EarthShape slope profiles
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB38877 | ENA |
REPOSITORIES: ENA
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Project description:Adverse experiences in childhood are associated with altered hypothalamic pituitary adrenal axis function and negative health outcomes throughout life. It is now commonly accepted that abuse and neglect can alter epigenetic regulation of HPA genes. Accumulated evidence suggests harsh parenting practices such as spanking are also strong predictors of negative health outcomes. We predicted harsh parenting at 2.5 years old would predict HPA gene DNA methylation similarly to abuse and neglect, and cortisol output at 8.5 years old. Saliva samples were collected three times a day across three days to estimate cortisol diurnal slopes. Methylation was quantified using the Illumina Infinium MethylationEPIC array BeadChip (850K) with DNA collected from buccal cells. We used principal components analysis to compute a summary statistic for CpG sites across candidate genes. The first and second components were used as outcome variables in mixed linear regression analyses with harsh parenting as a predictor variable. We found harsh parenting significantly predicted methylation of several HPA axis genes, including novel gene associations with AVPRB1, CRHR1, CRHR2, and MC2R (FDR corrected p < 0.05). Further, we found NR3C1 methylation predicted a steeper diurnal cortisol slope. Our results extend the current literature by demonstrating harsh parenting may influence DNA methylation similarly to more extreme early life experiences such as abuse and neglect. Further, we show NR3C1 methylation is associated with diurnal HPA function. Elucidating the molecular consequences of harsh parenting on health can inform best parenting practices and provide potential treatment targets for common complex disorders.
2021-04-01 | GSE147058 | GEO
Project description:Two alfalfa varieties, 'Chilean' (M. sativa ssp. sativa var. Chilean, drought sensitive) and 'Wisfal' (M. sativa ssp. falcata var. Wisfal, drought tolerant), with contrasting water use efficiency were subjected to water withholding for 11 days followed by re-watering. Samples were taken for well-watered plants and plants after five, eight, eleven days of drought stress as well as plants after recovery for one day following drought stress. Roots and shoots were sampled and analyzed separately by expression profiling using Affymetrix Medicago GeneChip.
2011-08-29 | E-MEXP-3320 | biostudies-arrayexpress
Project description:The goal of the ChIP-seq study was to investigate the distribution of the TATA-binding protein (TBP) across the human genome. TBP is the DNA-binding subunit of the basal transcription factor TFIID for RNA polymerase II (pol II) and it also participates in other complexes for the other RNA polymerase. The BTAF1 ATPase forms a stable complex with TBP and regulates its activity in pol II transcription. BTAF1 is believed to mobilize TBP from promoter and non-promoter sites. To test this hypothesis, TBP ChIP samples were prepared from human HeLa cervix carcinoma cells after knock-down of BTAF1 expression and compared to HeLa cells with a control knock-down of GAPDH. GAPDH is a cytosolic enzyme that participates in glycolysis, and its inactivation is not expected to affect the genomic distribution of TBP, and acts as negative control. ChIP samples were sequenced using SOLiD technology along with the INPUT sample to normalize the distribution of background signals within each of the two chromatin samples. 2 ChIP samples + one input sample
2010-03-02 | E-GEOD-17937 | biostudies-arrayexpress
Project description:Distribution of microbial generalists and habitat specialists in Chilean soils
| PRJEB38745 | ENA
Project description:The goal of the ChIP-seq study was to investigate the distribution of the TATA-binding protein (TBP) across the human genome. TBP is the DNA-binding subunit of the basal transcription factor TFIID for RNA polymerase II (pol II) and it also participates in other complexes for the other RNA polymerase. The BTAF1 ATPase forms a stable complex with TBP and regulates its activity in pol II transcription. BTAF1 is believed to mobilize TBP from promoter and non-promoter sites. To test this hypothesis, TBP ChIP samples were prepared from human HeLa cervix carcinoma cells after knock-down of BTAF1 expression and compared to HeLa cells with a control knock-down of GAPDH. GAPDH is a cytosolic enzyme that participates in glycolysis, and its inactivation is not expected to affect the genomic distribution of TBP, and acts as negative control. ChIP samples were sequenced using SOLiD technology along with the INPUT sample to normalize the distribution of background signals within each of the two chromatin samples.
2010-03-02 | GSE17937 | GEO
Project description:Different genes, especially cytokines, have been deregulated in the inflammatory environment of intestinal mucosa in ulcerative colitis patients. The effects of differential gene expression such as immunological factors have been described before, however, there is no evidence of alarmins deregulated by microRNAs impacting on the pathophysiology of UC. Our goal is to study deregulated genes in inflamed mucosa for microRNA pairing in a Chilean cohort of patients. We used microarrays to compare inflamed and non inflamed mucosa from chilean ulcerative colitis patients
2019-10-07 | GSE133060 | GEO
Project description:Peatlands of the Lehstenbach catchment (Germany) house so far unidentified microorganisms with phylogenetically novel variants of the dissimilatory (bi)sulfite reductase genes dsrAB. These genes are characteristic for microorganisms that reduce sulfate, sulfite, or some organosulfonates for energy conservation, but can also be present in anaerobic syntrophs. However, nothing is currently known regarding the abundance, community dynamics, and biogeography of these dsrAB-carrying microorganisms in peatlands. To tackle these issues, soils from a Lehstenbach catchment site (Schlöppnerbrunnen II fen) from different depths were sampled at three time points over a six-year period to analyze the diversity and distribution of dsrAB-containing microorganisms by a newly developed functional gene microarray and quantitative PCR assays. Members of novel, uncultivated dsrAB lineages (approximately representing species-level groups) (i) dominated a temporally stable but spatially structured dsrAB community and (ii) represented ‘core’ members (up to 1-1.7% relative abundance) of the autochthonous microbial community in this fen. In addition, denaturing gradient gel electrophoresis (DGGE)- and clone library-based comparison of the dsrAB diversity in soils from a wet meadow, three bogs, and five fens of various geographic locations (distance ~1-400 km), identified one Syntrophobacter-related and nine novel dsrAB lineages to be widespread in low-sulfate peatlands. Signatures of biogeography in dsrB-DGGE data were not correlated with geographic distance but could largely be explained by soil pH and wetland type, implying that distribution of dsrAB-carrying microorganisms in wetlands on the scale of a few hundred kilometers is not limited by dispersal but determined by contemporary environmental conditions. 36 dsrAB clones for chip evaluation, 33 hybridizations of labeled dsrAB RNA from environmental peatsoil samples
2010-11-26 | E-GEOD-24582 | biostudies-arrayexpress
Project description:A high-density oligonucleotide microarray that targets functional genes in marine microbial community was designed as a result of a multi-institutional effort. The design is based on nucleotide sequence data obtained with metagenomics and metatranscriptomics. The chip targets ~20000 gene sequences represented by 145 gene categories relevant to microbial metabolism in the open ocean and coastal environments. The three domains of life and also viruses are represented on the chip. Using this microarray we were able to compare the functional responses of microbial communities to iron and phosphate enrichments in samples from the North Pacific Subtropical Gyre. The response was attributed to individual lineages of microorganisms including uncharacterized strains. Transcription of 68% of the gene probes was detected from a variety of microorganisms, and the patterns of gene transcription indicated a relief from iron limitation and transition into nitrogen limitation. When combined with physicochemical descriptions of each system, the use of microarrays can help to develop a comprehensive understanding of the changes in microbially-driven processes. We analyzed three samples amended with phosphate and two sample amended with iron (III) after 48h of incubation
2013-03-07 | E-GEOD-44448 | biostudies-arrayexpress
Project description:Globally, there has been an increase in the frequency of landslides which is the result of slope failures. The combination of high intensity rainfall and high temperature resulted in the formation of acidic soil which is detrimental to the healthy growth of plants. Proper plant coverage on slopes is a prerequisite to mitigate and rehabilitate the soil. However, not all plant species are able to grow in marginal land. Thus, this study was undertaken to find a suitable slope plant species. We aimed to evaluate the effect of different soil pH on root profiles and growth of three different potential slope plant species namely, Melastoma malabathricum, Hibiscus rosa-sinensis and Syzygium campanulatum. M. malabathricum showed the highest tolerance to acidic soil as it recorded the highest plant height and photosynthetic rate. The root systems of M. malabathricum, H. rosa-sinensis and S. campanulatum were identified as M, VH- and R-types, respectively. The study proposed M. malabathricum which possessed dense and shallow roots to be planted at the toe or top of the slope while H. rosa-sinensis and S. campanulatum to be planted in the middle of a slope. S. campanulatum consistently recorded high root length and root length density across all three types of soil pH while M. malabathricum showed progressive increase in length as the soil pH increased. The root average diameter and root volume of M. malabathricum outperformed the other two plant species irrespective of soil pH. In terms of biomass, M. malabathricum exhibited the highest root and shoot dry weights followed by S. campanulatum. Thus, we propose M. malabathricum to be planted on slopes as a form of soil rehabilitation. The plant species displayed denser rooting, hence a stronger root anchorage that can hold the soil particles together which will be beneficial for slope stabilization.
| S-EPMC7451015 | biostudies-literature