Lake Chaohu
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA528168 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8758530_1.fastq.gz | Fastqsanger.gz | |||
| SRR8758530_2.fastq.gz | Fastqsanger.gz | |||
| SRR8758540_1.fastq.gz | Fastqsanger.gz | |||
| SRR8758540_2.fastq.gz | Fastqsanger.gz | |||
| SRR8758550_1.fastq.gz | Fastqsanger.gz |
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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:Deep Lake is a hypersaline system in Antarctica (68°33’36.8S, 78°11’48.7E) that is so saline it remains liquid at –20°C (DeMaere et al 2013). The lake is dominated by haloarchaea, comprising a low-complexity community that differs greatly to warm-hot latitude hypersaline systems, is hierarchical structured, and supports a high level of intergenera gene exchange. Metaproteomics was performed on biomass that was collected in the austral summer of 2008 by sequential size fractionation (20 – 3 µm, 3 – 0.8 µm, 0.8 – 0.1 µm). The data were integrated to obtain a systems level view of the active host-virus interactions occurring in this novel aquatic Antarctic system. DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JA, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe SG, Cavicchioli R (2013) High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110: 16939-16944
2015-07-21 | PXD001436 | 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.
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Project description:Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.
2021-08-19 | GSE158514 | GEO
Project description:The perfluoroalkyl substances (PFAAs) have received growing attention in recent years as emerging contaminants in the aquatic environment. The occurrence, removal and bioaccumulation of fourteen PFAAs (C4-C14 carboxylate; C4, C6, C8 sulfonates) were investigated in Lake Chaohu, China. The concentrations of the selected PFAAs in inflowing river, lake water and sewage treatment plant (STP) samples were analyzed by ultra performance liquid chromatograph (UPLC-MS/MS). The results showed that perfluorohexanesulfonic acid (PFHxS), perfluorobutane sulfonate (PFBS), perfluorobutyric acid (PFBA) and perfluoropentanoic acid (PFPeA), instead of perfluorooctanoic acid (PFOA), were predominant PFAAs in the inflowing river and lake water with maximum concentrations in the ranges of 52.2-1866 and 27-236 ng L-1, respectively. The highest concentrations of total PFAAs were detected in the western rivers. The effluents from seven STPs were likely important sources of PFAAs in surface water, and the amount of the daily fluxes in the effluent were 132 g for short-chain PFAAs and 109 g for long-chain PFAAs. PFAAs were widely detected in Chinese icefish (Neosalanx tangkahkeii taihuensis) collected from Lake Chaohu, with maximal concentrations ranging from 1.79 ng g-1 to 50.9 ng g-1. The logarithmic bioaccumulation factors of perfluorodecanoic acid (PFDA, 3.5), perfluorooctane sulfonate (PFOS, 3.35) and perfluorononanoic acid (PFNA, 3.31) indicated the bioaccumulation of these long-chain PFAAs. This study is useful for enhancing our understanding of the pollution profiles of PFAAs and their environmental health risk in the freshwater lake.
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