Project description:Gene expression was examined during four growth conditions which modulated antimicrobial secretion in B. ambifaria AMMD. A minimal salts medium (BSM; Hareland et al. 1975. J Bacteriol 121:272-85) with 0.05% yeast extract was used for all comparisons with the carbon source (4 g/L) and growth condition varied as follows: (i) liquid culture with glucose; (ii) liquid culture with glycerol; (iii) growth on agar with glucose, and (iv) growth on agar with glycerol. For the liquid cultures, 25 ml of growth medium was placed a 250 ml conical flask and inoculated with 0.5 ml of a starter culture of strain AMMD which had been optically adjusted to O.D. 1 at 600 nm and corresponded to a viable count of 10 million colony forming units per ml. After growth with shaking (150 rpm) for 30 h at 30 degrees Celcius, the O.D. 600 nm of the cultures was measured to enable an estimation of cell density to be made, they were then snap-chilled and harvested as previously described (Drevinek et al. 2008. BMC Infect Dis 8:121), and frozen at -80 degrees Celcius. Growth on agar was performed by laying a sterile 47 mm nitrocellulose filter (0.22 ?m) onto a plate of the BSM agar and the same starter culture of AMMD as used for the liquid growth spread over a 2 cm diameter circular area using a sterile cotton swab. The agar cultures were incubated for 30 h at 30 degrees Celcius, the filters removed to sterile 50 ml conical tubes and the bacteria washed off by gentle pipeting using 2 ml ice cold BSM (without any carbon source or yeast extract). This resuspension of surface grown bacteria was processed prior to RNA extraction in an exactly the same way as the liquid cultures
Project description:To study hepatic gene expression differences, liver samples from infected pigs (n = 10) were compared with liver samples from the non-infected control group (n = 5). Ten microarrays were performed, such that 5 randomly selected cDNA samples from the infected group were labeled with Oyster 550 (Genisphere Inc., Hatfield, PA, USA) and compared directly to 5 control animals labeled with Oyster 650 (Genisphere) analysing a pair of samples (one from an infected animal and one from a randomly chosen non-infected animal) on each microarray slide. The remaining five cDNA preparations from the infected group were labeled with Oyster 650 and compared in the same way to the five controls labeled with Oyster 550 on the remaining 5 microarray slides. This dye-swap design was applied to reduce variation due to dye effects and to provide as much biological replication as possible. Keywords: Disease state analysis Two-condition experiment, Disease vs. Control, Biological replicates: 10 disease replicates and 5 control replicates, 10 Microarrays comparing one disease replicate with one control replicate.
Project description:Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8<br>Comparison of transcript profiles between wild type Columbia and ccr1 (carotenoid and chloroplast regulatory) mutant, which contains a mutation in At1g77300 (SDG8)
Project description:Microarray analyses were performed on Arabidopsis thaliana plants overexpressing ERF6. In this way it was hoped that any changes in the Arabidopsis transcriptome caused by overexpression would provide clues as to the role this gene plays in vivo.<br>Arabidopsis thaliana plants were transformed with 35S::ERF6 or the empty vector pK2GW7 (used as a control). Total RNA was extracted from untreated 10-day old seedlings. Three separate arrays were performed (the RNA for each slide having been extracted from an independent biological replicate).
Project description:Comparison of N. gonorrhoeae nmb1650 knockout mutant and wild-type parent strains grown in capnoaerobic conditions (normal atmosphere +5% CO2)
Project description:Comparison of N. meningitidis nmb1650 knockout mutant and parental strains grown in capnoaerobic conditions (normal atmosphere +5% CO2)
Project description:Plants engineered for abiotic stress tolerance may soon be commercialized. The engineering of these plants typically involves the manipulation of complex multigene networks and may therefore have a greater potential to introduce pleiotropic effects than the simple monogenic traits that currently dominate the plant biotechnology market. Drought- tolerant Arabidopsis thaliana were engineered through overexpression of the transcription factor ABF3 in order to investigate unintended pleiotropic effects. In order to eliminate position effects, the Cre/lox recombination system was used to create control plant lines that contain identical T-DNA insertion sites but with the ABF3 transgene excised. This additionally allowed us to determine if Cre recombinase can cause unintended effects that impact the transcriptome. Microarray analysis of control plant lines that underwent Cre-mediated excision of the ABF3 transgene revealed only two genes that were differentially expressed in more than one plant line, suggesting that the impact of Cre recombinase on the transcriptome was minimal. In the absence of drought stress, overexpression of ABF3 had no effect on the transcriptome, but following drought stress, differences were observed in the gene expression patterns of plants overexpressing ABF3 relative to control plants. Examination of the functional distribution of the differentially expressed genes revealed strong similarity indicating that unintended pathways were not activated. In response to drought stress, overexpression of ABF3 results in a reprogramming of the drought response, which is characterized by changes in the timing or strength of expression of some drought response genes, without activating any unexpected gene networks. These results illustrate that important gene networks are highly regulated in Arabidopsis and that engineering stress tolerance may not necessarily cause extensive changes to the transcriptome.
Project description:The experiment's aim is to follow the population of E. coli cells before and after treatment with histones. The E. coli libraries consisted of MACH1 pSMART-LCKm carrying random fragments of 1, 2, 4 and 8 kb of E. coli genome. The selection procedure involved three rounds of histones treatment (same dose each time during 3h hours then recovery time of 2h before applying the next histone treatment, at the end a total of 15-16h).