Biology subjects

Xu, S.

Publications and source records attributed to Xu, S..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Identification of the bona fide active center of influenza A virus polymerase acidic protein as the antiviral target

The influenza virus PA protein, a core subunit of RNA polymerase, is critical for viral replication and a key antiviral target. Contrary to the prevailing view that its endonuclease active site resides in the N-terminal domain (PAn, residues 1-319), we identified a C-terminal truncation (PAc, 320-716) of H1N1 PA that retained high endonuclease activity, while PAn showed minimal activity. Crystal structural analysis revealed that PAc binds substrate RNA via the YDS motif (residues 393-395), with mutations abolishing RNA association. Surprisingly, baloxavir acid (BXA), a known PA inhibitor, specifically targeted PAc rather than PAn, supported by molecular docking showing higher binding affinity to PAc. Mutations at PAc-BXA interaction sites identified F707A as a potential drug resistance mutation. Virtual screening targeting PAc identified methotrexate as potent inhibitors (EC50 < 100 nM), which effectively suppressed viral replication in vitro and alleviated symptoms in influenza-infected mice. Our findings redefine PAs catalytic architecture and establish PAc as a novel platform for antiviral discovery, offering strategies to combat drug resistance through structure-guided inhibitor design.

microbiology↗

bioRxiv2025

Loss of miR-9-2 Causes Cerebral Hemorrhage and Hydrocephalus by Widespread Disruption of Cell-Type-Specific Neurodevelopmental Gene Networks.

MIR-9-2 is a broadly and highly expressed microRNA in the developing brain and is frequently deleted in 5q14.3 Microdeletion Syndrome, a rare but severe neurodevelopmental disorder. Despite this, little attention has been paid to the unique contributions of MIR-9-2 to neurodevelopment and disease. We find that deletion of this microRNA leads to embryonic cerebral hemorrhages and severe hydrocephalus, while disrupting gene networks across a wide range of cell types in the developing brain, thus revealing underappreciated and non-redundant molecular, cellular, and system-wide functions for MIR-9-2 in neurodevelopment.

neuroscience↗

bioRxiv2025

APOE knockout attenuates vascular graft fibrosis by limiting profibrotic macrophage formation through low-density lipoprotein receptor related protein 1

Vascular graft fibrosis can cause a decrease in cellular infiltration and capillary ingrowth in vascular walls and vascular stiffening. As such, there are still no vascular grafts that can be used in blood vessels where their diameters are less than 6 mm in patients. Although various approaches have been evaluated to mitigate implant-associated fibrosis, effective treatments remain quite limited. In this study, we demonstrated that APOE was significantly increased during vascular regeneration after graft implantation in vivo. APOE knockout (KO) increased compliance of regenerated aortas and reduced extracellular matrix (ECM) deposition in adventitia of the regenerated aortas. Using single cell RNA sequencing (scRNA-seq), a subset of profibrotic macrophages was found to be involved in graft fibrosis and APOE KO limited the formation of profibrotic macrophage formation during vascular regeneration. The interaction between APOE and low-density lipoprotein receptor related protein 1 (LRP1) partially mediated fibrotic differentiation of the macrophages. Profibrotic macrophages promoted graft fibrosis mainly through secretion of insulin-like growth factor-1 (IGF-1) that could support proliferation of fibroblasts. Finally, we showed that APOE knockdown in vivo using adeno-associated virus (AAV) improved the compliance of regenerated aortas and reduced ECM deposited in the adventitial areas by limiting formation of profibrotic macrophages. Collectively, these data indicate that APOE promotes the profibrotic transition of macrophages partially through LRP1, and the profibrotic macrophages increase the proliferation of fibroblasts via IGF-1. Inhibition of APOE by AAV can alleviate graft fibrosis occurring during vascular regeneration.

bioengineering↗

bioRxiv2025

Baseline expression of c-Myc defines the tissue specificity of oncogenic K-Ras

KRAS is among the most frequently mutated oncogenes in cancer. Yet, mutations in KRAS are common only in tumors originating from a subset of tissues. It is critical to understand the molecular mechanisms underlying this oncogene tissue specificity. Utilizing genetically engineered mouse models carrying a conditional oncogenic allele of Kras, we expressed activated K-Ras in adult tissues to investigate its specificity. We discovered that the ability of K-RasG12D to influence the fitness of cells in a given tissue is not determined by its canonical signaling through MAPK. Instead, low baseline expression of c-Myc renders tissues non-permissive to oncogenic K-Ras, a context that can be reversed in the liver by ectopically expressing c-Myc. This functions independently of the proliferative index of the tissue or the induction of cell cycle arrest or apoptosis. Our findings reveal the importance of the basal state of the tissue-inherent signaling network for determining oncogene specificity.

cancer biology↗

bioRxiv2025

A Photo-regulatable Intein Based Trans-Splicing tool for Protein and Organelle Relocalization to Different Subcellular Compartments

The dynamics of protein subcellular localization are intricately regulated, requiring new tools for controlling protein translocation to uncover the biological significance of post-translational regulation of protein localization. Here, we developed a new method, Protein Rerouting via INtein-mediated Trans-Splicing (PRINTS), which enables precise control of protein translocation across diverse subcellular compartments. By reconstituting functional signaling peptides, PRINTS can efficiently relocalize fluorescent proteins to the 26S proteasome, nucleus, mitochondria, plasma membrane, endomembrane organelles, and liquid-liquid phase separation (LLPS) condensates. Furthermore, we incorporated the optically regulated dimerization domain CRY2clust into the PRINTS system, achieving light-mediated control of protein entry into the cell membrane and LLPS membraneless compartments. Strikingly, we observed that HNRNPA1 promiscuously recruit CRY2- or intein-containing proteins into LLPS condensate, whereas FXR1, another LLPS protein showed minimal non-specific activity. PRINTS also allow organelle relocalization, such as LLPS condensates or mitochondria to cell membrane in a light-controllable manner. Overall, PRINTS provides a versatile and robust platform for manipulating protein and organelle subcellular translocations, offering a powerful tool to investigate the regulatory coordination and crosstalk between membranous and membraneless compartments in response to physiological needs.

cell biology↗

bioRxiv2025

Intertemporal choice across short and long time horizons: an fMRI study

This preregistered fMRI study investigates the neural mechanisms underlying intertemporal choices involving waiting and postponing. On a behavioral level, choices made regarding rewards available in seconds that require waiting compared to choices about rewards postponed to a number days are surprisingly similar. The explanation to this short/long time scales gap is lacking even after considering time perception and external factors, such as stress. To address that this study is the first to examine the overlapping and distinct neural circuitry involved in the intertemporal choices over seconds and days, and the waiting period within subject. Our results revealed considerable overlap in brain activation during choices that consider seconds and days delays to reward in the executive control (dACC, dlPFC) and prospection (PCC/precuneus, dmPFC) networks, but not in the valuation network. Consistent with existent literature we found the valuation network activation (both vmPFC and ventral striatum) being parametrically modulated by individual subjective values of delayed rewards. Overall, the key network determined through representational similarity and decoding analyses was prospection accounting for similarity in activation during decision making across time scales of delays and discriminating between waiting and postponing the reward. These findings enhance our understanding of the neural underpinnings of intertemporal choices and their implications for real-life decisions occurring across varying time horizons, such as paying to skip advertisements while watching videos or deciding on the next-day delivery service.

neuroscience↗

bioRxiv2025

Copper resistance predicts heritable transgenerational fitness variation in the clonal duckweed Spirodela polyrhiza

Transgenerational plasticity in the absence of genetic change can alter organismal fitness, yet we know little about the genetic basis of transgenerational fitness effects. Here, we explored whether transgenerational fitness effects can be predicted by the rate of vegetative reproduction, plant resistance and defence. Thereto, we exposed monoclonal, singledescendant lineages from 56 globally distributed genotypes of the clonal duckweed Spirodela polyrhiza to five generations of copper excess, followed by five generations without stress, and then measured plant fitness and phenotypes in both environments. Previous copper excess reduced fitness variation within each genotype and elicited heritable and reproducible fitness effects that depended on both the genotype and environment: genotypes that benefited from previous stress under recurring conditions suffered when the stress was absent, and vice versa. These transgenerational fitness effects were predicted best by copper resistance, explaining 30% of the intraspecific variation: the more susceptible a genotype, the more its offspring suffered from ancestral stress in the absence of recurrent stress; however, these offspring became more resistant to copper excess, likely by protecting the photosystem II. Together, these findings show that transgenerational fitness effects are heritable and variable and likely controlled by genes that regulate plant reproduction and defence.

evolutionary biology↗

bioRxiv2025

In vivo Calcium Imaging in the Near-Infrared II Window

Non-invasive deep-tissue calcium imaging of live mammals with high sensitivity and resolution is challenging owing to light scattering experienced by traditional calcium ion (Ca2+) indicators with excitation and emission wavelengths within 400-750 nm. Here, we report near-infrared II (NIR-II) calcium imaging beyond 1000 nm by exploring a natural protein derived from a bacterium (Thermochromatium tepidum) living in a calcium carbonate-rich environment. This highly photostable fluorescent protein enables NIR-II imaging of intracellular Ca2+ responses to stimulant drugs in cultured mammalian cells with sensitivity comparable to that of visible Ca2+ indicators. We achieve in vivo NIR-II imaging of Ca2+ transients in response to two different tumor treatment strategies in intact tumors with high sensitivity, resolution, and contrast, opening the possibility of non-invasive deep-tissue calcium imaging for assessing treatment efficacy longitudinally. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/661443v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@149504eorg.highwire.dtl.DTLVardef@37722borg.highwire.dtl.DTLVardef@2878a7org.highwire.dtl.DTLVardef@1091d0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

EF-G Mutations Reveal Correlation between Power Stroke and Translocation Fidelity in Protein Synthesis

One of the most essential biomolecular functions is the ribosome translocation for protein synthesis, in which the ribosome moves on the mRNA by primarily three nucleotides per step in the presence of elongation factor G (EF-G). The large conformational changes of EF-G generate significant mechanical force, referred to as power stroke. Quantification of power stroke remains under debate and its correlation with translocation fidelity has not been observed. In this work, we use quantum sensing techniques for measuring both the EF-G power stroke and its influence on ribosome translocation steps. Two EF-G mutants, H584K and Q508K, were expressed, with the mutated residues directly interacting with tRNA. H584K, which interacts on codon-anticodon minihelix, produced less power stroke of 60{+/-}6 pN and induced "-1" frameshifting, wherein the ribosome translocated only two nucleotides. In contrast, Q508K, which interacts with tRNA residue 37 immediately outside the codon-anticodon minihelix, exhibited a normal power stroke of 89{+/-}11 pN and maintained canonical 3-nucleotide translocation. These findings provide direct mechanistic evidence that the pivotal point and EF-G power stroke are critical for maintaining translocation fidelity and highlight the potential of quantum sensing for chemical biology.

biophysics↗

bioRxiv2025

Genomic Evidence for Males of Exceptional Reproductive Output (ERO) in Apes and Humans

It is widely suspected that a small percentage of males have exceptional reproductive output (ERO) but progeny numbers of males are rarely measurable, even in humans. If we define the variance ratio of reproductive-output in males and females as = VM/VF, the ERO hypothesis would predict >>1. Since autosomal, X, and Y chromosomes are found in males 1/2, 1/3, and 100% of the time, their DNA diversities can inform about . For example, autosomal and Y-linked diversities are governed, respectively, by (VM+VF)/2 and VM. When comparing the chromosomal diversities, appears to be near 20 for chimpanzees and orangutans, and 1-10 for gorillas. The exception is bonobos with < 1. In humans, the extensive genomic data are coupled to a theory, developed herein, that can filter out selection influences on Y-linked diversities. Hence, the estimation of is rigorous, yielding values near or above 20, depending on the population. When >10, the presence of ERO males is very likely. These analyses can be applied more generally to species with XY sex determination.

evolutionary biology↗

bioRxiv2025

MF-ProtDisMap: protein real-valued distance prediction with fusion of sequence and coevolutionary features

The precise estimation of protein inter-residue distances is essential for high-accuracy protein structure modeling. Currently, the prediction methods are predominantly based on MSA-derived coevolutionary features or language model-based sequence features. To effectively leverage the strengths of both methods, this study developed MF-ProtDisMap (Multi-Feature Protein Distance Map), an integrative framework that effectively combines both feature types to achieve superior real-valued distance prediction. Briefly, MSA Transformer is employed to extract the coevolutionary features from protein multiple sequence alignments, whereas ESM2 is used to capture long-range interactions and sequence-level features. To reduce the computational cost while maximumly represent fused feature information, we implement group pooling for feature dimensionality reduction and introduce Diff-former--a novel module combining a diffusion model with a triangular attention mechanism to enhance representation learning. MF-ProtDisMap achieved a MAE of 2.20 [A] and an RMSE of 3.40 [A] in the protein real-valued distance prediction task. The predicted distances can be converted into contact results, achieving ROC and PR values of 84.56% and 81.01%, respectively. These results demonstrate that MF-ProtDisMap outperforms state-of-the-art real-valued protein distance methods.

bioinformatics↗

bioRxiv2025

GABA-independent activation of GABAB receptor by mechanical forces

The heterodimeric GABAB receptor, composed of GB1 and GB2 subunits, is a metabotropic G protein-coupled receptor (GPCR) activated by the neurotransmitter GABA. GABA binds to the extracellular domain of GB1 to activate G proteins through GB2. Here we show that GABAB receptors can be activated by mechanical forces, such as traction force and shear stress, in a GABA-independent manner. This GABA-independent mechano-activation of GABAB receptor is mediated by a direct interaction between integrins and the extracellular domain of GB1, indicating that GABAB receptor and integrin form a novel type of mechano-transduction complex. Mechanistically, shear stress promotes the binding of integrin to GB1 and induces an allosteric re-arrangement of GABAB receptor transmembrane domains towards an active conformation, culminating in receptor activation. Furthermore, we demonstrate that shear stress-induced GABAB receptor activation plays a crucial role in astrocyte remodeling. These findings reveal a previously unrecognized function of GABAB receptor in mechano-transduction, uncovering a novel ligand-independent activation mechanism for GPCRs.

neuroscience↗

bioRxiv2025

SURFS and AlphaFold Reveal Ribosome Footprint Shift Caused by EF-Tu D81 Mutation

Protein synthesis relies on accurate mRNA decoding by tRNA, a process guided by EF-Tu. We investigated how mutations at a conserved residue, aspartate 81, affect EF-Tu function using GTPase assays, AlphaFold modeling, and quantum-sensing-based super-resolution force spectroscopy (SURFS). All D81 variants retained GTPase activity but impaired tRNA release, revealed by sub-nucleotide ribosome footprinting. AlphaFold3 modeling suggests that D81 mutations disrupt magnesium coordination and interaction with the sarcin-ricin loop in the GTP-bound state. AlphaFold2-based sequence-structure analysis indicates that D81 anchors coevolutionary constraints, and its mutation enables cryptic structural variation. These results show how a single conserved residue links catalytic coordination, allosteric communication, and evolutionary constraint, offering mechanistic insight into translation fidelity and demonstrating the utility of an unconventional force spectroscopy in probing ribosome dynamics.

biophysics↗

bioRxiv2025

Active learnings impact on student course performance in STEM varies by type and intensity

We updated a recent meta-analysis of active learnings impact on student achievement in undergraduate STEM courses by following the same protocol to evaluate studies published from 2010-2017. We screened 1659 papers, coded 1294, and found 210 that met five pre-established inclusion criteria and six pre-established criteria for methodological quality. After further dropping 76 studies with no exam scores data, 134 of these studies contained data on student performance on identical or equivalent exams. We found that on average, active learnings effect size on exam scores was 0.519 {+/-} 0.049, meaning that when students are in active learning classes, they perform roughly half a standard deviation higher on an identical exam. Funnel plots and sensitivity analyses indicated that these results were not due to sampling bias. Active learning had a positive impact on student outcomes regardless of class size, course level, or STEM discipline, though there was heterogeneity in the effects. All of these results are very similar when compared to earlier meta-analyses, however increased resolution in the studies analyzed here revealed two novel results. First, student performance was significantly better in courses that employed high-intensity active learning, defined as students being on task at least two-thirds of class time, versus lower-intensities. Additionally, there was significant heterogeneity in efficacy across different types of active learning employed. These results suggest that most, if not all types of active learning are effective, and that when innovating in their classes, instructors should continually work to increase active learning intensity. We urge caution in interpreting the results on active learning types, however, and propose a preliminary framework for making more-sophisticated and reliable analyses of variation in course design. Finally, the evidence presented here for active learnings impact on student outcomes creates a strong foundation for faculty professional development and administration.

scientific communication and education↗

bioRxiv2025

The XPF-like domain in SHOC1 required for homologous recombination and safeguarding autosome from meiotic silencing of unsynapsed chromatin

During meiosis, a group of evolutionarily conserved ZMM proteins plays essential roles in stabilizing the recombination intermediates and promoting crossover (CO) formation. In mice, SHOC1 forms a trimeric complex with the other two ZMM proteins, SPO16 and TEX11, to bind recombination intermediates after strand invasion. Although genetic variants of SHOC1 are clinically associated with meiotic arrest and male infertility, their precise molecular mechanisms and evolutionarily conserved functions in human gametogenesis remain enigmatic. Here, we delineated species-specific divergences between human and mouse SHOC1 complex, and identified a missense variant within the XPF-like domain in SHOC1 (c.A1769G:p.Q590R) that was associated with meiotic arrest and non-obstructive azoospermia (NOA). The disorder of the XPF-like domain in SHOC1 impaired DNA double-strand breaks repair by compromising its ability to bind branched DNA structures and the recruitment of M1AP, REDIC1, and ZMM factors to recombination intermediates, ultimately abolishing CO formation. Furthermore, the variant disrupted dynamic 3D chromatin structure in pachytene spermatocytes and induced defects in homologous chromosome synapsis. More importantly, the XPF-like domain in SHOC1 was revealed to prevent autosome intrusion into the sex body compartment, thereby safeguarding critical autosomal loci from meiotic silencing of unsynapsed chromatin (MSUC). Overall, our study demonstrated that the XPF-like domain in SHOC1 is required for homologous recombination and safeguarding autosome from MSUC in meiosis.

developmental biology↗

bioRxiv2025

FoldBench: An All-atom Benchmark for Biomolecular Structure Prediction

Accurate prediction of biomolecular complex structures is fundamental for understanding biological processes and rational therapeutic design. Recent advances in deep learning methods, particularly all-atom structure prediction models, have significantly expanded their capabilities to include diverse biomolecular entities, such as proteins, nucleic acids, ligands, and ions. However, comprehensive benchmarks covering multiple interaction types and molecular diversity remain scarce, limiting fair and rigorous assessment of model performance and generalizability. To address this gap, we introduce FoldBench, an extensive benchmark dataset consisting of 1,522 biological assemblies categorized into nine distinct prediction tasks. Our evaluations reveal critical performance dependencies, showing that ligand docking accuracy notably diminishes as ligand similarity to the training set decreases, a pattern similarly observed in protein-protein interaction modeling. Furthermore, antibody-antigen predictions remain particularly challenging, with current methods exhibiting failure rates exceeding 50%. Among evaluated models, AlphaFold 3 consistently demonstrates superior accuracy across the majority of tasks. In summary, our results highlight significant advancements yet reveal persistent limitations within the field, providing crucial insights and benchmarks to inform future model development and refinement.

bioinformatics↗

bioRxiv2025

TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques

Atherosclerosis progresses from fatty streaks to complex plaques, with rupture leading to life-threatening complications. Endothelial-to-mesenchymal transition (EndMT) is associated with advanced atherosclerotic plaques, but its role in plaque progression remains unclear. To investigate this, we analyzed the role of TWIST1, a key EndMT-driving transcription factor, in plaque development. Using single-cell RNA sequencing of atherosclerotic plaques from hypercholesterolemic mice with inducible deletion of Twist1 from endothelial cells (Twist1ECKO ApoE-/-) we demonstrate that Twist1 regulates endothelial cell heterogeneity by promoting cell states expressing EndMT markers. Cell tracking confirmed that Twist1 induces EndMT in advanced plaques. Mechanistically, we found that TWIST1 contributes to EndMT by promoting endothelial migration and proliferation through the transcriptional coactivator PELP1. Additionally, TWIST1 induces AEBP1 transcription, which upregulates COL4A1 to drive endothelial proliferation. Analyses of murine brachiocephalic plaques show that endothelial Twist1 promotes plaque growth, collagen deposition, and ACTA2-positive cell accumulation, hallmarks of plaque stability, while reducing necrosis and macrophage infiltration, features of plaque instability. Moreover, TWIST1 expression was associated with asymptomatic human carotid atherosclerosis and predicts favourable clinical outcomes. These findings challenge the prevailing view that EndMT destabilizes plaques, by suggesting that TWIST1-driven EndMT can promote plaque stability, offering new insights into atherosclerosis pathophysiology and therapeutic potential.

pathology↗

bioRxiv2025

Testicular mRNA-LNP Delivery: A Novel Therapy for Genetic Spermatogenic Disorders

Uniform testicular maturation arrest is a severe form of male infertility characterized by the presence of germ cells that do not complete spermatogenic development. It is usually caused by meiotic arrest with genetic variants and difficult to treat via drugs or surgery. mRNA-lipid nanoparticle (LNP) delivery is a promising therapeutic option for maturation arrest with monogenic variants via protein replacement therapy. Herein, a spermatocytes-tropic LNP (Pool1-LNP3) was identified via a library of 30 ionizable lipids screening. And in vivo delivery of this novel LNP composition using rete testis microinjection was showed to be high spermatocytes targeting with high transfection efficiency. Thereafter, it was revealed that in vivo delivery of Pool1-LNP3 encapsulating Msh5 mRNA could promote crossover formation and restore spermatogenesis in Msh5D486Y/D486Y mouse models with DSB recombination defects. Notably, the offspring without genomic integration was born using intracytoplasmic sperm injection (ICSI) derived from rescue of Msh5D486Y/D486Ymouse and embryo transfer. Furthermore, no obvious inflammation and histologic damage in any tissue were detected after in vivo delivery of mRNA-LNP. In addition, it was demonstrated that Maps mRNA-LNP3 recovered spermatogenesis in Maps KO mouse with meiotic arrest. Altogether, these findings suggested that this spermatocytes-tropic mRNA-LNP delivery could become a viable and broad applicable strategy for treatment of spermatogenic disorders with genetic defects, providing a foundation for future clinical application.

molecular biology↗