GNPS Metabolomics of thermal stress-induced coral blenching
Ontology highlight
ABSTRACT:
INSTRUMENT(S): ThermoTM Q-ExactiveTM mass spectrometer
ORGANISM(S): Coral
SUBMITTER: 
Jiying Pei
PROVIDER: MSV000088564 | GNPS | Tue Dec 14 11:03:00 GMT 2021
REPOSITORIES: GNPS
Similar Datasets
Project description:The bleaching model of P. decussata was built by heating from 26C to 35C in the aquarium, and the metabolite extract was analyzed by ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry.
2021-12-14 | MSV000088564 | MassIVE
Project description:Mouse livers were analyzed by lipidomics and urine by metabolomics.An Agilent Ultra-Performance Liquid Chromatography/Electrospray Ion Quadrupole Time-of-Flight-Mass Spectrometer (UPLC-ESI-QTOFMS) (Agilent, Santa Clara, CA) was utilized for lipid and other metabolites proofing in this work.
2023-06-07 | PXD041465 | Pride
Project description:Background: Shengyu decoction (SYD) is a classic and excellent prescription of traditional Chinese Medicine (TCM). The innovative use of SYD by Chinese medical master Prof. Qi Shi in the treatment of knee osteoarthritis (KOA) has achieved considerable clinical outcomes. However, the current weakness is the lack of study on the active ingredients and mechanisms of SYD. Purpose: To evaluate the role of SYD in reducing KOA cartilage damage as well as to explore the active ingredients and mechanisms of SYD. Methods: The KOA rat model and chondrocyte model were established. This study employed various molecular biology techniques to clarify the role of SYD in vivo and in vitro. Furthermore, the active ingredients and mechanisms of SYD were analyzed through ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS), RNA sequencing, molecular docking and surface plasmon resonance (SPR) experiment. Finally, rescue experiments were conducted to verify the mechanisms. Results: The results revealed that SYD could significantly reduce cartilage tissue lesions, inhibit inflammation and regulate proliferation-apoptosis balance. Transcriptome analysis showed an increase in the expression of Piezo1, Xbp1, Atf6 in KOA and SYD downregulated them. UPLC-Q-TOF-MS analysis revealed four bioactive compounds of SYD, which were further confirmed to directly interact with Piezo1 through molecular docking and SPR assays. Furthermore, SYD downregulated the calcium ion concentration, Piezo1 and ERS intensity. Meanwhile, in the rescue experiment, Yoda1, the agonist of Piezo1, antagonized the pharmacological effects of SYD. Conclusions: The present results provides strong evidence that SYD protected articular cartilage via inhibiting the Piezo1-mediated ERS signaling pathway. Overall, our work emphasizes the pivotal role of TCM in addressing medical challenges and provides new ideas for the treatment of KOA.
2025-08-06 | GSE301460 | GEO
Project description:The resveratrol-producing rice (Oryza sativa L.) inbred line, Iksan 526 (I.526), developed by the expression of the groundnut (Arachis hypogaea) resveratrol synthase 3 (AhRS3) gene in the japonica rice cultivar Dongjin, accumulated both resveratrol and its glucoside, piceid, in leaves and seeds. Especially, ultra-performance liquid chromatography (UPLC) analysis revealed that the biosynthesis of piceid reached peak levels at 20 days after heading (DAH) seeds. To investigate endogenous piceid biosynthesis genes (UGTs), total RNA samples of 20 DAH seeds was used for RNA-seq.
2020-12-20 | E-MTAB-9695 | biostudies-arrayexpress
Project description:We applied nanoscale liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (nanoLC/Q-TOF-MS/MS) and ultra-performance LC/Q-TOF-MS/MS technologies on tear samples obtained from 18 dry eye patients and 19 healthy controls for integrated proteomic and metabolomic analyses
2019-02-28 | PXD012917 |
Project description:DNA methylation is a key mechanism for regulation of DNA repair, DNA replication, and gene expression. In bacteria, DNA is modified by methylation on C5-cytosine (5mC), N6-adenine (6mA) and N4-cytosine (4mC). Metazoans were thought to only use 5mC to regulate gene expression until the recent discovery of N6-adenine methylation in DNA of diverse metazoan species, including mammals. Here we show by dot blot, immunoprecipitation with 4mC-specific antibodies, and ultra-high performance liquid chromatography coupled with triple-quadrupole mass spectrometry that 4mC also occurs in most eukaryotes. We further characterize 4mC sites on a near genome-wide scale by single molecule real time (SMRT) sequencing in the nematode C. elegans. In C. elegans, 4mC is found in all chromosomes but is relatively sparse on the X chromosome. 4mC is relatively enriched on introns, depleted on exons, and co-localizes with 6mA. In human cells, 4mC is anti-correlated with 5mC. Moreover, 4mC modifications are associated with increased gene expression. Transfection of human cells with a 4mC-modified luciferase reporter plasmid increases luciferase expression as compared to the unmethylated plasmid. These data suggest that 4mC promotes gene transcription, playing an opposing role to 5mC, which generally represses transcription. Thus 4mC modification of DNA is a previously unrecognized mechanism of gene regulation in eukaryotes, providing evidence for a complex epigenetic DNA code.
2018-09-01 | GSE86993 | GEO
Project description:<p>This dataset contains raw untargeted metabolomics data generated from esophageal tissue samples of rats in a reflux esophagitis (RE) model. The study aimed to characterize metabolic alterations associated with RE pathogenesis and to evaluate the regulatory effects of Shunwei Jiangni Decoction (SWJN), a modified traditional Chinese medicine formula derived from Banxia Xiexin Decoction. Male Wistar rats were divided into four groups: sham control (Control), RE model (Mod), SWJN low-dose (SWJN_L), and SWJN high-dose (SWJN_H). After 4 weeks of treatment, esophageal tissues were collected and subjected to untargeted metabolomics analysis using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF-MS) in both positive and negative ion modes. Metabolite features were extracted and annotated using the XCMS package and public databases (HMDB, Metlin, and self-built libraries). </p>
2026-04-10 | MTBLS14112 | MetaboLights
Project description:Gigantol is a bioactive compound in Dendrobium officinale with a wide range of pharmacological properties. This study developed an ultrahigh-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) method for quantifying gigantol, which was subsequently applied to assess its pharmacokinetics and tissue distribution in Kunming mice. Additionally, the effects of gigantol on peroxisome proliferator-activated receptors (PPARs) were investigated. The UHPLC-Q-TOF/MS method was validated following the guidelines provided by the FDA and EMA for bioanalytical methods. Pharmacokinetic analysis revealed that gigantol exhibits a non-linear kinetic profile. Tissue distribution studies demonstrated high concentrations of gigantol in the liver and lungs. RNA sequencing (RNA-seq) indicated significant enrichment of PPAR signaling pathways in the KEGG database during gigantol-induced gene expression changes in the liver of Kunming mice. Molecular fingerprinting, docking studies and dual luciferase reporter assays confirmed that gigantol is a dual PPARα/γ agonist. These findings provide valuable insights for preclinical research on gigantol.
2025-12-06 | GSE312718 | GEO
Project description:Background: Arachidonic acid (AA) metabolism pathway is dominant in metabolic programming after hypoxia exposure, but its biological function is disputed and require in-depth studies. In this research, we aimed at integrating plasma metabolomics and transcriptomics approaches to systematically explore its roles in response to acute hypoxia based on model of acute high-altitude exposure. Methods: Blood samples were taken from 53 enrolled subjects before and after their exposure to high altitude. Ultra-performance liquid chromatography- quadrupole time-of-flight mass spectrometry and RNA sequencing were performed to acquire corresponding metabolomic and transcriptomic profiling along with hypoxia exposure, separately. Influential modules comprising essential metabolites and genes were identified by weighted gene co-expression network analysis (WGCNA) after integrating metabolic information with phenotypic and transcriptomic datasets, respectively. Results: Enrolled individuals showed significant alterations in heart rate, SpO2, hemoglobin and Lake Louise Score (LLS) in response to hypoxia. Metabolomics profiling demonstrated that AA metabolism pathway was remarkable in these metabolic alterations. Integrated analysis of metabolomic and transcriptomic data revealed that increasing AA metabolism pathway might count for gas transport incapacitation and disorders in hemoglobin metabolism under hypoxia stimuli. Moreover, identified in further analysis and another cohort, excessively elevated AA metabolism pathway was involved in poor response to hypoxia. Conclusion: Our study, for the first time, constructed the maps of AA metabolism pathway in response to hypoxia; and revealed the crosstalk between phenotypic variation to hypoxia and AA metabolism pathway. These findings will not only advanced pathophysiological mechanisms for acute hypoxic diseases, but provided new insights into critical roles of AA metabolism pathway in development and prevention of these diseases.
2018-03-09 | GSE103940 | GEO
Project description:This study established a quantitative analysis method for moscatilin using ultrahigh-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) to investigate its pharmacokinetics and tissue distribution in Kunming mice. Additionally, RNA sequencing (RNA-seq) and network pharmacology were employed to elucidate the molecular mechanisms underlying moscatilin's therapeutic potential in liver diseases, including non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), viral hepatitis, liver injury, liver fibrosis, liver cirrhosis, and liver cancer. The analytical method was validated for selectivity, carryover, linearity, precision, accuracy, dilution integrity, matrix effect, recovery, and stability following US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) bioanalytical guidelines. Pharmacokinetic analysis revealed rapid absorption of moscatilin in vivo, with a bioavailability of 85.82%. Tissue distribution studies indicated widespread presence across various organs, with elevated concentrations in the lungs and liver. RNA-seq and network pharmacology analysis identified signal transducer and activator of transcription 1 (STAT1) and serine protease inhibitor clade E member 1 (SERPINE1) as potential targets for moscatilin in liver disease treatment.
2025-12-12 | GSE312822 | GEO