Waters in lakes East Lake and West Lake
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ABSTRACT:
PROVIDER: PRJNA956224 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:sediments in lakes East Lake and West Lake Raw sequence reads
| PRJNA956227 | ENA
Project description:Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.
2019-09-27 | GSE133502 | GEO
Project description:The consistent cold temperatures and large amount of precipitation in the Olympic and Cascade ranges of Washington State are thought to increase atmospheric deposition of contaminants in these high elevation locations. Total mercury and 28 organochlorine compounds were measured in composite, whole fish samples collected from 14 remote lakes in the Olympic, Mt. Rainer, and North Cascades National Parks. Mercury was detected in fish from all lakes sampled and ranged in concentration from 17 to 262 ug/kg wet weight. Only two organochlorines, total polychlorinated biphenyls (tPCB) and dichlorodiphenyldichloroethylene (DDE), were detected in fish tissues (concentrations <25 ug/kg wet weight). No organochlorines were detected in sediments (MRL ≈1-5 ug/kg), while median total and methyl mercury in sediments were 30.4 and 0.34 ug/kg (dry weight), respectively. Using a targeted rainbow trout cDNA microarray with known genes, we detected significant differences in liver transcriptional responses, including metabolic, endocrine, and immune-related genes, in fish collected from a contaminated lake compared to a lake with a lower contaminant load. Overall, our results suggest that local urban areas are contributing to the observed contaminant patterns, while the transcriptional changes point to a biological response associated with exposure to these contaminants in fish. Specifically, the gene expression pattern leads us to hypothesize a role for mercury in disrupting the metabolic and reproductive pathways in fish from high elevation lakes in western Washington. Keywords: High altitude lakes, mercury, salmonids, organochlorines
2007-05-01 | GSE6886 | GEO
Project description:Here we provide dataset from a proteomic experiment, using trypsin digestion, and reversed-phase chromatography (RPC) with tandem mass spectrometr (RPC-MS/MS), in order to relatively quantify the protein composition of skin mucus of Prussian carp Carassius gibelio. The main aim of the project is to identify the proteins specifically assotiated with fish inhabits euthophic shallow lakes lake Chany Lake (West Siberia).
2021-05-27 | PXD025974 | Pride
Project description:Lake trout (Salvelinus namaycush) are a top-predator species in the Laurentian Great Lakes that are often used as bioindicators of chemical stressors in the ecosystem. Although many studies are done using these fish to determine concentrations of stressors like legacy persistent, bioaccumulative and toxic chemicals, there are currently no proteomic studies on the biological effects these stressors have on the ecosystem. This lack of proteomic studies on Great Lakes lake trout is because there is currently no complete, comprehensive protein database for this species. In this research, we aimed to use proteomic methods and established protein databases from NCBI and UniProtKB to identify potential proteins in the lake trout species. The current study utilized heart tissue and blood from two separate lake trout. Our previous published work on the lake trout liver revealed 4,194 potential protein hits in the NCBI databases and 3,811 potential protein hits in the UniProtKB databases. In the current study, using the NCBI databases we identified 838 potential protein hits for the heart and 580 potential protein hits for the blood of the first lake trout (biological replicate 1). In the second lake trout (biological replicate 2), using the NCBI databases we identified 1,180 potential protein hits for the heart and 561 potential protein hits for the blood. Similar results were obtained using the UniProtKB databases. This study builds on our previous work by continuing to build the first comprehensive lake trout protein database. Through this investigation, we are also able to make observations as to protein homology through evolutionary relationships.
2021-12-30 | PXD023970 | Pride
Project description:Lake trout are used as bioindicators for toxics exposure in the Great Lakes ecosystem. However, there is no knowledge about lake trout proteome. Here we performed the first lake trout (Salvelinus namaycush) liver proteomics and searched the databases against (NCBI and UniProtKB) Salvelinus, Salmonidae, Actinopterygii and the more distant Danio rerio. In the NCBI search, we identified 4371 proteins in 1252 clusters. From these proteins, we found 2175 proteins in Actinopterygii 1253 in Salmonidae, 69 in Salvelinus and 901 in Danio rerio NCBI searches. In the UniProtKB search, we identified 2630 proteins in 1100 clusters. From these proteins, we found 317 in Actinopterygii, 1653 in Salmonidae, 37 in Salvelinus and 666 in Danio rerio UniProtKB searches. A similar outcome was also obtained from a technical replicate experiment. A large number of lake trout liver proteins were not in any Salvelinus databases, suggesting that lake trout liver proteins have homologues to some proteins from the Salmonidae family and Actinopterygii class, as well as to the species Danio rerio, a more highly studied Cypriniformes fish. Therefore, our study not only builds the first comprehensive lake trout protein database, but also establishes protein homology-based evolutionary relationships between the fish within their family and class, as well as distant-related fish (lake trout and zebrafish). In addition, this study opens the possibility of identifying evolutionary relationships (i.e. adaptive mutations) between various groups (i.e. zebrafish, Salmonidae, Salvelinus and lake trout) through evolutionary proteomics
2019-10-10 | PXD011924 | Pride
Project description:East Skaftar Cauldrons Subglacial Lake Metagenome
| PRJNA1086540 | ENA
Project description:This data is a case study done in the context of developing methods for assessing the taxonomic composition of microbial communities using metaproteomics. For this study with analyzed phototrophic biomats from two Soda Lakes in the Canadian Rocky Mountains using metaproteomics. For protein identification we generated a metagenome from which we predicted and annotated the protein sequences used to analyze the metaproteomes. The database is available in this PRIDE submission. Lake1 refers to Goodenough Lake (GEM, 51°19'47.64"N 121°38'28.90"W) and Lake2 referes to Last Chance Lake (LCM, 51°19'39.3" N 121°37'59.3"W).
2017-05-12 | PXD006343 | Pride
Project description:Today, many contaminants of emerging concern can be measured in waters across the United States, including the tributaries of the Great Lakes. However, just because the chemicals can be measured does not mean that they necessarily result in harm to fish and other aquatic species. Complicating risk assessment in these waters is the fact that aquatic species are encountering the chemicals as mixtures, which may have additive or synergistic risks that cannot be calculated using single chemical hazard and concentration-response information. We developed an in vitro effects-based screening approach to help us predict potential liver toxicity and cancer in aquatic organisms using water from specific Great Lakes tributaries: St. Louis River (MN), Bad River (WI), Fox River (WI), Manitowoc River (WI), Milwaukee River (WI), Indiana Harbor Canal (IN), St. Joseph River (MI), Grand River (MI), Clinton River (MI), River Rouge (MI), Maumee River (OH), Vermilion River (OH), Cuyahoga River (OH), Genesee River (NY), and Oswego River (NY). We exposed HepG2 cells for 48hrs to medium spiked with either field collected water (final concentration of environmental samples in the exposure medium were 75% of the field-collected water samples) or purified water. Using a deep neural network we clustered our collection sites from each tributary based on water chemistry. We also performed high throughput transcriptomics on the RNA obtained from the HepG2 cells. We used the transcriptomics data with our Bayesian Inferene for Sustance and Chemical Toxicity (BISCT) Bayesian Network for Steatosis to predict the probability of the field samples yielding a gene expression pattern consistent with predicting steatosis as an outcome. Surprisingly, we found that the probability of steatosis did not correspond to the surface water chemistry clustering. Our analysis suggests that chemical signatures are not informative in predicting biological effects. Furthermore, recent reports published after we obtained our samples, suggest that chemical levels in the sediment may be more relevant for predicting potential biological effects in the fish species developing tumors in the Great Lakes basin.
2022-12-01 | GSE146903 | GEO