions to attenuate G protein signaling and promote GPCR internalization and trafficking. While there are hundreds of diverse GPCRs, only two {beta}-arrestin isoforms ({beta}arrs) must recognize and engage this wide range of receptors with varied phosphorylation patterns. Traditional models suggest that {beta}arr activation requires displacement of its autoinhibitory C-tail by a phosphorylated GPCR C-terminus; however, this paradigm fails to explain how minimally phosphorylated GPCRs still complex with {beta}arrs. Using single-molecule Forster resonance energy transfer imaging and hydrogen-deuterium exchange mass spectrometry, we observe basal dynamics in which the {beta}arr1 C-tail spontaneously releases from the N-domain, transiently adopting an active conformation that can facilitate binding of the phosphorylated GPCR C-terminus. We further demonstrate the importance of an intermediate state of {beta}arr1 arising from spontaneous C-tail release stabilized by the membrane phosphoinositide PI(4,5)P2. Both PI(4,5)P2 and mutations in the proximal or middle regions of the C-tail shift {beta}arr1 towards a partially released state, revealing an allosteric connection that informs a refined model for {beta}arr activation. In this model, membrane engagement conformationally primes {beta}arrs prior to receptor binding, thereby explaining how {beta}arrs are recruited by diverse GPCRs, even those with limited C-terminal phosphorylation.

biophysics↗

bioRxiv2025

A Tandem Repeat Atlas for the Genome of Inbred Mouse Strains: A Genetic Variation Resource

Tandem repeats (TRs) are a significant source of genetic variation in the human population; and TR alleles are responsible for over 60 human genetic diseases and for inter-individual differences in many biomedical traits. Therefore, we utilized long-read sequencing and state of the art computational programs to produce a database with 2,528,854 TRs covering 39 inbred mouse strains. As in humans, murine TRs are abundant and were primarily located in intergenic regions. However, there were important species differences: murine TRs did not have the extensive number of repeat expansions like those associated with human repeat expansion diseases and they were not associated with transposable elements. We demonstrate by analysis of two biomedical phenotypes, which were identified over 40 years ago, that this TR database can enhance our ability to characterize the genetic basis for trait differences among the inbred strains.

genetics↗

bioRxiv2025

Development and application of a genotyping by target sequencing SNP array panel in Salix suchowensis

Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a genotyping by target sequencing SNP array panel to facilitate efficient genotyping. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.

genetics↗

bioRxiv2025

Individual heterogeneity drives a plant macroparasites life history

The population dynamics and life histories of macroparasites are fundamental to examine their impacts on hosts and ecosystems. Still, macroparasite population models often ignore parasite individual heterogeneity and are rarely applied to parasitic plants, where demographic strategies are less well understood. Using a 10-year dataset on European mistletoe (Viscum album), we examine how this macroparasites traits influence its performance. V. album survival and reproduction depend on its size and, to a lesser extent, height on the host tree, with a strong growth-reproduction trade-off. We parameterise these relationships in an integral projection model to compare the life history strategy of V. album with two other macroparasites and 490 free-living plants. Contrary to our hypothesis, V. album and other macroparasites do not follow an extreme strategy, suggesting that parasitic plants may not escape the life history constraints experienced by non-parasitic plants. Our results highlight how incorporating parasite heterogeneity can improve macroparasite models.

ecology↗

bioRxiv2025

Discover the Maze-like Pathway for Glabridin Biosynthesis

Tailoring enzymes diversify plant metabolite scaffolds through complex, context-dependent modifications, generating maze-like biosynthetic networks that complicate metabolic pathway reconstruction. Here, we systematically deconstructed and reconstructed the biosynthetic network of glabridin, a valuable skin-whitening isoflavone from Glycyrrhiza. By integrating metabolic pathway mining with genome and 183 transcriptomes, we identified four functional routes among sixteen theoretical possibilities and uncovered a previously uncharacterized, ladder-like multi-route tailoring network. Reconstruction of such architecture in yeast revealed metabolic redundancy and interconnectivity confer unexpected robustness, enabling higher production efficiencies compared to a single-route design. Further modular engineering enabled the de novo biosynthesis of glabridin in yeast. Our work establishes a framework for reconstructing metabolic mazes and demonstrates that multi-route architectures can be harnessed to enhance the robustness and productivity of cell factories.

synthetic biology↗

bioRxiv2025

Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV-1 V2 apex broadly neutralizing antibody development

Broadly neutralizing antibodies (bNAbs) are rarely elicited during HIV-1 infection. To identify obstacles to bNAb development, we longitudinally studied 122 rhesus macaques infected by one of 16 different simian-human immunodeficiency viruses (SHIVs). We identified V2 apex as the most common bNAb target and a subset of Envs that preferentially elicited these antibodies. In 10 macaques, we delineated Env-antibody coevolution from B cell priming to bNAb development. Antibody phylogenies revealed permissive developmental pathways guided by evolving Envs that contained few mutations in or near the V2 apex C-strand, which were a sensitive indicator of apex-targeted responses. The absence of such mutations reflected a failure in bNAb priming. These results indicate that efficiency of B cell priming, and not complexities in Env-guided affinity maturation, is the primary obstacle to V2 apex bNAb elicitation in SHIV-infected macaques and identify specific HIV-1 Envs to advance as novel vaccine platforms. One sentence summaryB cell priming is the primary bottleneck to HIV-1 V2 apex bNAb elicitation.

immunology↗

bioRxiv2025

Escherichia coli with a 57-codon genetic code

The near-universal genetic code of living organisms uses 64 codons to encode the 20 canonical amino acids in protein synthesis. Here we design and generate a variant of Escherichia coli with a 4 Mb synthetic genome in which we replace every known occurrence of six sense codons and a stop codon with synonymous codons. We thereby recode 105 codons to create an organism with a 57-codon genetic code; this organism - which we name Syn57 - uses 55 codons to encode the 20 canonical amino acids.

synthetic biology↗

bioRxiv2025

HIF-1α promotes osteogenic-angiogenic coupling response of BMSCs cell sheets

BackgroundThere is a critical need for management of vascularization in bone tissue engineering. The purpose of this study was to use HIF-1-transduced BMSCs fabricated prevascularized osteogenic cell sheets and explore HIF-1 promoted osteogenic-angiogenic coupling response of BMSCs cell sheets in vitro. MethodsHIF-1 was over-expressed by using a lentiviral vector, and transduced steadily in Wistar rats bone marrow mesenchymal stem cells(BMSCs). Real-time quantitative and western blot were performed to assess the expression level of HIF-1. Then, HIF-1/BMSCs were cultured to form osteogenic cell sheets(OCTs). ALP activity and Alizarin-red staining were performed respectively at day 14 and 21 to detect the characteristic of osteogenesis. Simultaneously, HIF-1/BMSCs were induced to differentiate into endothelial-like cells(iECs) for 14 days, and flow cytometry was further detected the conversion rates of HIF-1/BMSCs to iECs. Finally, iECs were seeded onto the OCTs to construct the prevascularized-osteogenic cell sheets (P-OCTs). In order to detect the role of HIF-1 involved in osteogenic-angiogenic coupling response of P-OCTs, Immunofluorescent staining for CD31 was performed on P-OCTs at 1, 3, 7, 14 days to check the formation of networks, and western blot of osteopontin(OPN) and osteocalcin (OCN) at 1, 7, 14 days to detect bone formation. Meanwhile, the none transduced BMSCs were as control. ConclusionBMSCs were transduced by Lenti-HIF-1 with optimal multiplicity of infection was 30(MOI=30), meanwhile, qPCR and western blot were performed to confirm this result. Next, the flow cytometric analysis results showed the conversion rate of BMSCs differentiated to iECs was 92.43%, which indicated BMSCs transduced by HIF-1 had a great superiority to differentiate into endothelial cells under experimental conditions. Then, ALP at day 14 and Alizarin-red staining at day 21 on OCTs showed an obvious osteogenic differentiation characteristic with more deep stained calcium nodules deposits than the control groups. Finally, we fabricated P-OCTs and observed iECs migrated reticulated fast and formed a large number of lumens and networks in experimental groups. At the same time, the results of Immunofluorescent staining for CD31 at day 1, 3, 7, 14 and osteogenic proteins expressions of OCN,OPN at day 1, 7, 14 showed that HIF-1 could promote osteogenic-angiogenic coupling response in P-OCTs significantly in vitro. All in all, the over-expressed HIF-1 of BMSCs cell sheets strategy can provide a new promising method for bone engineering, and we will detect further in vivo.

bioengineering↗

bioRxiv2025

Mesoscopic SCAPE Microscope with a Rescanned, Super-oblique Illumination Plane

Investigating structural and functional dynamics across large spatial scales in living organisms calls for volumetric microscopy that combines a wide field of view (FOV), high spatial resolution, and sufficient temporal resolution. Swept confocally-aligned planar excitation (SCAPE) microscopy offers a compelling balance of optical sectioning, cellular resolution, and high-speed volumetric imaging. However, extending SCAPE to mesoscopic scales has been hindered by the limited tilting angle of the oblique illumination light sheet achievable with commercial low-magnification objectives. Here, we present a mesoscopic SCAPE microscope that overcomes this constraint by implementing a super-oblique light sheet--tilted up to ~60{degrees} relative to the optical axis of a 0.5-NA primary objective--enabled by an air-to-water bridging reflector. In addition, we introduce a single-galvanometer, self-conjugating rescanning strategy that allows arbitrary customization of the optical-to-mechanical angle ratio. This innovation accommodates the reversed and modulated scan displacement of the reflected light sheet and preserves descanned epi-fluorescence detection. Together, these advancements enable our mesoscopic SCAPE microscope to achieve a lateral FOV of 5.0 mm x 2.9 mm, cellular-level spatial resolution (~9.4 m x ~5.9 m lateral, and ~6.0 m axial), and a volumetric imaging rate of 9 volumes per second.

bioengineering↗