Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in four lakes at low and high elevations of approximately 530 and 4,600 m a.s.l., respectively.

2021-02-03 | GSE156784 | GEO

bacterioplankton commmunity sequences

Project description:Bacterioplankton community structure from pacific southern ocean

| PRJEB45020 | ENA

Project description:Plankton from 10 Pampean shallow lakes were investigated using MiSeq

| PRJEB24133 | ENA

Assessing the Potential Ecological Impacts of Perfluorinated Chemicals (PFCs) in the liver and testis of male largemouth bass (Micropterus salmoides) in Minnesota Lakes

Project description:This study used an emerging analytical technology (cDNA microarrays) to assess the potential effects of PFC exposure on largemouth bass in TCMA lakes. Microarrays simultaneously measure the expression of thousands of genes in various tissues from organisms exposed to different environmental conditions. From this large data set, biomarkers (i.e., genes that are expressed in response to an exposure to known stressors) and bioindicators (e.g., suites of genes that correspond to changes in organism health) can be simultaneously measured to clarify the relationship between contaminant exposure and organism health. Based on current scientific literature, we hypothesized that gene expression patterns would be altered in fish exposed to PFCs (as compared with fish from reference lakes), and that the magnitude of these changes would correspond to the concentrations of PFCs present throughout TCMA lakes. Patterns of gene expression in largemouth bass observed across the TCMA lakes corresponded closely with PFC concentration. Concentrations of PFCs in largemouth bass varied significantly across the sampled lakes, where the lowest concentrations were found in Steiger and Upper Prior Lakes and the highest concentrations were found in Calhoun and Twin Lakes. Patterns of gene expression were most different (relative to controls) in fish with the highest PFC tissue concentrations, where fish from Twin and Calhoun Lakes were observed to have between 5437 and 5936 differentially expressed genes in liver and gonad tissues. Although gene expression patterns demonstrated a high degree of correlation with PFC concentrations, microarray data also suggest there are likely additional factors influencing gene expression patterns in largemouth bass in TCMA lakes.

2014-07-31 | GSE57684 | GEO

Regional Epigenetic Variation in Asexual Snail Populations among Urban and Rural Lakes

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

Bacterioplankton

Project description:Bacterioplankton community of Sansha Bay Metagenome, July 16 '21

| PRJNA747131 | ENA

Tissue Contaminants and Associated Transcriptional Response in Trout Liver from High Elevation Lakes of Washington

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

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