Ontology highlight
ABSTRACT:
PROVIDER: PRJNA630458 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparison of probe-target dissociations of probe Eub338 and Gam42a with native RNA of P. putida, in vitro transcribed 16s rRNA of P. putida, in vitro transcribed 16S rRNA of a 2,4,6-trinitrotoluene contaminated soil and an uncontaminated soil sample. Functional ANOVA revealed no significant differences in the dissociation curves of probe Eub338 when hybridised to the different samples. On the opposite, the dissociation curve of probe Gam42a with native RNA of P. putida was significantly different than the dissociation curves obtained with in vitro transcribed 16S rRNA samples. Keywords: Microbial diversity, thermal dissociation analysis, CodeLink microarray
2005-11-05 | GSE3525 | GEO
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO
Project description:C57BL6J mice were fed 200ug/kg body weight BPA or BPS for two weeks and then bred. Placenta tissue was collected at embryonic day 12.5, and dams received checmicals until this day. RNA-Seq was carried out on placenta tissue, and 13 genes were identified to have altered expression to a similar extent in BPA and BPS treated mice.
2020-01-16 | GSE141322 | GEO
Project description:Aims Structural analogues of bisphenol A (BPA), including BPS and BPF, are emerging environmental toxicants as their presence in the environment is rising since new regulatory restrictions were placed on BPA-containing infant products. The adipogenesis-enhancing effect of bisphenols may explain the link between human exposure and metabolic disease; Methods Adipose-derived progenitors were isolated from mice and exposed to various concentrations of BPS, BPA or BPF before induction of adipogenesis. RNAseq in BPS-exposed progenitors revealed modulation in redox pathways. The role of reactive oxygen species (ROS) was assessed by measuring the degree of adipogenesis in the presence or absence of antioxidants. ROS production and mitochondria function were determined by fluorescent assays. Fat mass was measured by TD-NMR in adult mice exposed to BPS during in utero establishment of the adipocyte progenitor pool, and in adult mice exposed to BPS after weaning. however, underlying molecular pathways remain unresolved. Results Exposure of progenitors to BPS, BPF, BPA or ROS generators enhanced lipid droplet formation and expression of adipogenic markers after induction of differentiation. ROS was higher in bisphenol-exposed cells, while co-treatment with antioxidants attenuated adipogenesis and abolished the effect of BPS. There was a loss of mitochondria membrane potential in BPS-exposed cells and mitochondria-derived ROS contributed to potentiation of adipogenesis by BPS and its analogues. Male mice exposed to BPS during gestation had higher adiposity, while postnatal exposure had no impact on adiposity in either sex. ROS act as signaling molecules in the regulation of adipocyte differentiation and mediate bisphenol-induced potentiation of adipogenesis.
2022-09-23 | GSE213781 | GEO
Project description:Bisphenol compounds (BPs) have various industrial uses and can enter the environment through various sources. To evaluate the ecotoxicity of BPs and identify potential gene candidates involved in the plant toxicity, Arabidopsis thaliana was exposed to bisphenol A (BPA), BPB, BPE, BPF, and BPS at a concentration of 1, 3, 10 mg/L for a duration of 14 days, and their growth status were monitored. At day 14, roots and leaves samples were collected for internal BPs exposure concentration detection, RNA-seq, and morphological observations. As shown in the results, exposure to BPs significantly disturbed root elongation, exhibiting a trend of stimulation at low concentration and inhibition at high concentration. Additionally, BPs exhibited pronounced generation of ROS, while none of the pollutants caused significant changes in root morphology. Internal exposure concentration analysis indicate that BPs tend to accumulate in the roots, with BPS exhibiting the highest level of accumulation. The results of RNA-seq indicate that shared 211 differently expressed genes (DEGs) of these 5 exposure groups are enriched in defense response, generation of precursor metabolites, response to organic substance, response to oxygen-containing, response to hormone, oxidation-reduction process and so on. Regarding unique DEGs in each group, BPS was mainly associated with the redox pathway, BPB primarily influenced seed germination, and in BPA, BPE and BPF were primarily involved in metabolic signaling pathways. Our results provide new insights for BPs induced adverse effects on Arabidopsis thaliana and suggest that the ecological risks associated with BPA alternatives cannot be ignored. At 14 d, roots in 3 mg/kg BPA, BPB, BPE, BPF and BPS exposure groups and the control were collected for RNA-seq analysis.
2023-12-19 | GSE250123 | GEO
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.
2016-08-02 | E-GEOD-85064 | biostudies-arrayexpress
Project description:Purpose: the goal of this study is to determine the changes in gene expression during EB differentiation after BPA, BPF and BPS treatments, as indications of potential developmental toxicity. Methods: Transcriptomics profiling for EB samples treated with 100 nM BPA, BPF, BPS or DMSO control at different time points were generated by RNA-seq, using a BGISEQ-500 platform. Reads were filtered and aligned to the reference genome with Bowtie2. Results: BPA, BPF and BPS disrupted many processes, during mESC global and neural differentiations, in very similar manners. In fact, analogous gene categories were differentially regulated by the three chemicals, at each time point, particularly the ones involved in cell-matrix and cell-cell adhesions, signal transduction pathways, and medical conditions such as cardiovascular diseases and cancer.
2019-09-30 | GSE120224 | GEO
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in EarthM-bM-^@M-^Ys biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling. Fifty four samples were collected from three soil types (Phaeozem,Cambisol,Acrisol) in three sites (Hailun, Fengqiu and Yingtan) along a latitude with reciprocal transplant; Both with and without maize cropping in each site; Three replicates in every treatments.
2013-10-30 | E-GEOD-51592 | biostudies-arrayexpress
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.
2016-08-02 | GSE85064 | GEO
Project description:A comparision of soil microbial functional genes of three types of subtropical broad-leaved forests Microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher alpha-diversity of functional genes but lower beta-diversity, and showed more complex functional gene networks.
2021-01-29 | GSE165723 | GEO