Project description:Transcriptionnal profiling comparing a V. Choleare ∆cpxR mutant harboring either (pBAD33-cpxR) or empty (pBAD33) grown for 1h under inducing conditions. Two independent experiments with a technical replicate for each.
Project description:Transcript abundance in Escherichia coli O157:H7 was determined in the presence or absence of pulsed expression of the small RNA, AsxR. AsxR was cloned under the control the arabinose inducible promoter Para. Escherichia coli O157:H7 str. TUV93-0 with pAsxR or empty vector was cultured in MEM-HEPES media to an OD600 of 0.8 and 0.2% arabinose added. 10min after addition of arabinose 10ml of cells were harvested and and pellets resuspended in 1ml of Trizol and total RNA isolated. RNAs were labelled using the SuperScript Plus indirect cDNA labelling System. Triplicate control RNAs were pooled and hybridised to seperate AsxR test RNAs on three microarays. Arrays were hybridised using the Maui hybridisation platform and Scann using and Axon Autoloader Scanner. GenePix software was used to analyse images and GPR files were analysed using Genespring 7.3.1.
Project description:The objective of this study was to identify changes in gene expression levels between wild-type and AE2-knockout colon. 7 wild-type and 7 AE2-null colon RNA samples were compared to identify genes that are differentially expressed in the colon of AE2 knockout mice. Total RNA was collected from both male and female wild-type and AE2-null colons (including both proximal and distal colon) when the mice were 18 days old. All pairs were gender- and aged-matched, and all mice were on a mixed 129 Black Swiss background. To facilitate statistical analysis and reduce any affects of Cy3 and Cy5 labeling, comparisons of two wild-type and two AE2-null samples were repeated using a dye flip.
Project description:The objective of this study was to identify changes in gene expression levels between wild-type and CFTR-knockout small intestine. CFTR-knockout mice (provided by Dr. Lane Clarke of the University of Missouri) were maintained on colyte. Keywords: gene expression comparison Four wild-type and four CFTR-knockout small intestinal RNA samples were compared. To facilitate statistical analysis and reduce affects of Cy3 and Cy5 labeling, comparison of two WT and two KO were repeated with a dye flip.
Project description:The objective of this study was to identify changes in gene expression levels between wild-type and NHE4-knockout stomach. 6 wild-type and 6 NHE4-knockout stomach RNA samples were compared. Total RNA was collected from both male and female adult (between 8 and 12 weeks of age) wild-type and NHE4-null mice on a mixed 129 Black Swiss background. With the exception of one, all comparisons were done between wild-type and NHE4-null samples from littermate age- and gender-matched siblings.
Project description:The objective of this study was to identify changes in gene expression levels between wild-type and NKCC1-knockout small intestine. 6 wild-type and 6 NKCC1-knockout small intestine RNA samples were compared. Total RNA was collected from both male and female 8-week old wild-type and NKCC1-null mice on an inbred FVB\N background. All comparisons were done between wild-type and NHE4-null samples from age- and gender-matched mice.
Project description:Candida albicans is an opportunistic fungal pathogen capable of causing superficial and systemic infections in humans. The ability of C. albicans to switch between various morphological forms depending on its host environment is thought to contribute to its virulence. Filamentous growth states are associated with tissue invasion, biofilm formation, evasion of innate host defences and mating. Although the mechanisms of activation of filamentous growth pathways are well understood, less is known about which factors control the negative regulation of filamentation. In this study, we have identified a previously uncharacterized Orf that shares sequence similarity with Saccharomyces cerevisiae Dig1p and Dig2p. Deletion of the gene encoding this Orf triggers invasive growth in C. albicans and so we have retained the yeast designation of Dig1 (for Down-regulation of Invasive Growth). Mutants lacking CaDIG1 form cultures of hyperpolarized cells, form robust biofilms, are highly invasive in vitro but not in vivo and are constitutively activated for the pheromone response. Deletion of key transcription factors that act downstream of Dig1p provide evidence to suggest that CaDig1 regulates filamentation and mating through multiple signalling pathways. Transcriptional analysis of the C. albicans dig1Δ/dig1Δ homozygous mutant versus the wild type (SN148) in the MTLa/alpha background. Four biological replicates of the mutant and the wild type were included in the analysis. Samples were grown at 30 °C in YPD medium plus uridine
Project description:Time series of infection of Sulfolobus solfataricus strain 2-2-12 cells infected with STIV are compared with uninfected cells over 32 h. Two-condition experiment, Control vs. Infected cells sampled at 5 time points (0, 8, 16, 24, 32 h post infection). Biological replicates: 3 control, 3 infected, paired samples independently grown. One replicate per array. Dye swaps.
Project description:Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly. We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more resistant to heat stress than MG1655. A microarray study of these strains subjected to sub-lethal heat-stress at 45°C was carried out. In E. coli O157 (Sakai), 380 genes responded significantly to the treatment compared to 410 genes in MG1655. Overnight cultures of E. coli O157 (Sakai) and E. coli K-12 MG1655 were grown in Neidhardt's EZ Rich Defined Medium and diluted 1:100 in 50 ml fresh medium in 125 ml Ehrlenmeyer flasks. The cultures were shaken at 37°C until the optical density (OD600) reached 0.4. Each culture was divided into 2 equal parts in identical flasks. One flask flask was transferred to a shaking water bath and incubated at 45°C for 10 min; the other flask was incubated at 37°C for 10 min. After incubation, the cultures were transferred to 50 mL centrifuge tubes and treated with RNAprotect™ to stabilise the mRNA. The experiment was performed 3 times on different days. Six custom-made microarray slides were used in this study; each slide was hybridised with labelled cDNA made from untreated and heated E. coli O157 (Sakai) or MG1655.