Ontology highlight
ABSTRACT:
PROVIDER: PRJNA642914 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12125664.fastq.gz | Fastqsanger.gz | |||
| SRR12125665.fastq.gz | Fastqsanger.gz | |||
| SRR12125666.fastq.gz | Fastqsanger.gz | |||
| SRR12125667.fastq.gz | Fastqsanger.gz | |||
| SRR12125668.fastq.gz | Fastqsanger.gz |
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Project description:Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, incur a wide variety of consequences depending upon host sensitivity. Juvenile pink salmon (Oncorhynchus gorbuscha) migrate from natal freshwater systems to the ocean at a young age relative to other Pacific salmon, and require rapid development of appropriate defences against marine pathogens. We analyzed the early transcriptomic responses of naïve juvenile pink salmon of sizes 0.3g (no scales), 0.7g (mid-scale development) and 2.4g (scales fully developed) to a low-level laboratory exposure with early moult stage L. salmonis. All infected size groups exhibited unique transcriptional profiles. Inflammation and inhibition of cell proliferation was identified in the smallest size class (0.3g), while increased glucose absorption and retention was identified in the middle size class (0.7g). Tissue-remodelling genes were also up-regulated in both the 0.3g and 0.7g size groups. Profiles of the 2.4g size class indicated cell-mediated immunity and possibly parasite-induced growth augmentation. Understanding a size-based threshold of resistance to L. salmonis is important for fisheries management. This work characterizes molecular responses reflecting the gradual development of innate immunity to L. salmonis between the susceptible (0.3g) and refractory (2.4g) pink salmon size classes.
2011-02-26 | GSE27528 | GEO
Project description:The oceans are now all affected by human activities. The study of the impact of pollution on the health status of exploited marine populations is essential to better understand the direct constraints that stress generates on growth, reproduction, immune system and, ultimately, on the reproductive success of animals. Interactions between different stressors can generate non-additive effects ("cocktail effects"), which makes experimental models under controlled conditions based on only one or a few "stressors" insufficient. Thus, quantitative proteomics was used to analyse muscle proteome of wild European pilchards evolving in the Mediterranean Sea with contrasting levels of organic and inorganic contamination. The prospects of researching biomarkers of health status that can be used as indicators of the status of a population or an ecosystem are of major interest for the monitoring and management of natural environments, hence promoting the conservation and management of marine species.
2024-01-30 | PXD037313 | Pride
Project description:The oceans are now all affected by human activities. The study of the impact of pollution on the health status of exploited marine populations is essential to better understand the direct constraints that stress generates on growth, reproduction, immune system and, ultimately, on the reproductive success of animals. Interactions between different stressors can generate non-additive effects ("cocktail effects"), which makes experimental models under controlled conditions based on only one or a few "stressors" insufficient. Thus, quantitative proteomics was used to analyse liver proteome of wild European pilchards evolving in the Mediterranean Sea with contrasting levels of organic and inorganic contamination. The prospects of researching biomarkers of health status that can be used as indicators of the status of a population or an ecosystem are of major interest for the monitoring and management of natural environments, hence promoting the conservation and management of marine species.
2024-01-30 | PXD037276 | Pride
Project description:Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, incur a wide variety of consequences depending upon host sensitivity. Juvenile pink salmon (Oncorhynchus gorbuscha) migrate from natal freshwater systems to the ocean at a young age relative to other Pacific salmon, and require rapid development of appropriate defences against marine pathogens. We analyzed the early transcriptomic responses of naïve juvenile pink salmon of sizes 0.3g (no scales), 0.7g (mid-scale development) and 2.4g (scales fully developed) to a low-level laboratory exposure with early moult stage L. salmonis. All infected size groups exhibited unique transcriptional profiles. Inflammation and inhibition of cell proliferation was identified in the smallest size class (0.3g), while increased glucose absorption and retention was identified in the middle size class (0.7g). Tissue-remodelling genes were also up-regulated in both the 0.3g and 0.7g size groups. Profiles of the 2.4g size class indicated cell-mediated immunity and possibly parasite-induced growth augmentation. Understanding a size-based threshold of resistance to L. salmonis is important for fisheries management. This work characterizes molecular responses reflecting the gradual development of innate immunity to L. salmonis between the susceptible (0.3g) and refractory (2.4g) pink salmon size classes. Six-condition experiment, 3 size groups each infected and uninfected, duplicate tanks. Biological replicates: 6 control, 6 infected for each size group. Sampled 6 days post exposure. cDNA samples with reference design (aRNA), two-color array.
2011-02-26 | E-GEOD-27528 | biostudies-arrayexpress
Project description:Soil metaproteome of two sites near mining operation in Southern Brazil
2019-03-12 | MSV000083557 | MassIVE
Project description:A variety of contaminants find their way to the marine sediments from different sources, and these contaminants can pose serious risks to the natural marine flora and fauna. For example, pyrethroids, which are a potent pesticide family, are often used in agriculture fields worldwide, and these find their way into the marine environment through run off. Further, pyrethroids are used in farmed Atlantic salmon cages in Chile, Great Britain and Norway. Ammonia is another contaminant that is used in agriculture in form of ammonia-rich fertilizer and can be carried during run-offs to localized rivers and streams. Ammonia is also detectable after emission of effluents from sewage treatment plants and industrial plants like oil refineries and meat processing plants. Contaminants may have short and long term effects on non-target organisms living in the water column or in the marine sediment. Importantly, the sediment ecosystem houses a variety of plants, animals and crustaceans, including the American lobster Homarus americanus. Lobster is the most fished crustacean in New Brunswick and Quebec and its resale and exportation produced over $1.6 billion in 2011. Due to its economic and environmental importance, it is essential to study the effects of contaminants present in its ecosystem. Sediment samples are often used as pollution markers during toxicity testing due to their tendency to accumulate hydrophobic contaminants. To better understand the possible effects of contaminants in sediment, a total gene expression study was developed using the marine amphipod Eohaustorius estuarius. A 10 day spike-in exposure was performed using ammonia and two pyrethroids, namely cypermethrin and deltamethrin. As pyrethroids and ammonia are known to have vastly different mechanisms of action in living organisms, we compared global gene expression patterns following exposure to ammonia against the patterns observed following exposure to pyrethroids. Total gene expression was measured by oligonucleotide microarray. The expression of five genes of interest involved in different biological processes such as metabolism, transcription, translation, immunity and stress, which were found to be differently expressed by microarray, was validated by RT-qPCR. A set of genes was identified that showed differential expression levels in a treatment-dependent manner, thus further highlighting the different mechanisms of action of ammonia and pyrethroids in the marine sediment. This study provides a proof of concept for the use of DNA microarrays with model crustaceans for the study of marine sediment contaminants. This specific study is aimed at evaluating the effect of ammonia and pyrethroid exposure on E.estuarius and to identify possible biomarkers of these exposures.
2014-09-01 | E-GEOD-54214 | biostudies-arrayexpress
Project description:Coastal Antarctic marine ecosystems play an important role in carbon cycling due to their highly productive seasonal phytoplankton blooms. Southern Ocean microbes are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12 ). Micronutrient limitation is a key driver of ecosystem dynamics and influences the composition of blooms, which are often dominated by either diatoms or the haptophyte Phaeocystis antarctica, each with varied impacts on carbon cycling. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remains poorly characterized. Using cultures, physiological analysis, and comparative ’omics we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12 , as previously suggested, and report new mechanistic insights of its B12 response in cultures of predominantly solitary and colonial cells. Proteomics coupled with proteogenomics detected a B12 -independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and is interreplaced with the B12 -dependent isoform (MetH) in replete conditions. Database searches returned homologs of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles and also bacterioplankton. Furthermore, MetE-fusion homologs were found to be expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12 -auxotrophic diatoms.
2023-02-27 | PXD031524 | Pride