Biology subjects

Xu, S.

Publications and source records attributed to Xu, S..

At least 181 records · Page 10Linked to original sources

bioRxiv2024

Terrestrial herbivory drives adaptive evolution in an aquatic community via indirect effects

Indirect ecological effects, which occur when the impact of one species on another is mediated by a third species or the shared environment, are ubiquitous in nature. Given the complexity of natural systems, indirect ecological effects were thought to be important in driving eco-evolutionary processes across community boundaries. However, we know remarkably little about such effects. Here we show that indirect effects of terrestrial insect (aphids) herbivory on macrophytes (duckweed) drives adaptive evolution of water fleas (Daphnia) in large outdoor aquatic mesocosms. Aphid herbivory reduced macrophyte growth and increased the abundance of phytoplankton, which in turn increased the abundance of Daphnia. Whole genome pool sequencing and phenotypic assays revealed an impact on the genetic compositions of the Daphnia populations and transplant experiments indicated that these evolutionary changes were adaptive. Furthermore, these changes in the aquatic community altered the interactions of the aphids and the macrophytes. These results demonstrate that indirect ecological effects can shape eco-evolutionary interactions between different communities.

evolutionary biology↗

bioRxiv2024

Novel regulator Fpr2 controls immune homeostasis via CCL4-dependent neutrophils

Polymorphonuclear leukocytes (PMNs) in Fpr2-deficient mice have significantly impaired bactericidal activity, yet the precise mechanism remains elusive. Our research unveiled the cellular heterogeneity of peripheral blood PMNs through single-cell RNA-sequencing (scRNA-seq) and identified two new neutrophil clusters related to bacterial infection, including a sterilization cluster named Neu_CSTA and a regulation cluster named Neu_CCL4. The lack of Fpr2 leads to an immune regulation imbalance of Neu_CCL4 on other clusters in uninfected conditions, resulting in persistent instability of PMNs in peripheral blood, elevated inflammatory factors, and increased NOX2 expression. Furthermore, our findings corroborate that the regulatory function of Neu_CCL4 on PMNs immune balance is closely tied to its high expression of the anti-inflammatory ligand Anxa1. Regulon analysis inferred by scRNA-seq and ChIP-seq data suggested that a specific transcription factor Elf4, could modulate the expression of Anxa1, thereby facilitating its regulatory impact on other clusters. In the infection state, there was a noted increase in intercellular interactions across different clusters, leading to a general improvement in the bactericidal activity of PMNs. In summary, our research revealed distinct functional cellular sub-populations of PMNs, discovered the potential regulatory mechanisms, and elucidated the essential roles of Fpr2 in their ability to resist infection.

immunology↗

bioRxiv2024

Accurate and Rapid Prediction of Protein pKa: Protein Language Models Reveal the Sequence-pKa Relationship

Protein pKa prediction is a key challenge in computational biology. In this study, we present pKALM, a novel deep learning-based method for high-throughput protein pKa prediction. pKALM uses a protein language model (PLM) to capture the complex sequence-structure relationship of proteins. While traditionally considered a structure-based problem, our results show that a PLM pre-trained on large-scale protein sequence databases can effectively learn this relationship and achieve state-of-the-art performance. pKALM accurately predicts the pKa values of six residues (Asp, Glu, His, Lys, Cys, and Tyr) and two termini with high precision and efficiency. It excels at predicting both exposed and buried residues, which often deviate from standard pKa values measured in solvent. We demonstrate a novel finding that predicted protein isoelectric points (pI) can be used to improve the accuracy of pKa prediction. High-throughput pKa prediction of the human proteome using pKALM achieves a speed of 4,965 pKa predictions per second, which is several orders of magnitude faster than existing state-of-the-art methods. The case studies illustrate the efficacy of pKALM in estimating pKa values and the constraints of the method. pKALM will thus be a valuable tool for researchers in the fields of biochemistry, biophysics, and drug design.

bioinformatics↗

bioRxiv2024

Reduced Hydrogen Sulfide Bioavailability Contributes to Cardiometabolic Heart Failure with Preserved Ejection Fraction

BackgroundHeart failure with preserved ejection fraction (HFpEF) is a significant public health concern with limited treatment options. Dysregulated nitric oxide-mediated signaling has been implicated in HFpEF pathophysiology, however, little is known about the role of endogenous hydrogen sulfide (H2S) in HFpEF. ObjectivesThis study evaluated H2S bioavailability in patients and two animal models of cardiometabolic HFpEF and assessed the impact of H2S on HFpEF severity through alterations in endogenous H2S production and pharmacological supplementation. We also evaluated the effects of the H2S donor, diallyl trisulfide (DATS) in combination with the GLP-1/glucagon receptor agonist, survodutide, in HFpEF. MethodsHFpEF patients and two rodent models of HFpEF ("two-hit" L-NAME + HFD mouse and ZSF1 obese rat) were evaluated for H2S bioavailability. Two cohorts of two-hit mice were investigated for changes in HFpEF pathophysiology: (1) endothelial cell cystathionine-{gamma}-lyase (EC-CSE) knockout; (2) H2S donor, JK-1, supplementation. DATS and survodutide combination therapy was tested in ZSF1 obese rats. ResultsH2S levels were significantly reduced (i.e., 81%) in human HFpEF patients and in both preclinical HFpEF models. This depletion was associated with reduced CSE expression and activity, and increased SQR expression. Genetic knockout of H2S -generating enzyme, CSE, worsened HFpEF characteristics, including elevated E/e ratio and LVEDP, impaired aortic vasorelaxation and increased mortality. Pharmacologic H2S supplementation restored H2S bioavailability, improved diastolic function and attenuated cardiac fibrosis corroborating an improved HFpEF phenotype. DATS synergized with survodutide to attenuate obesity, improve diastolic function, exercise capacity, and reduce oxidative stress and cardiac fibrosis. ConclusionsH2S deficiency is evident in HFpEF patients and conserved across multiple preclinical HFpEF models. Increasing H2S bioavailability improved cardiovascular function, while knockout of endogenous H2S production exacerbated HFpEF pathology and mortality. These results suggest H2S dysregulation contributes to HFpEF and increasing H2S bioavailability may represent a novel therapeutic strategy for HFpEF. Furthermore, our data demonstrate that combining H2S supplementation with GLP-1/glucagon receptor agonist may provide synergistic benefits in improving HFpEF outcomes. HighlightsO_LIH2S deficiency is evident in both human HFpEF patients and two clinically relevant models. C_LIO_LIReduced H2S production by CSE and increased metabolism by SQR impair H2S bioavailability in HFpEF. C_LIO_LIPharmacological H2S supplementation improves diastolic function and reduces cardiac fibrosis in HFpEF models. C_LIO_LITargeting H2S dysregulation presents a novel therapeutic strategy for managing HFpEF. C_LIO_LIH2S synergizes with GLP-1/glucagon agonist and ameliorates HFpEF C_LI

pharmacology and toxicology↗

bioRxiv2024

The impact of high-fat and obesogenic diets on brain volume in a commercially available mouse model of fatty liver disease

The obesity pandemic poses significant health challenges, despite recent advancements in weight loss medications. Mouse models fed obesogenic diets serve as invaluable tools for dissecting the pleiotropic mechanisms underlying weight gain. Here, we utilize these models to analyze brain morphometrics using MRI techniques, inspired by similar findings in human studies linking obesity to brain volume changes. We hypothesize that the mouse model of obesity will exhibit brain volume alterations akin to those observed in obese humans, potentially shedding light on the neurological implications of obesity. To test our hypothesis, mice were provided free access to either regular chow or a diet consisting of high fat and high sugar and MRI scans for total brain volumes as well as volumes of specific brain regions were estimated and compared between obese and control mice. We found that obesogenic diets resulted in [~]13% greater weight gain compared to control chow diets. MRI brain scans revealed reduced total brain volume in obese mice that trended towards significance. In contrast, analysis of specific brain volumes showed an increase in neocortical regions of obese mice, that were significant when compared to controls. In conclusion, diet-induced obesity mouse models are a readily available avatar for studying the obesity epidemic, with significant increases in body weight within a reasonable timeframe. While weight gain among individual mice fed obesogenic diets showed some variability, MRI brain scans were able to reveal significant differences, especially within different anatomical regions of the brain.

neuroscience↗

bioRxiv2024

High-speed 4D fluorescence light field tomography of whole freely moving organisms

Volumetric fluorescence imaging techniques, such as confocal, multiphoton, light sheet, and light field microscopy, have become indispensable tools across a wide range of cellular, developmental, and neurobiological applications. However, it is difficult to scale such techniques to the large 3D fields of view (FOV), volume rates, and synchronicity requirements for high-resolution 4D imaging of freely behaving organisms. Here, we present reflective Fourier light field computed tomography (ReFLeCT), a new high-speed volumetric fluorescence computational imaging technique. ReFLeCT synchronously captures entire tomograms of multiple unrestrained, unanesthetized model organisms over multi-millimeter 3D FOVs at 120 volumes per second. In particular, we applied ReFLeCT to reconstruct 4D videos of fluorescently labeled zebrafish and Drosophila larvae, enabling us to study their heartbeat, fin and tail motion, gaze, jaw motion, and muscle contractions with nearly isotropic 3D resolution while they are freely moving. As a novel approach for snapshot tomographic capture, ReFLeCT is a major advance towards bridging the gap between current volumetric fluorescence microscopy techniques and macroscopic behavioral imaging.

animal behavior and cognition↗

bioRxiv2024

High-efficiency discovery and structure-activity-relationship analysis of non-substrate-based covalent inhibitors of S-adenosylmethionine decarboxylase

Targeted covalent inhibitors (TCIs) form covalent bonds with targets following initial non-covalent binding. The advantages of TCIs have driven a resurgence in rational TCI design over the past decade, resulting in the approval of several blockbuster covalent drugs. To support TCI discovery, various computational methods have been developed. However, accurately predicting TCI reactivity remains challenging due to interference between non-covalent scaffolds and reactive warheads, leading to inefficiencies in computational screening and high experimental costs. In this study, we enhanced the SCARdock protocol, a validated computational screening tool developed by our lab, by incorporating quantum chemistry-based warhead reactivity calculations. By integrating these calculations with non-covalent docking scores, docking ranks, and bonding-atom distances, non-covalent and covalent inhibitors of S-adenosylmethionine decarboxylase (AdoMetDC) were correctly classified. Using the optimized SCARdock, we successfully identified twelve new AdoMetDC covalent inhibitors from 17 compounds, achieving a 70.6% hit rate. From these novel inhibitors, we analyzed the contributions of non-covalent interactions and covalent bonding, enabling a structure-activity relationship (SAR) analysis for AdoMetDC covalent inhibitors, which was previously unexplored with substrate-based inhibitors. Overall, this work presents an efficient computational protocol for TCI discovery and offers new insights into AdoMetDC inhibitor design. We anticipate that this approach will stimulate TCI development by improving computational screening efficiency and reducing experimental costs.

pharmacology and toxicology↗

bioRxiv2024

A critical affinity window for IgSF proteins DIP-α and Dpr10 is required for proper motor neuron arborization

For flies to walk properly, motor neurons (MNs) from the ventral nerve cord (VNC) need to reach the correct muscle, and arborize appropriately during development. The canonical view of how this is achieved is that cell surface proteins are expressed pre- and post-synaptically that bind to each other like molecular "lock-and-keys" that guide neurons to their targets. The binding affinities of these molecules can vary by more than 100-fold. In the fly leg neuromuscular system, three MNs express DIP- and their target muscles express its cognate partner, dpr10, both of which encode members of the Immunoglobulin superfamily (IgSF). Although, both of these molecules are necessary for the maintenance of MN-muscle contacts, the role that specific affinities play in this process has not been examined. Here we use knock-in mutations into DIP- and dpr10 that either decrease or increase the affinity between these two proteins. Compared to control animals, decreasing the affinity results in phenotypes similar to DIP- or dpr10 null animals, where MN axons fail to maintain contacts with their muscle targets and retract their filopodia, resulting in stunted and/or branchless axons. We also find that the three DIP--expressing motor neurons behave differently to the loss of affinity. Surprisingly, if the affinity increases past a certain threshold, a similar branchless phenotype is observed in adult legs. Live imaging during pupal development shows that MN filopodia are unable to productively engage their muscle targets and behavioral assays suggest that these defects lead to locomotor deficits. These data suggest that CAM affinities are tuned to a specific range to achieve proper neuronal morphology.

developmental biology↗

bioRxiv2024

Organoid Modeling and Single-Cell Profiling Uncover the Migration Mechanism of Smooth Muscle Cells in Moyamoya Disease

Moyamoya disease (MMD) is a chronic cerebrovascular disorder characterized by progressive occlusion of the intracranial arteries, resulting in severe ischemic or hemorrhagic stroke. The main characteristic of the affected vessels in MMD is arterial intimal thickening. However, there are no in vitro or in vivo models that can mimic its vascular characteristics. Moreover, the mechanisms underlying the intimal thickening remain unexplained. Here, we generated vascular organoids by differentiating human induced pluripotent stem cell derived from the peripheral blood of MMD patients, thereby creating an organoid model reflecting both the genetic background and characteristics of the affected vessels. Through single-cell sequencing, we found the increased vascular smooth muscle cell (VSMC) proportion and its functional abnormalities in MMD organoids. Proteomics and RNA sequencing identified abnormal TUBA4A and TUBB4B overexpression in both the organoids and patient serum. The following in vitro experiments demonstrated that TUBA4A and TUBB4B promote the contractile-to-synthetic phenotypic switching, migration and proliferation in VSMC. Further experiments identified the GJA1-mediated PI3K/AKT/KLF4 pathway as a key regulating pathway of these phenotypic changes in VSMCs. Our findings demonstrate that the abnormal expression of TUBA4A and TUBB4B in VSMC might be a significant contributor to the intimal thickening in the affected vessels of MMD.

cell biology↗

bioRxiv2024

Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis

Endosymbiotic gene transfer and import of host-encoded proteins are considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, obligate endosymbionts that are closely related to recently-described nitrogen-fixing organelles and share similar function as integral cell compartments. We report genomic analyses of two species which are highly divergent but share a common ancestor at the origin of the endosymbiosis. We found minimal evidence of genetic integration in E.clementina: nonfunctional diazoplast-to-nucleus DNA transfers and 6 host-encoded proteins of unknown function in the diazoplast proteome, far fewer than detected in other recently-acquired endosymbionts designated organelles. Epithemia diazoplasts are a valuable counterpoint to existing organellogenesis models, demonstrating that endosymbionts can function as integral compartments absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.

evolutionary biology↗

bioRxiv2024

Endothelial MICU1 protects against vascular inflammation and atherosclerosis by inhibiting mitochondrial calcium uptake

Atherosclerosis is triggered by endothelial activation and vascular inflammation, which is closely related to mitochondrial dysfunction. Mitochondrial calcium uptake 1 (MICU1), as the gatekeeper of mitochondrial Ca2+ homeostasis, is a critical player in mitochondrial function and implicated in a plethora of pathophysiological conditions. However, the role of MICU1 in the pathogenesis of vascular inflammation and atherosclerosis is unknown. We ask whether endothelial MICU1 can prevent vascular inflammation and atherosclerosis by maintaining mitochondrial homeostasis. We observed that vascular inflammation in response to LPS was aggravated in EC-specific Micu1 knockout mice (Micu1ECKO) and reduced in EC-specific Micu1 transgenic mice (Micu1ECTg). Furthermore, hypercholesterolemic Micu1ECKO mice also showed accelerated formation of atherosclerotic plaques, while Micu1ECTg mice protected against atherosclerosis. Mechanistically, MICU1 regulated mitochondrial Ca2+ influx, thereby reducing the expression of the mitochondrial deacetylase SIRT3 and the ensuing deacetylation of SOD2, leading to the burst of mitochondrial reactive oxygen species (mROS). Of clinical relevance, we identified decreased MICU1 level in endothelial layer of human atherosclerotic plaques, as well as in primary human aortic endothelial cells (HAECs) exposed to serum from patients with coronary artery diseases. Two-sample Wald ratio Mendelian randomization further revealed that increased expression of MICU1 was associated with decreased risk of coronary artery bypass grafting (CABG). Our findings unravel a critical and unrecognized role of MICU1 in preventing vascular inflammation and atherosclerosis by maintaining mitochondrial Ca2+ homeostasis.

molecular biology↗

bioRxiv2024

Outside-in engineering of cadherin endocytosis using a conformation strengthening antibody.

P-cadherin, a crucial cell-cell adhesion protein which is overexpressed in numerous malignant cancers, is a popular target for drug delivery antibodies. However, molecular guidelines for engineering antibodies that can be internalized upon binding to P-cadherin are unknown. Here, we use a combination of biophysical, biochemical, and cell biological methods to demonstrate that trapping the cadherin extracellular region in an X-dimer adhesive conformation, triggers cadherin endocytosis via a novel outside-in signaling mechanism. We show that the monoclonal antibody CQY684 traps P-cadherin in an X-dimer conformation and strengthens this adhesive structure. Formation of stable X-dimers results in the dissociation of p120-catenin, a suppressor of cadherin endocytosis, from the X-dimer cytoplasmic region. This increases the turnover of P-cadherin and targets the cadherin-antibody complex to the lysosome. Our results establish a previously unknown outside-in signaling mechanism that provides fundamental insights into how cells regulate adhesion and that can be exploited by anti-cadherin antibodies for intracellular drug delivery.

biophysics↗

bioRxiv2024

The clinical antiprotozoal drug halofuginone promotes weight loss by elevating GDF15 and FGF21

Obesity is a debilitating disease with increasing worldwide prevalence. Despite its high prevalence, specific pharmacologic intervention for obesity is challenging. Here, we report that halofuginone, an FDA-approved anti-scleroderma and anti-protozoal drug, is a promising anti-obesity agent in rodent models. Halofuginone suppressed food intake, increased energy expenditure, and resulted in weight loss in preclinical diet-induced obese mouse models, while also decreasing insulin resistance and hepatic steatosis. By combining genetic and pharmacological tools with transcriptomics, we identified that halofuginone increases FGF21 and GDF15 levels via ATF4. Using knockout mice, we show these hormones are both necessary for its anti-obesity effects. Thus, our study first reports the beneficial metabolic effects of halofuginone and underscores its utility to treat obesity and its associated metabolic complications.

pharmacology and toxicology↗

bioRxiv2024

FEDKEA: Enzyme function prediction with a large pretrained protein language model and distance-weighted k-nearest neighbor

Recent advancements in sequencing technologies have led to the identification of a vast number of hypothetical proteins, surpassing current experimental capabilities for annotation. Enzymes, crucial for diverse biological functions, have garnered significant attention; however, accurately predicting enzyme EC numbers for proteins with unknown functions remains challenging. Here, we introduce FEDKEA, a novel computational method that integrates ESM-2 and distance-weighted KNN (k-nearest neighbor) to enhance enzyme function annotation. FEDKEA first employs a fine-tuned ESM-2 model with four fully connected layers to distinguish from other proteins. For predicting EC numbers, it adopts a hierarchical approach, utilizing distinct models and training strategies across the four EC number levels. Specifically, the classification of the first EC number level utilizes a fine-tuned ESM-2 model with three fully connected layers, while transfer learning with embeddings from this model supports the second and third-level tasks. The fourth-level classification employs a distance-weighted KNN model. Compared to existing tools such as CLEAN and ECRECer, two state-of-the-art computational methods, FEDKEA demonstrates superior performance. We anticipate that FEDKEA will significantly advance the prediction of enzyme functions for uncharacterized proteins, thereby impacting fields such as genomics, physiology and medicine. FEDKEA is easy to install and currently available at: https://github.com/Stevenleizheng/FEDKEA

bioinformatics↗

bioRxiv2024

Study on the phenotypic diversity and comprehensive evaluation analysis of 43 ornamental peonies of Sect. Paeonia.

The peony of Sect. Paeonia was a perennial herbaceous plant with numerous ornamental varieties and riched diversity in flower color and shape. It has ornamental, edible, and medicinal value and a long history of cultivation in China. The study of phenotypic diversity of plants is an important foundation for plants of Sect. Paeonia breeding. This study conducted phenotypic diversity analysis, principal component analysis, and cluster analysis on 43 varieties of Sect. Paeonia germplasm resources. Phenotypic traits included 30 qualitative traits and 7 quantitative traits. Through genetic diversity analysis, principal component analysis, comprehensive evaluation, and cluster analysis, we ultimately concluded that plant samples had relatively rich genetic phenotype traits. In principal component analysis, the first 12 principal components have covered the vast majority of information for phenotypic traits. The comprehensive evaluation results of phenotypic traits indicate that the F values of each variety in the germplasm sample were all positive number. The degree of stamen petals played a key role in determining the phenotypic diversity of plants, and the shape of the cotyledons and leaflets may determine the plants stress resistance performance, which provides a reference for breeding new varieties of peonies of Sect. Paeonia.

plant biology↗

bioRxiv2024

Intra-subgenome regulation induces unbalanced expression and function among bread wheat homoeologs

The differential expression of homoeologous genes confers expression plasticity and facilitates the adaptation and domestication of major polyploid crops. However, how this homoeolog expression bias (HEB) is regulated remains elusive. Here, transcriptome analysis of 406 wheat (Triticum aestivum; AABBDD) accessions revealed great variation in HEB among accessions. We identified 14,727 QTLs regulating HEB (hebQTLs), indicating that HEB is genetically regulated and can be predicted using genotyping data. The hebQTLs only regulate the expression of homoeologs in the same subgenome and downregulate their expression to result in HEB, suggesting that intra-subgenomic rather than inter-subgenomic interactions induce HEB. Furthermore, non-hebQTL-regulated homoeologs have stronger biological functions, are under higher selection pressure and exhibit lower genetic diversity than hebQTL-regulated homoeologs and compensate for the downregulated expressions of hebQTL-regulated homoeologs. Our findings reveal how homoeolog expression is coordinated at the genetic level and provide an avenue for leveraging HEB to improve polyploid crops.

genomics↗

bioRxiv2024

Genome-Wide Association Study of Metabolic Traits in the Duckweed Spirodela polyrhiza

The exceptionally high growth rate and high contents of flavonoids make the giant duckweed Spirodela polyrhiza (L.) Schleid. (Arales: Lemnaceae) an ideal organism for food production and metabolic engineering. To facilitate this, identification of the genetic basis underlying growth and metabolic traits is essential. Here, we characterized the genetics underpinning the growth and contents of 42 metabolites in S. polyrhiza using a genome-wide association (GWA) approach. We found that biomass positively correlates with contents of many free amino acids, including L-Glutamine, L-Tryptophane and L-Serine, but negatively correlates with many specialized metabolites, such as flavonoids. GWA analysis showed that several candidate genes were simultaneously associated with several metabolic traits, qualifying them as targets for growth manipulation and metabolic engineering. Together, this study provides insights into the metabolic diversity of S. polyrhiza and its underlying genetic architecture, paving the way for industrial applications of this plant via targeted breeding or genetic engineering.

plant biology↗

bioRxiv2024

PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation

Preferentially Expressed Antigen in Melanoma (PRAME) and Ten-Eleven Translocation (TET) dioxygenase-mediated 5-hydroxymethylcytosine (5hmC) are emerging melanoma biomarkers. We observed an inverse correlation between PRAME expression and 5hmC levels in benign nevi, melanoma in situ, primary invasive melanoma, and metastatic melanomas via immunohistochemistry and multiplex immunofluorescence: nevi exhibited high 5hmC and low PRAME, whereas melanomas showed the opposite pattern. Single-cell multiplex imaging of melanoma precursors revealed that diminished 5hmC coincides with PRAME upregulation in premalignant cells. Analysis of TCGA and GTEx databases confirmed a negative relationship between TET2 and PRAME mRNA expression in melanoma. Additionally, 5hmC levels were reduced at the PRAME 5 promoter in melanoma compared to nevi, suggesting a role for 5hmC in PRAME transcription. Restoring 5hmC levels via TET2 overexpression notably reduced PRAME expression in melanoma cell lines. These findings establish a function of TET2-mediated DNA hydroxymethylation in regulating PRAME expression and demonstrate epigenetic reprogramming as pivotal in melanoma tumorigenesis. TeaserMelanoma biomarker PRAME expression is negatively regulated epigenetically by TET2-mediated DNA hydroxymethylation

cancer biology↗