Arabidopsis transcriptional profile in response to chromate (K2CrO4)
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ABSTRACT: Transcriptional profiling of Arabidopsis thalina seedlings in response to high (140 M-BM-5M) and low (20 M-BM-5M) concentrations of chromate (K2CrO4). Low concentrations of chromate (e.g. 40 M-BM-5M) promoted primary root growth, while high concentrations (e.g. 140 M-BM-5M) repressed growth and increased formation of root hairs, lateral roots and adventitious roots. Three-condition experiment, high (140 M-BM-5M) and low (20 M-BM-5M) concentrations of chromate (K2CrO4) vs non-chromate added (Control). Four biological replicates, one replicate per array.
Project description:Transcriptional profiling of 6 days-old Arabidopsis thaliana Col-0 seedlings transfered to alkamide decanamide-containing medium in a 1, 3, 7 and 14 d time course period. Keywords: Pharmacological A dye balanced modified loop design was implemented. Four biological replicates representing each sampling point were obtained by pooling in a 1:1 proportion shoot and root purified RNA from 120 randomly chosen seedlings. This experiment involved a total of sixteen sets of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across time points for the same treatment. This design allowed us to determine differences in gene expression between N-isobutyl decanamide-treated and control seedlings, and whether the differences were time dependent.
Project description:Five members of the Arabidopsis thaliana NF-YA gene family are strongly induced by several stress conditions via transcriptional and miR169-related posttranscriptional mechanisms. These transcription factors participate in gene regulation via two different mechanisms, one depending on binding to the CCAAT-box in the promoter of regulated genes and the other, independent of the CCAAT-box, in which NF-YA prevents the interaction of the NF-YB/YC heterodimer with transcription factors. Three biological and two technical (in swap) replicates for each genotype were obtained for each treatment (DMSO (mock) and estradiol 24h after induction). Mock samples were pooled and used as a reference.
Project description:Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns Cells were exposed to sodium arsenite (NaAsO2, Sigma) at concentrations of 0.08 M-BM-5M, 0.4 M-BM-5M and 2 M-BM-5M for 1, 2 and 8 weeks. A549 arsenic dose time response study.
Project description:Transcriptional profiling of three mexican maize landraces under 10, and 17 days stress and recovery irrigation A dye balanced modified loop design was implemented. Two biological replicates (pooling five representative plants) representing each sampling point for each genotype were obtained for purified RNA from 120 randomly chosen seedlings. This experiment involved a total of forty-eight (24 sets) of microarray hybridizations, including direct and dye swap comparisons between treatments as well as across the three landraces. This design allowed us to determine differences in gene expression between the three different landraces under drought stress (10 and 17 days) and at recovery irrigation compared to irrigated controls.
Project description:We investigated the effects of the flutamide (FLU) -induced liver injury in primary rat hepatocytes using our liver microfluidic biochips. Flutamide is used a non-steroidal anti-androgenic drug. Two flutamide concentrations, 10M-BM-5M and 100M-BM-5M, were used to expose the hepatocytes for 24h under perfusion. Primary rat hepatocytes were cultivated in microfluidic biochips and treated with 10 and 100M-BM-5M of flutamide for 24h
Project description:Legumes, in interaction with resistant rhizobia, combined both moderate tolerance and accumulation of metal(loids) in roots, with the ability to grow without nitrogen supply (Pajuelo et al., 2011). This quality has attracted attention for phytostabilisation of polluted soils (Reichman, 2007). Physiological studies suggest that low arsenite concentrations lead to a decrease of nodulation process (Dary et al., 2010; Pajuelo et al., 2008). Moreover, Lafuente et al. (2010) described a reduction in the expression patterns of nodulins genes in the presence of arsenite. Nevertheless, a global transcriptomic analysis has never been approached. In order to decipher the genetic regulation underlying the arsenite effect on the model symbiotic interaction Medicago-Sinorhizobium, we have performed a meta-analysis of three different hybridizations. These compare transcriptomic profiles of roots cultivated under different treatments (M-125 M-5M arsenite, M-1rhizobia).
Project description:Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns which could lead to altered gene expression Cells were exposed to sodium arsenite (NaAsO2, Sigma) at concentrations of 0.08 M-BM-5M, 0.4 M-BM-5M and 2 M-BM-5M for 1, 2 and 8 weeks.
Project description:The induction of genetic competence is a strategy used by bacteria to increase their genetic repertoire under stressful environmental conditions. Recently, Streptococcus pneumoniae has been shown to co-ordinate the uptake of transforming DNA with fratricide via increased expression of the peptide pheromone responsible for competence induction. Here, we document that environmental stress-induced expression of the peptide pheromone competence-stimulating peptide (CSP) in the oral pathogen Streptococcus mutans. We showed that CSP is involved in the stress response and determined the CSP-induced regulon in S. mutans by microarray analysis. Contrary to pneumococcus, S. mutans responds to increased concentrations of CSP by cell lysis in only a fraction of the population. We have focused on the mechanism of cell lysis and have identified a novel bacteriocin as the M-bM-^@M-^Xdeath effectorM-bM-^@M-^Y. Most importantly, we showed that this bacteriocin causes cell death via a novel mechanism of action: intracellular action against self. We have also identified the cognate bacteriocin immunity protein, which resides in a separate unlinked genetic locus to allow its differential regulation. The role of the lytic response in S. mutans competence is also discussed. Together, these findings reveal a novel autolytic pathway in S. mutans which may be involved in the dissemination of fitness-enhancing genes in the oral biofilm. Streptococcus mutans UA159 were grown with 2 uM CSP or without (uninduced control) to mid-log phase. Total RNA was extracted as described above. The cDNAs were prepared for hybridization using the PFGRC protocol. Microarray chips were scanned using a Gene Pix 4000B (Axon) and analyzed using the TM4 Microarray Software Suite (http://www.tm4.org/). Transcript levels were measured by cDNA hybridized to a fourfold redundant S. mutans microarray and averaged for three replicated hybridizations. Differential gene expression was based on a post-normalization cut-off of M-BM-1> twofold.
Project description:Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 66M-BM-5M. A time-dependent transcriptomic analysis using microarrays was performed at a non-toxic (100M-NM-<M) and a toxic (1mM) Cd dose. The reliability of microarray data was strengthened by real time RT-PCR validations. Altogether, 114 Cd responsive genes were revealed and a substantial subset of genes is related to metal homeostasis, drug detoxification, re-oxidization of cofactors and ATP production. This first genome-wide expression profiling study of archaeal cells challenged with Cd showed that T. gammatolerans withstands induced stress through pathways observed in both prokaryotes and eukaryotes but also through new and original strategies. T. gammatolerans cells challenged with 1mM Cd basically promote: 1) the induction of several transporter/permease encoding genes, probably to detoxify the cell; 2) the upregulation of Fe transporters encoding genes to likely compensate Cd damages in iron-containing proteins; 3) the induction of membrane-bound hydrogenase (Mbh) and membrane-bound hydrogenlyase (Mhy2) subunits encoding genes involved in recycling reduced cofactors and/or in proton translocation for energy production. By contrast to other organisms, redox homeostasis genes appear constitutively expressed and only a few genes encoding DNA repair proteins are regulated. We compared the expression of 27 Cd responsive genes in other stress conditions (Zn, Ni, heat shock, M-NM-3-rays), and showed that the Cd transcriptional pattern is comparable to other metal stress transcriptional responses (Cd, Zn, Ni) but not to a general stress response. Kinetics of gene expression changes induced by Cd were performed at two different concentrations (0.1mM and 1mM) and at 3 time points (30, 120 and 270 min). A 0.1mM Cd concentration did not affect the growth rate, whereas 1mM Cd induced a transitory growth arrest for 270min. Late exponentially growing cells (7x107 cells/mL) were exposed to Cd and were collected after 30min, 120 min and after 270 min. For each time point, four slides containing the 2157 oligonucleotide gene probes printed in duplicate were hybridized. The experiment was repeated twice leading to eight data sets per time point (four per biological replicate). Microarray analyses monitored 161 transcriptional changes (M-bM-^NM-^_Fold Change (FC)M-bM-^NM-^\M-bM-^IM-%2 and p-Value M-bM-^IM-$ 0.01) in response to Cd exposure corresponding to 114 unique genes i.e. 5,3% of T. gammatolerans gene content, most of them being upregulated. While about 25% of the upregulated genes exhibited a FC>3 with a maximum of almost 10 for one encoding a conserved hypothetical protein (tg0885, 1mM Cd at 120min), the large majority of the up- and down-regulated genes exhibited a 2 to 3-fold transcriptional change as already described in many archaeal transcriptomic studies.
Project description:To identify mediators of the osmotic stress response in Mycobacterium tuberculosis (Mtb), we performed transcriptional profiling of WT CDC1551 following treatment with 140 mM NaCl for 1 hr relative to an untreated control. 140 mM NaCl was chosen to reflect the approximate osmolarity of human plasma (i.e., 280 mOsm/L), which may be relevant during the course of infection. CDC1551 was treated with 140 mM NaCl for 1 h and compared to the same strain treated with 0 mM NaCl for 0 h. 4 biological replicates, independently grown and harvested. One replicate per array.