Maple Sap analysis from Ontario Canada
Ontology highlight
ABSTRACT:
ORGANISM(S): Sugar Maple Acer Saccharum
TISSUE(S): Plant
SUBMITTER: 
Justin Renaud
PROVIDER: ST001435 | MetabolomicsWorkbench | Fri Apr 17 00:00:00 BST 2020
REPOSITORIES: MetabolomicsWorkbench
Similar Datasets
Project description:The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methylation group is mainly decorated in the adenine, cytosine, and guanine base, or in the 2’-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m5U) hasn’t been discovered in mRNA of eukaryotes. In the current study, we established a method by N-cyclohexyl-N’-β-(4-methylmorpholinium) ethylcarbodiimide p-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry analysis (LC-ESI-MS/MS) for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1543 folds upon CMCT labelling. Using the developed method, we identified the distinct existence of m5U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methylation group of m5U originated from S-Adenosyl-L-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m5U will further uncover the functional roles of m5U in mRNA of mammals.
2019-07-30 | GSE135049 | GEO
Project description:We profile the transcriptional landscapes associated with acquisition of [ESI+], a prion scaffolded by Snt1, a core component of the Set3C histone deacetylase. We find that acquisition of [ESI+] leads to expression of otherwise silent, heterochromatic loci, proposing a new molecular means by which silent transcriptional states might be reversed.
2020-02-29 | GSE117624 | GEO
Project description:Background: Bone marrow stromal cells (BMSCs) have classically been cultured in media supplemented with 20% fetal bovine serum (FBS). As an alternative to FBS, pooled solvent detergent apheresis platelets, HPGF-C18, was evaluated for BMSC culture. Methods: A comparison of passage 2 BMSC growth revealed that 10% HPGF-C18 produced similar cell numbers as 20% FBS. Marrow aspirates from 5 healthy subjects were cultured for 4 passages in 10% HPGF-C18 or 20% FBS and were analyzed for proliferation, colony formation efficiency (CFE), surface marker expression, suppression of mixed lymphocyte reactions (MLRs), global gene and microRNA expression analysis. BMSC supernatant cytokine and growth factor concentrations were also compared. Results: Primary cultures of marrow aspirates in 10% HPGF-C18 and 20% FBS yielded similar numbers and CFE. After 4 passages, 10% HPGF-C18 and 20% FBS yielded similar numbers of BMSCs, surface marker expression patterns and immunosuppression effects. Gene and microRNA expression analysis revealed that BMSCs cultured under the two conditions had distinct expression profiles. Gene Set Enrichment Analysis (GSEA) revealed HPGF-C18-cultured BMSCs were enriched in metabolic processing and biosynthetic pathways; cell proliferation and cell cycle pathways; and immune response pathways. FBS-cultured BMSCs were enriched in MAPK signaling, TGF-beta signaling, cell adhesion and extracellular matrix pathways. Differently expressed microRNAs were related to the osteogenesis of BMSCs. Supernatant analysis found that HPGF-C18 BMSCs displayed higher levels of PEDF and TGFB1 and lower levels of IL6, VEGF, SDF1 and PLGF. Conclusions: Traditional measures; expansion, surface marker expression and inhibition of MLRs suggest that BMSC cultured in HPGF-C18 and FBS were similar, but analysis at the molecular level revealed many differences. BMSCs cultured in HPGF-C18 should be assessed in specific functional assays that reflect application-specific potency before substituting FBS with HPGF-C18.
2018-03-21 | GSE111495 | GEO
Project description:Transcriptional profiles of [ESI+]
| PRJNA482670 | ENA
Project description:The aim of this part of the wider project is to identify neuropeptide precursors, investigate cleavage sites on neuropeptide precursors and predict mature peptides in the sea anemone Nematostella vectensis. This was done to create a synthetic library of N. vectensis neuropeptides which were then used to test neuropeptide receptor candidates for activation by the different peptides.
2024-04-08 | PXD041235 | Pride
Project description:In order to understand the mechanisms underlying diabetes mellitus, we conducted a transcriptomic profiling of the liver from Macaca fascicularis with spontaneously occurred diabetes mellitus at their middle age compared with the monkeys fed with the same food and high-fat and high-sugar diet, respectively.
2022-05-05 | E-MTAB-10493 | biostudies-arrayexpress
Project description:We report the transcriptional profiles of the [ESI+] prion, as well as snt1∆, set3∆, and hos2∆ diploid cells.
2020-02-29 | GSE128672 | GEO
Project description:Claudin proteins are major constituents of epithelial and endothelial tight junctions (TJ), where they serve as regulators of paracellular permeability to ions and solutes. Claudin-18, a member of the large claudin family, is highly expressed in lung epithelium. To elucidate the role of claudin-18 in alveolar epithelial barrier function and fluid homeostasis, we generated claudin-18 knockout (C18 KO) mice. Increased alveolar fluid clearance (AFC) observed in C18 KO mice may have accounted for absence of lung edema despite increased alveolar solute permeability compared to wild type (WT) controls. Higher AFC in C18 KO mice was associated with higher Na-K-ATPase activity and increased expression of the Na-K-ATPase β1 subunit compared to WT controls. Consistent with in vivo findings, alveolar epithelial cell (AEC) monolayers derived from C18 KO mice exhibited lower transepithelial electrical resistance (RT) accompanied by increased solute and ion permeability without changes in ion selectivity. Expression of claudin-3 and claudin-4 was markedly increased in whole lung and in freshly isolated AEC from C18 KO mice, while claudin-5 was unchanged. In contrast, occludin, another major component of the TJ complex, was significantly decreased in C18 KO lung. Further analysis revealed rearrangements in the F-actin cytoskeleton in C18 KO MAECM. These findings demonstrate a crucial non-redundant role for claudin-18 in regulation of alveolar epithelial tight junction composition and permeability to ions and solutes. Importantly, increased AFC in C18 KO mice identifies additional roles for claudin-18 in alveolar fluid homeostasis beyond its direct contributions to barrier properties of the alveolar epithelium. Animals with a ubiquitous knockout (C18 KO) were obtained by crossing mice harboring a conditional (floxed) allele of claudin-18 (Cldn18F/F) with CMV-cre deleter mice to delete exons 2 and 3 by Cre/loxP recombination.
2014-04-06 | E-GEOD-48443 | biostudies-arrayexpress
Project description:Claudin proteins are major constituents of epithelial and endothelial tight junctions (TJ), where they serve as regulators of paracellular permeability to ions and solutes. Claudin-18, a member of the large claudin family, is highly expressed in lung epithelium. To elucidate the role of claudin-18 in alveolar epithelial barrier function and fluid homeostasis, we generated claudin-18 knockout (C18 KO) mice. Increased alveolar fluid clearance (AFC) observed in C18 KO mice may have accounted for absence of lung edema despite increased alveolar solute permeability compared to wild type (WT) controls. Higher AFC in C18 KO mice was associated with higher Na-K-ATPase activity and increased expression of the Na-K-ATPase β1 subunit compared to WT controls. Consistent with in vivo findings, alveolar epithelial cell (AEC) monolayers derived from C18 KO mice exhibited lower transepithelial electrical resistance (RT) accompanied by increased solute and ion permeability without changes in ion selectivity. Expression of claudin-3 and claudin-4 was markedly increased in whole lung and in freshly isolated AEC from C18 KO mice, while claudin-5 was unchanged. In contrast, occludin, another major component of the TJ complex, was significantly decreased in C18 KO lung. Further analysis revealed rearrangements in the F-actin cytoskeleton in C18 KO MAECM. These findings demonstrate a crucial non-redundant role for claudin-18 in regulation of alveolar epithelial tight junction composition and permeability to ions and solutes. Importantly, increased AFC in C18 KO mice identifies additional roles for claudin-18 in alveolar fluid homeostasis beyond its direct contributions to barrier properties of the alveolar epithelium.
2014-04-06 | GSE48443 | GEO
Project description:Gut commensal bacterial strains were cultured with or without added sugars (glucose, sucrose and kestose). The base culture medium without sugar added were modified based on the Yeast Casitone Fatty Acids (YCFA) broth. Samples were analyzed for proteomics using LC-MS/MS.
2023-06-08 | PXD037923 | Pride