Transcription profiling of yeast to determine polysome-associated mRNAs after 90 minutes of mRNA mistranslation induction
ABSTRACT: Polysome-associated transcriptome analysis in cells after 90 minutes of mistranslation induction comparing with a pool of mRNAs existent in cells without induction at several time points (Reference)
BACKGROUND: Organisms use highly accurate molecular processes to transcribe their genes and a variety of mRNA quality control and ribosome proofreading mechanisms to maintain intact the fidelity of genetic information flow. Despite this, low level gene translational errors induced by mutations and environmental factors cause neurodegeneration and premature death in mice and mitochondrial disorders in humans. Paradoxically, such errors can generate advantageous phenotypic diversity in fungi and b ...[more]
Project description:We have established Drosophila melanogaster as a model system for ocular hypertension by expressing wild-type human myocilin (MYOC) in the Drosophila eye. Here, we have created transgenic flies that express four clinically relevant mutant forms of MYOC (R342K, Q368X, D380N and K423E) in their eyes using the gmr-Gal4/UAS binary system. We compare and identify human glaucoma candidate genes based on the transcription profiles of flies that express wt-MYOC or mutant-MYOCs.
Project description:Transcriptome analysis in natural Saccharomyces cerevisiae as function of fermentation stage. Strains used were the reference strain S288C, two (06L3FF02 and 06L6FF20) isolates from the Bairrada wine region, Portugal, three (Lalvin EC-1118, Lalvin ICV D254 and AEB Fermol Rouge) wine yeast obtained commercially and one (J940047) isolate from a human patient. Fermentation was carried out in synthetic must MS300, in semi-anaerobic conditions. Cells were harvested at six time-points during fermentation: early exponential growth (T1), mid-exponential growth (T2), diauxic shift (T3), early stationary growth (T4) Mid-stationary growth (T5) and end of fermentation (T6). Hybridizations were carried out using a common reference design, using RNA obtained from S288C at T2, in dye-swap replicates, and four self-self hybridizations were performed using the common reference sample for control of the experiment background, in a total of 88 hybridizations.
Project description:We investigate the relevance of RNA integrity in gene expression analysis as well as analysis methods to accommodate the possible effects of degradation using paired tumour and normal samples from colorectal cancer patients undergoing colonic resection.
Project description:S. cerevisiae expressing the wild-type C. albicans G33 ser-tRNACAG and the mutant T33 ser-tRNACAG that trigger genetic code ambiguity were compared against control yeast using two-color oligo arrays
Project description:A parallel expression profiling of wild-type and loss-of-function mutants of Mla6 and Mla1 powdery mildew resistance alleles was conducted using Barley1 GeneChip. Barley plants were inoculated with powdery mildew isolate 5874 and first leaves were harvested at 6 time points after pathogen inoculation. This experiment was conducted in split-split-plot experimental design with 3 replications.
Project description:A large-scale time course expression profiling of wild type (Mla12/Rar1/Rom1) and mutants (mla12-M66, M82 (rar1-1), M100 (rar1-2) and rom1) of barley cultivar Sultan 5 was conducted to understand the molecular mechanisms of delayed powdery mildew resistance. Barley plants were inoculated with powdery mildew pathogen isolate 5874. First leaves of inoculated and non-inoculated plants were harvested at six time points after pathogen inoculation. The experiment was laid out in split-split-plot design with 180 experimental units (3 replications x 2 treatments (inoculated and non-inoculated) x 5 genotypes x 6 time points).
Project description:We performed a microarray analysis to compare the expression profile of azurin treated and untreated with different P-cadherin expression levels. We also compared the differentially expressed genes regulated by P-cadherin overexpression. Both cell lines presented an up-regulation of apoptosis mediated by p53 protein, endocytosis and vesicle-mediated transport. Conversely, invasive MCF-7/AZ.Pcad cells treated with azurin presented a decreased expression of genes associated with cell surface receptors and signal transduction, as well as genes associated with biological adhesion and migration. Azurin is a bacterial protein from Pseudomonas aeruginosa which exerts an inhibitory activity in cancer cells. In P-cadherin-overexpressing models, a bad prognosis marker in breast cancer increasing invasion and other malignant features, azurin decreases the invasion of cancer cells. We performed a microarray analysis to compare the expression profile of azurin treated cells with different P-cadherin expression levels. Azurin up-regulated apoptosis mediated by p53 protein, endocytosis and vesicle-mediated transport. In the contrary, in invasive MCF-7/AZ.Pcad cells, azurin decreased the expression of genes associated with cell surface receptors and signal transduction, as well as biological adhesion. Further, azurin decreased adhesion of cells to proteins from the Extracellular matrix (ECM) and altered protein expression of integrins α6, β4 and β1 and interfered with the ability of these cells to form mammospheres. Altogether, our results further enlighten the anti-cancer effects mediated by azurin in P-cadherin overexpression breast cancer models. Cells were exposed to azurin (100uM) for 48h, after which total RNA was extracted. Control cells were exposed during the same time to PBS buffer solution. Three independent samples for each condition were used treated with different azurin production batches.
Project description:The yeast transcriptomic response to quercetin, a naturally-occurring flavonol with antioxidant, anticancer and anti-ageing activities, was evaluated by differential gene expression analysis using a microarray containing probes for S. cerevisiae ORFeome. Samples obtained from BY4741 strain cells treated with 300uM quercetin were compared to control samples (obtained from cells incubated with vehicle) on dual-color microarray experiments. Three independent biological replicates and the respective dye-swap hybridizations were combined, in a total of 6 microarray hybridizations.
Project description:Mice were obtained from in house breeding of C57BL/6J and C57BL/6J-Chr 1A/Na breeding pairs (Jackson Laboratories, USA). To produce F1 hybrids, C57BL/6J females were mated with C57BL/6J-Chr 1A/Na males. The F1 hybrids were intercrossed, producing 82 F2 progeny (41 males and 41 females). Microarray analysis was performed on six pairs of affected and non-affected male animals from the F2 progeny selected on the basis of their motor activity levels (average daily levels of distance moved over a 3 days recording: 768±74 cm/hr (affected) versus 1765±175 cm/hr (non-affected)(p<0.0001).