Bacteria on Daphnia obtusa
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ABSTRACT:
PROVIDER: PRJEB18674 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Daphnia obtusa isolate:FS6 Genome sequencing and assembly
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Project description:Transcriptomics studies are more likely to achieve predictive results when they rely on tissue- and cell-specific transcriptional data. Identification of cell types in novel model organisms by their transcriptional profiles is difficult without data on transcriptional differences among major tissues and anatomical features. Here we report the first dataset on tissue- and organ-specific transcriptomics in freshwater plankton crustacean Daphnia magna, reporting markers of eggs, hemocytes, gut, carapace, antennae and head (as well as the remaining carcass).
2024-04-19 | GSE264123 | GEO
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:Epigenetic mechanisms have been found to play important roles in environmental stress response and regulation. These can, theoretically, be transmitted to future unexposed generations, yet few studies have shown persisting stress-induced transgenerational effects, particularly in invertebrates. Here, we focus on the aquatic microcrustacean Daphnia, a parthenogenetic model species, and its response to salinity stress. Salinity is a serious threat to freshwater ecosystems and a relevant form of environmental perturbation affecting freshwater ecosystems. We exposed one generation of D. magna to high levels of salinity (F0) and found that the exposure provoked specific methylation patterns that were transferred to the three consequent non-exposed generations (F1, F2 and F3). This was the case for the hypomethylation of six protein-coding genes with important roles in the organisms’ response to environmental change: DNA damage repair, cytoskeleton organization and protein synthesis. This suggests that epigenetic changes in Daphnia are particularly targeted to genes involved in coping with general cellular stress responses. Our results highlight that epigenetic marks are affected by environmental stressors and can be transferred to subsequent unexposed generations. Epigenetic marks could therefore prove to be useful indicators of past or historic pollution in this parthenogenetic model system. Furthermore, no life history costs seem to be associated with the maintenance of hypomethylation of across unexposed generations in Daphnia following a single stress exposure.
2018-08-20 | GSE107340 | GEO
Project description:Daphnia (Daphnia pulex) is a small planktonic crustacean and a key constituent of aquatic ecosystems. It is commonly used as a model organism for studying environmental toxic challenges. In the past decade, a Daphnia genomic information and proteomic dataset has been developed. This dataset has expanded the opportunity to relate toxicological effects with “Daphnia proteomics” as it integrates proteomic knowledge in Daphnia, those approach will provide greater insights for toxicological research. In order to exploit Daphnia for ecotoxicological research, information on the post-translational modification (PTM) of proteins is necessary as this is a critical regulator of biological processes. Acetylation of lysine (Kac) is a reversible and highly regulated PTM that is associated with diverse biological functions. However, a comprehensive description of Kac in Daphnia is not yet available. Here, to understand the cellular distribution of lysine acetylation in Daphnia, we identified 98 acetylation sites in 65 proteins by immunoprecipitation using an anti-acetyllysine antibody and an liquid chromatography system supported by mass spectroscopy. We identified 28 acetylated sites connected with metabolic proteins and 6 acetylated enzymes associated with the TCA cycle in Daphnia. From GO and KEGG enrichment analyses, we showed that Kac in D. pulex is highly enriched in proteins associated with metabolic processes. Our data provide the first global analysis of lysine acetylation in D. pulex. The expanded proteomic dataset will be an important resource for the functional analysis of Kac in D. pulex and it will be nice to have a first step done using a promising future model organism.
2016-01-05 | PXD002441 | Pride
Project description:Cationic antimicrobial peptides (CAPs) are promising novel alternatives to conventional antibacterial agents, but the overlap in resistance mechanisms between small-molecule antibiotics and CAPs is unknown. Does evolution of antibiotic resistance decrease (cross-resistance) or increase (collateral sensitivity) susceptibility to CAPs? We systematically addressed this issue by studying the susceptibilities of a comprehensive set of antibiotic resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic resistant bacteria frequently showed collateral sensitivity to CAPs, while cross-resistance was relatively rare. We identified clinically relevant multidrug resistance mutations that simultaneously elevate susceptibility to certain CAPs. Transcriptome and chemogenomic analysis revealed that such mutations frequently alter the lipopolysaccharide composition of the outer cell membrane and thereby increase the killing efficiency of membrane-interacting antimicrobial peptides. Furthermore, we identified CAP-antibiotic combinations that rescue the activity of existing antibiotics and slow down the evolution of resistance to antibiotics. Our work provides a proof of principle for the development of peptide based antibiotic adjuvants that enhance antibiotic action and block evolution of resistance.
2018-03-29 | GSE96706 | GEO
Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
2024-09-02 | PXD040304 | Pride
Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
2024-09-02 | PXD040228 | Pride
Project description:To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. 2016. We found that methylation percentage across the genome of Daphnia spp. follows a bimodal distribution. Furthermore, CpG methylation in Daphnia predominantly occurs at coding regions. Although methylation levels significantly decrease towards the 3’ end of a gene with a significant drop in methylation levels from one exon to the neighbouring intron, there is a clear spike in relative methylation levels between exon and intron boundaries, which may be linked to regulation of splicing. We further demonstrate that DNA methylation in Daphnia is responsive to intrinsic and extrinsic factors. We also compared the methylation and gene expression correlations found in Daphnia to publicly available dataset from two other invertebrate species (Apis mellifera and Nasonia vitripennis) and two vertebrate species (Homo sapiens and Mus musculus). We observed that similar to other invertebrates, Daphnia’s genome is sparsely methylated at a lower level and the methylation is predominantly focused at gene body while in vertebrate species the genome is heavily methylated (global methylation). Although the level and distribution of methylation across CpG sites is different between vertebrates and invertebrates it is possible that methylation density at coding regions has the same function between vertebrates and invertebrates. We demonstrate evolutionary conservation of a positive correlation between high methylation density at coding regions and gene expression across vertebrates and invertebrates, leading to potentially ensuring continuous high expression of genes required throughout the life in both vertebrates and invertebrates.
2018-12-11 | GSE103939 | GEO