Influence of Water Chemistry on Toxicogenomics of Chronic Lead Toxicity to the Fathead Minnow (Pimephales promelas)
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ABSTRACT:
ORGANISM(S): Pimephales promelas
SUBMITTER: Edward Mager
PROVIDER: E-GEOD-8404 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Toxicogenomics of water chemistry influence on chronic lead exposure to the fathead minnow (Pimephales promelas).
Mager Edward M EM Wintz Henri H Vulpe Chris D CD Brix Kevin V KV Grosell Martin M
Aquatic toxicology (Amsterdam, Netherlands) 20080212 3
Establishment of water quality criteria (WQC), intended to protect aquatic life, continues to rely principally on water hardness (i.e. Ca(2+)) for lead (Pb) despite growing evidence that other chemical parameters also strongly influence toxicity. To more clearly define the water chemistry parameters mediating Pb toxicity, we evaluated the effects of hardness as CaSO(4) and dissolved organic carbon (DOC) as humic acid during chronic (150 days) exposures to the fathead minnow. Measured Pb concentr ...[more]
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Project description:Considerable interest and controversy has arisen over the potential effects of seismic surveys carried out during exploration for oil and gas deposits. Regarding fish, there is a concern that intense sound sources, such as seismic airguns, may injure their auditory system. In this study, salmonid cDNA microarrays, reciprocal suppression subtractive hybridization (SSH) cDNA libraries and quantitative reverse transcription – polymerase chain reaction (QPCR) were used to identify and study a responsive gene set in the inner ear of Atlantic salmon (Salmo salar) following seismic airgun exposure. Microarray analyses on pooled seismic exposed inner ear RNA versus pooled control inner ear RNA revealed 79 unique transcripts (passing background threshold) that were greater than 1.75-fold differentially-regulated by acoustic stress on at least 3 of the 4 slides in the study (including at least one dye-swap). QPCR analyses of 8 microarray-identified transcripts of interest revealed a significant up-regulation (P<0.05) of transcripts encoding nicotinamide riboside kinase 2 (1.89-fold) and hemoglobin subunit alpha-4 (3.78-fold), and a significant down-regulation (P<0.05) of a transcript encoding C14orf159 protein (1.35-fold). QPCR analyses also confirmed an overall up-regulation of transcripts encoding growth hormone I (7.78-fold), c-type lectin receptor A (2.20-fold) and retinol binding protein I (1.24-fold), however these differences were not considered to be statistically significant (P<0.05) due to the high biological variability in the seismic exposed group for these transcripts of interest. A total of 683 expressed sequence tags (ESTs) generated from SSH cDNA salmon ear libraries enriched for genes responsive to seismic airgun noise have been deposited in the GenBank dbEST. Targeted gene discovery in salmon ear allowed for the identification of novel transcripts, including some with sensory-relevant functional annotations, and represents a significant contribution to salmonid hearing research. Initial results demonstrate that genomics has the potential to greatly enhance our understanding of the impact of seismic airguns on gene and molecular pathways involved in hearing, and provide valuable molecular biomarkers that can act as an early warning sensor to acoustic stress. Juvenile Atlantic salmon (Salmo salar) smolt were obtained from North Water Products Ltd., Daniel’s Harbour, NL and held at ambient seawater temperature, in a flow-through system supplied with air at the Northwest Atlantic Fisheries Centre, St. John’s, NL. Two weeks prior to seismic airgun exposures, fish were divided into two 1m3 cages, one each for control (non-exposed) and exposed groups, in a 15,000L aquarium at ambient seawater temperature (0.2°C). Each cage was placed the same distance from the water intake and airstones were placed next to each cage. Fish were fasted for two days prior to exposure. Sixteen control (non-exposed) fish from one cage were sampled prior to seismic activity. Immediately following sampling of control fish, seventeen fish in the remaining cage were placed 2m from a 10in3 Texas Instruments airgun. Fish were subjected to 50 exposures, 1 exposure every 10 seconds, at an average sound pressure level of 204 dB peak-to-peak relative to 1µPa; considered to be a worse case scenario within a few hundred meters of a survey vessel. Seventeen seismic exposed fish were sampled 16 h following exposure. The only aquarium available that was suitable for seismic airgun exposures was not designed to have a regulated photoperiod. For this reason the fish were held under a constant daylight regime. Fish were collected by dip-net and euthanized by severing the spinal cord. The inner ears from each salmon were removed, placed immediately in RNase-free 2 ml tubes, and then flash frozen in liquid nitrogen. RNA isolated from the right inner ear of the 12 seismic exposed and 12 control individuals that gave the highest total RNA yields were used to generate 2 mRNA pools (a “seismic” pool and a “control” pool). Each sample contributed 4.0 µg column purified total RNA to each pool. Comparisons were made for the seismic exposed mRNA pool compared to the control (non-exposed) mRNA pool using the consortium for Genomic Research on All Salmonids Project (cGRASP) 16K (salmonid) cDNA array and the 3DNA Array 900 Detection Kit and instructions (Genisphere). Technical quadruplicate slides including 2 dye-swaps were run for the comparison. Slide GG003_011: Cy5-labeled control ear, Cy3-labeled seismic Slide GG003_012: Cy5-labeled control ear, Cy3-labeled seismic Slide GG003_013: Cy3-labeled control ear, Cy5-labeled seismic Slide GG003_014: Cy3-labeled control ear, Cy5-labeled seismic
2012-02-28 | E-GEOD-33257 | biostudies-arrayexpress
Project description:Juvenile rainbow trout were fed Biodiet starter (4% body weight per day) with MeHg added at 0, 0.5, 5 and 50 ppm for six weeks. Atomic absorption spectrometry was applied to measure the level of MeHg in the whole fish body. Trout at six weeks were sampled from each group for gene expression analysis by cGRASP 16K cDNA microarrays. MeHg-exposed rainbow trout did not show overt signs of toxicity, nor were significant differences seen in mortality, length, mass, or condition factor. The chronic accumulation of total Hg in trout exhibited dose- and time-dependent patterns. The dysregulated genes have multiple functional annotations, such as involving metabolism, cellular development, ion binding and homeostasis, stress response, immune response, transcriptional regulation, hemolytic development, and apoptotic pathways. These results show that numerous molecular pathways involved in the growth and development of multiple organ systems are disrupted by exposure to moderate levels of dietary MeHg. The dysregulated genes will be selected by further analysis and used as biomarkers for MeHg exposure in aquatic environments. Juvenile rainbow trout (Oncorhynchus mykiss, average body 0.118g) were fed Biodiet Starter (Bio-Oregon) 4% of body weight per day with MeHg added at 0ppm, 0.5ppm, 5ppm and 50ppm (with ethanol as vehicle). Trout at six weeks were sampled from each group for gene expression analysis. Total RNA from individual fish was isolated using Trizol reagent (Invitrogen) and further purified using the RNeasy MiniElute cleanup kit (Qiagen).RNA of ten fish from control group was pooled as a common reference, and total RNA of five individual fish from control and MeHg-treated groups were randomly selected for microarray experiment. cDNA was synthesized from 1 M-NM-<g pooled RNA using SuperScript II Reverse Transcriptase (Invitrogen) according to the manufacturerM-bM-^@M-^Ys protocol. The common reference cDNA targets were labeled with Cy3 and cDNA of individual fish from each group was labeled with Cy5 using the Array 900 Expression Array Detection kit (Genisphere) according to the manufacturerM-bM-^@M-^Ys protocol. The labeled cDNA targets were hybridized to cGRASP 16K cDNA microarrays at 50M-BM-0C for 16 hours. Following the first hybridization, arrays were washed in 2X SSC, 0.2% SDS solution at 50 C 1 x 15 min, 2X SSC 1 x 15 min at room temperature, then 0.2X SSC for 1 x 15 min at room temperature. The fluorescent labeling hybridization (50 C for 4hr) utilized the Genisphere 3DNA Cy3 and Cy5 capture reagents in formamide hybridization buffer. The slides were washed as described above, and the arrays were dried by centrifugation. were scanned using the ScanArray Express (PerkinElmer) at 10 um resolution. The TIFF images of arrays were generated with ScanArray Express software and the intensities of raw data of two-channel arrays were collected by the ImaGene 6.0 (BioDiscovery). Statistical analysis of microarray data was performed using scripts written in R language with LIMMA package.
2013-06-01 | E-GEOD-32429 | biostudies-arrayexpress
Project description:Paper Abstract. Extrapolating toxicological sensitivity information across species can require the use of highly conservative safety factors as prescribed by ecological risk assessment protocols. The objective of our study was to use multipule factors to understand the dynamics of stress responses by comparing ecotoxicological, developmental, and genomic data to quantitatively determine the relative sensitivity of two common model aquatic vertebrates to assess the potential for developing refined safety factors among species. Larval (3-d old) zebrafish (Danio rerio) and fathead minnows (Pimephales promelas) were concurrently exposed in 96-h static exposures to the widely-used military energetic compound cyclotrimethylenetrinitramine (RDX). Endpoints assessed included mortality, incidence of vertebral deformities, swimming behavior, and differential gene (transcript) expression. Analytically verified treatment concentrations ranged from 0.9 to 27.7 mg/L RDX. While RDX concentrations prepared for exposures included 0, 0.9, 1.8, 3.5, 7.5, 15.0, and 30.0 mg/L, analytically verified treatment concentrations were 0, 0.88, 1.75, 3.46, 6.96, 13.79, and 27.7 mg/L, respectively. Changes in prepared RDX concentrations and analytically verified treatment concentrations are a result of chemical breakdown, a well known characteristic of RDX Our results indicated a higher sensitivity to RDX in P. promelas than in D. rerio in both mortality (LOECs 13.79 and 27.7 mg/L, respectively) and vertebral deformity (LOECs 13.79 and >13.79, respectively) endpoints. Swimming behavior was assessed in 10 min behavioral trials using Noldus EthoVision® digital tracking software. Swimming behavior trials indicated non-significant trends of decreased velocity, distance moved, and increased meander (change in direction per cm traveled) for P. promelas. No such trends were apparent in D. rerio swimming behavior. A comprehensive genomic analysis is in progress to determine the genes, gene ontology elements, metabolic pathways and metabolic networks affected in common among species in the RDX exposure. Taken as a whole, the ecotoxicological, developmental and genomic results will provide valuable insights into the similarity in response among these fish species to RDX. Three-day-old fathead minnow (FHM, Pimephales promelas) or Zebrafish (ZF, Danio rerio) fry were exposed to either control water or one of six concentrations of RDX (0.9, 1.9, 3.8, 7.5, 15, or 27.7 mg/L) in 96-h exposures. However, microarray analysis was only performed on FHM exposed to 0, 0.9, 1.9, 7.5, or 15 mg/L RDX and ZF exposed to 0, 0.9, 1.9, 3.8, 7.5, or 15 mg/L RDX due to insufficient tissue for microarray analysis due to animal death at the other RDX concentrations. The experimental design was based on the U.S. EPA (2002) acute testing method for P. promelas, test method 2000.0 and included four replicates per treatment with ten fish per replicate. Whole fish (10 fish per replicate) were investigated for differential expression in response to RDX exposure.
2011-02-08 | E-GEOD-27067 | biostudies-arrayexpress
Project description:The federally endangered Okaloosa darter (Etheostoma okaloosae) is found almost exclusively on the Eglin Air Force Base in the Choctawhatchee Bay watershed of Florida. Portions of this limited habitat are threatened with erosion of soils, altered hydrology, and impaired water quality. One stream reach in particular, East Turkey Creek, has demonstrated potential water quality problems including poor invertebrate bioassessment scores (IBI), uncharacteristically high conductivity values, and low numbers of Okaloosa darters. General water quality (dissolved oxygen, specific conductance, pH, temperature, and relative turbidity and primary productivity) was characterized in both the potentially impacted East Turkey Creek and a reference stream (Long Creek). Water quality was assessed during a 30 day exposure using passive samplers for both non-polar and polar effluent parameters. Metal loading in the system was assessed via fish tissue burdens in resident Pteronotropis hypseleotris. Additionally, microarray analysis was performed on gonad and liver tissue from fathead minnows, Pimephales promelas, after 48-h exposures to water collected from the two creeks and brought into the laboratory. Gene expression changes were evident at the site below the influence of a wastewater spray field sited along East Turkey Creek, suggesting that anthropogenic compounds in the effluent waters may have affected both liver and testis function and could be related to account the general decrease in populations of the Okaloosa darter. Array hybridizations were performed using a single color design. Four biological replicates consisting of four different individuals were analyzed for each of the treatments (University of Florida control, and each of five sites). Site C was left out of subsequent analysis for publication, due to poor characterization of the site. Two Samples were left out of the normalization/analysis due to QC failure. Therefore, there are only 3 replicates of the "testis, site A water, exposed 48 h." and "liver, site E water, exposed 48 h." groups.
2010-08-11 | E-GEOD-23521 | biostudies-arrayexpress
Project description:We investigated the effects of chronic TCDD exposure on global gene expression in developing rainbow trout (Oncorhynchus mykiss). Juvenile rainbow trout (0.18M-BM-10.01g) were fed Biodiet starter with TCDD added at 0, 0.1, 1, 10 and 100ppb, and ten fish were sampled and pooled from each group for microarray experiments at 28 days after initiation of the exposure. Gene expression analysis was performed using the Genomics Research on All Salmonids Project (cGRASP) 16K cDNA microarrays. TCDD-responsive whole body transcripts identified in the microarray experiments have putative functions involved in various biological processes including cellular process, metabolic process, biological regulation, and response to stimulus. In addition, TCDD caused leisons in multiple organ systems in juvenile rainbow, including skin, oropharynx, liver, gas bladder, intestine, pancreas, nose and kidney. Juvenile rainbow trout (0.18M-BM-10.01g) were fed Biodiet starter (Bio-Oregon) (4% body weight per day) with TCDD added at 0, 0.1, 1, 10 and 100 ppb. Fish were sampled after 28 days. Total RNA from individual fish was isolated using TRIzol reagent (Invitrogen). Total RNA of ten control trout were pooled as a common reference which were labeled with Cy3. Total RNA of ten fish of each treatment were labeled wih Cy5. cDNA were synthesized using SuperScript II Reverse Transcriptase (Invitrogen) (1 M-NM-<g pooled RNA per synthesis). Targets were labeled using the Array 900 Expression Array Detection kit (Genisphere) following the manufacture protocol. 1M-BM-5g RNA of pooled ten control fish were labled with Cy3 and 1M-BM-5g RNA of pooled ten TCDD-treated fish were labled with Cy5, then day-swap was performed. Two arrays were run for each comparison. Microarrays were scanned at 10 M-BM-5m resolution using a ScanArray Express (PerkinElmer Life Sciences, Inc, Boston, MA). The photomultiplier tube settings (PMT) for Cy3 and Cy5 were 70 and 65-66, respectively. TIFF images of arrays were generated with ScanArray Express software (PerkinElmer). Fluorescence intensity data for Cy3 and Cy5 channels were extracted from TIFF images using ImaGene 7.5 software (BioDiscovery Inc., El Segundo, CA). Background correction, data transformation (setting background corrected values < 0.01 to 0.01), Lowess normalization, and analysis (e.g. fold-change calculations) were performed using GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA)
2013-04-05 | E-GEOD-45779 | biostudies-arrayexpress
Project description:We investigated the effects of chronic TCDD exposure on global gene expression in developing rainbow trout (Oncorhynchus mykiss). Juvenile rainbow trout(0.18M-BM-10.01g) were fed Biodiet starter with TCDD added at 0, 0.1, 1, 10 and 100ppb, and ten fish were sampled and pooled from 10 ppb group at 7, 14, 28 and 42 days for microarray experiments after initiation of the exposure. Gene expression analysis was performed using the Genomics Research on All Salmonids Project (cGRASP) 16K cDNA microarrays. TCDD-responsive whole body transcripts identified in the microarray experiments have putative functions involved in various biological processes including response to stimulus, cell wall organization or biogenesis, growth and cell proliferation. In addition, TCDD caused leisons in multiple organ systems in juvenile rainbow, including skin, oropharynx, liver, gas bladder, intestine, pancreas, nose and kidney. Juvenile rainbow trout (0.18M-BM-10.01g) were fed Biodiet starter (Bio-Oregon) (4% body weight per day) with TCDD added at 0, 0.1, 1, 10 and 100 ppb. Fish were sampled and from 10 ppb group at 7, 14, 28 and 42 days for microarray experiments after initiation of the exposure. Total RNA from individual fish was isolated using TRIzol reagent (Invitrogen).Total RNA of ten control trout were pooled as a common reference which were labeled with Cy3. Total RNA of ten fish of each treatment were labeled wih Cy5. cDNA were synthesized using SuperScript II Reverse Transcriptase (Invitrogen) (1 M-NM-<g pooled RNA per synthesis). Targets were labeled using the Array 900 Expression Array Detection kit (Genisphere) following the manufacture protocol. 1M-BM-5g RNA of pooled ten control fish were labled with Cy3 and 1M-BM-5g RNA of pooled ten TCDD-treated fish were labled with Cy5, then day-swap was performed. Two arrays were run for each comparison. Microarrays were scanned at 10 M-BM-5m resolution using a ScanArray Express (PerkinElmer Life Sciences, Inc, Boston, MA). The photomultiplier tube settings (PMT) for Cy3 and Cy5 were 70 and 65-66, respectively. TIFF images of arrays were generated with ScanArray Express software (PerkinElmer). Fluorescence intensity data for Cy3 and Cy5 channels were extracted from TIFF images using ImaGene 7.5 software (BioDiscovery Inc., El Segundo, CA). Background correction, data transformation (setting background corrected values < 0.01 to 0.01), Lowess normalization, and analysis (e.g. fold-change calculations) were performed using GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA)
2013-04-05 | E-GEOD-45780 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-04-05 | E-GEOD-45781 | biostudies-arrayexpress
Project description:We describe here transcripts induced after infection of zebrafish with Spring Viremia Carp Virus (SVCV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in internal organs (pooled spleen, head kidney). Also, transcripts from resistant fishes to viral infection one month after inoculation were studied. Three different experiments were performed to get three biological replicates. Fishes were divided into two groups in each experiment. First group was infected by immersion with SVCV 10^7 pfu/ml, second group was used as a control of non-infected fishes. 6 fishes per group were sacrificed two days post infection, whereas the rest of the infected fishes from the three experiments were maintained for 30 days in the aquariums and then survivors (six for experiment) were sacrificed. This submission includes three biological replicate groups for the non-infected fish and the two days post-infected fish, and two biological replicate groups for the 30 days post-infected fish.
2013-11-04 | E-GEOD-42263 | biostudies-arrayexpress
Project description:Vibriosis caused by Vibrio vulnificus on eels represents an important threat for this specie under culture conditions. Development of new transcriptomic tools is essential to increase the knowledge of eel biology, that nowadays is scarcer. Therefore, using previous results obtained by 454 sequencing of the eel immune-enriched transcriptome, an eel-specific custom microarray have been designed. Gills transcriptomic pattern were analyzed as a principal portal of entry for pathogens in fish after 1h of bath infection with Vibrio vulnificus to describe gill immune response. Moreover, two different strains were used, vibro vulnificus wild type (R99) and rtx double mutant (CT285), to asses the virulence of these pathogen caused by MARTX. Adult european eels were bath infected with two Vibrio vulnificus strains, the wild type and double Rtx mutant (CT285). After 0, 3, 12h post-infection eel gills were sampled. Three individuals per experimental point were sampled, including a Control group and a Handling control group. Obtaining a total of 24 samples. The transcriptomic profile was described for each individual sample.
2013-03-15 | E-GEOD-45163 | biostudies-arrayexpress