Project description:Comparison of P. putida type strain crude extract with P. putida type strain phenotype evading myxobacterium C. ferrugineus predation.
Project description:Direct comparison of FACS sorted EGFP positive brain macrophages vs pooled Total Brain extract Keywords: Direct pairwise comparison
Project description:Direct comparison of FACS sorted EGFP positive renal macrophages vs pooled Total Kidney extract Keywords: Direct pairwise comparison
Project description:Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium M9 with glucose
Project description:These transcriptomic data are used in two distinct but subsequent and complementary studies:(i) the role of the mfsR gene on the expression of the mfsABC operon as well as on its own promoter, (ii) the role of the mfsR operon on the activation of the core genes of ICEclc. ICEclc-specific gene expression in Pseudomonas putida UWC1 was measured during exponential phase and the subsequent stationary phase (sole carbon and energy sources : 10mM 3-chlorobenzoate). 6 genotypes were tested: (i) wild type P. putida UWC1 ICEclc (strain nM-BM-02737) ; (ii) P. putida UWC1 ICEclc-KmR19033 (strain nM-BM-02961) ; (iii) P. putida UWC1 ICEclcM-bM-^HM-^F'mfsR (strain nM-BM-04322) ; (iv) P. putida UWC1 ICEclcM-bM-^HM-^F'orf17984 (strain nM-BM-04372) ; (v) P. putida UWC1 ICEclcM-bM-^HM-^F'tciR (strain nM-BM-04321) ; (vi) P. putida UWC1 ICEclcM-bM-^HM-^FmfsR-M-bM-^HM-^F'orf17984 (strain nM-BM-03543). For each strain, in each phase, 3 or 4 replicates were used.
Project description:We analyzed the expression profile of wild-type strain and ttha1564 deletion mutant strain of Thermus thermophils HB8 under alkylating condition. In wild type strain, 107 genes and 96 genes were over 2-fold up- and under 0.5-fold down-regulated by alkylation, respectively. In ttha1564 deletion mutant, 35 genes and 12 genes were over 2-fold up- and under 0.5-fold down-regulated by alkylation, respectively. Keywords: stress response comparison The T. thermophilus HB8 wild-type and delta ttha1564 strains were cultured in TT medium (0.4%(w/v) polypeptone, 0.2%(w/v) yeast extract, 0.1%(w/v) NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, (pH 7.5)) at 70°C until the OD600 reached 0.8. The cultures were then divided into two flasks and an equal volume of TT medium prewarmed at 70°C was added. One of the media culture of each strain contained 100 micro g/ml MNNG. We confirmed that the cells can continue to grow in TT medium containing 100 micro g/ml MNNG but DNAs are alkylated sufficiently (Onodera, 2011). After further cultivation at 70°C for 10 min, the diluted cultures were collected into an equal of 100% ethanol and stored at -80°C. The procedures used for extraction of crude RNA, synthesis of cDNA, labeling of cDNA fragment, hybridization to a TTHB8401a520105F GeneChip (Affymetrix) and data analysis were basically the same as those described previously (Agari et al., 2008; Shinkai et al., 2007). To determine the mRNA expression level of each sample, image data for the three independent samples were processed.
Project description:We observed the expression profile of the total mRNA of TTHB212 deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TR) medium at 70°C compared with that of wild type. Keywords: cell type comparison Three wild-type and mutant T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 5 h for wild-type and 7 h for TTHB212 deletion mutant, respectively, and then crude RNA was extracted. In order to compare mRNA expression in the TTHB212 deletion mutant with that of wild type, the expression of each mRNA was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.
Project description:We investigated the effects of the crude extract of a South African medicinal plant, Cotyledon orbiculata, on cell survival of colon (HCT116) cancer cell lines. Using RNASeq, we discovered that the extract interfered with mRNA regulatory pathways. Here, we found that the extract of Cotyledon orbiculata, a South African medicinal plant, had an anti-proliferative effect in cancer cells, mediated by apoptosis induced by alternative splicing of hnRNPA2B1 and BCL2L1.