Transcription profiling of Saccharomyces cerevisiae early response to the antimalarial drug quinine
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Sandra Santos
PROVIDER: E-GEOD-18037 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:In this study, we used the eukaryotic model Saccharomyces cerevisiae to better understand quinine’s mode of action and the mechanisms underlying the cell response to the drug. We performed a transcriptional profiling of the yeast response to a quinine concentration that exerted a very slight effect over cellular growth.
2009-09-11 | GSE18037 | GEO
Project description:The world-wide used herbicide alachlor is among the priority substances listed in the European Water Framework Directive. We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to alachlor at concentrations exerting slight to moderate levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the lowest observed effect concentration (LOEC; ~8% growth inhibition) and the 20%-inhibitory concentration (IC20), compared to control cells not exposed to the herbicide (CT02). Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 110 or 200 mg/L of ALA (corresponding to the LOEC and the IC20, respectively, of alachlor) or in medium non-supplemented with the herbicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with each concentration of alachlor versus controls were carried out independently. For each exposure condition, independent biological triplicates were processed and analysed.
2011-08-27 | E-GEOD-28677 | biostudies-arrayexpress
Project description:Nitrogen assimilation in plants is a tightly regulated process that integrates developmental and environmental signals. The legume-rhizobial symbiosis results in the formation of a specialized organ called root nodule, where the rhizobia fixes atmospheric nitrogen into ammonia. Ammonia is assimilated by the plant enzyme glutamine synthetase, which is specifically inhibited by PPT. The expression of key genes related to the regulation of root nodule metabolism will likely be affected by glutamine synthetase inhibition. We used microarrays to detail the global programme of gene expression in response to Glutamine synthetase inhibition in root nodules and identified genes differentially expressed over a time course. Medicago truncatula nodulated plants (20 days post inoculation) were treated with 0.25 mM of PPT. Root nodules were harvested at 4, 8 and 24 hours after PPT application. As a control, root nodules collected just before PPT application were used (PPT 0h). Three biological replicates consisting of pools of root nodules harvested from five distinct plants were used for RNA extraction and hybridization on Affymetrix GeneChips.
2012-05-08 | E-GEOD-34155 | biostudies-arrayexpress
Project description:Pyrimethanil (PYR) is a world-wide used fungicide approved for use in plant protection products in Agriculture, and with some (eco)toxicological concerns.We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to PYR at concentrations exerting moderate to median levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the 20% and 50%-inhibitory concentrations of PYR (IC20 and IC50, respectively), compared to control cells not exposed to the fungicide (CT02). Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 20 and 110 mg/L of PYR (corresponding to the PYR IC20 and IC50, respectively), or in medium non-supplemented with the fungicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with both concentrations of PYR and with control cells were carried out together. For each exposure condition, independent biological triplicates were processed and analysed.
2014-05-23 | E-GEOD-53126 | biostudies-arrayexpress
Project description:Gene list with increasing of expression in 2-fold or more after EZH2 knockdown in PC3 cells
2008-04-24 | E-MEXP-1581 | biostudies-arrayexpress
Project description:Arabinogalactan proteins are proteoglycans known to have important roles during cell growth and development, namelly during pollen tube growth. A microarray experiment was performed on agp6 agp11 pollen tubes to search for genetic interactions in the context of pollen tube growth. RNA from wt and mutant pollen tubes was extracted after 8h of in vitro germination and hybridized on Affimetrix microarrays.
2012-10-31 | E-GEOD-40861 | biostudies-arrayexpress
Project description:Oxidative stress can arise when in vitro propagated plants developed under low light conditions are exposed to high light during transfer to ex vitro conditions. In such a situation, among the many potential stresses to which the transferred plant can be exposed, oxidative stress is commonly experienced, most likely brought about by absorption of light energy in excess of that required for very low levels of photosynthetic metabolism. In vitro propagated grapevine when transferred to ex vitro conditions with a 4 fold increase in PPFD shows an initial inhibition of PET accompanied by an accumulation of H2O2, suggesting a signal for the upregulation in gene expression and antioxidant enzyme activity, which peaked at 48h after transfer of in vitro grapevine to ex vitro growing conditions. When in vitro propagated plants are exposed to high light upon transfer to ex vitro oxidative stress symptoms occur. To determine whether the underlying pathways activated at the transfer of in vitro grapevine to ex vitro conditions reflect the processes occurring upon light stress we used microarrays. Leaves were harvested from in vitro grown plants immediately prior to transfer to ex vitro condition and 48h after transfer to compare gene expression before and after exposure of these plants to the high light conditions typical of ex vitro growth.
2011-02-10 | E-GEOD-27180 | biostudies-arrayexpress
Project description:Experimental research on the effects of abiotic stress over grapevine has mainly focused on water shortage. The adaptation of plants to stress is a complex response triggered by cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Approaches such as array-based transcript profiling allow assessing the expression of thousands of genes in control and stress tissues. The variety Aragonês, used in wine production, was subjected to controlled individual abiotic stresses, WS and HS. Physiological effects were confirmed by measuring photosynthesis light curves at ambient CO2 and stepwise increasing irradiances. To assess physiological effects of stress treatments, light responses (A/I) curves were measured on the third fully expanded leaf from four plants per treatment and in the control, immediately after heat stress, and when Ψw was -0.9 MPa in water stress.
2012-03-27 | E-GEOD-36849 | biostudies-arrayexpress
Project description:We did transcription profiling on the effect of glucosamine in Saccharomyces cerevisiae using Research Genetics strains BY4741 (wild type) and 5251 (fks1). Yeast cells exposed to glucosamine in YPD growth medium show a significant increase in chitin content in the lateral cell wall. Likewise, cell wall stress caused by a gene deletion e.g., fks1 also results in elevated chitin. By comparing our data for fks1 with those from the literature we confirmed a strong induction of genes responsive to cell wall integrity, environmental stress as well as genes involved in cell signaling. Wild type cells treated with 15 mM glucosamine for 2 hours did not show any significant change in their transcription profile although the chitin level doubled during this time. For cells continuously exposed to glucosamine (steady state) there was a moderate transcription response, 105 genes showed a two-fold or higher change. The largest groups of up-regulated genes were those involved in mating, sporulation and cell cycle arrest. The largest group of down-regulated genes pertained to mitochondrial respiration. There was little overlap between those genes that have altered transcription from glucosamine treatment and those responsive to the fks1 mutation.
2007-07-07 | E-GEOD-441 | biostudies-arrayexpress
Project description:Aldehyde dehydrogenase 7A1 (ALDH7A1) is a metabolic enzyme that converts aldehydes to carboxylates. Here, we find that the reductive consequence of this catalytic activity, which generates NADH (nicotinamide adenine dinucleotide, reduced form) from NAD (nicotinamide adenine dinucleotide), underlies how ALDH7A1 coordinates a broad inhibition of the intracellular transport pathways. Studying vesicle formation by the Coat Protein I (COPI) complex, we elucidate that NADH generated by ALDH7A1 targets Brefeldin-A ADP-Ribosylated Substrate (BARS) to inhibit the fission stage. Moreover, defining a physiologic role for the broad transport inhibition exerted by ALDH7A1, we find that it acts to reduce energy consumption during hypoxia and starvation to promote cellular energy homeostasis. These findings uncover a non-canonical function of ALDH7A1, and also an unexpected way that NADH acts in cellular energetics. Moreover, the findings advance the understanding of intracellular transport by elucidating how multiple pathways can be coordinated, as well as defining physiologic circumstances in which this coordination occurs.
2019-09-12 | PXD014645 | Pride