Ketogulonicigenium vulgare cells: Acid-stressed vs. Control
Ontology highlight
ABSTRACT: Transcriptional profiling of K. vulgare cells, co-cultured with Bacillus megaterium, comparing control untreated cells with cells treated with pH 4.0 for 2 h. Differentially expressed genes in acid-stressed cells were analyzed. The aim was to investigate the mechanisms of K. vulgare in response to acid stress on global gene expression. Two-condition experiment, acid-stressed (pH 4.0) cells vs. control cells. Biological replicates: 3 control replicates, 3 acid-stressed replicates.
Project description:Transcriptional profiling of K. vulgare cells co-cultured with Bacillus megaterium compared to K. vulgare mono-cultured cells. Differentially expressed genes in co-cultured and mono-cultured K. vulgare cells were analyzed. The aim was to investigate the mechanisms of B. megaterium stimulating K. vulgare propagation on global gene expression. Two-condition experiment: co-cultured K. vulgare and B. megaterium cells vs. mono-cultured K. vulgare cells. Biological replicates: 3 co-cultured replicates, 3 mono-cultured replicates.
Project description:Transcriptional profiling of K. vulgare cells, co-cultured with Bacillus megaterium, comparing control untreated cells with cells treated with pH 4.0 for 2 h. Differentially expressed genes in acid-stressed cells were analyzed. The aim was to investigate the mechanisms of K. vulgare in response to acid stress on global gene expression.
Project description:The hepatitis B virus X protein (HBx) has been implicated as an oncogene in both epigenetic modifications and genetic regulation during hepatocarcinogenesis, but the underlying mechanisms are not entirely clear. Long non-coding RNAs (lncRNAs), which regulate gene expression with little or no protein-coding capacity, are involved in diverse biological processes and in carcinogenesis. We asked whether HBx could promote hepatocellular carcinoma (HCC) by regulating the expression of lncRNAs.In this study, we investigated the alteration in expression of lncRNAs induced by HBx using microarrays, and our results indicate that HBx transgenic mice have a specific profile of liver lncRNAs compared with wild-type mice. For these experiments, six each of 20-month-old male HBx-transgenic mice and wild-type C57BL/6 mice were sacrificed and the livers were removed. Every three livers were pooled as one sample; therefore, each group was represented by two samples. The total RNA was extracted from the four samples and used for microarray experiments. Mouse LncRNA Array (4 x 44K, ArrayStar, Rockville, MD) were used to monitor the expression level of approximately 14000 lncRNAs identified from the NCBI RefSeq, UCSC, RNAdb2.0, NRED, Fantom3.0 and UCRs. LncRNAs differentially expressed were identified by comparing expression levels in HBx-transgenic mice and wild-type mice.
Project description:Liver regeneration has important implications because many therapeutic strategies for the surgical treatment of liver diseases, such as removal of liver tumors and liver transplantation, depend on the ability of the liver to regenerate physically and functionally. Recent studies reported that lncRNAs control cell proliferation in hepatocellular carcinoma (HCC). However, the role of lncRNAs in liver regeneration and the overall mechanisms remain largely unknown. To address this issue, we carried out a genome-wide lncRNA microarray analysis during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points. The results revealed differential expression of thousands of lncRNAs during liver regeneration. Six-week-old male wildtype C57Bl/6 mouse liver samples were obtained at 0, 1.5, 12, and 24 hours after 2/3 PH, and three mice were analyzed for each time point. Total RNA was isolated using Trizol.Mouse Stringent LncRNA Array (4 x 44K, ArrayStar, Rockville, MD) were used to monitor the expression level of approximately 14000 lncRNAs identified from the NCBI RefSeq, UCSC, RNAdb2.0, NRED, Fantom3.0 and UCRs. LncRNAs differentially expressed were identified by comparing expression levels during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points.
Project description:T. rubrum was treated with PH11B,a potent eucaryotic fatty acid synthase inhibtor. A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and transcriptional profiles of the responses to PH11B were determined. Some class-specific and mechanism-independent changes in gene expression were found. Keywords: fatty acid synthase inhibition The expression profiles of Trichophyton rubrum treated with PH11B were compared to those of Trichophyton rubrum without drug. Each treatment has three replicates.
Project description:DNA microarray was applied to characterize the whole-genome expression profiles of placentas during ICP development. Pregnant women were categorized evenly into three groups: healthy group; mild ICP, with serum bile-acid concentration ranging from 10M-bM-^@M-^S40 uM; and severe ICP, with bile-acid concentration >40 uM.
Project description:Metabolic engineering of Saccharomyces cerevisiae for efficient monoterpenes production was mostly restricted by the limited tolerance to these chemicals. Understanding of the molecular mechanisms underlying the tolerance of S. cerevisiae to monoterpenes was essential for the de novo biosynthesis these chemicals in S. cerevisiae. In this study, commercial oligonucleotide microarray assays were performed to investigate the global response of S. cerevisiae to typical monoterpene D-limonene under transcriptional level. Yeast cell treated with sublethal dose of D-liomonene, gene change profiles were investigated at transcription level and the microarry data were also verified with quantitative real time PCR. D-limonene induced gene expression in Saccharomyces cerevisiae at early logarithmic phase was measured at 2 hours after exposure to doses of 0.02% (v/v) D-limonene. Three independent experiments were performed for each experiment (control or 2 hours).
Project description:Genome-wide expression profiling has been performed in malignant HepG2 cells and compared to the expression in normal human hepatocytes. 56 ucRNAs, representing 11% of all ucRNAs analyzed, were aberrantly and significantly (p<0.05) expressed in malignant HepG2 cells compared to non-malignant human hepatocytes. RNA was extracted from three separate biological samples for each analysis using Trizol reagent (Invitrogen, Carlsbad, CA). Total RNA (5 M-NM-<g) was reverse transcribed using biotin end-labeled random oligonucleotide primers and cDNA was hybridized to a custom microarray (OSU-CCC 4.0), which includes sense and antisense probes to all 481 human ultraconserved reported by Bejerano et al, each spotted in duplicate. Biotin-containing transcripts were detected using streptavidinM-bM-^@M-^SAlexa647 conjugate, scanned and analyzed using an Axon 4000B scanner and the GenePix 6.0 software (Axon Instruments, Downingtown, PA). The mean fluorescence intensity of replicate spots were subtracted from background and normalized using the global median method. We selected ucRNAs measured as present in all the three replicates. Differentially expressed ucRNAs were identified using the Class Comparison Analysis of BRB tools version 3.6.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). The criterion for inclusion of a gene in the gene list was a p-value < 0.05.
Project description:Feed restriction and L-carnitine infusion are known to affect the liver metabolism of dairy cows. In the present experiment the effects on liver transcriptome of feed restriction and L-carnitine abomasal infusion and the interaction of the two in mid-lactation Holstein dairy cows was assessed. Data clearly indicated a lack of transcriptomics effect by L-carnitine but a strong effect due to feed restriction. The functional analysis identified a overall reduction of cholesterol synthesis and oxidative phosphorylation and data suggested an increase flux toward gluconeogenesis and fatty acid oxidation. The liver biopsy was performed after 14 days of treatment in 8 Holstein dairy cows in a 2 x 2 factorial arrangment with 5 days washout between treatments. A dye-swap reference design (reference = mixture of RNA from several bovine tissues) was used.