Project description:Environmental fluctuations lead to a rapid adjustment of the physiology of Escherichia coli, necessitating changes on every level of the underlying cellular and molecular network. Thus far, the vast majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. Here we incorporate the metabolite composition together with gene expression data in order to provide a more comprehensive insight on system level stress adjustments by describing detailed time-resolved E. coli response to five different perturbations (cold, heat, oxidative stress, lactose diauxie, and stationary phase). The metabolite response is more specific as compared to the general response observed on the transcript level and is reflected by much higher specificity during the early stress adaptation phase and when comparing the stationary phase response to other perturbations. Despite these differences, the response on both levels still follows the same dynamics and general strategy of energy conservation as reflected by rapid decrease of central carbon metabolism intermediates coinciding with down regulation of genes related to cell growth. Application of co-clustering and canonical correlation analysis on combined metabolite and transcript data identified a number of significant condition dependent associations between metabolites and transcripts. The results confirm and extend existing models about co-regulation between gene expression and metabolites demonstrating the power of integrated systems oriented analysis.
Project description:Melatonin (N-acetyl-5-methoxytryptamine) is a ubiquitous indolamine that plays important roles in biological processes in different organisms. Recently, it has been found to have a important role in the antioxidant response in yeast. In this study the transcriptomic response to mild oxidative stress driven by Saccharomyces cerevisiae strain QA23 supplemented to different concentrations of melatonin (5 and 25 µM) is assessed.
Project description:Oxidative stress may play a role in normal aging. SKN-1 is a transcription factor necessary for intestine development in Caenorhabditis elegans, which also regulates the response to oxidative stress post-embryonically. Using DNA microarrays, we found that oxidative stress induces the antioxidant response, the heat shock response, and detoxification genes, while the expression of genes involved in homeostasis, development, and reproduction were decreased. Both up-regulated and down-regulated genes can be wholly, partially, or not at all dependent on SKN-1 action. However, induction of the heat shock response by oxidative stress was not affected by SKN-1 removal. Keywords: stress response
Project description:Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress. We used microarrays to study the genome-wide temporal response of the yeast S. cerevisiae to oxidative stress induced by cumene hydroperoxide. Keywords: time course
Project description:Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress. We used microarrays to study the genome-wide temporal response of the yeast S. cerevisiae to oxidative stress induced by cumene hydroperoxide. Keywords: time course
Project description:The goal of this study was to use microarrays to identify genes differentially regulated under conditions of formaldehyde stress relative to two other stress conditions (oxidative, osmotic) in an effort to identify genes that might be involved in a formaldehyde-specific stress response, rather than a general stress response, in the model methylotroph Methylobacterium extorquens AM1. Two color experiment, three treatments, three biological replicates per treatment, and two technical (dye swap) replicates per biological replicate: formaldehyde-stressed vs. unstressed cells; oxidative-stressed vs. unstressed cells; and osmotic-stressed vs. unstressed cells.
Project description:The aim of this study is to characterize the systemic stress response (SSR) induced in patients undergoing colorectal cancer (CRC) surgery. The project is a clinical prospective study. Blood samples will be collected from 30 patients on the day before CRC-surgery, and 1, 2, 3 and 10 days after surgery. A specimen from the resected tumor tissue will also be collected and sent for immunohistochemical analysis. Whole blood gene expression profiling will be performed to gain knowledge of the genetic changes in immunological, inflammatory and oxidative stress-related factors initiated by surgery. Peripheral immunological cells, proteins and cytokines will be analysed by FLOW and ELISA methods, and the functional capacity of NK-cells will also be defined for each time point. Furthermore, tumor tissue will be analyzed for invasion of immunological cells. At each time point, the patients will be asked to fill out a validated patient reported outcome measure with questions concerning clinical outcome parameters related to recovery after CRC-surgery