Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1191028 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The fitness and reproductive output of fishes can be affected by environmental disturbances. In this study, transcriptomics and label-free proteomics were combined to investigate Atlantic salmon (Salmo salar) sampled from three different field locations within the Baltic Sea (Baltic Main Basin (BMB), Gulf of Finland (GoF) and Bothnian Sea (BS)) during marine migration. The expression of several stress related mRNAs and proteins of xenobiotic metabolism, oxidative stress, DNA damage and cell death were increased in salmon from GoF compared to salmon from BMB or BS. Respiratory electron chain and ATP synthesis related gene ontology-categories were upregulated in GoF salmon whereas those associated with RNA processing and synthesis, translation and protein folding decreased. Differences were seen also in metabolism and immune function related gene expression. Comparisons of the transcriptomic and proteomic profiles between salmon from GoF and salmon from BMB or BS suggest environmental stressors, especially exposure to environmental contaminants, as a main explanation for differences. Salmon feeding in GoF are thus “disturbed by hazardous substances”. The results may also be applied in evaluating the conditions of pelagic ecosystems in the different parts of Baltic Sea.
2015-01-26 | PXD001453 | Pride
Project description:In this study, transcriptomics was used to investigate Atlantic salmon (Salmo salar) sampled from three different field locations within Baltic Sea (Baltic Main Basin (CBS), Gulf of Finland (GoF) and Bothnian Sea (BS)) during marine migration. RNA labeling, hybridizations, and scanning were performed by the Finnish Microarray and Sequencing Centre in Turku Centre for Biotechnology.
2015-01-23 | E-MTAB-3041 | biostudies-arrayexpress
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.
2013-08-24 | GSE50164 | GEO
Project description:Behçet syndrome (BS) is a chronic, multisystemic inflammatory condition with unanswered questions regarding its pathogenesis, classification, and rational therapeutics. A microarray-based comparative genome-wide expression analysis was performed to elucidate the molecular mechanisms of BS and identify any potential therapeutic targets. Twenty-nine BS patients (B) and 15 age and sex-matched control subjects (C) were recruited. Patients with BS were grouped as mucocutaneous (M), ocular (O), and vascular (V) according to their clinical phenotypes. GeneChip Human Genome U133 Plus 2.0 arrays were used for gene expression profiling on peripheral blood samples of the patients and the control subjects. Following the documentation of the differentially expressed gene (DEG) sets, the data were further evaluated with bioinformatics analysis/visualization and enrichment tools. Validation of the microarray data were performed using real-time qRT-PCR. When p<0.05 and fold change >2.0 were chosen, the following numbers of DEGs were obtained; B vs. C: 28, M vs. C: 20, O vs. C: 8, V vs. C: 555, M vs. O: 6, M vs. V: 324, O vs. V: 142. Venn diagram analysis indicated only two genes, CLEC12A and IFI27, in the intersection of M vs. C ∩ O vs. C ∩ V vs. C. Another noteworthy gene appeared as CLC in the DEG sets. Cluster analyses successfully clustered distinct clinical phenotypes of BS. While innate immunity-related biological processes were enriched in the M group, adaptive immunity-specific biological processes were significantly enriched in the O and V groups. Distinct clinical phenotypes of BS patients displayed distinct expression profiles. In Turkish patients with BS, expression differences regarding the genes CLEC12A, IFI27, and CLC seemed to be operative in BS pathogenesis. Based on these findings, future research should consider the immunogenetic heterogeneity of BS clinical phenotypes. Two anti-inflammatory genes, namely CLEC12A and CLC, may be valuable as therapeutic targets and may also help design an experimental model in BS.
2023-03-31 | GSE209567 | GEO
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-08-24 | E-GEOD-50164 | biostudies-arrayexpress
Project description:Bisulphite (BS) converted DNA from 2 paternal uniparental diploidies (pUPDs), one maternal (mUPD) and 5 control leukocytes samples were hybridized to the Infinium HumanMethylationEPIC BeadChip (Illumina), obtaining the BS DNA methylation profiles across approximately 850,000 CpGs. In addition, the 5 control leukocyte samples were also coverted using oxidative bisulphite (oxBS) treatment. The selective chemical oxidation of 5-hydroxymethylcytosine (5hmC) to 5-formylcytosine (5fC) and the deamination of the latter to uracil during the BS conversion allowed the quantification of independent 5-methylcytosine (5mC) and 5hmC methylation levels at every single CpG.
2018-07-11 | GSE103738 | GEO
Project description:RNA chemical modifications have been found to play important biological functions. Among which, the 5-methylcytosine (m5C) modification has been reported to participate in viral replication through affecting RNA processing, such as export, decay, translation and so on. In this study, we performed bisulfite sequencing (BS-seq) on HBV 1.1-mer-transfected huh7 cells to identify the m5C sites in HBV mRNA and their function in virus replication was verified. To investigate the mechanism by which m5C methyltransferase NSUN2 suppresses HBV replication, altered global m5C levels in host genes in HBV 1.1-mer-transfected cells were examined by BS-seq. We found that the m5C modification of genes associated with antiviral immunity changed significantly after viral infection. Our study provide new molecular insights into the mechanism of HBV-mediated IFN inhibition
2023-11-07 | GSE246879 | GEO
Project description:Characterization and comparison study of foeniculum vulgare for BS and BP products.
2024-02-19 | MSV000094122 | GNPS
Project description:Bisulphite (BS) and oxidative bisulphite (oxBS) converted DNA from 4 normal human placentas were hybridized to the Illumina HumanMethylation450 Beadchip v1.2, obtaining the BS and oxBS DNA methylation profiles across approximately 450,000 CpGs. By using the oxBS treatment, the selective chemical oxidation of 5-hydroxymethylcytosine (5hmC) to 5-formylcytosine (5fC) and the deamination of the latter to uracil during the BS conversion allowed the quantification of independent 5-methylcytosine (5mC) and 5hmC methylation levels at every single CpG. In consequence, this data set characterizes the genome-wide distribution of 5hmC in the human placenta offerring a high-confidence list of intervals enriched for 5hmC in this tissue.
2017-09-12 | GSE93429 | GEO
Project description:Evaluating the potential human health and ecological risks associated with exposures to complex chemical mixtures in the environment is one of the main challenges of chemical safety assessment and environmental protection. There is a need for approaches that can help to integrate chemical monitoring and biological effects data to evaluate risks associated with specific chemicals present in the environment. In the present study water samples from five locations near two wastewater treatment plants in the St. Croix River basin on the border of MN and WI, USA were analyzed for 127 contaminants including wastewater indicators, pharmaceuticals, and a number of natural and synthetic steroids. Prior knowledge about chemical-gene interactions was used to develop site-specific knowledge assembly models (KAMs) that were used to formulate hypothesis concerning possible biological effects of exposure to the chemicals detected at each location and suggest assays and endpoints for follow-up investigation. Additionally empirical hepatic gene expression data were collected for fathead minnows (Pimephales promelas) exposed in situ, for 12 d, at each location using a high density oligonucleotide microarray. Empirical gene expression data were analyzed to identify functional annotation terms enriched among the lists of differentially-expressed probes. However, the general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses, based on prior knowledge.
2016-05-11 | GSE81263 | GEO