Ontology highlight
ABSTRACT:
PROVIDER: PRJNA386070 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Increasing utilization and human population density in the coastal zone is widely believed to place increasing stresses on the resident biota, but confirmation of this belief is somewhat lacking. While we have solid evidence that highly disturbed estuarine systems have dramatic changes in the resident biota (black and white if you will), we lack tools that distinguish the shades of grey. In part this lack of ability to distinguish shades of grey stems from the analytical tools that have been applied to studies of estuarine systems and perhaps more important is the insensitivity of the biological end points that we have used to assess these impacts. In this paper we will present data on the phenotypic adjustments as measured by transcriptomic signatures of a resilient organism (oysters) to land use practices in the surrounding watershed using advanced machine learning algorithms. We will demonstrate that such an approach can reveal subtle and meaningful shifts in oyster gene expression in response to land use. Further, the data shows that gill tissues are far more responsive and provide superior discrimination of land use classes than hepatopancreas and that transcript encoding proteins involved in energy productions, protein synthesis and basic metabolism are more robust indicators of land use than classic biomarkers such as metallothioneins, GST and cytochrome P450. Keywords: Comparative genomics, ecogenomics. Tissue differences, impacts of land use and contaminants on gene expression.
2009-07-01 | GSE14793 | GEO
Project description:Impact of Amazon land-use change on genomic diversity
| PRJNA432584 | ENA
Project description:Increasing utilization and human population density in the coastal zone is widely believed to place increasing stresses on the resident biota, but confirmation of this belief is somewhat lacking. While we have solid evidence that highly disturbed estuarine systems have dramatic changes in the resident biota (black and white if you will), we lack tools that distinguish the shades of grey. In part this lack of ability to distinguish shades of grey stems from the analytical tools that have been applied to studies of estuarine systems and perhaps more important is the insensitivity of the biological end points that we have used to assess these impacts. In this paper we will present data on the phenotypic adjustments as measured by transcriptomic signatures of a resilient organism (oysters) to land use practices in the surrounding watershed using advanced machine learning algorithms. We will demonstrate that such an approach can reveal subtle and meaningful shifts in oyster gene expression in response to land use. Further, the data shows that gill tissues are far more responsive and provide superior discrimination of land use classes than hepatopancreas and that transcript encoding proteins involved in energy productions, protein synthesis and basic metabolism are more robust indicators of land use than classic biomarkers such as metallothioneins, GST and cytochrome P450. Keywords: Comparative genomics, ecogenomics. Tissue differences, impacts of land use and contaminants on gene expression. Oysters were collected from 11 tidal creeks in Georgia, South Carolina and North Carolina at sites variously impacted by human development. A total of 267 individuals were examined for gene expression profiles in gill and hepatopancreas tissues for a total of 534 arrays. The data were filtered though standard tools and ultimately analyzed using advance machine learning techniques.
2009-07-01 | E-GEOD-14793 | biostudies-arrayexpress
Project description:Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH-controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased pH above a threshold (~ 6.2) lead to carbon loss through increased decomposition following alleviation of acid-retardation of microbial growth. However, loss of carbon with intensification in near neutral-pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to tradeoffs with stress alleviation and resource acquisition. Thus, less intensive management practices in near neutral-pH soils have more potential for carbon storage through increased microbial growth efficiency; whereas, in acidic soils microbial growth is a bigger constraint on decomposition rates.
2018-07-26 | PXD010526 | Pride
Project description:The availability of organic carbon represents a major bottleneck for the development of soil microbial communities and the regulation of microbially-mediated ecosystem processes. However, there is still a lack of knowledge on how the lifestyle and population abundances are physiologically regulated by the availability of energy and organic carbon in soil ecosystems. To date, functional insights into the lifestyles of microbial populations have been limited by the lack of straightforward approaches to the tracking of the active microbial populations. Here, by the use of an comprehensiv metaproteomics and genomics, we reveal that C-availability modulates the lifestyles of bacterial and fungal populations in drylands and determines the compartmentalization of functional niches. This study highlights that the active diversity (evaluated by metaproteomics) but not the diversity of the whole microbial community (estimated by genome profiling) is modulated by the availability of carbon and is connected to the ecosystem functionality in drylands.
2017-07-07 | PXD003572 | Pride