Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1299799 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:The zebra mussel is present in Spain since early 2000,s, when it was discovered in the lower part of the Ebro river. To study the gene expression pattern of different populations of zebra mussel a long the Ebro River we use a custom microarray developed in our laboratory, using 4057 publicly available DNA sequences from Dreissena polymorpha and other related genera. Also it was used an external sampling site located in Sitjar Dam, about 200km form the Ebro river. Transcriptome profiles were analysed using the gills of individuals collected in the same period (20-23 March) to diminish seasonal effects. A total of 755 transcripts changed significantly their mRNA levels among the sites of the study (ANOVA p<0.01, fc ±1.5). Genes encoding for xenobiotic, energetic and calcium metabolism and cell proliferation were those showing the highest differences among populations. Geographical origin appeared as the major driver of the differences among the studied populations, as the transcriptomic profiles from four populations collected within a radius of few km around the Flix factory clustered together and separated from those from other distant populations both upstream the Ebro River or in the Sitjar dam.
2012-10-10 | GSE41416 | GEO
Project description:The zebra mussel is present in Spain since early 2000,s, when it was discovered in the lower part of the Ebro river. To study the gene expression pattern of different populations of zebra mussel a long the Ebro River we use a custom microarray developed in our laboratory, using 4057 publicly available DNA sequences from Dreissena polymorpha and other related genera. Also it was used an external sampling site located in Sitjar Dam, about 200km form the Ebro river. Transcriptome profiles were analysed using the gills of individuals collected in the same period (20-23 March) to diminish seasonal effects. A total of 755 transcripts changed significantly their mRNA levels among the sites of the study (ANOVA p<0.01, fc M-BM-11.5). Genes encoding for xenobiotic, energetic and calcium metabolism and cell proliferation were those showing the highest differences among populations. Geographical origin appeared as the major driver of the differences among the studied populations, as the transcriptomic profiles from four populations collected within a radius of few km around the Flix factory clustered together and separated from those from other distant populations both upstream the Ebro River or in the Sitjar dam. Differences on gene expression pattern were measure in gills of Dreissena polymorpha in different populations in five populations along the Ebro river and one population in Sitjar dam. The collection of samples were done during Srping (March). For the microarray it was used 2 replicates of each sites of the study.
2012-10-10 | E-GEOD-41416 | biostudies-arrayexpress
Project description:<p>Bivalves serve as an ideal ecological indicator; hence, their use by the NOAA Mussel Watch Program to monitor environmental health. This study aimed to expand the baseline knowledge of using metabolic end points in environmental monitoring by investigating the dreissenid mussel metabolome in the field. Dreissenids were caged at four locations along the Maumee River for 30 days. The mussel metabolome was measured using nuclear magnetic resonance spectroscopy, and mussel tissue chemical contaminants were analyzed using gas or liquid chromatography coupled with mass spectrometry. All Maumee River sites had a distinct mussel metabolome compared to the reference site and revealed changes in the energy metabolism and amino acids. Data also highlighted the importance of considering seasonality or handling effects on the metabolome at the time of sampling. The furthest upstream site presented a specific mussel tissue chemical signature of pesticides (atrazine and metolachlor), while a downstream site, located at Toledo's wastewater treatment plant, was characterized by polycyclic aromatic hydrocarbons and other organic contaminants. Further research into the dreissenid mussel's natural metabolic cycle and metabolic response to specific anthropogenic stressors is necessary before successful implementation of metabolomics in a biomonitoring program. </p>
2024-06-03 | MTBLS6311 | MetaboLights