GNPS - Metabolome vs Metagenome Project
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis
ORGANISM(S): Staphylococcus Aureus (ncbitaxon:1280) Staphylococcus Haemolyticus (ncbitaxon:1283) Klebsiella (ncbitaxon:570) Bacillus <bacterium> (ncbitaxon:1386) Enterobacter Sp. (ncbitaxon:42895) Acinetobacter Pittii (ncbitaxon:48296) Pantoea Conspicua (ncbitaxon:472705)
SUBMITTER: Kasthuri Venkateswaran
PROVIDER: MSV000080102 | GNPS | Fri Aug 26 16:46:00 BST 2016
REPOSITORIES: GNPS
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Project description:We evaluated the effect of methanol (MeOH) fixation on adult murine dentate gyrus (DG) single cell suspensions processed with droplet-based scRNA-seq.
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Project description:During senescence of detached rice leaves, tryptophan (Trp) and Trp-derived secondary metabolites such as serotonin and 4-coumaroylserotonin accumulated in concert with methanol (MeOH) production. This senescence-induced MeOH induction was closely associated with levels of pectin methylesterase (PME)1 mRNA and PME enzyme activity. Exogenous challenge of detached rice leaves with 1% MeOH accelerated Trp and serotonin biosynthesis with induction of the corresponding genes. No other solvents including ethanol resulted in a Trp-inducing effect. This MeOH-induced Trp synthesis was positively regulated by abscisic acid but negatively regulated by cytokinin, suggesting hormonal involvement on the action of MeOH. Endogenous overproduction or suppression of MeOH either by PME1 overexpression or RNAi gene silencing revealed that PME1 overexpressing lines produced twofold higher Trp levels with elevated Trp biosynthetic gene expression, whereas RNAi lines showed twofold reduction in Trp level in healthy control rice leaves, suggesting that MeOH acts as an endogenous elicitor to enhance Trp biosynthesis. Among many transcription factors induced following MeOH treatment, the WRKY family showed significant induction patterns of which WRKY14 appeared to play a key regulatory role in MeOH-induced Trp and Trp-derived secondary metabolite biosynthesis.
2011-01-03 | GSE26387 | GEO
Project description:Pseudomonas aeruginosa PA14 was precultured in SCFM2, and the OD600 was adjusted to 0.05 in 8 ml of SCFM2, in 6-well flat bottom cell culture plates. Gliotoxin (20 µM) or MeOH (solvent control) was added at log phase (optical density at 600 nm [OD600] = 0.3), and the cultures were incubated statically for an additional 4 h. 5 ml of each culture (triplicate) was then immediately added to an equal volume of RNA-later.
2023-03-30 | E-MTAB-12785 | biostudies-arrayexpress
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2015-08-03 | E-GEOD-71296 | biostudies-arrayexpress
Project description:All above ground organs of higher plants are ultimately derived from shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, and monocot SAMs such as maize are comprised of two cell layers, a single cell layered tunica (L1) and a corpus (L2). Although recent research has revealed roles of these cell layers in the SAM, intra- and inter-cell-layer signaling networks involved in organ development remain largely unknown except for a few differentially expressed genes. Here, we used Illumnia technology to conduct RNA-seq of L1 and L2 cell layers in maize B73 maize shoot apical meristem. Single sequencing library was constructed for L1 and L2 cell layer. Each library was sequenced using 2 lanes on a Solexa flow cell. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.
2013-01-28 | E-GEOD-16868 | biostudies-arrayexpress
Project description:Low molecular weight (LMW) peptides and proteins (LMWPs, < 30 kDa) in human plasma, serving as potential biomarkers or drug targets, are endowed with a wealth of biological and clinical research values. However, the extraction of LMW species is retarded by high-abundance proteins (HAPs) and therein large dynamic concentration ranges of proteins in plasma. Here we present an optimized MeOH/MTBE-based organic solvent precipitation approach that combining the efficient protein precipitation and effective delipidation (referred here as MeOH/MTBE) to enrich LMWPs from human plasma. The Tricine-SDS-PAGE analysis showed that MeOH/MTBE can not only maximally deplete HAPs but also effectively extract LMWPs from human plasma. By coupling with Top-Down Proteomics (TDP) strategy, MeOH/MTBE enabled the identification of 725 peptides derived from 158 proteins on average from human plasma, which should represent the largest number to our best knowledge with regard to TDP-based single LC-MS/MS acquisition. When combined with Bottom-Up Proteomics (BUP) strategy, MeOH/MTBE allowed for the identification of 376 proteins from human plasma. Notably, 155 out of 376 identified proteins (41.2%) were found to be with a molecular weight under 30 kDa, which further proved the efficient enrichment of LMWPs from human plasma by MeOH/MTBE approach. Moreover, concentrations of the identified proteins were found to span 5-6 orders of magnitude according to the PaxDb dataset. Additionally, many low abundant peptides including 25 neuropeptides and 19 smORF-encoded polypeptides (SEPs) derived from long noncoding RNAs (lncRNAs) were detected. Taken together, the MeOH/MTBE approach described here represents a simple, rapid and reproducible methodology for efficient and sensitive analysis of LMWPs and low abundant proteins from human plasma, which will greatly facilitate the selective identification and quantification of LMWPs from human plasma and accelerate the discovery rate of potential biomarkers and drug targets.
2020-07-07 | PXD016957 | Pride
Project description:Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH into toxic formaldehyde (FA). Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and the modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. Here, we demonstrate directly that study volunteers displayed increasing concentrations of MeOH and FA in their blood plasma when consuming citrus pectin, ethanol and red wine. A microarray analysis of white blood cells (WBC) in volunteers after pectin intake showed various responses for 30 differentially regulated mRNAs. Most of the mRNAs were somehow involved in the pathogenesis of Alzheimer's disease (AD). There was also a decreased synthesis of hemoglobin mRNA, HBA and HBB, the presence of which in WBC RNA was not a result of red blood cells contamination because erythrocyte-specific marker genes did not show significant change. A qRT-PCR analysis of volunteer WBC after pectin and red wine intake confirmed the complicated dependence between plasma MeOH content and the mRNA accumulation of previously identified genes, namely GAPDH and SNX27, and MME, SORL1, DDIT4, HBA and HBB genes revealed in this study. We hypothesized that human plasma MeOH, which is replenished from endogenous and exogenous sources (diet), has an impact on the WBC mRNA levels of genes involved in AD pathogenesis and signaling.
2014-06-10 | GSE58364 | GEO
Project description:Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH into toxic formaldehyde (FA). Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and the modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. Here, we demonstrate directly that study volunteers displayed increasing concentrations of MeOH and FA in their blood plasma when consuming citrus pectin, ethanol and red wine. A microarray analysis of white blood cells (WBC) in volunteers after pectin intake showed various responses for 30 differentially regulated mRNAs. Most of the mRNAs were somehow involved in the pathogenesis of Alzheimer's disease (AD). There was also a decreased synthesis of hemoglobin mRNA, HBA and HBB, the presence of which in WBC RNA was not a result of red blood cells contamination because erythrocyte-specific marker genes did not show significant change. A qRT-PCR analysis of volunteer WBC after pectin and red wine intake confirmed the complicated dependence between plasma MeOH content and the mRNA accumulation of previously identified genes, namely GAPDH and SNX27, and MME, SORL1, DDIT4, HBA and HBB genes revealed in this study. We hypothesized that human plasma MeOH, which is replenished from endogenous and exogenous sources (diet), has an impact on the WBC mRNA levels of genes involved in AD pathogenesis and signaling.
2014-06-10 | GSE58349 | GEO
Project description:Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH into toxic formaldehyde (FA). Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and the modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. Here, we demonstrate directly that study volunteers displayed increasing concentrations of MeOH and FA in their blood plasma when consuming citrus pectin, ethanol and red wine. A microarray analysis of white blood cells (WBC) in volunteers after pectin intake showed various responses for 30 differentially regulated mRNAs. Most of the mRNAs were somehow involved in the pathogenesis of Alzheimer's disease (AD). There was also a decreased synthesis of hemoglobin mRNA, HBA and HBB, the presence of which in WBC RNA was not a result of red blood cells contamination because erythrocyte-specific marker genes did not show significant change. A qRT-PCR analysis of volunteer WBC after pectin and red wine intake confirmed the complicated dependence between plasma MeOH content and the mRNA accumulation of previously identified genes, namely GAPDH and SNX27, and MME, SORL1, DDIT4, HBA and HBB genes revealed in this study. We hypothesized that human plasma MeOH, which is replenished from endogenous and exogenous sources (diet), has an impact on the WBC mRNA levels of genes involved in AD pathogenesis and signaling.
2014-06-10 | GSE58348 | GEO
Project description:During senescence of detached rice leaves, tryptophan (Trp) and Trp-derived secondary metabolites such as serotonin and 4-coumaroylserotonin accumulated in concert with methanol (MeOH) production. This senescence-induced MeOH induction was closely associated with levels of pectin methylesterase (PME)1 mRNA and PME enzyme activity. Exogenous challenge of detached rice leaves with 1% MeOH accelerated Trp and serotonin biosynthesis with induction of the corresponding genes. No other solvents including ethanol resulted in a Trp-inducing effect. This MeOH-induced Trp synthesis was positively regulated by abscisic acid but negatively regulated by cytokinin, suggesting hormonal involvement on the action of MeOH. Endogenous overproduction or suppression of MeOH either by PME1 overexpression or RNAi gene silencing revealed that PME1 overexpressing lines produced twofold higher Trp levels with elevated Trp biosynthetic gene expression, whereas RNAi lines showed twofold reduction in Trp level in healthy control rice leaves, suggesting that MeOH acts as an endogenous elicitor to enhance Trp biosynthesis. Among many transcription factors induced following MeOH treatment, the WRKY family showed significant induction patterns of which WRKY14 appeared to play a key regulatory role in MeOH-induced Trp and Trp-derived secondary metabolite biosynthesis. Total RNAs were extracted from the detached rice leaves with 1% MeOH or distilled water for 1 d, and gene expression was compared between the two groups with two replicates. DW, detached leaves in distilled water for 1 day; MeOH (2-replications), methanol treated detached leaves at the same time point as control. 2 sets of separately normalized data; DW-MeOH(1) and MeOH(2).
2011-01-03 | E-GEOD-26387 | biostudies-arrayexpress