Project description:This was a 1500+ sample run taken in both positive and negative mode. This submission is just for the positive data.
These are fungal extracts grown by the Cichewicz Lab, prepared by Thillini P, and run on the McCall Lab Q Exactive Plus for the joint Natural Product libraries building grant.
These samples had previously had malaria docking on them. at this point of the study, the results of the docking are kept blind for data analysis.
Project description:This study aimed to identify the mode of action of Schisandra chinensis water extracts (SCW) and Schisandra chinensis ethanol extracts (SCE) in SW1783 cell line.
Project description:In this study, we have characterized and compared the effects of differently prepared chamomile extracts and characteristic pure compounds on the T cell redox milieu as well as on the migration, activation, proliferation, and cytokine production of primary human T cells. Futhermore, nCounter based gene expression profiling was performed on the most promising extracts (Chamomile aqueous total fermented-CT, aqueous toot fermented-CR, and ethanolic flower-CF) and pure compounds (Apigenin-Ap and Chamazulene-Cz) to identify the genes related to different T cell functions, that were targeted by the different treatment conditions.
Project description:<h4>Introduction</h4>Chronic inflammation is a hallmark of chronic wounds and inflammatory skin diseases. Due to a hyperactive and prolonged inflammation triggered by proinflammatory immune cells, transitioning to the repair and healing phase is halted. T cells may exacerbate the proinflammatory milieu by secreting proinflammatory cytokines. <i>Chamomilla recutita</i> L. (chamomile) has been suggested for use in several inflammatory diseases, implying a capability to modulate T cells. Here, we have characterized and compared the effects of differently prepared chamomile extracts and characteristic pure compounds on the T cell redox milieu as well as on the migration, activation, proliferation, and cytokine production of primary human T cells.<h4>Methods</h4>Phytochemical analysis of the extracts was carried out by LC-MS/MS. Primary human T cells from peripheral blood (PBTs) were pretreated with aqueous or hydroethanolic chamomile extracts or pure compounds. Subsequently, the effects on intracellular ROS levels, SDF-1α induced T cell migration, T cell activation, proliferation, and cytokine production after TCR/CD3 and CD28 costimulation were determined. Gene expression profiling was performed using nCounter analysis, followed by ingenuity pathway analysis, and validation at protein levels.<h4>Results</h4>The tested chamomile extracts and pure compounds differentially affected intracellular ROS levels, migration, and activation of T cells. Three out of five differently prepared extracts and two out of three pure compounds diminished T cell proliferation. In line with these findings, LC-MS/MS analysis revealed high heterogeneity of phytochemicals among the different extracts. nCounter based gene expression profiling identified several genes related to T cell functions associated with activation and differentiation to be downregulated. Most prominently, apigenin significantly reduced granzyme B induction and cytotoxic T cell activity.<h4>Conclusion</h4>Our results demonstrate an anti-inflammatory effect of chamomile- derived products on primary human T cells. These findings provide molecular explanations for the observed anti-inflammatory action of chamomile and imply a broader use of chamomile extracts in T cell driven chronic inflammatory diseases such as chronic wounds and inflammatory skin diseases. Importantly, the mode of extract preparation needs to be considered as the resulting different phytochemicals can result in differential effects on T cells.
Project description:To establish contamination profiles, the sperm donors with normal sperm counts were analyzed using an Infinium HumanMethylation450 array. Somatic cell lysis, sperm isolation, DNA extraction, and bisulfite conversion were performed as described by Aston et al. The bisulfite converted sperm DNA was hybridized to Illumina Infinium HumanMethylation450K microarrays at the University of Utah and run as recommended by the manufacturer (Bibikova et al. 2011). Unpaired blood samples were extracted using Qiagen's DNeasy Blood and Tissue kit and bisulfite converted using Zymo's EZ DNA Methylation kit. All procedures were performed according to the instructions of the manufacturer. Four permutations were run on each sample, including pure blood, half blood and half sperm by DNA concentration, half blood and half sperm by cell count, and pure sperm (n = 16). Concentration was normalized using a spectrophotometer. A Makler cell counting chamber was used to count white blood cells and sperm, which were then normalized in a 1:1 ratio.
Project description:We wanted to measure the transcriptomic changes of P.aeruginosa (PAO1 strain) when treated with plant extracts (Melastoma dodecandrum Lour, and Potentilla indica) and antibiotics (triclosan, rifampicin, gentamicin and ciprofloxacin) against DMSO control to aid in understanding the mode of action of our plant extracts. PAO1 samples were treated with plant extracts and antibiotics at MIC, for 24h at 37°C with OD readings taken at 600 nm every 10 mins using a microplate reader.
Project description:Nontarget analysis by LC-HRMS (UHLPC Q Exactive) of seawater, river water and drinking water samples analyzed by DIA negative mode [ESI]-.
Project description:apply C8 column and 7.5 minutes run to feces, small intestine and large intestine samples from mice under negative polarity mode in ddMS2.
Project description:In this project, Q-Exactive HF(Thermo Fisher Scientific,San Jose,CA) was used to acquire mass spectrometry (MS) data for 7 samples in Data Independent Acquisition (DIA) mode. Quantification of peptides and proteins was performed using Spectronaut™ and MSstats software packages