Project description:ddMS2 data of C2C12 treated with Carnitine, untreated C2C12, water and carnitine in water using polar C18 column in Q Exactive Plus
Project description:ddMS2 in positive polarity for swab recovery of chemicals from desk top after sampling different concentrations using PRM in Q Exactive Plus.
Project description:ddMS2 run of mouse lung tissue and plasma extract using C8 column in 7.5-minute gradient and positive polarity mode in Q Exactive plus.
Project description:Ribosome profiling provides an opportunity to not only assess how the relative abundance of ribosome association with mRNAs changes in different conditions, but to look more closely at where along mRNAs those ribosomes bind. Here, we used ribosome profiling to calculate the ribosome polarity scores and changes in ribosome footprint read density in both aggregate and gene-specific ways. We profiled a time course of acute glucose starvation followed by glucose readdition and a multi-day growth course through the diauxic shift into stationary phase. We found that ribosome polarity became positive in postdiauxic shift conditions relative to log phase. In acute starvation, polarity shifted positive at our earliest time points but did not continue to do so at later time points. This is consistent with a read density analysis which demonstrated increased density on the 3’ half of genes after glucose starvation. Additionally, we performed ribosome profiling in samples that had glucose added back following acute starvation and observed a wave of new ribosome movement near the start codon and approximately 2,000 nucleotides downstream on open reading frames after one and five minutes of readdition, respectively. Our ribosome profiling analysis suggested that elongation slows during starvation which leads to a buildup of ribosomes on the 3’ halves of mRNAs. Further, it also indicated ribosomes previously built up can resume translation upon glucose readdition. We used reporter assays to corroborate these findings in vivo. Together, these results demonstrate how yeast regulate translation in response to glucose starvation.
Project description:Microarray analysis of the effect of L-carnitine supplementation on global expression of Sachharomyces cerevisiae cultures in logarithmic growing conditions and after exposure to H2O2 induced oxidative stress; L-Carnitine plays a well documented role in eukaryotic energy homeostasis by acting as a shuttling molecule for activated acyl residues across intracellular membranes. This activity is supported by carnitine acyl-transferases and transporters, and is referred to as the carnitine shuttle. However, several pleiotropic and often beneficial effects of carnitine in humans have been reported that appear to be unrelated to the shuttling activity, but little conclusive evidence regarding the molecular networks that would be affected by carnitine exist. We have recently demonstrated a protective role of carnitine in oxidative stress in yeast that is independent of the carnitine shuttle. A DNA microarray-based global gene expression analysis identified Cyc3p, a cytochrome c heme lyase, as being important for carnitine's protective impact in oxidative stress conditions. These findings establish a direct genetic link to a carnitine-related phenotype that is independent of the shuttle system. The data suggest that the yeast Saccharomyces cerevisiae should provide a useful model for further elucidation of carnitine's physiological roles. Experiment Overall Design: Yeast cultures was grown to mid-log phase with and without carnitine supplementation to a final concentration of 100 mg/L. A second set was grown to mid log phase, with and without carnitine supplementation and exposed to 0.4 mM H2O2 for 30 min. The experiments were performed using biological duplicate.
Project description:rs07-01_carnitine - carnitine effect - Effect of carnitine on the transcriptome of A. thaliana - Our objective is the description of the existence of an intracellular transport depend on the carnitine at Arabidopsis thaliana. For that, we planned the study of the response of the transcriptome in the presence of exogenic L-carnitine. Seedlings WT are cultivated on medium MS, 6 independent times. At 144h, the seedlings are collected and pools are formed with 3 samples. We proceed in the same way for the seedlings which are cultivated on medium MS containing L-carnitine 5mM. Keywords: treated vs untreated comparison
Project description:Feed restriction and L-carnitine infusion are known to affect the liver metabolism of dairy cows. In the present experiment the effects on liver transcriptome of feed restriction and L-carnitine abomasal infusion and the interaction of the two in mid-lactation Holstein dairy cows was assessed. Data clearly indicated a lack of transcriptomics effect by L-carnitine but a strong effect due to feed restriction. The functional analysis identified a overall reduction of cholesterol synthesis and oxidative phosphorylation and data suggested an increase flux toward gluconeogenesis and fatty acid oxidation.
Project description:Chagas disease is a parasitic infection originally endemic to latinamerican countries but now spreaded worldwide that can be transmitted congenitally. Current specific therapy involves benznidazole, however, other therapies may modify gene expression that can change genetic expression profile, allowing cell programming to provide a more unfavorable environment for intracellular parasite development. Herein, microarray analysis was performed to Human Umbilical Vein Endothelial Cells (HUVEC), treated with benznidazole and the anti-inflammatory drugs aspirin or simvastatin, and infected with T. cruzi, the causative agent of Chagas disease.
Project description:Large intestine samples from mice infected with 50,000 Trypanosoma cruzi parasites or left uninfected. One week post-infection, mice were treated with carnitine, benznidazole or vehicle. Animals were euthanized after 10 days of treatment and organs collected. Metabolites were extracted with 50% methanol followed by 3:1 dichloromethane-methanol and analyzed by C8 chromatography, with positive mode ddMS2 data collection (data-dependent).