In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
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ABSTRACT: S. aureus SA564 and SA564-codY-mutant were grown in bovine aqueous humor, bovine vitreous humor and a chemically defined medium. Samples were extracted in midlog phase and affymetrix microarray processing was performed.
Project description:Effect of anaerobic growth condition on gene expression profile of Pseudomonas aeruginosa PA14 grown in cystic fibrosis sputum with 100 mM nitrate added
Project description:Analysis of binding profile of the Polycomb group proteins Pho and dSfmbt (PhoRC complex) in Drosophila melanogster at two developmental stages (embryos and larvae).
Project description:Whole-genome tiling arrays were used to validate deletions and tandem duplications that were inferred based on next-generation sequencing data. The arrays were generated for six samples of the Drosophila melanogaster Genetic Reference Panel (DGRP) as well as the Berkeley reference strain. Structural variations (SVs) were assessed by comparing probe intensities within the region of interest between the sample for which the SV was predicted and the reference strain.
Project description:Analysis of binding profile of the Polycomb group protein Ph and of GlcNAc sites in Drosophila melanogaster larvae. <br><br>Note some of the protocols for this experiment were changed in May 2010.
Project description:Genomic DNA was collected from ies6d or ino80d after undergoing 40 or 80 generations post-sporulation of IES6/ies6 or 20 or 40 generations post-sporulation of INO80/ino80 heterozygous diploid strains, respectively. (1 day = 10 generations.) Genomic DNA was then amplified, and hybridized to a whole genome tiling microarray. Copy number variation was measured relative to a G1 arrested wild type sample.
Project description:YbjN, an enterobacteria-specific protein, is a multicopy suppressor of ts9 temperature sensitivity in Escherichia coli. Microarray study revealed that the expression level of ybjN was inversely correlated with the expression of flagellar, fimbrial and acid resistance genes. Over-expression of ybjN significantly down-regulated genes involved in the citric acid cycle, glycolysis, the glyoxylate shunt, oxidative phosphorylation, and amino acid and nucleotide metabolism. On the other hand, over-expression of ybjN up-regulated toxin-antitoxin modules, the SOS responsive pathway, cold shock proteins and starvation-induced transporter genes. Our results collectively suggest that YbjN may play important roles in regulating bacterial multicellular behaviors, metabolism and survival under various stress conditions in Es. coli. A total of 8 samples were analyzed: E. coli wild type strain (2 replicates); E. coli ybjN mutant strain (3 replicates); E. coli ybjN over-expression strain (3 replicates).