Ontology highlight
ABSTRACT:
PROVIDER: PRJNA555584 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:It is widely accepted that in many food webs, the trophic transfer efficiency among primary producers and herbivores is determined by the nutritional value of primary producers. In pelagic freshwater and marine ecosystems, secondary production by herbivorous crustacean zooplankton is often limited by the seston's content of essential ω3 polyunsaturated fatty acids (ω3 PUFAs). However, little is known about the genetic network behind the positive relationship between phytoplankton ω3 PUFA content and zooplankton growth and reproduction. In our experimental study, we analysed gene expression changes of the freshwater cladoceran Daphnia magna under different food regimes differing in their ω3 PUFA composition. To disentangle ω3 PUFA effects from other factors, we fed D. magna with different pure phytoplankton cultures (i.e., algal and cyanobacterial diets) with or without supplementing the essential ω3 PUFA eicosapentaenoic acid (EPA). As hypothesized, we observed enhanced growth on diets supplemented with EPA. We applied an Illumina RNA-seq approach to D. magna from different diet treatments to find and monitor genes that are regulated dependent on EPA availability. Of 26,646 potential protein products (mapped to the D. magna genome), we identified transcriptomic signatures driven by the different food sources. Further analyses revealed specific candidate genes involved in EPA metabolism, irrespective of the basal food source. This allows a first functional annotation of previously uncharacterized genes involved in the EPA-specific response of D. magna and may finally provide a link to molecular processes connected to ω3 PUFA metabolism and conversion and thus trophic transfer efficiency in pelagic food webs.
2018-01-22 | GSE107545 | GEO
Project description:The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps.
2017-10-26 | PXD008048 | Pride
Project description:The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps.
2017-10-27 | PXD008039 | Pride
Project description:We describe the first dental proteomic profiles of Iron Age individuals (c2000-1000 years B.P), collected from the site of Long Long Rak rock shelter (LLR) in northwest Thailand. A bias toward the preservation of small, acidic and hydrophobic amino acids is observed. It is evident that the 212 proteins identified (2 peptide, FDR <1%) comprise a palimpsest of alterations that occurred both ante-mortem and post-mortem. Conservation of particular amino acids has contributed to the identification of amelogenin peptides. A novel MRM method for sexing individuals using the amelogenin protein is described, with four teeth indicating male origin. Stable isotope analysis using carbon and oxygen isotopes highlights the strongly C3 based (~80%) diet of the Long Long Rak cemetery people, which probably comprised rice combined with protein from freshwater fish among other food items. The combination of pathway and isotopic analysis adds weight to the relatively simple C3 based diets having contributed to the enrichment of pathways associated with metabolic conditions and shows capacity for harboring these conditions prior to death. The combination of proteomics and stable isotope analysis provides a complementary strategy for assessing the demography, diet, lifestyle and possible diseases experienced by ancient populations.
2019-02-25 | PXD009418 | Pride
Project description:Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
| PRJEB31133 | ENA
Project description:Diatoms represent one of the largest groups of Stramenopiles. In the phytoplankton biodiversity, they dominate oceanic and freshwater ecosystems, and contribute significantly to biogeochemical cycles. They are primary producers at the base of food webs, capturing dissolved CO2, inorganic nitrogen, phosphorus, sulfur, etc., and are important carriers of carbon and silicon to the ocean interior. Whereas extensive studies of P. tricornutum response to a lack of nitrogen have been reported from transcriptomics to metabolomics and lipidomics, changes occurring at the proteome level are still missing. Here we aimed at providing a reference dataset, corresponding to the proteomic changes occurring when Phaeodactylum tricornutum cells were cultivated in either a nitrogen-rich or a nitrogen-poor medium.
2022-09-29 | PXD033328 | Pride