Chlamydomonas reinhardtii transcriptional responses to cerium dioxide nanoparticles
Ontology highlight
ABSTRACT:
ORGANISM(S): Chlamydomonas reinhardtii
SUBMITTER: Tim Williams
PROVIDER: E-MTAB-2454 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Daphnia are an important and widely studied model species in ecological and toxicological studies throughout the world and an official (OECD) recommended test organism. Their small size, wide distribution and easy growth conditions make this an organism ideal for functional genomics based studies, including metabolic profiling and transcriptomics. In this study we used an integrated systems approach in which transcriptomic, metabolomic and energetic responses of juvenile (4 days old) daphnids were evaluated in response to exposure to two poly aromatic hydrocarbons (pyrene and fluoranthene) and binary mixtures thereof. In addition, these responses were linked to responses measured during chronic experiments (21 days) assessing survival, growth and reproductive traits. Custom Daphnia magna microarrays were used to assess transcriptomic changes. Hierarchical cluster analysis did not result in a clear distinction between the single compounds suggesting similar molecular modes of action. Cluster analysis with both the single compounds and the binary mixture treatments resulted in a separation of treatments based on differences in toxic ratios rather than component differences. Changes in the metabolic profiles of the organisms were investigated using Nuclear Magnetic Resonance spectroscopy and Gas and Liquid Chromatography Mass Spectrometry. These multivariate metabolomic datasets were analysed with Principal Components Analysis and Partial Least Squares Discriminant Analysis. The major metabolite changes responsible for the differences observed indicated a disturbance in aminosugar metabolism in all cases. The study demonstrates the potential of âomicsâ to provide screening tools for monitoring of the freshwater environment â in invertebrate species - which is reasonably rapid, cost-effective and has the potential to greatly increase the amount of information obtained from aquatic toxicology testing. Two independent experiments were performed, each with two biological replicates. As a result, every treatment was measured four times with the exception of the two highest mixtures doses where we only had two available replicates. In general, a universal reference design was used in which the reference sample was a pool composed of aliquots from all samples. Dye-bias effects were accounted for by labeling two samples of every treatment with Cy3 and two with Cy5. Exp1Rep1 (reference Cy3, sample Cy5); Exp1Rep2 (reference Cy5, sample Cy3); Exp2Rep1 (reference Cy5, sample Cy3) and Exp2Rep2 (reference Cy3, sample Cy5)
2010-05-16 | E-GEOD-16869 | biostudies-arrayexpress
Project description:Monuron (1,1-dimethyl-3-(4-chlorophenyl) urea) is a non-selective phenylurea herbicide, widely used in the developing countries, however concerns have been raised about it toxicity and carcinogenicity. Monuron was evaluated by the National Toxicology Program (1988) and shown to be a male rat-specific renal carcinogen; however the mechanism of carcinogenesis is unknown. In this study we have examined the effect of sub-cytotoxic exposure to monuron (250M-BM-5M) at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E). In addition we examined the short term exposure of MON in kidney and liver of exposed rats. We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of monuron. NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to chlorothalonil dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.1 M-NM-<M CHL) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point. Eight Wistar-derived rats where bred in the Life Science Support Unit at Liverpool John Moores University male rats (190-240g) 7-9 weeks of age were used in this study. Four rats being dosed with MON at 40mg/kg body weight on day 1 and 400mg/kg body weight on days 2 and 3, at 5ml/kg in corn oil. Four control animals were dosed with corn oil at 5ml/kg. Seventy two hours after the last dose all rats were killed by a rising concentration of carbon dioxide, the liver and kidneys quickly removed and immersed in RNAlater.
2015-02-16 | E-GEOD-51163 | biostudies-arrayexpress
Project description:Non-alcoholic fatty liver disease (NAFLD) is the number one cause of chronic liver disease worldwide, with 25% of these patients developing nonalcoholic steatohepatitis (NASH). NASH significantly increases the risk of cirrhosis and decompensated liver failure. Past studies in rodent models have shown the knockout of glycine-N-methyltransferase (GNMT) results in rapid pro-gression of steatosis, fibrosis, and hepatocellular carcinoma. However, the attenuation of GNMT in subjects with NASH and the molecular basis for its impact on the disease process are still unclear. To address this knowledge gap, we show the reduction of GNMT protein levels in the liver of NASH subjects compared to healthy controls. To gain insight into the impact of decreased GNMT in the disease process, we performed global label-free proteome studies on the livers from a murine Western diet-based model of NASH. Histological and molecular characterization of the animal model demonstrate high resemblance to the human disease.
2022-04-04 | PXD030781 | Pride
Project description:We used microarrays to analyze gene expression changes in liver after treatment of rats with two compounds from drug development (R1, R2) to identify potential effects related to hepatotoxicity. Experiment Overall Design: Compound R1 or R2, or vehicle control, was given for either 24h or 2 weeks (336h) at different doses.
2009-08-09 | E-GEOD-17388 | biostudies-arrayexpress
Project description:In this study we tested and modeled the hepatotoxic potential of locked nucleic acid-containing phosphorothioated antisense oligonucleotide (ASOs) gapmers designed to target human BACH1 and PAR-2 transcripts. Using RNA extracted from mouse livers we compared expression profiles of off-target (i.e. genes other than the intended target that were predicted by RNArcher software to fully or partially interact with a given ASO) and ‘background’ genes (not identified as potential targets). The analysis revealed a correlation between the number of potent unintended interactions (fold change ≤ -0.5 with an associated p-value ≤ 0.01) and the severity of liver phenotype. A subsequent pathway analysis has not shown any common patterns, suggesting that the adverse effects emerged through divergent mechanisms. We propose that efforts should be focussed on designing and progressing ASOs with lowest number of putative off-target genes, which will minimize the chances of encountering potent interactions and hence adverse liver phenotypes.
2017-08-02 | E-MTAB-5180 | biostudies-arrayexpress
Project description:In this study, Lemna minor was used to investigate ecotoxic modes-of-action (MoA) at the gene expression level. For this purpose, mRNA sequencing was applied to plant RNA extracted from L. minor exposed to the herbicide bentazon in a shortened version of the OECD guideline test No. 221 (OECD TG 221). L. minor is commonly used as a non-target model organism to determine ecotoxicological effects of xenobiotics. As bentazon is one of the five most frequently detected pesticides in European groundwater, it is known for its environmental impact. Therefore, aquatic organisms, especially plants like L. minor, may be affected by its photosynthesis inhibition. The aim of our study was to determine a molecular fingerprint of the substance in order to identify potential biomarkers for its MoA. Therefore, we applied bioinformatics approaches to functionally annotate the previously unannotated reference genome of L. minor. Our functional annotation pipeline is in principle applicable to any organism with an available reference genome and thus greatly facilitates the identification of gene functions for poorly annotated organisms. The observed effects at the molecular level showed promising results for the development of OMICs as screening methods as well as for the identification of biomarkers for the toxicity of bentazon in L. minor.
2022-07-15 | E-MTAB-11460 | biostudies-arrayexpress
Project description:In this study, Lemna minor was used to investigate ecotoxic modes-of-action (MoA) at the gene expression level. For this purpose, mRNA sequencing was applied to plant RNA extracted from L. minor exposed to the pharmaceutical atorvastatin in a shortened version of the OECD guideline test No. 221 (OECD TG 221). L. minor is commonly used as a non-target model organism to determine ecotoxicological effects of xenobiotics. Since atorvastatin (and statins in general) are frequently used pharmaceuticals, they can be found in the aquatic environment. In humans, they are used as cholesterol-lowering agents due to their hydroxymethylglutaryl-CoA reductase (HMGR) inhibitory effect. Analogously, in L. minor, atorvastatin can also inhibit the plant’s HMGR, which is involved in phytosterol synthesis. The aim of our study was to determine a molecular fingerprint of the substance in order to identify potential biomarkers for its MoA. Therefore, we applied bioinformatics approaches to functionally annotate the previously unannotated reference genome of L. minor. Our functional annotation pipeline is in principle applicable to any organism with an available reference genome and thus greatly facilitates the identification of gene functions for poorly annotated organisms. The observed effects at the molecular level showed promising results for the development of OMICs as screening methods as well as for the identification of biomarkers for the toxicity of atorvastatin in L. minor.
2022-07-15 | E-MTAB-11459 | biostudies-arrayexpress
Project description:To elucidate how does the gene expression profiles of whole transcriptome of P.fucata response to acute and gradual seawater acidification and warming, and which genes or functional gene clusters are involved in the stress response to enviromental stressors, we have employed microarray as a tool to identify genes in these stress. For acute temperature and acidity stress treatment, oysters were added into the tanks immediately with the maintaining conditions of temperature 25M-BM-11 M-BM-0C and 31M-BM-11 M-BM-0C, acidity pH7.8M-BM-10.05 and pH7.5M-BM-10.05, salinity 33M-BM-11M-bM-^@M-0 in recirculating seawater. The temperatures and pH values in the studies were near future levels and predicted for 2100 and 2300. The pallial zone of mantle were collected and preserved on the hours of 72 after treatment for subsequent studies. All the collected mantles above were snap-frozen in liquid nitrogen, and stored at -80M-BM-0C. The conditions of salinity 33M-BM-11M-bM-^@M-0, 19M-BM-11 M-BM-0C and pH8.1M-BM-10.05 (~380 ppm CO2) in pre-culture tanks was as a control. In total, 15 mantle tissue samples from 15 individuals were used for the microarray analysis and 3 samples were used as control .Three biological replicates were employed in each treatment.
2014-05-02 | E-GEOD-57171 | biostudies-arrayexpress
Project description:In this study we have examined the effect of sub-cytotoxic exposure to aristolochic acids (1.65µM) at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E). We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of aristolochic acids in rat renal proximal cells. NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to aristolochic acid dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.65 ?M) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point.
2015-07-02 | E-GEOD-68687 | biostudies-arrayexpress
Project description:In autoimmune diseases, accumulation of activated leukocytes correlates with inflammation and disease progression, and therefore, disruption of leukocyte trafficking is an active area of research. The protein kinase Tpl2 (MAP3K8) regulates leukocyte inflammatory responses and is also being investigated for therapeutic inhibition during autoimmunity. Herein, we addressed the contribution of Tpl2 to the regulation of macrophage chemokine and chemokine receptor expression and subsequent migration in vivo using a mouse model of Tpl2 ablation. We found that gene expression of the chemokine ligands CCL2, CCL7, CXCL2, and CXCL3 as well as the chemokine receptors CCR1 and CCR5 were reduced in macrophages from the bone marrow and peritoneal cavities of tpl2-/- mice following stimulation with LPS. LPS stimulation repressed chemokine receptor expression of CCR1, CCR2 and CCR5. Notably, LPS-induced repression of CCR1 and CCR5 was significantly enhanced in Tpl2-deficient macrophages and was observed to be dependent upon Erk activation and independent of PI3K and mTOR signaling. Consistent with alterations in chemokine and chemokine receptor expression, tpl2-/- macrophages were defective in trafficking to the peritoneal cavity following thioglycollate-induced inflammation. Overall, this study demonstrates a Tpl2-dependent mechanism for macrophage expression of both chemokine receptors and their ligands and provides further insight into how Tpl2 inhibition may disrupt inflammatory networks in vivo. microarray was used to profile the genome-wide expression patterns in Tpl2 wild-type and deficient macrophage.
2014-06-03 | E-GEOD-48338 | biostudies-arrayexpress