Ontology highlight
ABSTRACT:
PROVIDER: PRJNA482277 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7549730_1.fastq.gz | Fastqsanger.gz | |||
| SRR7549730_2.fastq.gz | Fastqsanger.gz | |||
| SRR7549750_1.fastq.gz | Fastqsanger.gz | |||
| SRR7549750_2.fastq.gz | Fastqsanger.gz | |||
| SRR7549770_1.fastq.gz | Fastqsanger.gz |
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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:Per- and polyfluoroalkyl substances (PFAS) are a diverse family of industrially significant synthetic chemicals infamous for extreme environmental persistence and global environmental distribution. Many PFAS are bioaccumulative and biologically active mainly due to their tendency to bind with various proteins. These protein interactions may be the most important element in determining the accumulation potential and tissue distribution of individual PFAS. Trophodynamics studies including aquatic food webs present inconsistent evidence for PFAS biomagnification. This study strives to identify whether the observed variability in PFAS bioaccumulation potential among species could correspond with interspecies protein composition differences. Specifically, this work compares the perfluorooctane sulfonate (PFOS) serum protein binding potential and the tissue distribution of ten perfluoroalkyl acids (PFAAs) detected in alewife (Alosa pseudoharengus), deepwater sculpin (Myoxocephalus thompsonii), and lake trout (Salvelinus namaycush) of the Lake Ontario aquatic piscivorous food web. To identify interspecies differences in PFAS-binding serum proteins, fish sera were pre-equilibrated with PFOS, fractionated by serial molecular weight cut-off filter fractionation, followed by liquid chromatography–tandem mass spectrometry analysis of the tryptic protein digests and the PFOS extracts of each fraction. This workflow identified similar serum proteins for all fish species. However, serum albumin was only identified in lake trout, suggesting apolipoproteins are likely the primary PFAA transporters in alewife and deepwater sculpin sera. PFAA tissue distribution analysis provided supporting evidence for interspecies variations in lipid transport and storage, which may also contribute to the varied PFAA accumulation in these species.
2023-03-11 | PXD039145 | Pride
Project description:Effect of temperature variation on zebra fish health and behaviour Water temperature is an important environmental parameter that influences the distribution and the health of fishes. Moreover, temperature has a central role in ectothermic animals affecting their physiology and behaviour. The aim of this study was to determine the effects of ambient temperature on the molecular mechanism and the behavioural responses in ZF (Danio rerio) (ZF) a widely used animal model for environmental "omics" genomics researches. A global proteomic analysis was performed on fish brains to investigate physiological and biochemical changes that may occur from the exposure to this environmental stressor at the central nervous system level. Behavioural investigations were performed using a Y-Maze task to evaluate how temperature variations may affect swimming performance, the response to novelty and the spatial memory. Adult specimens of wild type ZF were kept at three different temperatures: 18 °C, 34 °C and 26 °C (used as a control) for 21 days. Proteomic data revealed 202XXX differentially expressed proteins across acclimation groups. These proteins are involved in energy metabolism, mitochondrial regulation and cytoskeletal organization. Temperature variation was able to alter swimming performance in adult ZF and to induce variations in the novel ambient exploration and in the acquisition and consolidation of spatial memory. This study indicates that moderate temperature variations can elicit biochemical changes that may affect fish health and behaviour. This combined approach may provide insights into mechanisms supporting thermal adaptation and plasticity in fishes.
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Project description:Our main objectives wereto investigate the molecular mechanisms involved in metal toxicity and detoxification in the field using juvenile yellow perch subjected to differents levels of this metal exposure. Recent local adaptation to pollution has been evidenced in several organisms inhabiting environments heavily contaminated by metals. Nevertheless, the molecular mechanisms underlying adaptation to high metal concentrations are poorly understood, especially in fishes. Yellow perch (Perca flavescens) populations from lakes in the mining area of Rouyn-Noranda (QC, Canada) have been faced with metal contamination for about 90 years. Here, we examine gene transcription patterns of fish reciprocally transplanted between a reference and a metal-contaminated lake and also fish caged in their native lake. After four weeks, 111 genes were differentially transcribed in metal-naïve fish transferred to the metal-contaminated lake, revealing a plastic response to metal exposure. Genes involved in the citric cycle and beta-oxidation pathways were under-transcribed, suggesting a potential strategy to mitigate the effects of metal stress by reducing energy turnover. However, metal-contaminated fish transplanted to the reference lake did not show any transcriptomic response, indicating a reduced plastic response capability to sudden reduction in metal concentrations. Moreover, the transcription of other genes, especially ones involved in energy metabolism, was affected by caging. Overall, our results highlight environmental stress response mechanisms in yellow perch at the transcriptomic level and support a rapid adaptive response to metal exposure through genetic assimilation. Comparison between fish Op and OpâOp using a pairwise design corresponding to the cage experiment in the reference lake Opasatica (Op), comparison between fish Du and DuâDu using a pairwise design corresponding to the cage experiment in the metal contaminated lake Dufault (Du), comparison between fish from reference lake transplanted to the metal contaminated lake (OpâDu) and fish from reference lake caged in their own lake (OpâOp) using pairwise design corresponding to the experiment of metal contamination, comparison between fish from metal contaminated lake transplanted to the reference lake (DuâOp) and fish from the metal contaminated lake caged in their own lake (DuâDu) using pairwise design corresponding to the depuration experiment.
2016-01-11 | E-GEOD-76723 | biostudies-arrayexpress
Project description:Understanding biological diversity and distribution patterns at multiple spatial scales is a central issue in ecology. Here, we investigated the biogeographical patterns of functional genes in soil microbes from 24 arctic heath sites using GeoChip-based metagenomics and principal coordinates of neighbour matrices (PCNM)-based analysis. Functional gene richness varied considerably among sites, while the proportions of each major functional gene category were evenly distributed. Functional gene composition varied significantly at most medium and broad spatial scales, and the PCNM analyses indicated that 14-20% of the variation in total and major functional gene categories could be attributed primarily to relatively broad-scale spatial effects that were consistent with broad-scale variation in soil pH and total nitrogen. The combination of variance partitioning and multi-scales analysis indicated that spatial distance effects contributed 12% to variation in functional gene composition，whereas environmental factors contributed only 3%. This relatively strong influence of spatial as compared to environmental variation in determining functional gene distributions contrasts sharply with typical microbial phylotype/species-based biogeographical patterns in the Arctic and elsewhere. Our results suggest that the distributions of soil functional genes cannot be predicted from phylogenetic distributions because spatial factors associated with historical contingencies are relatively important determinants of their biogeography.
2014-12-10 | GSE63927 | GEO
Project description:Our main objectives wereto investigate the molecular mechanisms involved in metal toxicity and detoxification in the field using juvenile yellow perch subjected to differents levels of this metal exposure. Recent local adaptation to pollution has been evidenced in several organisms inhabiting environments heavily contaminated by metals. Nevertheless, the molecular mechanisms underlying adaptation to high metal concentrations are poorly understood, especially in fishes. Yellow perch (Perca flavescens) populations from lakes in the mining area of Rouyn-Noranda (QC, Canada) have been faced with metal contamination for about 90 years. Here, we examine gene transcription patterns of fish reciprocally transplanted between a reference and a metal-contaminated lake and also fish caged in their native lake. After four weeks, 111 genes were differentially transcribed in metal-naïve fish transferred to the metal-contaminated lake, revealing a plastic response to metal exposure. Genes involved in the citric cycle and beta-oxidation pathways were under-transcribed, suggesting a potential strategy to mitigate the effects of metal stress by reducing energy turnover. However, metal-contaminated fish transplanted to the reference lake did not show any transcriptomic response, indicating a reduced plastic response capability to sudden reduction in metal concentrations. Moreover, the transcription of other genes, especially ones involved in energy metabolism, was affected by caging. Overall, our results highlight environmental stress response mechanisms in yellow perch at the transcriptomic level and support a rapid adaptive response to metal exposure through genetic assimilation.
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Project description:Gymnocypris przewalskii przewalskii is distributed in Qinghai Lake, the largest inland saltwater lake in China. It is the only Cyprinidae fish in the Qinghai Lake water system and has extremely strong adaptability to the ecological environment with high salinity. G. p. przewalskii originates from the freshwater species Gymnocypris eckloni eckloni in the Yellow River and has a freshwater subspecies, Gymnocypris przewalskii ganzihonensis, distributed in the Ganzi River. Therefore, G. p. przewalskii is considered an ideal material for studying the high salt adaptation of plateau fish. Previous studies have characterized the evolutionary basis of highland adaptation in G. p. przewalskii; however, its adaptability to highly saline aquatic environments remains elusive. In the current study, we performed physiological, histological, genomic and transcriptomic analyses to investigate the phenotypical adaptation of G. p. przewalskii to a high saline environment and the underlying genomic and regulatory bases.
2024-08-30 | PXD055442 |
Project description:BACKGROUND: The transcript levels of many genes exhibit significant variation in tissue samples from inbred laboratory mice. A microarray experiment was designed to separate transcript abundance variation across samples from adipose, heart, kidney, and liver tissues of C57BL/6J mice into within-mouse and between-mouse components. Within-mouse variance captures variation due to heterogeneity of gene expression within tissues, RNA-extraction, and array processing. Between-mouse variance reflects differences in transcript levels between these genetically identical mice. Many biological sources can contribute to heterogeneous transcript levels within a tissue sample including inherent stochasticity of biochemical processes such as intrinsic and extrinsic noise within cells and differences in cell-type composition which can result from heterogeneity of stem and progenitor cell populations. Differences in global signaling patterns between individuals and micro-environmental influences such as interactions with pathogens and cage mates can also contribute to variation, but are likely to contribute more to the between-mouse variance component. RESULTS: The nature and extent of transcript abundance variation differs across tissues. Adipose has the largest total variance and the largest within-mouse variance. Liver has the smallest total variance, but it has the most between-mouse variation. Genes with high variability can be classified into groups with correlated patterns of expression that are enriched for specific biological functions. Variation between mice is associated with circadian rhythm, growth hormone signaling, immune response, androgen regulation, lipid metabolism, and the extracellular matrix. Genes showing correlated patterns of within mouse variation were also associated with biological functions, spatial connectivity of stochastic variation and heterogeneity of cell types within tissues. CONCLUSIONS: Genetically identical mice are individuals and they can experience different outcomes for medically important traits. This is reflected in the stochastic variation in gene expression observed between genetically identical mice. Much of the stochasticity has organismal, tissue, or spatial connectivity. Prior knowledge of the genes and functional classes of genes that are likely to vary in the absence of experimental perturbations, whether these are genetic or environmental, can inform experimental design decisions and the interpretation of gene expression data. Variation in gene expression in genetically identical mice sheds light on the impact of stochastic and micro-environmental factors and their phenotypic consequences.
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