Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1041936 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Understanding the biogeographical patterns and underlying drivers of microbial functional diversity is essential for anticipating climate change impacts on ecosystem functioning worldwide. However, this matter remains scarcely addressed in freshwater ecosystems. Using the high-throughput gene array GeoChip 4.0, we show that functional gene alpha diversity and compositon differ across mountains, alpha diversity declines towards high elevations and compositional turnover increases with larger elevational distances. Both continental- and mountain-scale patterns were primarily driven by climatic variables.
2020-06-22 | GSE128826 | GEO
Project description:Edwardsiella tarda is a Gram-negative bacterial pathogen that can infect a wide range of freshwater and marine fish. However, the immune evasion mechanisms of Edwardsiella tarda is not fully understood. We found that Edwardsiella tarda infection generally significantly upregulated and downregulated a lot of immune-related genes of zebrafish ZF4 cells using RNA-seq technology.
2017-02-14 | GSE81773 | GEO
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment.
2017-05-30 | GSE82310 | GEO
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. This is the RNA-seq experiment, DNA methylation data (bisulfite-seq) is provided under accession number GSE82310.
2021-11-03 | GSE186925 | GEO
Project description:Freshwater environments such as rivers receive effluent discharges from wastewater treatment plants, representing a potential hotspot for antibiotic resistance genes (ARGs). These effluents also contain low levels of different antimicrobials including biocides and antibiotics such as sulfonamides that can be frequently detected in rivers. The impact of such exposure on ARG prevalence and microbial diversity of riverine environment is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration (<4 g L-1) of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a microflume system. This system was a semi-natural in-vitro microflume using river water (30 L) and sediment, with circulation to mimic river flow. A combination of ‘omics’ approaches were conducted to study the impact of SMX exposure on the microbiomes within the microflumes. Metaproteomics did not show differences in ARGs expression with SMX exposure in water.
2021-07-06 | PXD023822 | Pride
Project description:Global climate change increasingly polarizes environments, presenting unprecedented challenges to many organisms (Smol, 2012). Polarization occurs not only in the spatial dimension, producing greater desert drought and tropical rainfall, for example, but also in the temporal dimension by making a local environment more variable over time. Many organisms survive these fluctuating environmental conditions by manifesting multiple distinct phenotypes through developmental processes that enable phenotypic plasticity (Pigliucci et al., 2006; Parsons et al., 2011). As with early development, these processes are expected to strictly regulate gene expression to canalize phenotype, despite the genetic diversity within populations (Alberch, 1982; Riska, 1986, Pigliucci et al., 1996). For plasticity to evolve, natural selection must act on genes that regulate trait variation, e.g, those conferring norms of reaction to a specific set of conditions. Despite the importance of these reaction norms for coping with environmental challenges, the genetic framework underlying phenotypic plasticity remains poorly defined, making it impossible to study how they function, differ among natural populations, and evolve. Here we used arsenic, a chemical inhibitor of salinity acclimation, to identify genes involved in transforming the gill from its freshwater to its seawater architecture in the euryhaline teleost Fundulus heteroclitus. Linear model interaction terms associated with the combined effect of arsenic and salinity challenge revealed an antagonistic relationship between arsenic exposure and salinity acclimation Exposure to arsenic during salinity acclimation yielded gene expression values similar to those observed in unexposed fish that remained in a stable environment, demonstrating that arsenic prevents changes in gene expression that normally enable osmotic plasticity. The gene sets defined by the interaction terms showed reduced inter-individual variation, suggesting unusually tight control, consistent with the hypothesis that they participate in a canalized developmental response. Evidence that natural selection acts to preserve their canalized gene expression was obtained by referencing three populations that differ in their adaptive tolerance to salinity changes (Whitehead et al., 2011). Specifically, populations adapted to withstand the widest salinity range showed both reduced transcriptional variation in genes enabling gill plasticity and an increased osmoregulatory capacity, highlighted by more stable plasma chloride concentrations in response to an osmotic challenge. Finally, we observed significantly fewer associations between genes underlying trait variation and their transcriptional regulators compared to genes that responded to only arsenic or salinity. Collectively, our results demonstrate that phenotypic plasticity converges on a molecular solution that parallels early development, in which the expression of phenotypic plasticity genes and phenotypes are canalized in part by reducing trans-regulatory complexity. 36 Sample comparisons with fish gills exposed to freshwater, freshwater to seawater for 1 hour, freshwater to seawater for 1 hour with arsenic, freshwater to seawater for 24 hours, freshwater to seawater for 24 hours with arsenic, and freshwater with arsenic for 48 hours
2014-10-02 | E-GEOD-47035 | biostudies-arrayexpress