Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1088994 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:28 Streptomyces strains isolated from common scab lesions of potato tubers from a wide geographic range in Norway, were selected for microarray analysis. The selected strains were subjected to species identification by microarray, 16S phylogenetic analysis and PCR; and microarray-based comparative genome analysis. To our knowledge, this is the first report of S. turgidiscabies and S. europaeiscabiei in Norway.
2010-05-01 | GSE20487 | GEO
Project description:Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we hypothesized that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the “coenzyme” category have been examined, including a gene cluster encoding for the co-factor pyrroloquinoline quinone (PQQ). When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides a new engineering strategy for improving polyketide production and discovering new biosynthetic gene clusters.
2024-03-01 | GSE256209 | GEO
Project description:28 Streptomyces strains isolated from common scab lesions of potato tubers from a wide geographic range in Norway, were selected for microarray analysis. The selected strains were subjected to species identification by microarray, 16S phylogenetic analysis and PCR; and microarray-based comparative genome analysis. To our knowledge, this is the first report of S. turgidiscabies and S. europaeiscabiei in Norway. 28 Norwegian Streptomyces strains were hybridized in duplicates, one S.turgidiscabies strain (St32) and one S.scabies strain (ATCC49173) were hybridized in 4 replicates. Two out of 64 hybridizations failed (replicate hybridizations of Norwegian strains 33 and 44), for a total of 62 samples. Normalization was based on log-ratios against reference strain.
2010-04-30 | E-GEOD-20487 | biostudies-arrayexpress
Project description:Alam2010 - Genome-scale metabolic network of
Streptomyces coelicolor
This model is described in the article:
Metabolic modeling and
analysis of the metabolic switch in Streptomyces
coelicolor.
Alam MT, Merlo ME, STREAM
Consortium, Hodgson DA, Wellington EM, Takano E, Breitling
R.
BMC Genomics 2010; 11: 202
Abstract:
BACKGROUND: The transition from exponential to stationary
phase in Streptomyces coelicolor is accompanied by a major
metabolic switch and results in a strong activation of
secondary metabolism. Here we have explored the underlying
reorganization of the metabolome by combining computational
predictions based on constraint-based modeling and detailed
transcriptomics time course observations. RESULTS: We
reconstructed the stoichiometric matrix of S. coelicolor,
including the major antibiotic biosynthesis pathways, and
performed flux balance analysis to predict flux changes that
occur when the cell switches from biomass to antibiotic
production. We defined the model input based on observed
fermenter culture data and used a dynamically varying objective
function to represent the metabolic switch. The predicted
fluxes of many genes show highly significant correlation to the
time series of the corresponding gene expression data.
Individual mispredictions identify novel links between
antibiotic production and primary metabolism. CONCLUSION: Our
results show the usefulness of constraint-based modeling for
providing a detailed interpretation of time course gene
expression data.
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MODEL1507180005.
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2015-07-30 | MODEL1507180005 | BioModels
Project description:Novel transaminase and laccase from Streptomyces spp. using combined identification approaches
| PRJNA739376 | ENA
Project description:Bioprospecting bioactive compounds from Streptomyces sp.
| PRJNA792017 | ENA
Project description:The generation of cell-based three dimensional (3D) nerve tissue is an attractive subject to improve graft survival and integration into host tissue for neural tissue regeneration or to model biological events in stem cell differentiation. However, although 3D organotypic culture strategy has been well established for 3D nerve tissue formation of pluripotent stem cells to study underlying biology in nerve development, cell-based nerve tissue have not been developed using human postnatal stem cells with therapeutic potential of stem cell-based therapy. Here, we established culture strategy for the generation of in vitro cell-based 3D nerve tissue from postnatal stem cells from apical papilla (SCAPs) of tooth, which is known to be originated from neural crest-derived ectomesenchyme. A stem cell population capable of differentiating into neural cell lineages was generated during the ex-vivo expansion of SCAPs in the presence of EGF and bFGF, and SCAPs differentiated into neural cells showing neural cell lineage-related molecular and gene expression profiles with morphological change under neural inductive culture condition. Moreover, we showed the first evidence that 3D cell-based nerve-like tissue with axon and myelin structure could be generated from SCAPs via 3D organotypic culture using an integrated bioprocess composing of polyethylene glycol (PEG) microwell-mediated cell spheroid formation and subsequent dynamic culture in a high aspect ratio vessel (HARV) bioreactor. In conclusion, our study propose that the culture strategy provide a novel approach to develop in vitro engineered nerve tissue using SCAPs and a foundation to study biological events in neural differentiation of postnatal stem cells.
2016-11-01 | GSE74701 | GEO
Project description:In this study, we describe the isolation and identification of Streptomyces isolates collected from traditional medicinal plants’ rhizosphere during a campaign in Hamedan Province, Iran. Traditional medicinal plants represent a rich and unique source for the isolation of Streptomyces and new antimicrobial compounds. This strain was isolated from the rhizosphere of Helichrysum rubicundum
2024-01-04 | PXD042019 | Pride