Effect of surface waters from Eglin Air Force Base on gene expression in fathead minnow (Pimephales promelas)
Ontology highlight
ABSTRACT:
ORGANISM(S): Pimephales promelas
SUBMITTER: Daniel Spade
PROVIDER: E-GEOD-23521 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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.
2010-08-11 | GSE23521 | GEO
Project description:The goal of this study was to use global gene expression as a diagnostic tool to compare hepatic gene expression patterns in both male and female FHM in streams with the lowest and highest reproductive success, and potentially identify a suite of mRNA transcripts indicative of reproduction in a population The goal of this study was to compare differences in hepatic mRNA expression between gender at high and low egg-producing streams, not differences between individual streams. A k-means cluster analysis was performed using eggs/pair/day on the original 17 streams to delineate 3 clusters: high, medium and low. From that analysis, FHM from 6 of the original 17-streams used in Crago et al. (2010) were chosen for the microarray experiment (Fig. 1, Table 1). In this study the experimental condition is reproductive success; High versus Low reproductive success. The streams grouped into High Reproductive Success were Oak Creek-2007 (2313 eggs), Point Creek (1277 eggs), Meeme Creek (1164 eggs) and Baird Creek (967 eggs). The streams grouped into Low Reproductive Success were: Ashwaubenon Creek (0 eggs), Devils Creek (541 eggs) and Oak Creek-2006 (642 eggs). Multiple regression analysis using the 22 sediment and water quality characteristics measured in the 6 streams with the highest (n = 4 and lowest (n = 3) streams demonstrated that there were no differences amongst the streams in regards to measure sediment and water variables. .5 One array was run for each gender from each stream. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. There were 14 arrays used in this study, 7 for males, 7 for females from individual rivers. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. In the case of Oak Creek, which was sampled in both years, there was a large difference in egg production between two years. Therefore separate arrays were run for Oak Creek 2006 and Oak Creek 2007. All streams chosen had overall survival rates of at least 80% through the 21-day sampling period, except Devils River. The survival rate for Devils River was at 100% until four days prior to the end of the experiment when six fish died or escaped.
2014-04-09 | E-GEOD-56604 | biostudies-arrayexpress
Project description:In 2013, two large-scale Florida manatee (Trichechus manatus latirostris) mortality episodes were reported on separate coasts of Florida. The east coast mortality episode was associated with an unknown etiology in the Indian River Lagoon (IRL). The west coast mortality episode was attributed to a persistent Karenia brevis algal bloom or ‘red tide’ centered in Southwest Florida. To investigate these two mortality episodes, proteomic experiments using two-dimensional difference gel electrophoresis (2D-DIGE) followed by protein identification using liquid chromatography-tandem mass spectrometry (LC-MS/MS) were conducted, along with a separate gel-free analysis using isobaric tags for relative and absolute quantification (iTRAQ) LC-MS/MS. In comparison to the control group, manatees from the IRL, an area associated with an unknown mortality episode, displayed increased levels of several proteins in their serum samples. These increased proteins, which were identified in the iTRAQ experiment, included kininogen-1 isoform 1 (average ratio 1.38), protein AMBP (1.38), histidine-rich glycoprotein (1.34), properdin (1.30), and complement C4-A isoform 1 (1.25). In the red tide group, ceruloplasmin (2.32), pyruvate kinase isozymes M1/M2 isoform 3 (2.29), angiotensinogen (2.08), complement C4-A isoform 1 (1.83), and complement C3 (1.42) were increased. The proteins kininogen-1 isoform 1, histidine-rich glycoprotein, complement C4-A isoform 1, angiotensinogen, and complement C3 were also identified in increased levels in the 2D-DIGE experiment (Table 2b). These proteins are associated with acute-phase response, amyloid formation and accumulation, copper and iron homeostasis, the complement cascade pathway, and other important cellular functions. The increased level of complement C4 protein observed in both the red tide and unknown mortality episode groups was confirmed through the use of Western Blot.
2021-08-30 | PXD002470 | Pride
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4212 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4211 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4210 | GEO
Project description:Aspergillus flavus is one of the major fungal molds that colonize peanut in the field and during storage. The impact to human and animal health and to economy in agriculture and commerce are significant since this mold produces the most potent natural toxins, aflatoxins, which are carcinogenic, mutagenic, immunosuppressive, and teratogenic. A strain of marine Bacillus megaterium isolated from the Yellow Sea of East China was evaluated for its effect to inhibit aflatoxin formation through down-regulating aflatoxin pathway gene expression in A. flavus as demonstrated by genechip analysis in liquid medium and peanuts. The results showed that aflatoxin accumulation in potato dextrose broth liquid medium and liquid minimal medium was almost totally (more than 98%) inhibited by B. megaterium. The expression of many of the aflatoxin biosynthetic genes in the fungus was confirmed to be turned down. Some of the target genes down-regulated by B. megaterium within the whole genome and within the aflatoxin pathway gene cluster (aflF, aflT, aflS, aflJ, aflL, aflX) were identified. These target genes could be used for controlling aflatoxin contamination in crops such as corn, cotton, and peanut. Importantly, the expression of the regulatory gene aflS was found to be significantly down-regulated. The effect of B. megaterium on aflatoxin biosynthesis and genes expression of pathogen was firstly tested in potato dextrose broth (PDB) and glucose minimal salts medium (MM). The cell suspension of B. megaterium (concentration in PDB and MM was finally adjusted to 108 CFU/ml) or sterile distilled water as a control was added into the 100 ml beaker flask containing 15 ml PDB or MM, respectively. Then 100 M-NM-<l of spore suspension (5 M-CM-^W 106 spores/ml) of A. flavus were added into each beaker flask. After 48 h of incubation at 28M-BM-0C at 200 rpm, mycelia were collected, fresh frozen with liquid nitrogen, ground to a fine powder in liquid nitrogen, and stored at -80M-BM-0C for further analysis. The effect of B. megaterium on aflatoxin biosynthesis and genes expression in the A. flavus fungal pathogen was also tested in two types of peanut kernels, UF 715133-1 and Jinhua 1012, respectively. Peanut kernels were wounded (6 mm diameter and approximately 3 mm deep) using a sterile borer and then 20 M-NM-<l of 1 M-CM-^W 108 CFU/ml cell suspension of B. megaterium was inoculated on wounded peanut kernels respectively. Sterile distilled water was also used for inoculation as control. Two hours after bacterial inoculation, 10 M-NM-<l A. flavus spore suspension was inoculated into each wound at a concentration of 106 spores/ml. The kernels were placed in artificial weather chamber to maintain high humidity (85%) and incubated at 28M-BM-0C for 7 days. Each treatment was replicated three times with 20 peanut kernels in each test. The mycelia on kernels were harvested at day 7 and fresh frozen immediately in liquid nitrogen, ground into powder, and stored at -80M-BM-0C for further analysis.
2013-10-22 | E-GEOD-51469 | biostudies-arrayexpress
Project description:A 6K oligonucleotide microarray (TSKMLO) was designed as a community resource for researchers interested in domestic turkey muscle biology as it pertains to growth and development and their association with downstream meat quality. A series of quality control experiments performed to assess the functionality of the newly constructed array, which included a set of validation hybridizations performed in order to initially assess the functionality and repeatability of the newly designed TSKMLO array. Strong correlations between these test comparisons confirmed that the array was able to hybridize fluorescently-labeled aRNA samples from turkey skeletal muscle at different developmental stages, that there was little dye bias, and that results were repeatable.
2010-02-01 | GSE19452 | GEO
Project description:Remaining adult bees in colonies suffering from CCD at apiaries in Florida, California and Pennsylvania were collected during the winter of 2006-2007. The health of CCD colonies was scored at the time of collection as either ï¾severeï¾ or ï¾mildï¾ depending on the apparent strength of the colony. ï¾Historicalï¾ bees, collected prior to the appearance of CCD and hence ostensibly healthy, were collected in 2004 and 2005 from colonies set up on new equipment and not receiving any miticide treatments from apiaries of The Pennsylvania State University near State College, PA. A combination looped, common-reference microarray design was used to compare historical and CCD samples with each other; a blend of RNA isolated from healthy colonies (collected near Urbana, IL in July 2007) served as reference. The microarray experiment compared the guts of bees from mildly and severely afflicted colonies collected in apiaries experiencing CCD on the East Coast (Florida and Pennsylvania) and West Coast (California) with a common reference.
2009-08-15 | E-MEXP-2292 | biostudies-arrayexpress
Project description:Three surface waters in Gainesville, Florida were used in a 48 hour whole effluents exposure to assess gene expression profiles of male fathead minnow liver. Microarray analysis was used to determine changes in gene expression of exposed fish to waters from a site downstream of a wastewater treatment plant (streamwater), a wastewater treatment plant (wastewater), and a lake (stormwater). Differences in gene expression between fish exposed to collected waters and controls were observed. Number of altered genes and biological processes were 1028 and 18 for stormwater; 787 and 19 for streamwater; and: 575 and 12 for wastewater. In general, the effects observed in all exposed fish were related with fatty acid metabolism, DNA repair, oxidation-reduction process, cell wall catabolic process and apoptosis. All exposed fish showed altered expression of genes related with DNA damage repair. In particular fish exposed to stormwater and streamwater showed downregulation of several key intermediates transcripts of cholesterol. The presence and environmental persistence of perfluorinated chemicals (PFCs) in these waters, the resemblance in known effects on transcripts with those found in this study, suggest that the set of genes differentially regulated in fathead minnows after 48 hours of exposure may be attributed to exposure to PFCs. Three surface water sites were chosen for effluent collection in Gainesville, Florida: A lake (stormwater), surface water downstream of a wastewater treatment plant (streamwater), and a wastewater treatment plant effluent used for landscaping irrigation (wastewater). Water from each site was collected two days prior to the fish exposure experiment using Chemfluor ® tubing and a 120 liters steel barrels coated with polyester resin (gel coat) to avoid cross-contamination. Three barrels for each effluent were collected during day 1. Water from the barrel was transported to the laboratory and pumped into four fiberglass cylinders in the aquatic toxicology facility. Water from each cylinder was then pumped into four replicate aquariums per treatment and kept for 1 day without fish (pre-treatment). On day 2, four male fathead minnows from a common tank were transferred to each replicate aquarium and kept for 48 hours, with one 75% water change after first 24 hours. The exposure system consisted of 40 L glass aquaria. Each exposure was conducted in quadruplicate and each aquarium contained the four male fish in 25 L of treatment water . The water used in the control treatment was carbon filtered, dechlorinated tap water. The positions of the treatment tanks were randomized and test initiation times were staggered to ensure an exposure/sampling interval of 48 h. The fish were not fed during the experiment. The temperature range of the water was 24-26 °C with a photoperiod of 16 h light: 8 h dark. Liver was isolate from 4 males indviduals for each treatment except for control group (3 individuals).
2012-04-24 | E-GEOD-37550 | biostudies-arrayexpress