Catostomus macrocheilus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA175537 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin Correlation between contaminant exposure and gene expression profiles of wild largescale suckers collected from three different sites in the Columbia River. At each site, liver samples of six to eight different fish were analyzed using microarrays.
2013-12-04 | E-GEOD-41016 | biostudies-arrayexpress
Project description:Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin
2013-12-04 | GSE41016 | GEO
Project description:Catostomus macrocheilus Transcriptome or Gene expression
| PRJNA166979 | ENA
Project description:Catostomus commersonii (white sucker) Transcriptome or Gene expression
| PRJNA282680 | ENA
Project description:GBS data for hybridization among Catostomus species
| PRJNA275447 | ENA
Project description:The bacterium Serratia marcescens is a common contaminant of contact lens cases and lenses. Serratamolide is one of the secreted hemolytic/cytotoxic factors which contribute to the virulence of this opportunistic pathogen (PMID 22615766). A newly identified transcription factor (eepR) is essential for serratamolide production (PMID 25897029). In the present study, we used immortalized human corneal-limbal epithelial (HCLE) cells (PMID 12766048) as targets for the secreted products of either wild-type (WT) S. marcescens or an isogenic eepR mutant. Microarray data showed that at sub - cytotoxic levels, the secretome of WT bacteria stimulated a > 2-fold response in 712 unique characterized genes. Analysis showed that immune/inflammatory response pathways are significantly enriched in these genes. The scaled response of eepR, ((eepR - control)/(WT – control)), was < 0.5 for 418 of these 712 genes (59%). Pathway analysis of these 2-fold attenuated genes confirmed that they too represented immune/inflammatory responses. These data demonstrate that the serratamolide-deficient eepR mutant evokes a much weaker immune/inflammatory response from a clinically relevant cellular target than does the wild-type bacterium.
2015-12-31 | GSE71320 | GEO
Project description:Initial work for profiling contaminant response in Phaeodactylum cells exposed to contaminants and non contaminant stressors
2012-01-11 | GSE34988 | GEO
Project description:Adaptation of C. elegans to hypertonic environments involves the accumulation of the organic osmolyte glycerol via transcriptional upregulation of the glycerol biosynthestic enzyme gpdh-1. A number of mutants, termed osmotic stress resistant (osr) mutants, have been identified. osr mutants cause constitutive upregulation of gpdh-1 and confer extreme resistance to hypertonicity. We tested the hypothesis that osr mutants broadly activate a gene expression program normally activated by osmotic stress in wild type animals using Affymterix microarray analysis of the hypertonic stress response in wild type animals and of constituitive gene expression changes in five osr mutants.
2009-12-04 | GSE19310 | GEO
Project description:Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification. Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure. To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Gene expression was analyzed using principal component analysis, differential expression testing, and gene co-expression networks, and the results correlated to season, location, and contaminant burden. Season had a significant impact, with over 30% of genes differentially expressed between spring/summer and winter months. Geographic location exhibited lesser effects on the transcriptome, with 15% of genes differentially expressed between the northern Gulf of Mexico and the southeastern U.S. Atlantic locations. Despite a large overlap between the seasonal and geographical gene sets, the pathways altered in the observed gene expression profiles were somewhat distinct. Co-regulated gene modules and differential expression analysis both identified epidermal development and cellular architecture pathways to be expressed at lower levels in animals from the northern Gulf of Mexico. Although contaminant burdens measured were not significantly different between regions, some correlation with contaminant loads in individuals was observed among co-expressed gene modules, but these did not include classical detoxification pathways. Instead, this study identified other, possibly downstream pathways, including those involved in cellular architecture, immune response, and oxidative stress, that may prove to be contaminant responsive markers in bottlenose dolphin skin.
2016-12-06 | GSE90941 | GEO