Project description:An exponentially growing culture of strain R6 in AGCH at OD620nm=0.4 was either non-treated or treated with two LVX concentrations: 0.125 ug/ml LVX (0.5x MIC of R6) and 2.5 ug/ml LVX (10x MIC of R6). Samples were taken before treatment (0 min), at 15, 30 and 60 min in the non-treated culture, and at 5, 15 ,30 and 60 min in the LVX treated cultures
Project description:We have analyzed the transcriptomes of Dickeya dadantii wild type, fis and hns strains in condition of DNA relaxation induced by novobiocin, a DNA gyrase inhibitor. For DNA relaxation novobiocin was added for 15 min to 100µg/ml final concentration to exponentially growing wild type, hns and fis strains (OD600= 0.2) grown in M63 medium supplemented by sucrose 0.2% (w/v). At this concentration, novobiocin has no impact on D. dadantii growth The micro-arrays used in this study were custom designed and produced by Roche NimbleGen, Inc. (Madison, WI) based on the annotated sequence of D. dadantii, available at Genbank accession number n° CP002038, which comprises 4597 CDS. The 4plex expression micro-arrays consist of 60-mer oligonucleotides, triplicated in three blocks on the array (5 oligonucleotides per CDS). For micro-array analyses, cDNA was synthesized, labeled and hybridized by Roche NimbleGen Inc.
Project description:For Staphylococcus aureus it was shown previously that aminocoumarinecoumarin antibiotics such as novobiocin lead to immediate down-regulation of recA expression and thereby inhibition of the SOS response, the mutation frequency and the recombination capacity. Aminocoumarinecoumarin function by inhibition of the ATPase activity of the gyrase subunit B. Here we analysed the global impact of the DNA relaxing agent novobiocin on gene expression in S. aureus. By use of a novobiocin resistant mutant, it became evident that the change in recA expression is due to gyrase inhibition. Microarray analysis and Northern blot hybridization revealed that the expression of a distinct set of genes is increased (e.g. recF-gyrB-gyrA, rib operon and ure operon M-bM-^@M-&)), or decreased (e.g. arlRS, recA, lukA, hlgC, fnbA) by novobiocin. The two-component ArlRS system was previously found to decrease the supercoiling level in S. aureus. Thus, down-regulation of arlRS might in part compensate for the relaxing effect of novobiocin. Novobiocin resulted in down-regulation of several of arlRS repressed target genes in an arl mutant. Global analysis and gene mapping of supercoiling sensitive genes did not give indications that they are clustered in the genome. Promoter fusion assays confirmed that responsiveness of a given gene is intrinsic to the promoter region but independent of the chromosomal location. The results indicate that molecular property of the spacers of a given promoter dictatesa given promoter rather than chromosomal topology dictates the responsiveness towards changes in supercoiling rather than chromosomal topology. We analyzed S. aureus global gene expression changes to the treatment of novobiocin
Project description:Huntington’s disease is a genetic disease caused by a single mutation. It is characterised by progressive movement, emotional and cognitive deficits. R6/2 transgenic mice carrying the Huntington’s disease mutation have a progressive neurological phenotype, including deterioration in cognitive function. The mechanism underlying the cognitive deficits in R6/2 mice is unknown, but dysregulated gene expression, reduced neurotransmitter levels and abnormal synaptic function are present before the cognitive decline becomes pronounced. Our goal here was to ameliorate the cognitive phenotype in R6/2 mice using a combination drug therapy (tacrine, moclobemide and creatine) aimed boosting neurotransmitter levels in the brain. Treatment from 5 weeks of age prevented deterioration in two different cognitive tasks until at least 12 weeks. However, motor deterioration continued unabated. Microarray analysis of global gene expression revealed that many genes significantly up- or down-regulated in untreated R6/2 mice had returned towards normal levels after treatment. Thus dysregulated gene expression was reversed by the combination treatment in the R6/2 mice and probably underlies the observed improvements in cognitive function. Our study shows that cognitive decline caused by a genetic mutation can be slowed by a combination drug treatment, and gives hope that cognitive symptoms in HD can be treated. Keywords = HD Keywords = Huntingtin Keywords = cognitive disorder Keywords = R6/2 Keywords = transgenic mice Keywords = gene expression Keywords = microarray Keywords: ordered
Project description:We describe a more detailed survey undertaken to detect candidate CNVs in a panel of 20 Asian cultivated rice and the genome-wide characteristics of CNVs in subspecies and groups. These resources allowed us to analyze genetic structure as indicated by CNVs, to implicate the biological roles of CNVs, and to identify candidate CNVs that are likely to occur independently in groups and contribute to differences between the subspecies. a panel of 20 accessions