Biology subjects

Xi, J.

Publications and source records attributed to Xi, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Plasma membrane PI4P recruits SNAP47 to mediate SNARE-dependent AMPAR exocytosis during synaptic potentiation

The synaptic delivery of the AMPA-type glutamate receptors (AMPARs) is crucial for longterm potentiation (LTP) of excitatory synapses, yet the mechanisms underlying neuronal activity-dependent AMPAR exocytosis at the plasma membrane (PM) remain unclear. We previously demonstrated that the PM synthesis of the phosphoinositide PI4P is enhanced upon LTP induction and that PM PI4P, not PI(4,5)P2, is required for activity-induced AMPAR exocytic trafficking. Here, we show that AMPARs are exocytosed at PI4P-enriched dendritic PM microdomains in potentiated hippocampal neurons. The Q-SNARE SNAP47 binds PI4P via its pleckstrin homology (PH)-like domain. This interaction recruits SNAP47 to the PM, promoting the exocytic fusion of AMPAR vesicles through the SNAP47-Syntaxin-3-VAMP2 SNARE complex. In the hippocampus, the SNAP47-PI4P interaction is necessary for both LTP and long-term memory. Our findings reveal a mechanistic role for PI4P in mediating activity-dependent, SNARE-driven fusion of AMPAR exocytic vesicles with the PM.

neuroscience↗

bioRxiv2026

A GPX4 phosphorylation switch by FGFR1 guards against ferroptosis

Ferroptosis is driven by lipid peroxidation, yet the mechanisms by which cells rapidly adjust their sensitivity to ferroptosis in response to extracellular cues remain elusive. We identify a direct phosphorylation switch controlling the activity of glutathione peroxidase 4 (GPX4), the core ferroptosis regulator. The receptor tyrosine kinase FGFR1 directly binds and phosphorylates GPX4 at Tyr180/Tyr196 in a kinase-dependent manner, requiring its Tyr730 as a docking site. This phosphorylation enhances GPX4s catalytic activity and suppresses ferroptosis. In cardiac ischemia/reperfusion injury, the FGFR1-GPX4 axis is suppressed, and a selective FGFR1 agonist (FGF-1{Delta}NT) reactivates it to protect against ferroptosis-mediated damage. Critically, a phosphorylation-deficient GPX4 knock-in mouse exhibits hypersensitivity to injury and non-responsive to this agonist, proving that GPX4 phosphorylation is essential. Our findings reveal a rapid mechanism for regulating ferroptosis via GPX4 tyrosine phosphorylation, directly linking receptor tyrosine kinase signaling to ferroptosis, and offering new strategies for treating ischemic-and other ferroptosis-associated diseases.

Cell Biology↗

bioRxiv2026

Mapping distribution of invasive plant species and uncertainty using citizen science, remote sensing, and deep learning

Invasive plants pose a major environmental problem, threatening biodiversity, altering ecosystem functions, and causing economic loss. Climate change is altering environmental conditions, potentially facilitating the spread of invasive plant species, posing challenges for ecosystem management and biodiversity conservation. Accurate predictions of invasive species distributions are therefore essential for effective monitoring and early intervention. Species distribution models (SDMs) have become an important tool for predicting species habitats, but many studies rely on traditional machine learning approaches, focus on single-species predictions and overlook uncertainty associated with future climate scenarios. This study aims to evaluate the performance of a deep learning-based SDM framework, Deepbiosphere, for predicting both native and invasive plant species distributions on a regional scale, the US state of Michigan, and to assess how climate scenario uncertainty influences spatial predictions of invasive species risk particularly on two focal invasive species. Results show that Deepbiosphere outcompeted other baseline models by on average of 10.98% with a mean AUC-ROC of 0.79 across 1553 vascular plant species. For two invasive species Rhamnus cathartica and Ailanthus altissima, Deepbiosphere respectively improved modeling accuracy by an average of 56.41% and 74.99%, suggesting its enhanced predictive capability for invasive species. Current predictions indicated that R. cathartica is already broadly suitable across much of Michigan, whereas A. altissima is currently more restricted to southern regions. Under future climate scenarios, both species were projected to expand northward, with a particularly strong expansion signal for A. altissima. Prediction uncertainty was spatially heterogeneous, where general circulation models (GCMs) were the dominant source of uncertainty across most of the state. By integrating citizen science, remote sensing, and deep learning, we produced high-resolution risk-uncertainty maps for key invasive species and highlighted the importance of explicitly mapping uncertainty to support more informed invasive species management under climate change.

ecology↗

bioRxiv2026

DeepSRFusion: a point cloud deep learning framework for super-resolution particle fusion

Deciphering the spatial organization of macromolecular complexes in their native context is central to structural biology. Particle fusion in single-molecule localization microscopy offers a unique capability for high-resolution structural reconstruction in situ. However, existing methods face significant challenges from large rotational perturbations and sparse labeling, resulting in compromised accuracy and substantial computational cost. We present DeepSRFusion, a self-supervised pretraining framework for three-dimensional super-resolution particle fusion. By representing single-molecule point clouds as Gaussian Mixture Models, DeepSRFusion integrates data-driven feature learning with physical imaging constraints. A two-stage optimization strategy with dynamic template updating enhances robustness, and a novel Clustering Error metric quantifies fusion quality. Nanometer-scale validation on both simulated and experimental datasets demonstrates high reconstruction fidelity and structural consistency with cryo-electron microscopy and AlphaFold3. DeepSRFusion remains effective under challenging imaging conditions, including large 3D rotations, sparse labeling, high localization uncertainty, and limited particle numbers, while achieving over 100-fold speedups compared to current methods. It resolves fine structural features with a measured spatial resolution of 1.60 {+/-} 0.10 nm, sufficient to distinguish ~10 nm spaced protein pairs and visualize tilted internal substructures within macromolecular assemblies. DeepSRFusion provides a powerful tool for high-precision structural analysis in native cellular environments.

biophysics↗

bioRxiv2026

Histology-Aware Graph for Modeling Intercellular Communication in Spatial Transcriptomics

Cell-cell communication (CCC) is essential to how life forms and functions. Recent tools achieve single-cell-resolved CCC inference utilizing spatial transcriptomics (ST). However, most ignore the modeling of tissue contexts surrounding cells, causing high false-positive/negative rates. Here, we propose HARMONIC, a CCC inference method integrating multimodal ST and hematoxylin and eosin (H&E)-stained images. HARMONIC causally modeling the transcriptomic-to-contextual relationships for CCC inference. The state-of-the-art performance was verified across ST platforms, species and healthy/diseased status, on both synthetic and biological samples. HARMONIC was applied in various real-world scenarios, especially on tissues with clear morphological boundaries, including cortical layers in mouse brain, medullary-cortex structures in mouse kidney, as well as tumor-stromal/immune interface. Significant refinement of false-positive/negative predictions was observed compared to ST-only CCC tools.

bioinformatics↗

bioRxiv2026

DNA synthesis inside the hepatitis B virus creates a high-energy spool

The Hepatitis B Virus (HBV) capsid assembles around an RNA pregenome which is reverse-transcribed into double-stranded DNA. It remains unclear how this DNA, which is stiff, bulky, and has significant negative charge, is accommodated within the capsid. The organization of the genome will answer this and lend insight into the viral reverse transcription reaction. We determined the structures of mature HBV and Duck HBV, finding that the DNA forms a spool that is coaxial with the capsids fivefold symmetry and interacts with charges on the capsid interior. We calculate that the energy of DNA bending would create a metastable capsid that just awaits a trigger for DNA release. Thus, we see how nature has created a fragile energy minimum that enables genome uncoating.

microbiology↗

bioRxiv2025

A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics

Spatial transcriptomics (ST) platforms are limited by spatial resolution, sensitivity to low expression levels, alignment with tissue structures, and the balance across tissue complexity. Computational enhancement typically targets a single challenge, e.g., super-resolution using hematoxylin and eosin (H&E) images or sensitivity enhancement with single-cell RNA sequencing (scRNA-seq). However, most ignore the interdependence across challenges, yielding biologically inconsistent enhancement. Here we introduce FOCUS, a foundational generative model for unified ST enhancement, conditioned on H&E images, scRNA-seq references, and spatial co-expression priors. With large-scale pretrained encoders, FOCUS uses a modular design for multimodal integration and a cross-challenge coordination strategy to target co-occurring challenges, enabling joint optimization. FOCUS was trained and comprehensively benchmarked on >1.7 million H&E-ST pairs and >5.8 million single-cell profiles, demonstrating state-of-the-art performance across ten ST platforms, on both individual and coupled challenges. The real-world utility and generalizability were validated on a rare suprasellar tumor, papillary craniopharyngioma, and an unseen ST platform (Open-ST) for primary and metastatic head and neck squamous cell carcinoma.

bioengineering↗

bioRxiv2025

Nuclear N-Glycosylation Redefines the Glycoscape and Directs Cell Identity

Glycans modify nucleic acids, proteins and lipids in fundamental biological processes, but have long been considered confined to the secretory pathway and cell surface. Here, we challenge this view with evidence that N-glycosylation, a ubiquitous glycan modification, occurs within cell nuclei across tissues and species, exhibiting cell type-dependent abundance and localization patterns. Using a multi-faceted approach, we show that numerous classical membrane and secreted glycoproteins localize to the nucleus with N-glycan modifications, exemplified by the cell adhesion molecule L1CAM. Mechanistically, we show that the N-glycosylated L1CAM is transported to the nucleus by KPNB1, where it transcriptionally modulates neuronal differentiation. Moreover, this nuclear N-glycosylation event contributes to neurodevelopmental disorders and is pharmacologically reversible. These findings revise the cellular geography of N-glycosylation and expand the known routes of protein trafficking, and highlight nuclear N-glycosylation pathways as potential therapeutic entry points for developmental disorders.

cell biology↗

bioRxiv2025

Gold Nanocages as Scattering Contrast Agents for Optical Coherence Tomography

We report a scattering-dominant agent that significantly enhances optical coherence tomography (OCT) imaging contrast. The agent is based on gold nanocages, which exhibit a surface plasmon resonance (SPR) peak around 780 nm and a scattering cross-section that exceeds the absorption cross-section. The synthesis protocol for these nanocages is provided in detail. The optical properties of the gold nanocages were characterized using OCT imaging and further validated with integrating sphere measurements. OCT contrast enhancement was demonstrated through imaging of tissue phantoms containing embedded nanocages, as well as ex vivo imaging of mouse tissues and in vivo imaging of a mouse tumor following intravenous administration of PEGylated gold nanocages. To the best of our knowledge, this may be the first demonstration of scattering-dominant OCT contrast agents utilizing structured gold nanoparticles.

bioengineering↗

bioRxiv2025

Gold Nanocages with a Long SPR Peak Wavelength as Contrast Agents for Optical Coherence Tomography Imaging at 1060 nm

There has been growing interest in optical coherence tomography (OCT) imaging at a wavelength of 1060 nm. However, potential contrast agents for OCT imaging at this specific wavelength has not been thoroughly investigated. In this study, we present the synthesis and optical characterization of gold nanocages with a small edge length ([~]65 nm) and a surface plasmon resonance peak around 1060 nm. These nanocages represent a class of potential contrast agents for OCT at 1060 nm. OCT imaging experiments were conducted on phantoms and in vivo mouse tissues using a 1060-nm swept-source OCT system, demonstrating significant enhancement in imaging contrast due to the presence of the gold nanocages. GRAPHICAL ABSTRACTGold nanocages with a long SPR peak wavelength as OCT imaging contrast agents at 1060 nm O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/642209v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@179a727org.highwire.dtl.DTLVardef@1cd1e4eorg.highwire.dtl.DTLVardef@180ce47org.highwire.dtl.DTLVardef@166a779_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

C. elegans LET-381/FoxF and DMD-4/DMRT control development of the mesodermal HMC endothelial cell

Endothelial cells form the inner layer of blood vessels and play key roles in circulatory system development and function. A variety of endothelial cell types have been described through gene expression and transcriptome studies; nonetheless, the transcriptional programs that specify endothelial cell fate and maintenance are not well understood. To uncover such regulatory programs, we studied the C. elegans Head Mesodermal Cell (HMC), a non-contractile mesodermal cell bearing molecular and functional similarities to vertebrate endothelial cells. Here, we demonstrate that a Forkhead transcription factor, LET-381/FoxF, is required for HMC fate specification and maintenance of HMC gene expression. DMD-4, a Dmrt transcription factor, acts downstream of and in conjunction with LET-381 to mediate HMC fate specification and gene expression maintenance. DMD-4, independently of LET-381, also represses the expression of genes associated with a different, non-HMC, mesodermal fate. Our studies uncover essential roles for FoxF transcriptional regulators in endothelial cell development, and suggest that the identity of FoxF co-functioning target transcription factors promotes specific non-contractile mesodermal fates.

developmental biology↗

bioRxiv2024

Interpretable high-resolution dimension reduction of spatial transcriptomics data by DeepFuseNMF

Spatial transcriptomics (ST) technologies have revolutionized tissue architecture studies by capturing gene expression with spatial context. However, high-dimensional ST data often have limited spatial resolution and exhibit considerable noise and sparsity, posing significant challenges in deciphering subtle spatial structures and underlying biological activities. Here, we introduce SpaHDmap, an interpretable dimension reduction framework that enhances spatial resolution by integrating ST gene expression with high-resolution histology images. SpaHDmap incorporates non-negative matrix factorization into a multimodal fusion encoder-decoder architecture, enabling the identification of interpretable, high-resolution embeddings. Furthermore, SpaHDmap can simultaneously analyze multiple samples and is compatible with various types of histology images. Extensive evaluations on synthetic and real ST datasets from various technologies and tissue types demonstrate that SpaHDmap can effectively produce highly interpretable, high-resolution embeddings, and detects refined spatial structures. SpaHDmap represents a powerful approach for integrating ST data and histology images, offering deeper insights into complex tissue structures and functions.

bioinformatics↗

bioRxiv2024

An automated microfluidic platform for toxicity testing based on Caenorhabditis elegans

Humans are frequently exposed to a multitude of chemicals daily, necessitating efficient methods for rapidly assessing toxicity and potential health risks. Microfluidics has shown promise as an intelligent tool for rapid compound testing, owing to its flexibility in integrating with automated devices. The article introduces an automated microfluidic platform, based on Caenorhabditis elegans (C. elegans), designed for chemical toxicity testing. This platform consists of three modules - worm culture, monitoring, and image analysis - which enable automated worm culturing, drug delivery, periodic monitoring, and automated phenotypic analysis. Researchers have designed a bridged microfluidic chip that permits worms to move freely during experiments and established an economical monitoring module for long-term tracking and periodic imaging. Furthermore, they have developed an automated image analysis algorithm to automatically determine worm bending frequency. The platform was subsequently utilized for long-term toxicological assessments of the organophosphate pesticide and environmental pollutants. Results indicated that the platform can effectively evaluate the general and developmental impacts of chemicals. The automated microfluidic worm analysis platform holds significant potential for applications in drug safety assessmentand drug screening research, contributing to human health and industry advancement.

bioengineering↗

bioRxiv2024

Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics

Spatial transcriptomics (ST) technologies represent a significant advance in gene expression studies, aiming to profile the entire transcriptome from a single histological slide. These techniques are designed to overcome the constraints faced by traditional methods such as immunostaining and RNA in situ hybridization, which are capable of analyzing only a few target genes simultaneously. However, the application of ST in histopathological analysis is also limited by several factors, including low resolution, a limited range of genes, scalability issues, high cost, and the need for sophisticated equipment and complex methodologies. Seq-Scope--a recently developed novel technology--repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, thereby overcoming these limitations. Here we provide a detailed step-by-step protocol to implement Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell that allows for the profiling of multiple tissue sections in an area of 7 mm x 7 mm or larger. In addition to detailing how to prepare a frozen tissue section for both histological imaging and sequencing library preparation, we provide comprehensive instructions and a streamlined computational pipeline to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology. KEY POINTSO_LIThe protocol outlines a method for repurposing an Illumina NovaSeq 6000 flow cell as a spatial transcriptomics array, enabling the generation of high-resolution spatial datasets. C_LIO_LIThe protocol introduces a streamlined data analysis pipeline that produces a spatial digital gene expression matrix suitable for various single-cell and spatial transcriptome analysis methods. C_LIO_LIThe protocol allows for the capture of histology images from the same tissue section subjected to spatial transcriptomics analysis and allows users to precisely align the transcriptome dataset with the histological image using fiducial marks engraved on the flow cell surface. C_LIO_LILeveraging commonly available Illumina equipment, the protocol offers researchers ultra-high submicrometer resolution in spatial transcriptomics analysis with a comprehensive pipeline, rapid turnaround, cost efficiency, and versatility. C_LI

genomics↗

bioRxiv2023

Initiation of a ZAKa-dependent Ribotoxic Stress Response by the Innate Immunity Endoribonuclease RNase L

RNase L is a regulated endoribonuclease in higher vertebrates that functions in antiviral innate immunity. Interferons induce OAS enzymes that sense double-stranded RNA of viral origin leading to synthesis of 2,5-oligoadenylate (2-5A) activators of RNase L. However, it is unknown precisely how RNase L inhibits viral infections. To isolate effects of RNase L from other effects of double-stranded RNA or virus, 2-5A was directly introduced into cells. Here we report that RNase L activation by 2-5A causes a ribotoxic stress response that requires the ribosome-associated MAP3K, ZAK. Subsequently, the stress-activated protein kinases (SAPK) JNK and p38 are phosphorylated. RNase L activation profoundly altered the transcriptome by widespread depletion of mRNAs associated with different cellular functions, but also by SAPK-dependent induction of inflammatory genes. Our findings show that 2-5A is a ribotoxic stressor that causes RNA damage through RNase L triggering a ZAK kinase cascade leading to proinflammatory signaling and apoptosis. HighlightsO_LIRNase L signals antiviral innate immunity from the ribosome C_LIO_LIThe ribotoxic stress response requires the MAP3K ZAK C_LIO_LIRNA cleavage leads to transcription of proinflammatory genes C_LIO_LIZAK contributes to apoptosis downstream of RNase L activity C_LI

immunology↗

bioRxiv2023

Collaborative Augmented Reconstruction for Scaled Production of 3D Neuron Morphology in Mouse and Human Brains

Digital reconstruction of the intricate 3D morphology of individual neurons from microscopic images is widely recognized as a crucial challenge in both individual research laboratories and large-scale scientific projects focusing on cell types and brain anatomy. This task often fails both conventional manual reconstruction and state-of-the-art automatic reconstruction algorithms, even many of which are based on artificial intelligence (AI). It is also critical but challenging to organize multiple neuroanatomists to produce and cross-validate biologically relevant and agreeable reconstructions in scaled data production. Here we propose an approach based on collaborative human intelligence augmented by AI. Specifically, we have developed a Collaborative Augmented Reconstruction (CAR) platform for neuron reconstruction at scale. This platform allows for immersive interaction and efficient collaborative-editing of neuron anatomy using a variety of client devices, such as desktop workstations, virtual reality headsets, and mobile phones, enabling users to contribute anytime and anywhere and take advantage of several AI-based automation tools. We have tested CARs applicability for challenging mouse and human neurons towards a scaled and faithful data production. Our data indicate that the CAR platform is suitable for generating tens of thousands of neuronal reconstructions used in our companion studies.

neuroscience↗

bioRxiv2023

Decoding human in vitro terminal erythropoiesis originating from umbilical cord blood mononuclear cells and pluripotent stem cells

Ex vivo RBC production generates unsatisfactory expansion, {beta}-globin expression, and maturation of erythroid cells. The underlying mechanisms behind these limitations and ex vivo terminal erythropoiesis from different origins are largely unexplained. In this study, we mapped an atlas of ex vivo terminally differentiated cells from umbilical cord blood mononuclear cells (UCBMNs) and pluripotent stem cells (PSCs), and observed the differential regulatory dynamics of erythropoiesis from these two origins at a single-cell resolution. We detected the presence of hematopoietic stem progenitor cells (HSPCs), erythroid progenitor (e.g., CFU-E), and non-erythroid cells (e.g., macrophages) in the terminal populations. We observed that UCBMN-derived erythropoiesis is more active than PSC-derived erythropoiesis in terms of the cell cycle, stress erythropoiesis, and autophagy at single cell resolution, which may provide new insights into the limitations in cell expansion, globin expression, and maturation in ex vivo RBC production, respectively. We verified that a stress-erythropoiesis-related gene, TRIB3, increases the expression of globin genes in ex vivo erythropoiesis. As the major unexpected component detected in terminally differentiated cells, CFU-E were further characterized as having high- or low- expansion capacity based on CD99 expression, which generally decreased over erythropoiesis. By inhibiting CD99 gene expression using antagonists, we increased reticulocyte production in the population. Heterogeneous CFU-Es also exist in bone marrow. Moreover, decreased CD99 expression mediates the interactions between macrophages and CFU-E during ex vivo erythropoiesis. Overall, our results provide a reference for facilitating the development of strategies to improve ex vivo RBC regeneration. HighlightsO_LIWe performed scRNA-seq and cell typing of late stage UCBMN- and PSC-derived cells C_LIO_LIStress erythropoiesis, autophagy and cell cycle related gene expression different in two origins C_LIO_LICD99high progenitor cells are a proliferating colony forming unit erythroid subpopulation C_LI

cell biology↗

bioRxiv2022

PIF4/HEMERA-mediated daytime thermosensory growth requires the Mediator subunit MED14

While moderately elevated ambient temperatures do not trigger stress responses in plants, they do significantly stimulate the growth of specific organs through a process known as thermomorphogenesis. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including Arabidopsis thaliana. Although it is well known that PIF4 promotes plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is not clear. Our previous studies demonstrated that HEMERA (HMR), a transcriptional co-activator of PIF4, promotes the thermo-induced expression of PIF4 target genes through its nine-amino-acid transactivation domain (9aaTAD). In this report, we investigate the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 is identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 is required for the thermal induction of PIF4 target genes but has a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirm that the expression of numerous PIF4/HMR-dependent, auxin-related genes requires MED14 at warm temperatures. Moreover, PIF4 and HMR physically interact with MED14 and both are indispensable for the association of MED14 with the promoters of these thermoresponsive genes. Taken together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature. One-sentence summaryThe Mediator subunit MED14 promotes thermomorphogenesis by interacting with PHYTOCHROME-INTERACTING FACTOR 4 and HEMERA to induce the expression of growth-promoting genes at elevated temperatures.

plant biology↗