Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20242 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| FWWU01.dat.gz | Other | |||
| FWWU01.fasta.gz | Fasta.gz | |||
| FWWU01.master.dat | Other | |||
| FWWU01.dat.gz | Other |
Items per page: 5 1 - 4 of 4 |
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Project description:Draft genome sequence of Deinococcus sp. KR-1
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Project description:Comparison of gene expression of KR Primary and KR 1 cell lines KR Primary cells are established from lung tumors of Kras mice. This cell line was injected into B6 mice intratracheally and then KR 1 cell line was established.
2016-12-31 | GSE84163 | GEO
Project description:A 13-(4-isopropylbenzyl)berberine derivative (named KR-72) was synthesized and examined for antifungal activities against various human pathogenic fungi. The synthesized compound exhibited remarkably enhanced antifungal activity than berberine and berberrubine. Regardless of the potent antifungal activity of KR-72, its mode of action and the physiological impacts of the drug on fungal metabolism remain elusive. In this study, we performed the DNA microarray-based transcriptome analysis to identify KR-72 responsive genes and employed reverse genetics approaches to characterize their functions in Cryptococcus neoformans, which causes fatal meningoencephalitis in humans. First, KR-72 treatment altered in remodeling of transcriptome profiles in C. neoformans. Genes involved in translation and transcription were mostly upregulated, while those involved in cytoskeleton, intracellular trafficking, lipid and carbohydrate metabolism and energy production were downregulated. Supporting this, KR-72 has a strong synergistic effect with a calcineurin inhibitor FK506, while it has an antagonistic effect with polyene drug. Finally, KR-72 treatment promoted expression of ECM16, NOP14, HSP10, and MGE1, which we proved to be essential for the growth of C. neoformans. Among them, KR-72 mediated induction of MGE1 also appeared to hamper the viability of C. neoformans, potentially through impaired cell cycle or DNA repair system. This study will proposed mode of action for KR-72.
2014-02-26 | GSE55337 | GEO
Project description:A 13-(4-isopropylbenzyl)berberine derivative (named KR-72) was synthesized and examined for antifungal activities against various human pathogenic fungi. The synthesized compound exhibited remarkably enhanced antifungal activity than berberine and berberrubine. Regardless of the potent antifungal activity of KR-72, its mode of action and the physiological impacts of the drug on fungal metabolism remain elusive. In this study, we performed the DNA microarray-based transcriptome analysis to identify KR-72 responsive genes and employed reverse genetics approaches to characterize their functions in Cryptococcus neoformans, which causes fatal meningoencephalitis in humans. First, KR-72 treatment altered in remodeling of transcriptome profiles in C. neoformans. Genes involved in translation and transcription were mostly upregulated, while those involved in cytoskeleton, intracellular trafficking, lipid and carbohydrate metabolism and energy production were downregulated. Supporting this, KR-72 has a strong synergistic effect with a calcineurin inhibitor FK506, while it has an antagonistic effect with polyene drug. Finally, KR-72 treatment promoted expression of ECM16, NOP14, HSP10, and MGE1, which we proved to be essential for the growth of C. neoformans. Among them, KR-72 mediated induction of MGE1 also appeared to hamper the viability of C. neoformans, potentially through impaired cell cycle or DNA repair system. This study will proposed mode of action for KR-72. The six slides of Cryptococcus_neoformans 3X20K are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted under 2 conditions (with or without treatment of KR-72 with H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A). We use the KR-72 non-treated RNAs from this experiment as a control RNA. We use Cy5 as Sample dye and Cy3 as a control dye.
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Project description:The extreme radiation resistance of Deinococcus bacteria requires the radiation-stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation-induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo-IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively. Binding of IrrE to RDRM-containing DNA or interaction of IrrE with DNA-bound DdrO was not observed. The data are in line with IrrE being a zinc peptidase, and indicate that increased zinc availability, caused by oxidative stress, triggers the in vivo cleavage of DdrO unbound to DNA. Transcriptomics and proteomics of Deinococcus deserti confirmed the IrrE-dependent regulation of predicted RDR regulon genes and also revealed additional members of this regulon. Comparative analysis showed that the RDR regulon is largely well conserved in Deinococcus species, but also showed diversity in the regulon composition. Notably, several RDR genes with an important role in radiation resistance in Deinococcus radiodurans, for example pprA, are not conserved in some other radiation-resistant Deinococcus species.
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Project description:kRas (KR) tumors grow faster when expressing kRas and HPV E6E7 (KHR). The hypothesis was to test for differences in gene expression between KR and KHR oral tumors.
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Project description:To elucidate the (possibly sumo dependent) binding sites of L3MBTL2, wild type L3MBTL2, L3MBTL2-Flag and L3MBTL2-KR-Flag ChIPs from HEK293 cells were analyzed via ChIPseq
2014-01-14 | E-MTAB-1731 | biostudies-arrayexpress
Project description:Slow-growing Korat chicken (KR) is an alternative to broiler chickens that has been used as a national tool to support smallholder farmers due to a higher selling price of KR meat. However, the individual variability of feed efficiency (FE) within a KR stockbreeding results in a lack of competitiveness. Therefore, improvement of FE of KR is of major importance to improve the profitability of livestock production enterprises. Here, we selected two groups of KR with divergent feed conversion ratios (FCR). We performed RNA-sequencing in order to profile KR jejunal transcriptome and to identify the transcriptional variations and biological pathways implied in response to divergent FCR. The biological pathways involved were revealed by enrichment of the Gene Ontology (GO) terms, and the Kyoto Encyclopedia of Gene and Genome (KEGG) pathways. The results showed that main pathways involved in KR FCR divergence were related to immune response, glutathione metabolism, vitamin transport and metabolism, lipid metabolism, and maturation, development and growth. This is the first study to investigate the molecular genetic mechanisms affecting the FCR values in jejunum of slow-growing chicken. This study will be useful in the line-breeding programs for slow growing chickens to improve FE in the stockbreeding and its profitability.
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