Where a label such as “”Fe limitation”" appears, it denotes a transcriptome that can be considered a positive control. Where no such label appears, a suitable positive control data set was lacking. To further demonstrate the potential to diagnose metabolic activities from transcript ranks, we conducted a more comprehensive analysis of relationship between the presence or absence of glucose and the ranks of selected gene transcripts. Fifty eight samples were identified in which no glucose was present in the medium. Eleven samples were identified selleck kinase inhibitor in which glucose was the sole or

predominant carbon source. Differences in the ranks of pairs of genes, identified by inspection, were found Selleckchem BMS 907351 to discriminate the glucose-present and glucose-absent data sets (Figure 4A). The drip-flow biofilm data group with the glucose-present comparators, as expected. The six glucose-absent points that overlap with the glucose-present cluster are from a single investigation in which glycerol was the predominant carbon source. The extensive commonality of pathways for catabolism of glucose

and glycerol may explain this overlap. Figure 4 Discrimination of glucose metabolism (A) and homoserine lactone quorum sensing (B) based on differences in transcript ranks. Open symbols are glucose-absent or quorum sensing negative comparators in panels A and B, respectively. Filled symbols are glucose-present and quorum sensing positive comparators in panels A and B, respectively. Stars indicate drip-flow biofilm samples. The genes appearing in these graphs are annotated as: PA5564, gidB, glucose inhibited division protein B; PA3187, probable ATP-binding component

of ABC transporter; PA2634, aceA, isocitrate lyase; PA3186, glucose/carbohydrate outer membrane porin OprB precursor; PA0485, conserved hypothetical protein; PA3724, lasB, elastase; PA3281, hypothetical protein; rhlA, rhamnosyltransferase Cisplatin manufacturer chain A. Alvarez-Ortega and Harwood [15] identified genes induced under conditions of low oxygen concentration. From their results, we identified a subset of seven genes that were particularly strongly induced by low oxygen and whose transcript rank increased monotonically with decreasing oxygen concentration. Figure 3B compares the rank for these seven genes between drip-flow biofilms in this study and the Alvarez-Ortega and Harwood [15] data. The rankings of the transcripts for the biofilm were consistent with low oxygen concentrations for six of seven transcripts. This comparison indicates that the biofilm experienced oxygen limitation. A recent investigation reported 117 genes induced by transferring P. aeruginosa from aerobic to anaerobic conditions [24]. Thirty-five genes appearing on this list also appear in Table 3, a significant overlap (p = 3 × 10-12; random chance would predict an overlap of approximately 2 genes).