Blood plasma proteome of Japanese medaka fish exposed to humic acid
Ontology highlight
ABSTRACT:
ORGANISM(S): Cellular Organisms
SUBMITTER: Victor Zgoda
PROVIDER: PXD025857 | JPOST Repository | Fri Apr 29 00:00:00 BST 2022
REPOSITORIES: jPOST
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Project description:Medaka fish were exposed to several concentrations of humic acid. Changes in liver protein profiles of control and exposed fish were studied using LC-MS/MS analysis.
2021-07-14 | PXD025749 | JPOST Repository
Project description:A microarray-based transcriptome profiling was performed to provide a better understanding of the effects of maleic acid on human. Gene expression profiles of human neuroblastoma SH-SY5Y cells exposed to three concentrations of maleic acid (10, 50 and 100 μM) for 24 h were analyzed.
2017-03-14 | GSE86510 | GEO
Project description:The anabolic androgen 17M-NM-2-trenbolone (TB) can cause masculinization and reduce fecundity of fish. However, the underlying mechanisms of various biological pathways including metabolism, biosynthesis etc. are largely unknown. Here, we evaluated the effects of TB using the medaka DNA microarray representing 36,398 genes. Larval medaka, Oryzias latipes, (within 24 hrs posthatch) were exposed to TB at various concentrations (2, 6, 20, 60, 100, 200 ng/L) for up to 7 days. Dose-response relationships in gene expression levels of the categorized genes were analyzed using the cumulative chisquared method. Microarray analyses of the TB-exposed larvae showed that 117 and 32 genes were determined as up and down-regulated genes, respectively. The most significant GO term for biological process identified within this gene list was lipid metabolic process, which contained 26 genes in up-regulated genes. In this category, M-bM-^@M-^\cholesterol biosynthetic processM-bM-^@M-^] was highlighted as an important subcategory with 15 genes, including hydroxymethylglutaryl-CoA synthase cytoplasmic, squalene monooxygenase, lanosterol synthase etc. RT-PCR measurements in these genes were consistent with the microarray results in the direction and magnitude of these changes in gene expression. On the other hands, in the category of M-bM-^@M-^\sexual differentiation and developmentM-bM-^@M-^], genes related to hypothalamic-pituitary-gonadal (HPG) axis were not affected by TB treatment except for one gene encoded to cytochrome P450 19A1. Genes related to oogenesis, such as choriogenins and vitellogenins were weakly down regulated at 2-200 ng/L of TB. Our findings demonstrate that genes encoding cholesterol synthesis pathway via the mevalonate pathway were controlled by TB in larval medaka. TB concentrations used were 0 (control), 2, 6, 20, 60, 100 and 200 ng/L for 7 days of exposure. Each TB treatment had 90 larval medaka for each chamber. At day 7 of the exposures, triplicate samples (30 larvae/sample) from each chamber respectively were collected, flash-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.
2013-02-14 | E-GEOD-35908 | biostudies-arrayexpress
Project description:Recently, omics techniques have been widely applied to the discovery of potential bio-markers and explore triggering mechanism. To get a more comprehensive diagnosis of HBCD impacts on marine medaka (Oryzias melastigma), the larvae (within 24 hours post-hatch) were exposed to gradient doses of HBCD. After exposure for 7 days, the profiles of genes expression were examined using a custom-commercial 26, 430-oligonucleotide arrays (4×44K) of Japanese medaka which is shared much genomic information with marine medaka.At the end of the treatment period, 30 larvae/sample were pooled for RNA extraction and labeled by One-Color. A total of twelve independent arrays: three control (DMSO), three low-concentration HBCD (0.2 nM) exposures, three medium-concentration HBCD (2 nM) exposures, and three high-concentration HBCD (20 nM) exposures.
2013-07-31 | GSE49362 | GEO
Project description:Recently, omics techniques have been widely applied to the discovery of potential bio-markers and explore triggering mechanism. To get a more comprehensive diagnosis of HBCD impacts on marine medaka (Oryzias melastigma), the larvae (within 24 hours post-hatch) were exposed to gradient doses of HBCD. After exposure for 7 days, the profiles of genes expression were examined using a custom-commercial 26, 430-oligonucleotide arrays (4M-CM-^W44K) of Japanese medaka which is shared much genomic information with marine medaka.At the end of the treatment period, 30 larvae/sample were pooled for RNA extraction and labeled by One-Color. A total of twelve independent arrays: three control (DMSO), three low-concentration HBCD (0.2 nM) exposures, three medium-concentration HBCD (2 nM) exposures, and three high-concentration HBCD (20 nM) exposures. The larvae of marine medaka (within 24 hours post-hatch) were exposed to to 0 (control), 0.2nM, 2nM and 20nM of HBCD (dimethyl sulfoxide with a final concentration of 1:30000 v/v water) for 7 days. Each HBCD treatment had three replicates with 100 larvae for each Petri dish. At the end of the treatment period, 30 larvae/sample were pooled for RNA extraction. A total of twelve independent arrays: three control (DMSO), three low-concentration HBCD (0.2 nM) exposures, three medium-concentration HBCD (2 nM) exposures, and three high-concentration HBCD (20 nM) exposures.
2013-07-31 | E-GEOD-49362 | biostudies-arrayexpress
Project description:Currently, the novel brominated flame retardant, 1,2,5,6-tetrabromocyclooctane (TBCO), is considered as a potential replacement for hexabromocyclododecane (HBCD). As such, use of TBCO could increase significantly in the near future. Therefore, this study investigated the toxicity of TBCO in order to assess its potential toxicological risks to aquatic organisms. Embryos of Japanese medaka (Oryzias latipes) were exposed to 10, 100 and 1,000 μg/L TBCO, and molecular responses were characterized by use of transcriptomics (RNAseq) and proteomics in embryos exposed to 100 μg/L TBCO that were collected on the day of hatch. TBCO was accumulated in embryos by 0.43-1.3×104 30 fold and the rate of accumulation was 1.7-1.8 day-131 . Number of days to hatch and success of hatching of embryos exposed to the two greatest concentrations of TBCO were impaired. Consistent with effects on hatching, proteins that were less abundant were enriched in pathways of embryo development and hatching. Responses of the transcriptome and proteome to TBCO also were used to predict adverse effects of TBCO. Functionally grouped gene ontology terms indicated that TBCO might impair contraction of cardiac muscle and vision, and these effects were confirmed by use of targeted bioassays designed to evaluate cardiac and visual performance. Results of this study provided a comprehensive understanding of effects of TBCO on medaka at early-life stages. Also, the study illustrated the power of “omics” approaches to explain and predict phenotypic responses to the exposure with chemicals.
2017-06-29 | PXD003823 | Pride
Project description:The anabolic androgen 17β-trenbolone (TB) can cause masculinization and reduce fecundity of fish. However, the underlying mechanisms of various biological pathways including metabolism, biosynthesis etc. are largely unknown. Here, we evaluated the effects of TB using the medaka DNA microarray representing 36,398 genes. Larval medaka, Oryzias latipes, (within 24 hrs posthatch) were exposed to TB at various concentrations (2, 6, 20, 60, 100, 200 ng/L) for up to 7 days. Dose-response relationships in gene expression levels of the categorized genes were analyzed using the cumulative chisquared method. Microarray analyses of the TB-exposed larvae showed that 117 and 32 genes were determined as up and down-regulated genes, respectively. The most significant GO term for biological process identified within this gene list was lipid metabolic process, which contained 26 genes in up-regulated genes. In this category, “cholesterol biosynthetic process” was highlighted as an important subcategory with 15 genes, including hydroxymethylglutaryl-CoA synthase cytoplasmic, squalene monooxygenase, lanosterol synthase etc. RT-PCR measurements in these genes were consistent with the microarray results in the direction and magnitude of these changes in gene expression. On the other hands, in the category of “sexual differentiation and development”, genes related to hypothalamic-pituitary-gonadal (HPG) axis were not affected by TB treatment except for one gene encoded to cytochrome P450 19A1. Genes related to oogenesis, such as choriogenins and vitellogenins were weakly down regulated at 2-200 ng/L of TB. Our findings demonstrate that genes encoding cholesterol synthesis pathway via the mevalonate pathway were controlled by TB in larval medaka.
2013-02-14 | GSE35908 | GEO
Project description:We assess gene expression patterns upon 17beta-estradiol (E2) exposure to Japanese medaka (Oryzias latipes) in order to appere the E2 effects using DNA microarray analysis. Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, fish were sacrificed and mRNA was extracted for gene expression analysis. In an effort to link gene expression changes to effects on higher levels of biological organization, sex characteristics, gonadal histology, GSI, and egg production and fertility were examined. In microarray experiments, the correlation factors between the controls were from 0.91 to 1.00 among control samples. We observed highly induced O. latipes Gene Indices (OLGI) related to egg-yolk protein such as vitellogenin and L-SF precursor etc., which were significantly affected in a concentration-dependent manner by E2 exposure. To clarify the function of expressed genes by E2 treatments, we selected statistically expressed genes from the microarray experiments. We found 190 genes and 72 genes which were statistically expressed in E2 treatment as induced and repressed genes, respectively. In the induced gene list, there were characteristic induced-genes in the categories of lipid metabolism, stress (oxidative stress, DNA and protein damage), and apoptosis with MAPK pathway. On the other hands, there were characteristic repressed genes in the categories of heat shock protein. Our result may suggest that gene expressions in yolk medaka is able to be used for detection of E2 effect by DNA microarray analysis. Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration and time-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, three independent samples (one sample contained thirty whole medakas) were sacrificed and mRNA was extracted for gene expression analysis.
2010-05-01 | E-GEOD-17633 | biostudies-arrayexpress
Project description:The present research aimed to investigate peripheral blood gene expression profiling as a minimally invasive surrogate approach to study silica-induced pulmonary toxicity. Rats were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days). Pulmonary damage and blood gene expression profiles were determined at various latency periods (0 - 16 weeks). Silica exposure resulted in pulmonary toxicity and this was evidenced by histological changes in the lungs and elevation of LDH activity, and total protein and albumin contents in the bronchoalveolar lavage fluid (BALF) of the rats. Microarray analysis of global gene expression profiles in the blood of the rats identified genes that were differentially expressed in response to silica exposure and toxicity. The number of significantly differentially expressed genes in the blood of silica exposed rats correlated with the severity of silica-induced pulmonary toxicity. Genes involved in biological functions such as inflammatory response, cancer, pulmonary damage, oxidative stress, energy metabolism, fibrosis, etc, were found differentially expressed in the blood of the silica exposed rats compared with the controls. Induction of pulmonary inflammation in the silica exposed rats, as suggested by differential expression of inflammatory response genes in the blood, was supported by significant increases in the number of macrophages and infiltrating neutrophils as well as the activity of pro-inflammatory chemokines – MCP1 and MIP2, observed in the BALF of the silica exposed rats. A silica-responsive blood gene expression signature developed using the gene expression data predicted with significant accuracy the exposure of rats to lower concentrations (1 and 2 mg/m3) of silica. Taken together our findings suggest the potential application of peripheral blood gene expression profiling as a minimally invasive and efficient surrogate approach to detect and study silica-induced pulmonary toxicity.
2011-12-02 | GSE27023 | GEO
Project description:Recent research has highlighted that the polyphenols Quercetin (Q) and Tannic acid (TA) are capable of extending the lifespan of C. elegans. To gain a deep understanding of the underlying molecular genetics, we analyzed the global transcriptional patterns of nematodes exposed to Quercetin or Tannic acid concentrations that are non-effective (in lifespan extension), lifespan extending or toxic.
2012-02-03 | GSE35354 | GEO