PhoD and phoX alkaline phosphatase genes in soil
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ABSTRACT:
PROVIDER: PRJEB11367 | ENA |
REPOSITORIES: ENA
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Project description:Two primer sets targeting phoD alkaline phosphatase were compared using 454-sequencing on six grassland soils.
| PRJEB7946 | ENA
Project description:phoD alkaline phosphatase genes and transcripts were studied at different pH levels and P fertilization intensities in a lowland grassland
| PRJEB9272 | ENA
Project description:To exploit the therapeutic mechanism of our proposed alkaline phosphatase-controllable and red light-activated RNA modification approach at the genetic level, we established an RNA-modified group (f-RCP+660 nm) and non-RNA-modified group (RCP+660 nm) in HepG2 cells.
2022-11-09 | GSE217510 | GEO
Project description:Phosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution of phoD genes using whole-genome and metagenome databases. phoD alkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity of phoD, we developed a new set of primers which targets phoD genes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 different phoD operational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalent phoD genes identified in these soils were affiliated with the orders Actinomycetales (13 to 35%), Bacillales (1 to 29%), Gloeobacterales (1 to 18%), Rhizobiales (18 to 27%), and Pseudomonadales (0 to 22%). The primers also amplified phoD genes from additional orders, including Burkholderiales, Caulobacterales, Deinococcales, Planctomycetales, and Xanthomonadales, which represented the major differences in phoD composition between samples, highlighting the singularity of each community. Additionally, the phoD bacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity of phoD in soil and represent a valuable tool for the study of phoD alkaline phosphatase in environmental samples.
| S-EPMC4579420 | biostudies-literature
Project description:Serum alkaline phosphatase (ALP) concentration is a prognostic factor for osteosarcoma in multiple studies, though its biological significance remains incompletely understood. To determine whether gene expression patterns differed in osteosarcoma from patients with differing serum ALP concentrations, microarray analysis was performed on 18 primary osteosarcoma samples and six osteosarcoma cell lines from dogs with normal and increased serum ALP concentration. No differences in gene expression patterns were noted between tumors or cell lines with differing serum ALP concentration using a gene-specific two-sample t-test. Using a more sensitive empirical Bayes procedure, DCUN1D1 was increased in both the tissue and cell lines of the normal ALP group. Using QPCR, differences in DCUN1D1 expression between the two groups failed to reach significance. The homogeneity of gene expression patterns of osteosarcoma associated differing serum ALP concentrations are consistent with previous studies suggesting serum ALP concentration is not associated with intrinsic differences of osteosarcoma cells. A total of 18 canine primary osteosarcoma tumor samples were used in this study. 9 tumor samples were from patients having a normal serum alkaline phosphatase concentration. 9 tumor samples were from patients having an increased serum alkaline phosphatase concentration. There were no reference tissues or controls used in this study.
2014-11-19 | E-GEOD-63476 | biostudies-arrayexpress
Project description:Alkaline phosphatase (ALP) is known to be a marker for several somatic stem cells and cancer cells. We found that human squamous cell carcinoma HeLa cells are comprised by ALP-positive and negative cells. Single cell-derived colony assay revealed that the former cells are labile with respect to ALP activity, but the latter are stable. We cloned ALP-negative cells from the HeLa cells, and named H-1 clone. DNA microarray analysis revealed that gene expression pattern of H-1 cells is almost the same with that of their parental HeLa cells, but several genes for glycoprotein hormone alpha chain, ras-related and estrogen-regulated growth inhibitor, ALP, and Frizzled-10 was respectively 18.2, 9.6, 9.2 and 10.5M-bM-^@M-^Sfold are upregulated in the HeLa cells. Although there is no evidence that the ALP-positive cells are cancer stem cells (CSCs) at present, HeLa cells comprised by ALP-positive and -negative cells may be a good model for CSC study in future. HeLa cells consist of two cell types, namely alkaline phosphatase (ALP)-positive and negative cells. To distinguish gene expression pattern between these two types of cells, microarray analysis was performed using HeLa cells (parental cell line; a mixture of ALP-positive and negative cells) and H-1 cells, ALP-negative cells derived from HeLa cells
2013-04-23 | E-GEOD-42222 | biostudies-arrayexpress
Project description:The functional coupling of calcium-mediated signalling and alkaline tolerance has been demonstrated in multiple fungi. The applied relevance of such interplay extends most notably to fungal pathogens of man where the physiological pH of serum and tissues exerts considerable alkaline stress. Drugs targeting the calcium-dependent phosphatase, calcineurin, are potent antifungal agents but also perturb human calcineurin signalling, it has therefore been postulated that abrogation of fungal alkaline tolerance could offer a valuable therapeutic adjunct. To study the interdependency of pH- and calcium-mediated intracellular signalling in the major human fungal pathogen A. fumigatus, we examined the transcriptional response following exposure to 200 mM calcium chloride or alkaline pH (pH 8.0).
2015-09-30 | GSE60786 | GEO
Project description:biochar return in Soda saline-alkaline land Metagenome
| PRJNA659907 | ENA
Project description:soil from saline and alkaline land Raw sequence reads
| PRJNA563235 | ENA