Ontology highlight
ABSTRACT:
PROVIDER: PRJNA988297 | ENA |
REPOSITORIES: ENA
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Project description:Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of non-lineage specific genes was conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.
2015-03-07 | GSE62763 | GEO
Project description:Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of non-lineage specific genes was conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families. Whole transcriptome dual color arrays were used to discover differentially expressed genes following sub-lethal exposure to five cyanobacteria in D. pulex. RNA was isolated from eight independent and concurrently replicated exposures of Daphnia to control and five cyanobacteria conditions. RNA was hybridized to microarrays using a standard, control vs. treated design that included dye swaps. Cyanobacteria were Anabaena (ANA), Aphanizomenon (Aph), Cylindrospermopsis (Cyl), Nodularia (Nod) and Oscillatoria (Osl).
2015-03-07 | E-GEOD-62763 | biostudies-arrayexpress
Project description:Mass developments of toxin-producing cyanobacteria are frequently observed in freshwater ecosystems due to eutrophication and global warming. These mass developments can partly be attributed to cyanobacterial toxins, such as protease inhibitors (PIs), which inhibit digestive serine proteases of Daphnia, the major herbivore of phytoplankton and cyanobacteria. To date, mechanisms of this inhibition in the gut of the crustacean Daphnia magna are not known. Here, we characterize a single serine protease, chymotrypsin 448 (CT448), which is present in the gut of the crustacean D. magna.
2018-10-04 | PXD010978 | Pride
Project description:In the past years, the research focus on the effects of microplastics (MP) on aquatic organisms extended from marine systems towards freshwater systems. An important freshwater model organism in the MP field is the cladoceran Daphnia, which plays a central role in lacustrine ecosystems and has been established as a test organism in ecotoxicology. To investigate the effects of MP on Daphnia magna, we performed a chronic exposure experiment with polystyrene MP under strictly standardized conditions. Chronic exposure of D. magna to PS microparticles led to a significant reduction in body length and number of offspring. To shed light on underlying molecular mechanisms induced by microplastic ingestion in D. magna, we assessed the effects of PS-MP at the proteomic level.
2021-07-07 | PXD025108 | Pride
Project description:Cellular uptake and cytotoxicity data from neural cells treated with microplastics were compared and contrasted. Transcriptomic data obtained by RNA-seq from astrocytes treated with microplastics was assessed further.
2024-03-01 | GSE256038 | GEO
Project description:Microplastics represent a growing environmental concern for the oceans due to their potential capability to adsorb different classes of pollutants, thus representing a still unexplored source of exposure for aquatic organisms. In this study polystyrene (PS) microplastics were characterized for their capability to adsorb pyrene (PYR) as model compound for polycyclic aromatic hydrocarbons, and transfer this chemical to filter feeding mussels Mytilus galloprovincialis. Gene expression analyses of Mytilus galloprovincialis exposed to polystyrene (PS) microplastics and to polystyrene contaminated with pyrene (PS-PYR) have been performed trough a DNA microarray platform.
2014-12-27 | GSE57460 | GEO
Project description:Background/Objectives: The waterflea Daphnia is an interesting candidate for biore- generative life support systems (BLSS). These animals are particularly promising be- cause of their central role in the limnic food web and its mode of reproduction. How- ever, the response of Daphnia to altered gravity conditions has to be investigated, especially on the molecular level, to evaluate the suitability of Daphnia for BLSS in space. Methods: In this study, we applied a proteomic approach to identify key proteins and pathways involved in the response of Daphnia to simulated microgravity gener- ated by a 2D-clinostat. We analysed 5 biological replicates using 2D-DIGE proteomic analysis. Results: We identified 109 protein spots differing in intensity (p < 0.05). Substan- tial fractions of these proteins are involved in actin microfilament organisation, in- dicating the disruption of cytoskeletal structures during clinorotation. Furthermore, proteins involved in protein folding were identified, suggesting altered gravity in- duced break-down of protein structures in general. In addition, simulated micro- gravity increased the abundance of energy metabolism related proteins, indicating an enhanced energy demand of Daphnia. Conclusion: The affected biological processes were also described in other studies using different organisms and systems either aiming to simulate microgravity con- ditions or providing real microgravity conditions. Moreover, most of the Daphnia protein sequences are well conserved throughout taxa, indicating that the response to altered gravity conditions in Daphnia follows a general concept.
2015-09-08 | PXD002096 | Pride
Project description:There is global concern regarding the fate and effects of microplastics in the environment, particularly in aquatic systems. In this study, ethylene acrylic acid copolymer particles were evaluated in a chronic toxicity study with the aquatic invertebrate, Daphnia magna. The study design included a natural particle control treatment (i.e., silica) in order to discern any potential physical effects of a particlefrom intrinsic toxicity of the test material. In addition to the standard endpoints of survival, growth, and reproduction, the transcriptomic profile of control and ethylene acrylic acid copolymer-exposed D. magna were evaluated at the termination of the 21-day toxicity study. No significant effects on D. magna growth, survival, or reproduction were observed in the study in comparison to both particle and untreated control groups. Significant transcriptomic alterations were induced in the highest treatment level of 2.3 x 1012 particles of the ethylene acrylic acid copolymer/ L in key pathways linked to central metabolism and energy reserves, oxidative stress, as well as ovulation and molting indicating a global transcriptomic response pattern. To put the results in perspective is challenging at this time, since, to date, microplastic environmental monitoring approaches have not been equipped to detect particles in the nano size range. However, the results of this study indicate that ethylene acrylic acid copolymer microplastics in the upper nano-size range are not expected to adversely affect D. magna growth, survival, or reproductive outcomes at concentrations up to 1012 particles/L.
2020-07-31 | GSE149738 | GEO