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:Japanese medaka (Oryzias latipes) embryos were exposed to two concentrations of the water accommodated fractions and chemically-enhanced water accommodated fractions of two types of diluted bitumen (dilbit). Chemical-dispersion did not significantly alter transcriptional responses to dilbit toxicity but may have acted through alternative mechanisms to give similar phenotypic responses, such as normal swim bladder development. This study identified novel biomarkers in fish with or without visual malformations exposed to dilbit that can be used to assess aquatic ecosystem health. Microarray analyses identified novel biomarkers and gene networks in dilbit-exposed malformed embryos that were not evident in unaffected dilbit-exposed fish or in controls.
2020-05-12 | GSE142734 | 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:The Nation’s streams and rivers contain several contaminants in the form of complex mixtures. These cocktails of chemicals are not equivalent in concentrations, some pollutants such as nutrients can be found in the range of mg/L (macro-pollutants) but others components (micro-pollutants) such as endocrine disrupting chemicals (EDCs) are in amounts thousands to millions of times less concentrated ug/L to ng/L. These mixtures hamper the determination of particular effects of contaminants in aquatic biota. Nonetheless, the fact that toxicity is preceded by alteration in gene expression in an organism allows the use of gene expression profiling (from microarray studies) to detect early toxic effects and identify mechanisms of action. The microarray technology, a collection of DNA fragments attached to a solid surface, can be used to measure the expression levels of large numbers of genes. This facilitates establishment of links between toxicants and effects on biota. In urban waters, micropollutants such as EDCs, are known to cause effects at very low concentrations. One common class of EDCs found in low levels in urban waters is the class of perfluorochemicals (PFCs). Previously, we observed that urban waters with wastewater influence containing PFCs in the 300 ng/L range exerted effects in fish by altering the expression of cholesterol metabolism and DNA repair genes in the liver. To determine whether low concentrations in the range of the PFCs found in the environment can elicit gene expression changes, we investigated the impact of 7 different types of PFCs in a controlled laboratory study by exposing fathead minnows for 48h to environmentally relevant concentrations of PFCs. Additionally, we use blood as starting material for microarray analysis in order to explore non-invasive techniques. No fish mortality was observed in any treatment exposures, but gene expression was altred. Surprisingly, low levels of PFCs that we used altered gene expression in fish liver and blood. Several of the same genes were altered in both liver and blood from exposed fish. Micorarray analysis yields information on altered molecular pathways that predict changes at higher levels of biological organization such as survival and reproduction.
2014-01-30 | GSE54506 | GEO
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:Despite recent knowledge of the potential environmental impact that compounds present in municipal wastewater effluents, including contaminants of emerging concern (CECs), may have, the implications of fish exposure to this contaminant mixtures are not completely understood. The effects caused by effluent CECs may be subtle and diverse, thus the need for sensitive and comprehensive tools such as gene expression to detect such responses. In this study, we conducted laboratory exposures that examined plasma concentrations of vitellogenin (VTG), changes in secondary sexual characteristics and gene expression in sexually mature male fathead minnows (Pimephales promelas) exposed to environmentally realistic (0.5%) and higher (5%) concentrations of municipal wastewater effluents. Secondary and primary treated effluents were used. Several of the 32 CECs investigated were detected, including pharmaceuticals, personal care products, hormones, current use pesticides and industrial compounds. The percent of males with detectable levels of VTG was higher in fish exposed to effluent treatments. An increased number of males with changes in secondary sexual characteristics (e.g. development of ovipositors), was observed in fish exposed to 5% effluent treatments. Gene expression data indicated that overall expression patterns were characteristic to each effluent. Higher numbers of differentially expressed genes were observed in fish exposed to primary treated effluent when compared to controls. Differentially expressed genes belonged to several functional categories, including xenobiotic metabolism, estogenicity and energy/metabolism processes. Gene expression data provided information to understand some of the mechanisms behind the effects observed at higher biological levels. To investigate gene expression responses resulting from exposure to POTW effluents, two laboratory experiments were conducted using effluent from San Diego (Point Loma; SD) and Los Angeles (Hyperion; LA). The LA effluent received secondary treatment and the SD effluent received advanced primary treatment. Treatments used during exposures consisted of negative controls (moderately hard water), positive controls (E2), and 0.5% and 5% effluent concentrations. The 0.5% concentration of effluent represented an environmentally realistic exposure level. The 5% effluent concentration represented a higher level at which we expected biological responses. The exposures lasted 14 days. Treatments: EFFHa = 5% primary treated effluent EFFHb = 5% secondary treated effluent EFFLa = 0.5% primary treated effluent E2a = Estradiol, positive control for primary effluent E2b = Estradiol, positive control for secondary effluent CTRLa = Moderately hard water, negative control for primary effluent CTRLb = Moderately hard water, negative control for secondary effluent
2011-05-18 | E-GEOD-29350 | biostudies-arrayexpress
Project description:The pollution of the environment with microplastics has been recognized as an emerging threat worldwide. Due to an exponential increase in production of plastic over the last eight decades and its longevity in the environment, accumulating amounts of microplastic are polluting rivers, lakes and the ocean. Their entry pathways are diverse and still only incompletely understood. Since microplastics are usually defined smaller than 5 mm, it can be ingested by a wide range of aquatic organisms including teleost fish. There are different approaches to study the detrimental effects of pollutants on aquatic organisms. On the one hand, generic baseline parameters such as growth and mortality are regularly considered, often accompanied by established stress parameters such as cortisol, heat shock proteins or lipid oxidation. The conflicting findings to date suggest that these parameters might not be sensitive enough to indicate the physiological effects of environmentally relevant microplastic concentrations. For this reason, more sophisticated biological approaches could provide new insights into whether and how microplastics harm fish. To date, proteomic approaches have been used only sporadically when investigating the effects of microplastic exposure on aquatic organisms. So far, this approach has not been used to address potential microplastic impacts in fish. In the present study, a proteomic approach was trialed alongside established methods in an investigation of fish experiencing long-term exposure to environmentally relevant concentrations of microplastics. Two groups of rainbow trout (Oncorhynchus mykiss were exposed to microplastic concentrations and sizes currently encountered in wild fish and an increased concentration, expected to occur in the near future. These groups where compared to a control group maintained in MP free conditions. Five fish of each treatment were sampled at three time points (week 1, week 4, week 17). The experiments were performed in triplicates, resulting in 45 samples used in the proteomic analysis.
2022-08-08 | PXD033331 | Pride
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: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.
2010-05-01 | GSE17633 | GEO