Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27117 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Marine sediment microbial communities from Kolumbo Volcano mats, Greece - white/grey mat metagenome
| PRJNA337731 | ENA
Project description:Marine sediment microbial communities from Santorini caldera mats, Greece - red mat metagenome
| PRJNA336970 | ENA
Project description:Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme’s response (R2, 0.51–0.80, p < 0.01 in all cases). Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide (latitude 62.2°S–16°N, MAT –1.4ºC–29.5ºC) validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility, confirm the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response
2023-02-07 | PXD039714 | Pride
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.
2014-09-01 | GSE54214 | GEO
Project description:Chemical analysis of the compounds present in sediment, although informative, often is not indicative of the downstream biological effects that these contaminants exert on resident aquatic organisms. More direct molecular methods are needed to determine if marine life is affected by exposure to sediments. In this study, we used an aquatic multispecies microarray and q-PCR to investigate the effects on gene expression in juvenile sea bream (Sparus aurata) of two contaminated sediments defined as sediment 1 and 2 respectively, from marine areas in Northern Italy.
2011-01-01 | E-TABM-1146 | biostudies-arrayexpress
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:Lipidomic analysis carried out on postmortem human brain tissue from cases with FTD carrying inherited mutations in the GRN gene, or repeat expansions in the C9orf72 gene, and age-matched control cases. Tissue was sampled from the heavily affected superior frontal grey and white matter, and less heavily affected superior parietal grey and white matter.
2023-01-19 | ST002452 | MetabolomicsWorkbench
Project description:Microglia are brain-resident, myelin-phagocytosing cells, yet their role in lesion initiation in grey and white matter regions in multiple sclerosis (MS) is unclear. We isolated primary microglia from both, occipital cortex and corpus callosum, of 10 MS and 11 control donors and studied their transcriptional profile by RNA sequencing, thereby identifying regional and MS-associated changes. Identification of pathways underlying regional differences showed a relatively increased type I interferon response in cortical grey matter microglia, while white matter microglia more highly expressed NF-κB pathway genes. In normal-appearing white matter MS tissue, lipid metabolism genes were increased, suggesting processing of myelin by microglia already in areas seemingly devoid of MS pathology. Normal-appearing grey matter MS microglia showed increased activation of glycolysis and metal ion homeostasis, possibly reflecting microglia reacting to iron depositions. Notably, expression of genes associated with microglia homeostasis were hardly changed, suggesting that subtle regional changes in MS-associated microglia do not yet affect their resting state.
2019-03-13 | GSE111972 | GEO
Project description:Saline sediment microbial communities from Etoliko Lagoon, Greece - sediment metagenome
| PRJNA593590 | ENA