GNPS - SEED - Cheetah diet / liver necrosis study -- data with LC RT shift
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis
ORGANISM(S): Acinonyx Jubatus (ncbitaxon:32536)
SUBMITTER: 
Julia Gauglitz
PROVIDER: MSV000083689 | GNPS | Mon Apr 15 15:10:00 BST 2019
REPOSITORIES: GNPS
Similar Datasets
Project description:Metabolic analysis of cheetah fecal samples and environmental samples, standard methanol extraction. Data was acquired using a Bruker Daltonics maXis Impact and C18 RP-UHPLC. Positive polarity acquisition of LC-MS/MS.
| MSV000082969 | GNPS
Project description:Raw reads obtained from environmental samples of otter (excrements) that represent what the animal has eaten.
| PRJEB38720 | ENA
Project description:Aflatoxins are toxic and carcinogenic polyketide metabolites produced by fungal species, including Aspergillus flavus and A. parasiticus. The biosynthesis of aflatoxins is modulated by many environmental factors, including the availability of a carbon source. The gene expression profile of A. parasiticus was evaluated during a shift from a medium with low concentration of simple sugars, Yeast Extract (YE), to a similar medium with sucrose, Yeast Extract Sucrose (YES). Total RNA and aflatoxins (B1, B2, G1, and G2) were quantified from fungal mycelia harvested pre- and post-shifting. When compared to YE media, YES caused temporary reduction of the aflatoxin levels detected at 3 hours post-shifting and they remained low well past 12 hours post-shift. Aflatoxin levels did not exceed the levels in YE until 24 hrs post shift, at which time point a 10-fold increase was observed over YE. Microarray analysis comparing the RNA samples from the 48 hr YE culture to the YES samples identified a total of 2120 genes that were expressed across all experiments, including most of the aflatoxin biosynthesis genes. One-way Analysis of Variance (ANOVA) identified 56 genes that were expressed with significant variation across all time points. Three genes responsible for converting norsolorinic acid to averantin were identified among these significantly expressed genes. The potential role of these genes involvement in the regulation of aflatoxin biosynthesis is discussed. Keywords: time course, media shift, Aspergillus, aflatoxin
2007-10-01 | GSE8038 | GEO
Project description:Liver samples of mice harboring liver-specific deletion of Lats2 (Lats2-CKO) were compared to WT mice. This effect was tested along with the effect of diet - high cholesterol diet (Paigen-PD) vs. normal chow (ND).
2016-03-17 | GSE68824 | GEO
Project description:Genetic and environmental factors mediate via different physiological and molecular processes a shifted energy balance leading to overweight and obesity. Significant progress in understanding the molecular mechanisms of appetite regulation and control of food consumption was made when the hypothalamus was identified as an important player in regulating energy and glucose homeostasis by sensing circulating hormones and nutrients. To get insights in the underlying processes involved in energy intake and weight gain, we compared hypothalamic tissue of mice kept on a high-fat or control diet for 10 days by a proteomic approach. Using 2D difference gel electrophoresis in combination with LC-MS/MS we observed significant abundance changes in 16 protein spots. One isoform of the protein DJ-1 was elevated in the high fat diet group in the analyzed three different mouse strains SWR/J, C57BL/6N and AKR/J. Large scale validation of DJ-1 isoforms in individual samples and tissues confirmed a shift in the pattern of DJ-1 isoforms towards more acidic isoforms in several brain and peripheral tissues after feeding a high-fat diet for 10 days. The identification of an oxidation of cysteine 106 as well as a 2-succinyl modification of the same residue by mass spectrometry not only explains the isoelectric shift of DJ-1 but also links our results to similar shifts of DJ-1 observed in neurodegenerative disease states under oxidative stress. We hypothesize that DJ-1 is a common physiological sensor involved in both nutrition-induced effects and neurodegenerative disease states. Peak lists of MS/MS spectra acquired on the HCT ion trap (Bruker Daltonics, Bremen, Germany) were generated using the software tool Data Analysis (version 4 SP4 Build 281, Bruker Daltonics) with default parameters. For peptide and protein identification using MASCOT 2.4.1, peak lists were correlated with the Swiss-Prot part of the UniProtKB release 12/2012 including a reverse decoy version of all entries resulting in a total of 33,160 mus musculus sequences. All searches were performed for peptides with charge states 2+, 3+ and 4+ with tryptic specificity allowing one missed cleavage. No fixed modification was set, oxidation of methionine was considered as variable modification. Ion trap MS/MS spectra were accepted with cut off scores of 30 as well as mass tolerance of 0.4 Da was applied for MS and MS/MS experiments. Only proteins with at least 2 identified peptides were considered to be identified. Raw files from the LTQ Orbitrap ELITE were further processed for protein and peptide identification and quantification using the MaxQuant software suite version 1.3.0.5 (Max Planck Institute of Biochemistry, Planegg, Germany) mainly with default parameters. Within the software suite database searches were carried out using 16,615 mouse sequences from the SwissProt part of UniProtKB (release June 2013) applying the following parameters: mass tolerance Fourier transformed mass spectra (Orbitrap) first/second search: 20 ppm / 6 ppm, mass tolerance fragment spectra (linear ion trap): 0.5 Da, no fixed modification was specified. For variable modifications methionine oxidation, acetylation at protein N-termini and carbamidomethylation were considered as well as one of the following modifications per search event: trioxidation of cysteines, 2-succinylation of cysteines. Peptides and proteins were accepted at a false discovery rate of 1 % and proteins identified with a minimum of two peptides.
2014-03-26 | PXD000379 | Pride
Project description:Autophagy or ‘self-eating’ is a conserved and essential route for recycling intracellular constituents in eukaryotes. For plants, autophagy supports robust crop performance by regulating traits such as nitrogen-use efficiency, carbon allocation, reproduction, grain fill, and protection against various environmental stresses. To define the autophagic mechanisms underlining nutrient partitioning, which are used to sustain plant fitness during rapid growth of sink tissues, we applied a comprehensive multi-omic approach using maize (Zea mays) mutants lacking the core autophagy component ATG12. A sink tissue of particular interest are seeds, which require massive investments of fixed carbon for development. The transcriptome, proteome, metabolome, and ionome of developing seeds from atg12 mutants at 8 and 18 days after pollination (DAP) were analyzed. Developing atg12 seeds exhibited pronounce transcriptional reprogramming at 8 DAP, which may contribute to the observed hyperaccumulation of proteins, metabolites, and ions at 18 DAP. Collectively, this multi-omic approach should provide new perspectives into the adaptive role(s) of autophagy in coordinating nutrient allocation.
2023-03-10 | PXD022863 | Pride
Project description: Not available
| S-EPMC2938094 | biostudies-literature
Project description:Primary outcome(s): Development of Gene - Environmental interaction risk score methodology and Gene - Environmental Risk Score (GERS) of colorectal cancer;Development of high risk criteria that could be applied final GERS prediction model
Study Design: Observational Study Model : Cohort, Time Perspective : Other(Prospective+Retrospective), Enrollment : 270000, Biospecimen Retention : Collect & Archive- Sample with DNA, Biospecimen Description : whole blood, serum, urine
| 2509007 | ecrin-mdr-crc
Project description:D. vulgaris is a model sulfate reducing bacteria whose genome encodes a high number of two component systems, including 29 DNA-binding response regulators (RRs) whose functions are unknown, but are very likley to be important to the environmental lifestyle of the organism. We determined the gene targets for 24 of these RRs using purified His-tagged RR and sheared genomic DNA in an in vitro DAP-chip (DNA-affinity-purified - chip) assay. For each RR, one target was identified first using gel shift assays, and qPCR was used to ensure that the target was enriched in the RR-bound DNA before the samples were hybridized to a tiling array. Based on the peaks generated by the array analysis, we determined that at least 200 genes are regulated by two component systems in this organism. We also predicted binding site motifs and validated them for 15 RRs using gel shift assays. In vitro DAP-chip for 28 response regulators where RR-bound enriched DNA is compared to input total genomic DNA
2011-05-31 | E-GEOD-25163 | biostudies-arrayexpress