Villard_deRham_0810
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Celine Delucinge
PROVIDER: E-MTAB-2096 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Over 20% of Earth’s terrestrial surface is underlain by permafrost that represents one of the largest terrestrial carbon pools, with an estimated ~1700 Pg of carbon (C) contained in the upper 3 m of permafrost. Models estimate that C release from thawing permafrost might represent the largest new transfer of C from the biosphere to the atmosphere as the climate warms. Here we investigated microbial community phylogeny, genetic functional potential gene expression, and protein production patterns along a natural thaw gradient, including permafrost, the seasonally thawed active layer and nearby thawed thermokarst bog, using a combination of molecular “omics” approaches: metagenomics (MG), metatranscriptomics (MT) and metaproteomics (MP). Highlights from these analyses reveal energy yielding microbial processes and potential strategies for microbial survival in permafrost soils, and linkages between biogeochemical process rates and –omics measurements. The results provide new knowledge about microbial life and activity potential in permafrost, the potential importance of iron reduction as a survival strategy under frozen conditions in mineral soils, and the importance of methanogenesis following thaw. The multi-omics strategy demonstrated here enables better mechanistic understanding of the ecological strategies utilized by soil microbial communities in response to climate change. Associated metagenomics data available at the EBI Metagenomics portal under the accession number <a href="https://www.ebi.ac.uk/metagenomics/projects/SRP052575">SRP052575</a>.
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Project description:In order to uncover the biological processes affected in glial cells by aging, we analyzed microarray gene expression of the Schwann cell-rich mouse sciatic nerve at 17 time-points throughout life, from day of birth until senescence. In addition, we combined these data with the microarray gene expression data of myelin 56 day-old mouse mutants carrying deletions of either Pmp22, SCAP or Lpin1. Seven mice were dissected per developmental or aging time-point. Both sciatic nerves were isolated from each mouse and tissues were pooled per time-point to extract total RNA. For the mutants and their wild-type littermates, sciatic nerves were dissected from three mice per genotype. Tissues were not pooled, which generated triplicates per genotype. Total RNA was extracted, purified and quality-controlled. For each condition, 300 ng of total RNA was used to synthesize cRNA using the Illumina TotalPrep RNA amplification kit (Ambion). The cRNA was then quantified, quality controlled and hybridized to the MouseWG-6 v1 expression Beadchips (Illumina) according to the manufacturerM-^Rs instructions.
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Project description:Steroid-refractory acute rejection is a risk factor for inferior renal allograft outcome. We aimed to gain insight into the mechanisms underlying steroid resistance by identifying novel molecular markers of steroid-refractory acute rejection. Eighty-three kidney transplant recipients (1995-2005), who were treated with methylprednisolone during a first acute rejection episode, were included in this study. Gene expression patterns were investigated in a discovery cohort of 36 acute rejection biopsies, and verified in a validation cohort of 47 acute rejection biopsies. In the discovery set, expression of metallothioneins (MT) was significantly (P<0.000001) associated with decreased response to steroid treatment. Multivariate analysis resulted in a predictive model containing MT-1 as an independent covariate (AUC=0.88, P<0.0000001). In the validation set, MT-1 expression was also significantly associated with steroid resistance (P=0.029). Metallothionein expression was detected in macrophages and tubular epithelial cells. Parallel to the findings in patients, in vitro experiments of peripheral blood mononuclear cells from 11 donors showed that non-response to methylprednisolone treatment is related to highly elevated MT levels. High expression of metallothioneins in renal allografts is associated with resistance to steroid treatment. Metallothioneins regulate intracellular concentrations of zinc, through which they may diminish the zinc-requiring anti-inflammatory effect of the glucocorticoid receptor. Transcriptional profiles of 40 renal allograft biopsy samples were analyzed using Illumina HumanRef-8 v3.0 BeadChips (Illumina, San Diego, CA). Expression profiles were investigated in total RNA isolated from biopsy samples of 18 patients with steroid responsive acute rejection and 18 patients with steroid resistant acute rejection. Four biopsies, taken during acute decrease of graft function but with no histomorphologic indication of rejection, were included as controls.
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