Project description:Drosophila harbor substantial genetic variation for antibacterial defense. We allowed wild-caught Drosophila melanogaster to evolve a defense response to systemic infection with the human opportunistic pathogen, Pseudomonas aeruginosa over 10 generations. We performed genome wide transcriptional profiling in selected lines relative to control lines (not infected, but were exposed to the same bottleneck in population size as their paired selected lines by randomly selecting a set of individuals to found the next generation, and then infected at the end of the 10 generations), to identify specifically the genetic basis of the evolved immune response.
Project description:Wolbachia is a vertically transmitted intracellular bacteria that infect most than 60% of insect species. The strains wMelPop and wMel were introduced in the dengue virus vector Aedes aegypti, naturally not infected by Wolbachia. Recently, it was shown that those two strains inhibit dengue virus replication into their new host, A. aegypti (Moreira et al. 2009 and Walker et al. in preparation). The aim of this project is to look at the transcriptional response of Aedes aegypti to infection with wMel and wMelPop and try to find some genes or pathway potentially involved in the viral interference.Four laboratory lines of A. aegypti were used throughout this study. The PGYP1 and Mel2 lines were generated by transinfection with wMelPop and wMel strains respectively. PGYP1.tet and Mel2tet lines were treated with the antibiotic tetracycline and cured from Wolbachia infection (McMeniman et al., 2009 and Walker et al in preparation). The Mosquitoes were reared under standard laboratory conditions (26 ± 2 °C, 12:12 light/dark cycle, 75% relative humidity). Mosquito larvae were fed 0.1mg/larvae of TetraMin Tropical Tablets once a day. Adults were transferred to cages (measuring 30 x 30 x 30 cm) at emergence at 400 individuals per cage. Adults were supplied with a basic diet of 10% sucrose solution (Turley et al., 2009).
Project description:Examine the dose response characteristics of a set of eight artificial transcripts (IVT) when spiked into a Universal Human RNA background at different copy numbers. The experiment was designed to <br>(i) evaluate the technical reproducibility of array data generated on the Agilent Whole Human 44K array with use of a set of external RNA controls <br> (ii) employ two panels of the same external RNA controls, which differed in copy number between panels, in order to simulate normal and disease states. We employed 8 different pools which were comprised of 8 different external RNA standards in a total human reference RNA background. Each different standard was present at a different copy number within any single pool (see file: E-MEXP-2670.additional.zip). Each control was present at a different concentration in each of the 8 pools. Standard microarray analysis was performed on the data and the differences in abundance between external RNA controls determined in terms of fold change differences.
Project description:Comparison of transcript profiles of E. coli LZ41 and LZ54 fishns mutant strains containing drug-resistant alleles of different topoisomerase genes to distinguish gene transcripts associated either with relaxation or hypernegative supercoiling in absence of transcriptional regulator FIS and H-NS.
Project description:Comparison of transcript profiles of E. coli LZ41fishns and LZ54fishns strains containing drug-resistant alleles of different topoisomerase genes to distinguish gene transcripts associated either with relaxation or hypernegative supercoiling.
Project description:Hyphae and conidia, representing the two developmental stages of the fungus, were examined separately in this study.<br><br>RNA from hyphae or conidia incubated in plasma in RPMI/HEPES without neutrophils was used as reference, and was co-hybridized with the query samples obtained from the corresponding sets incubated with neutrophils.<br><br>Each biological replicate was carried out with neutrophils obtained from a different donor, and the RNA samples associated with each neutrophil source was paired separately with a corresponding reference sample prepared at the same time.<br><br>
Project description:A pilot program for monitoring proficiency in microarray facilities using three replicates of two different RNA sources. Participating laboratories prepared and hybridized targets from the six RNA samples using their own protocols. The entire process was repeated three times over a nine-month period and included approximately fifteen distinct laboratories in each testing round.
Project description:U2OS cells were infected with shRNA vector targeting Ark5 or control vector, selected on puromycin for 48hrs, seeded on 5cm dishes at 20% confluency and harvested in triplicate 48hrs later