coli genes during lambda phage induction. Histograms count number of genes significantly up-regulated (black) or down-regulated (grey) at each time interval. Genes were grouped according to the NCBI COG classification scheme [49]. Categories

with an (*) were enriched in down-regulated genes (Fisher exact test, false discovery rate < 0.05): carbon catabolism, cell processes, cell structure, central metabolism energy metabolism, and transport. Figure 4: A) Diagram of the linear (integrated) lambda phage genome, color-coded by lifecycle stage (blue = lysogenic, yellow = early lytic, red = late lytic). B) (wild type phage) and C) (Lambda-P27): gene expression ratios during prophage induction are shown relative to an untreated ""mock induction"" control and log2 transformed. Genes arranged by order on the lambda genome. References 1. Osterhout RE, Figueroa AZD2281 chemical structure IA, GSK-3 inhibitor Keasling JD, Arkin AP: Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol 2007, 7:82.PubMedCrossRef”
“Background Bacterial biofilms are defined as sessile communities of bacteria that form on air-liquid or liquid–solid interfaces, or even intracellularly [1]. Due to their high resistance to any attempts of removing them, biofilms have a profound impact in many clinical settings, including catheter-associated

urinary tract infections [2], periodontitis [3], and otitis [4], as well as click here Pseudomonas aeruginosa infections of cystic fibrosis patients [5]. Much research has been done on disease mechanisms relating to the biofilm lifestyle. Yet, many of the see more early studies do not consider that growth conditions for the bacteria differ across the biofilm and also change with time. As one example, bacteria residing within the fully matured biofilm have limited access to nutrients and oxygen, but are also well protected from anti-microbials, as well as the host immune system. In contrast, bacteria that grow at the surface of the three-dimensional structure or are still in the early phases of biofilm formation would have better access to nutrients and oxygen, but are also more exposed to anti-microbials. Some temporal studies of gene

expression in biofilms were done years ago [6]. Spatial studies have been done more recently. These were facilitated by advances in microscopy techniques, as well as the development of fluorescent probes [7–9]. Fusions of gene promoters to the structural genes of fluorescence proteins were used to study heterogeneity in biofilms of several bacterial species. This was done to measure: i) spatial gene regulation in biofilm of Bacillus subtilis[10], ii) real-time spatial gene expression in Geobacter sulfurreducens electricity producing biofilm [11], iii) quantitative gene expression in biofilm of Salmonella[12], iv) single cell gene expression in B. subtilis biofilm [13], and v) the effect of inhibitors on Pseudomonas aeruginosa biofilm [14].