Field application of a new low density stress response microarray STREM
Ontology highlight
ABSTRACT:
ORGANISM(S): Mytilus californianus Mytilus edulis Magallana gigas Mytilus galloprovincialis
PROVIDER: GSE97099 | GEO | 2019/04/04
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling of the digestive gland tissue of female mussel Mytilus galloprovincialis exposed to nickel along with a temperature gradient Background: The exposure of marine organisms to stressing agents may affect the level and pattern of gene expression. Although many studies have examined the ecological effects of heat stress on mussels, little is known about the physiological mechanisms that might be affected by co-exposure to heat stress and environmental contaminants such as nickel (Ni). In the present work we investigated the effects of simultaneous changes in temperature and Ni supply on lysosomal membrane stability (LMS) and malondialdehyde accumulation (MDA) in the digestive gland (DG) of the blue mussel Mytilus galloprovincialis (Lam.). To shed some light into how the molecular response to environmental stressors is modulated, we employed a cDNA microarray with 1,673 sequences to measure the relative transcript abundances in the DG of mussels exposed to Ni along with the temperature increase. Temperature and Ni rendered additive effects on LMS and MDA accumulation, increasing the toxic effects of metal cations. Ni loads in DG tissues was also affected by co-exposure to 26°C. In animals exposed only to heat stress, functional genomics analysis of the microarray data (171 DEGs) revealed 7 biological processes, largely dominated by the up-regulation of folding protein-related genes, and the down regulation of genes involved in cell migration and cellular component assembly. Exposure to Ni at 18°C and 26°C rendered respectively 188 and 262 DEGs showing distinct pattern in term of biological processes. In particular, the response of mussels exposed to Ni at 26°C was characterized by the up regulation of proteolysis, ribosome biogenesis, response to unfolded proteins and catabolic-related genes as well as the down-regulation of genes encoding cellular metabolic processes. Our data provide new insights on the transcriptomic response in mussels challenging temperature increases and Ni exposure and should be carefully considered in view of the biological effects of heat stress and particularly in polluted areas.
2013-06-19 | GSE48062 | GEO
Project description:Development of a new low density stress response microarray to evaluate biological effects of contaminants in Mytilus sp: laboratory validation. Background: Despite the increasing use of mussels in environmental monitoring, their genome and gene functions remain weakly explored. Recently several cDNA microarrays were proposed in Mytilussp, however partial putatively identified transcripts are provided rendering very difficult the generation of robust transcriptional responses in term of pathwaysidentification. In this study we developed a new medium density oligonucleotide microarray with 476 probes covering the same number of well identified genes representing 16 Biological processes at cellular and tissue levels among the most important in mussel’s response to stress (Lysosomal activity, DNA Metabolism, Translation, Mitochondrial activity, Carbohydrate metabolism, Heat choc response, Oxydatif stress, Proteolysis, Phase I and II detoxification, Metal resistance, Endocrine disruptors, Endocytosis, Macrophage, Pumps, Cytoskeleton, Adhesion to substrate). Our new platform STREM (STress Response Microarray in Mytilussp) consists of eight sub-arrays with 3 repetitions for each target in each sub-array. To assess the potential use of the new array, we tested the effect of three Benzo[a]pyren (B[a]P) concentrations, a relevant environmental contaminants in two mussel’s tissues; gills and digestive gland. Our data provided clues about the higher sensitivity of the new array. Moreover transcriptional data were confirmed using Q-RT-PCR and the possible implication in biological role by conventional biomarkers of stress (oxidative stress biomarkers) as well as immune-histochemical analysis (Tubulin).
2017-08-17 | GSE84605 | GEO
Project description:Transcriptional profiling of the digestive gland tissue of female mussel Mytilus galloprovincialis exposed to nickel along with a temperature gradient Background: The exposure of marine organisms to stressing agents may affect the level and pattern of gene expression. Although many studies have examined the ecological effects of heat stress on mussels, little is known about the physiological mechanisms that might be affected by co-exposure to heat stress and environmental contaminants such as nickel (Ni). In the present work we investigated the effects of simultaneous changes in temperature and Ni supply on lysosomal membrane stability (LMS) and malondialdehyde accumulation (MDA) in the digestive gland (DG) of the blue mussel Mytilus galloprovincialis (Lam.). To shed some light into how the molecular response to environmental stressors is modulated, we employed a cDNA microarray with 1,673 sequences to measure the relative transcript abundances in the DG of mussels exposed to Ni along with the temperature increase. Temperature and Ni rendered additive effects on LMS and MDA accumulation, increasing the toxic effects of metal cations. Ni loads in DG tissues was also affected by co-exposure to 26M-BM-0C. In animals exposed only to heat stress, functional genomics analysis of the microarray data (171 DEGs) revealed 7 biological processes, largely dominated by the up-regulation of folding protein-related genes, and the down regulation of genes involved in cell migration and cellular component assembly. Exposure to Ni at 18M-BM-0C and 26M-BM-0C rendered respectively 188 and 262 DEGs showing distinct pattern in term of biological processes. In particular, the response of mussels exposed to Ni at 26M-BM-0C was characterized by the up regulation of proteolysis, ribosome biogenesis, response to unfolded proteins and catabolic-related genes as well as the down-regulation of genes encoding cellular metabolic processes. Our data provide new insights on the transcriptomic response in mussels challenging temperature increases and Ni exposure and should be carefully considered in view of the biological effects of heat stress and particularly in polluted areas. Digestive gland tissue from individual animals in different experimental conditions were analyzed in a complete loop design. Dual color competitive hybridizations (Control M-bM-^@M-^\16M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\20M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\16M-BM-0C+CuM-bM-^@M-^], M-bM-^@M-^\20M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\20M-BM-0C+CuM-bM-^@M-^], M-bM-^@M-^\24M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0C+CuM-bM-^@M-^], M-bM-^@M-^\16M-BM-0C+CuM-bM-^@M-^] vsM-bM-^@M-^]20M-BM-0C+CuM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0C+CuM-bM-^@M-^]; M-bM-^@M-^\20M-BM-0C+CuM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0C+CuM-bM-^@M-^]) including label swap. Single individuals. Four biological replicates. One replicate per array.
2013-06-19 | E-GEOD-48062 | biostudies-arrayexpress
Project description:Transcriptional profiling of the digestive gland tissue of female mussel Mytilus galloprovincialis exposed to copper along with a temperature gradient Background: Global warming is a major factor that may affect biological organization, especially in marine ecosystems and in coastal areas that are particularly subject to anthropogenic pollution. We evaluated the effects of simultaneous changes in temperature and copper concentrations on lysosomal membrane stability of the blue mussel Mytilus galloprovincialis (Lam.). Temperature and copper exerted additive effects on lysosomal membrane stability, exacerbating the toxic effects of metal cations present in non-physiological concentrations. Mussel lysosomal membrane stability was positively related toscope for growth, indicating possible effects of increasing temperature on mussel populations in metal-polluted areas. To clarify the molecular response to environmental stressors, we used a cDNA microarray with 1,700 sequences to measure the relative transcript abundances in the gills of mussels exposed to copper (40µg/L) and a temperature gradient (16°C, 20°C, and 24°C). In animals exposed only to heat stress, hierarchical clustering of the microarray data revealed three main clusters, which were largely dominated by down-regulation of translation-related differentially expressed genes, drastic up-regulation of folding protein-related genes, and genes involved in chitin metabolism. The response of mussels exposed to copper at 24° C was characterized by an opposite pattern of the genes involved in translation, most of which were up-regulated, as well asthe down-regulation of genes encoding heat shock proteins and microtubule-based movement proteins. Our data provide novel information on the transcriptomic modulations in mussels facing temperature increases and high copper concentrations; these data highlight the risk of marine life exposed to toxic chemicals in the presence of temperature increases due to climate change.
2012-10-31 | GSE41899 | GEO
Project description:Contaminants of Emerging Concern (CECs) are a class of chemicals that can spread throughout the environment causing adverse biological and ecological effects. Through the different classes of CECs, the occurrence of pharmaceutical drugs such as natural and synthetic estrogens, is well documented in the aquatic environment. In this study mussels (Mytilus galloprovincialis), chosen as model organism, were exposed to the synthetic hormone 17 α-Ethinylestradiol (EE2), the primary component in contraceptive pills. Mussels were exposed to a single concentration of EE2 ( 5 ng/L) of EE2 in a semi-static and time-dependent experiment. The total period of exposure was 28 days and the mussels were analysed 14 days (T14) and 28 days (T28) after treatment. RNA-Seq analysis showed signs of stress with significant differential expression at 99 genes (T14 compared to controls), 73 genes (T28 compared to controls) and 103 DEGs after two weeks of exposure. EE2 treatment resulted in up-regulation of 3 gene/proteins for lipid transport/metabolism and 7 gene/proteins upregulated encoding immune and antibacterial function.
2022-05-15 | GSE188198 | GEO
Project description:Cathepsin D is reportedly to be closely associated with tumor development, migration and invasion, but its pathological mechanism is not fully elucidated. We aimed to evaluate phenotypic changes and molecular events in response to cathepsin D knockdown. Lowering endogenous cathepsin D abundance (CR) induced senescence in HeLa cells, leading to reduced rate of cell proliferation and impaired tumorigenesis in a mouse model. Quantitative proteomics revealed that compared with control cells (EV), the abundances of several typical lysosomal proteases were decreased in the lysosomal fraction in CR cells. We further showed that cathepsin D knockdown caused increased permeability of lysosomal membrane and ROS accumulation in CR cells, and the scavenging of ROS by antioxidant was able to rescue cell senescence. Despite the increased ROS, the proteomic data suggested a global reduction of redox-related proteins in CR cells. Subsequent analysis indicated that the transcriptional activity of nuclear factor erythroid-related factor 2 (Nrf2), which regulates the expression of groups of antioxidant enzymes, was down-regulated by cathepsin D knockdown. Importantly, Nrf2 over-expression significantly reduced cell senescence. Although transient oxidative stress promoted the accumulation of Nrf2 in the nucleus, we showed that the Nrf2 protein exited nucleus if oxidative stress persisted. In addition, when cathepsin D was transiently knocked down, the cathepsin-related events followed a sequential order, including lysosomal leakage during the early stage, followed by oxidative stress augmentation, and ultimately Nrf2 down-regulation and senescence. Our results suggest the roles of cathepsin D in cancer cells in maintaining lysosomal integrity, redox balance and Nrf2 activity, thus promoting tumorigenesis.
2015-12-17 | PXD002844 | Pride
Project description:Mytilus galloprovincialis (Lmk, 1819) is economically relevant bivalve specie. In Adriatic Sea, periodical temperatures increases define optimal growth conditions for Dinoflagellate spp which can reach high concentrations also in filter-feeding mussels, thus causing potential human health problems. The most commonly used methods for the detection of Diarrhoeic Shellfish Poisoning biotoxins have either a low sensitivity or are too expensive to be used for routine tests. Genomic tools, such as microarray platforms, provide a reliable and alternative solution to overcome these problems. In this study we used a mussel cDNA microarray for studying gene expression changes in mussels exposed to Okadaic acid. Mussels collected in the Gulf of Trieste, located in Northern Adriatic Sea, were fed with Okadaic acid-spiked invertebrates for five weeks. In a time course experiment we were able to describe an early acute response just from the first 4th day time point. Among the differentially expressed genes we found a general up-regulation of stress proteins and proteins involved in cellular synthesis. Overall, we identified 34 transcripts candidate as useful markers to monitor OA-induced stress in mussels. This study contributes to the characterization of many potential genetic markers that could be used in future environmental monitoring, and could lead to explore new mechanisms of stress tolerance in marine mollusc species. Keywords: Time course, stress response Loop Design experiment including 5 time points (T0 = control samples, T1 = 3 days post treatment, T2 = 1 week post treatment, T4 = 3 weeks post treatment, T6 = 5 weeks post treatment). 3 biological replicates were done for a total number of 15 samples
2010-05-05 | E-GEOD-14885 | biostudies-arrayexpress
Project description:Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice.
2010-11-11 | GSE25206 | GEO
Project description:Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. The rice variety IR-64 was germinated and allowed to grow for 5 d at 37 C and then transferred to Hewitt solution for growth. After 10 d of growth, seedlings of uniform size and growth were treated with 100 µM of Cr (VI), As (V), Cd, and Pb under standard physiological conditions of 16 h light (115 μmol m−2 s−1) and 8 h dark photoperiod at 25 ± 2 C for 24 h. Total RNA was extracted from the treated rice roots and microarray was performed using one-cycle target labeling and control reagents (Affymetrix platform).
2010-11-11 | E-GEOD-25206 | biostudies-arrayexpress
Project description:Transcriptional profiling of the digestive gland tissue of female mussel Mytilus galloprovincialis exposed to copper along with a temperature gradient Background: Global warming is a major factor that may affect biological organization, especially in marine ecosystems and in coastal areas that are particularly subject to anthropogenic pollution. We evaluated the effects of simultaneous changes in temperature and copper concentrations on lysosomal membrane stability of the blue mussel Mytilus galloprovincialis (Lam.). Temperature and copper exerted additive effects on lysosomal membrane stability, exacerbating the toxic effects of metal cations present in non-physiological concentrations. Mussel lysosomal membrane stability was positively related toscope for growth, indicating possible effects of increasing temperature on mussel populations in metal-polluted areas. To clarify the molecular response to environmental stressors, we used a cDNA microarray with 1,700 sequences to measure the relative transcript abundances in the gills of mussels exposed to copper (40M-BM-5g/L) and a temperature gradient (16M-BM-0C, 20M-BM-0C, and 24M-BM-0C). In animals exposed only to heat stress, hierarchical clustering of the microarray data revealed three main clusters, which were largely dominated by down-regulation of translation-related differentially expressed genes, drastic up-regulation of folding protein-related genes, and genes involved in chitin metabolism. The response of mussels exposed to copper at 24M-BM-0 C was characterized by an opposite pattern of the genes involved in translation, most of which were up-regulated, as well asthe down-regulation of genes encoding heat shock proteins and microtubule-based movement proteins. Our data provide novel information on the transcriptomic modulations in mussels facing temperature increases and high copper concentrations; these data highlight the risk of marine life exposed to toxic chemicals in the presence of temperature increases due to climate change. Digestive gland tissue from individual animals in different experimental conditions were analyzed in a complete loop design. Dual color competitive hybridizations (Control M-bM-^@M-^\16M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\20M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\16M-BM-0C+CuM-bM-^@M-^], M-bM-^@M-^\20M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\20M-BM-0C+CuM-bM-^@M-^], M-bM-^@M-^\24M-BM-0CM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0C+CuM-bM-^@M-^], M-bM-^@M-^\16M-BM-0C+CuM-bM-^@M-^] vsM-bM-^@M-^]20M-BM-0C+CuM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0C+CuM-bM-^@M-^]; M-bM-^@M-^\20M-BM-0C+CuM-bM-^@M-^] vs M-bM-^@M-^\24M-BM-0C+CuM-bM-^@M-^]) including label swap. Single individuals. Four biological replicates. One replicate per array.
2012-10-31 | E-GEOD-41899 | biostudies-arrayexpress