Project description:Tuberculosis (TB) remains a major public health problem and we lack a comprehensive understanding of how Mycobacterium tuberculosis (M. tb) infection impacts host immune responses. We compared, at two timepoints, the induced immune response to TB antigen, BCG and IL-1β stimulation between latently M. tb infected individuals (LTBI) and active TB patients. The immune response was assessed using the TruCulture system with a Null stimulation. samples were tested by Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC MS/MS) for a total of 696 metabolites.
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.
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.
Project description:The experiment is part of a study using systems biology approach to analyze muscle gene expression and UPLC-MS based plasma lipidomics profiling data to illuminate relevant biological pathways and to find potential biomarker candidates related to statin-induced changes in muscle metabolism.
2007-03-01 | E-TABM-116 | biostudies-arrayexpress
Project description:Evaluation of VITEK MS VER. 3.0 MALDI-TOF
Project description:Using well-characterized cell line models for seminoma (Tcam-2, n=15) and EC (NT2, n=15), we characterized their metabolite profiles using ultraperformance liquid chromatography coupled with Q-TOF mass spectrometry (UPLC/Q-TOF MS).
Project description:<p>This study presents untargeted LC–MS/MS metabolomics and lipidomics datasets comparing CON and MAL experimental groups acquired in both positive and negative electrospray ionization modes. For quality control, a pooled QC sample was prepared by mixing equal volumes of all study samples and was analyzed alongside extracted samples. Separation was performed using an Agilent Infinity 1200 UPLC system coupled to an Agilent 6540 Quadrupole Time-of-Flight mass spectrometer (Q-TOF) in data-dependent acquisition (DDA) mode over an m/z range of 50–1000. Chromatographic separation used an Agilent Poroshell column (2.1 × 100 mm, 1.9 μm) with mobile phases (A) 0.1% formic acid in water and (B) 0.1% formic acid in acetonitrile, at 0.4 mL/min, 30 °C, and 10 μL injection volume. The ESI source settings were: gas temperature 250 °C, gas flow 10 L/min, nebulizer 35 psi, sheath gas 250 °C at 11 L/min, capillary 3.5 kV, fragmentor 75 V, and oct RF 750 V; acquisition rate was 2 spectra/s. MS/MS fragmentation used a rolling collision energy of 10–20–40 V. Raw Q-TOF data were processed using Progenesis QI to generate aligned feature tables (m/z, retention time, and intensity; default sensitivity level 3; S/N ≥ 3). Internal standards were removed prior to downstream analysis. Putative annotation was performed using an in-house PMDB combined with HMDB (mass error ≤ 10 ppm; MS/MS match ≥ 35). Features were filtered using a 50% rule, missing values were imputed with minimum values, intensities were sum-normalized, features with QC RSD > 30% were removed, and the matrix was log10-transformed. Statistical analysis included OPLS-DA using the R package ropls (v1.6.2) and significance assessment using VIP > 1 and Student’s t-test (p < 0.05). The deposited files include raw vendor data (.d) for both ion modes and the processed data matrices used for analysis.</p>
Project description:Intrauterine growth restriction (IUGR) is one of the most common adverse pregnancy outcomes with high risk of perinatal morbidity and mortality, and affects up to 7% of pregnancies. Here, seven pairs of placentas were employed for whole genomic promoter DNA methylation profiling and some of the candidate differentially methylated promoters were further validated in additional twelve pairs of samples. Consistent with previous report, our results further indicated that IUGR associated placentas harbored a distinct promoter DNA hypomethylation pattern and the result was further confirmed byultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS)