Bacillus sp. OTC-L18
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1158002 | ENA |
REPOSITORIES: ENA
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Project description:The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 often faces salt stress in its natural habitats. One-color microarrays was used to investigate transcriptome expression profiles of Bacillus sp. N16-5 adaptation reactions to prolonged grown at different salinities (0%, 2%, 8% and 15% NaCl) and the initial reaction to suddenly alter salinity from 0% to 8% NaCl.
2015-01-03 | GSE64621 | GEO
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Project description:Background: Treatment of head and neck squamous cell carcinoma (HNSCC) remains challenging and the survival rates of affected patients remain poor. A three-dimensional organotypic co-culture (3D-OTC) model where patient derived tumor tissue is cultured on human-derived fibroblasts (dermal equivalent, DE) was evaluated regarding its comparability to primary tumor tissue and the identification of potential individualized therapeutic targets. Methods: 3D-OTC models were cultured from n=10 HNSCC patients for up to 21 days. The growth pattern at the DE was compared to tumor budding of corresponding resection specimens. Furthermore, we immunohistochemically determined the immune cell infiltrate of primary tumor tissue and corresponding 3D-OTC models. Spatially resolved gene expression analysis (“Xenium in situ”) was performed for separate regions of interest within the 3D-OTC specimens and within primary tumor tissue. Up-regulated and down-regulated genes of the 3D-OTC samples were included in gene set enrichment analysis and up-regulated genes between invasive (invading the DE) and non-invasive tumor cells within the 3D-OTC samples were included in drug sensitivity analyses using publicly available cell line data. Results: The growth pattern observed at the DE was associated with tumor budding in primary tumor tissue. The density of CD3-/CD20-/CD56-positive cells was lower in 3D-OTC samples compared to primary tumor tissue. No such changes were observed for CD68-positive cells and no significant changes in the density of the immune cell infiltrate were detected during the cultivation period. The centroids and dispersion of the gene expression of the 3D-OTC samples did not differ from the corresponding primary tumor tissue. The regions of interest within the 3D-OTC samples showed distinct functional states in gene set enrichment analysis. The comparison of genes up-regulated in invasive tumor parts of the 3D-OTC samples with cell line data revealed potential therapeutic targets. Conclusion: The 3D-OTC model morphologically and transcriptomically resembles primary tumor tissue and its biology while preserving the tumor microenvironment. Furthermore, the 3D-OTC model allows the standardized evaluation of tumor tissue by the definition of transcriptomically separate regions of interest and thus, could help to evaluate the impact of personalized therapeutic interventions on the tumor and its microenvironment in vitro.
2026-05-11 | GSE324934 | GEO
Project description:The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 often faces salt stress in its natural habitats. One-color microarrays was used to investigate transcriptome expression profiles of Bacillus sp. N16-5 adaptation reactions to prolonged grown at different salinities (0%, 2%, 8% and 15% NaCl) and the initial reaction to suddenly alter salinity from 0% to 8% NaCl. Salt induced gene expression was measured when culture was grown on different salinities (0%, 2%, 8% and 15% NaCl) to mid-logarithmic phase. And salt induced gene expression was also measured at 0 min, 10 min, 30 min, 60min, 120min after a sudden change salinity from 0% to 8% NaCl.
2015-01-03 | E-GEOD-64621 | biostudies-arrayexpress
Project description:gamma proteobacterium L18 Genome sequencing and assembly
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Project description:Alkaline hemicellulytic bacteria Bacillus sp. N16-5 has abroad substrate spectrum and exhibits great growth ability on complex carbohydrates. In order to get insight into its carbohydrate utilization mechanism, global transcriptional profiles were separately determined for growth on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan, pectin and carboxymethyl cellulose by using one-color microarrays.
2014-06-17 | GSE38276 | GEO
Project description:Lactococcus garvieae strain:L18 Genome sequencing and assembly
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