Ontology highlight
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PROVIDER: PRJNA1145100 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Potential sources of microbial colonizers in initial soil ecosystem after retreat of an Alpine glacier
| PRJEB8572 | ENA
Project description:fungi communities on glacier retreat Raw sequence reads
| PRJNA353892 | ENA
Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. From an ecological point of view, three ecosystems can be differentiated in glaciers: the supraglacial ecosystem, the subglacial ecosystem and the englacial ecosystem. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of microbial populations, the type of metabolism and the biogeochemical cycles. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by autotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautrotophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the less studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a true trophic chain and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. The cells were harvested and their proteins were extracted and analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI/TOF/TOF). Several proteins and enzymes were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
2019-08-29 | PXD010060 | Pride
Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. From an ecological point of view, three ecosystems can be differentiated in glaciers: the supraglacial ecosystem, the subglacial ecosystem and the englacial ecosystem. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of microbial populations, the type of metabolism and the biogeochemical cycles. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by autotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautrotophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the less studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a true trophic chain and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. The cells were harvested and their proteins were extracted and analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI/TOF/TOF). Several proteins and enzymes were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
2019-08-29 | PXD010185 | Pride
Project description:Meditation and other alternative practices have long been known to promote various health benefits, presumably by fostering a blood and tissue environment that enhances resilience to stress. Here, we used an integrated, multidisciplinary approach that couples quantitative electroencephalography (qEEG), biometrics, molecular, and biochemical data at multiple time points to investigate the impact of mind-based interventions on the body in a cohort of twins during an intensive week-long meditation retreat. We aim to show the feasibility of a novel design aimed to address individual changes controlling for intersubject trait variation (via twin control) and explore the role of genetic background on multi-omic factors during meditation. Interestingly, twin pairs showed significant spectral power correlations while in separate rooms and only one twin was meditating. These similarities were not observed in mismatched twin pairs. Heart rate dynamics assessments showed alignment among twin pairs that were absent between unmatched pairs. In addition, changes in gene expression, metabolites, and cytokines in blood plasma associated with specific meditative states showed patterns of change related to time points. Twin sets were similar in multiple domains before the start of the retreat, showed considerable divergence at the mid-point, and looked more similar by the end of the retreat. To our knowledge, this study is novel within the twin research paradigm and is a first step toward exploring the effects of meditation in twins.
2025-02-03 | GSE252632 | GEO
Project description:Purpose: The goal of this study was to characterized the transcriptome profiles of whole-blood cells from 388 specimens obtained from 106 individuals before and after the meditation retreat at four-time points (T1–T4) by RNA sequencing (RNA-Seq). T1 samples were collected 5-8 weeks before the retreat, T2 samples were collected on the day of retreat before starting the meditation method, T3 samples were collected immediately after the retreat, and T4 samples were collected three months after the retreat. Methods: The human blood samples were collected into PAXgene Blood RNA Tubes and stored at -80°C freezer. Before RNA extraction the samples were removed from -80°C and incubated overnight at room temperature. The samples were randomized before RNA extraction to eliminate any time point or age or sex or batch effect. Manufacturer’s protocol of manual purification of total RNA from human whole blood was followed (Qiagen, cat #762164). RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina). Results: We applied a comprehensive systems biology approach starting with whole blood gene expression profiling combined with multi-level bioinformatic analyses to characterize the co-expression, transcriptional, and protein-protein interaction networks to identify meditation-specific core network after an advanced eight-day Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were downregulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon (IFN) signaling were upregulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients. Conclusions: The present proof-of-principle study demonstrates that the immune system can be voluntarily influenced by non-pharmaceutical interventions like yoga and meditation. This suggests that meditation as a behavioral intervention could have important implications for treating various conditions associated with excessive or persistent inflammation with a dampened immune system profile.
2021-10-01 | GSE174083 | GEO
Project description:Quantifying and characterising organic carbon and microbes in newly developed soils following glacier retreat in northern latitudes
| PRJEB68336 | ENA
Project description:Early mouse development is accompanied by dynamic changes in chromatin modifications, including G9a-mediated histone H3 lysine 9 dimethylation (H3K9me2), which is essential for embryogenesis. Here we show that H3K9me2 directs repression of 2-cell stage specific genes in nascent embryos to facilitate preimplantation development. Thereafter, genome-wide accumulation of H3K9me2 is crucial for postimplantation development, and coincides with redistribution of EZH2-dependent histone H3 lysine 27 trimethylation (H3K27me3). Loss of G9a or EZH2 results in upregulation of distinct gene sets involved in processes such as cell cycle regulation as well as germline and embryonic development. Accumulation of H3K9me2 not only occurs at promoters and gene bodies, but also extends to active enhancer elements to promote their developmentally-linked silencing. This epigenetic mechanism is important for priming gene regulatory networks in epiblast cells undergoing rapid cell proliferation in preparation for critical cell fate decisions. Examination of 2 histone modification in 3 cell types and transcriptional analysis of G9a and Ezh2 KO epiblasts and Whole genome bisulfite sequencing in two cell types
2015-11-09 | E-GEOD-70355 | biostudies-arrayexpress
Project description:Liver dysfunction is associated with diseases ranging from metabolic disorders to hepatocellular carcinomas (HCC). Here we employed single-cell RNA-sequencing to extensively characterise the cellular landscape of human liver, from development to disease. We analysed ~212,000 cells representing human fetal liver, HCC and mouse liver. Our analysis revealed a remarkable fetal-like reprogramming of the tumor microenvironment (TME). Specifically, the HCC ecosystem displayed features reminiscent of fetal development, including the re-emergence of fetal-associated endothelial cells (PLVAP+/VEGFR2+), and fetal-like (FOLR2+) tumor-associated macrophages (TAMs). In a cross-species comparative analysis, we discovered remarkable similarity of gene expression and regulatory networks between mouse embryonically-seeded, fetal-liver and FOLR2+ tumor macrophages. Spatial transcriptomics further corroborated a shared onco-fetal ecosystem between fetal-liver and HCC. Furthermore, gene regulatory analysis, spatial transcriptomics, and in vitro functional assays implicated VEGF and NOTCH signaling in maintaining onco-fetal ecosystem. Taken together, we report a shared immunosuppressive onco-fetal ecosystem between the human fetal-liver and HCC. Our results unravel a previously unexplored onco-fetal reprogramming of tumor ecosystem, provides a novel target for therapeutic interventions in HCC and also opens up avenues for identifying similar paradigms in other cancers and disease states.
2020-09-24 | GSE156625 | GEO
Project description:Liver dysfunction is associated with diseases ranging from metabolic disorders to hepatocellular carcinomas (HCC). Here we employed single-cell RNA-sequencing to extensively characterise the cellular landscape of human liver, from development to disease. We analysed ~212,000 cells representing human fetal liver, HCC and mouse liver. Our analysis revealed a remarkable fetal-like reprogramming of the tumor microenvironment (TME). Specifically, the HCC ecosystem displayed features reminiscent of fetal development, including the re-emergence of fetal-associated endothelial cells (PLVAP+/VEGFR2+), and fetal-like (FOLR2+) tumor-associated macrophages (TAMs). In a cross-species comparative analysis, we discovered remarkable similarity of gene expression and regulatory networks between mouse embryonically-seeded, fetal-liver and FOLR2+ tumor macrophages. Spatial transcriptomics further corroborated a shared onco-fetal ecosystem between fetal-liver and HCC. Furthermore, gene regulatory analysis, spatial transcriptomics, and in vitro functional assays implicated VEGF and NOTCH signaling in maintaining onco-fetal ecosystem. Taken together, we report a shared immunosuppressive onco-fetal ecosystem between the human fetal-liver and HCC. Our results unravel a previously unexplored onco-fetal reprogramming of tumor ecosystem, provides a novel target for therapeutic interventions in HCC and also opens up avenues for identifying similar paradigms in other cancers and disease states.
2020-09-24 | GSE156626 | GEO