SigmaPlot 2002 for Windows version 8.02 (SPSS, Chicago, IL, USA) and Paint Shop Pro
version 7.04 (Jasc Software) were used for conducting statistical analyses and creating graphs. To find the optimal PCR conditions for the selective detection of viable H. pylori, samples containing a mixture of dead and viable bacteria were used. The dead bacteria were produced artificially by treating viable bacterial samples with 70% EtOH for 20 min to obtain dead bacterial cells. Bacterial death was confirmed by the absence of any H. pylori colonies on bacterial culture media (data not shown), although some H. pylori might have acquired viable, Alectinib concentration but non culturable, forms. Different concentrations of EMA (0, 1, 5, 10, and 50 μM) and PMA (0, 5, 10, 50, and 100 μM) were added to both viable and dead H. pylori samples, in order to determine the ideal conditions for selective removal of genomic DNA from dead bacteria without loss of DNA from viable bacteria. After treatment of EtOH-killed H.
pylori samples with 10 μM EMA, we found that most of the genomic DNA was still present. In addition, treatment of viable H. pylori samples with EMA at concentrations as low as 1 μM resulted in loss of genomic DNA (Fig. 1a), showing that addition of EMA before PCR may not be useful for discriminating between viable and dead bacteria. PMA concentrations of up to 50 μM did not result in loss of genomic DNA from viable bacteria, although loss of genomic DNA did occur at 100 μM PMA (Fig. 1b). In contrast, treatment of EtOH-killed bacteria with PMA resulted
in significant genomic DNA loss for concentrations of up to 10 μM, and not all genomic DNA was detectable Ulixertinib at 50 and enough 100 μM concentrations (Fig. 1b). Thus, 50 μM was determined to be the most suitable PMA concentration for treating samples before PCR for selective detection of viable H. pylori. To further investigate genomic DNA loss after EMA and PMA treatments, these agents were added to viable and EtOH-killed H. pylori samples at concentrations of 5 μM and 50 μM, respectively; and the amounts of genomic DNA measured and compared by using a spectrophotometer. PMA affected the genomic DNA of viable H. pylori (reduced by 20.4 ± 3.1%, bar B in Fig. 2), but had a significant effect (P < 0.05) on dead bacteria with removal of most genomic DNA (reduced by 91.1 ± 1.2%, bar E in Fig. 2). In contrast, EMA had also a significant effect (P < 0.05) on the genomic DNA of viable H. pylori causing a DNA loss of about 77.3 ± 3.9% (Fig. 2). Viable and dead H. pylori cells were examined under a fluorescence microscope after addition of SYTO 9 and EMA and SYTO 9 and PMA to test the ability of EMA and PMA to pass through the cell membranes (Fig. 3). SYTO 9 plus PMA treated viable bacteria were not stained since PMA cannot penetrate viable H. pylori (Fig. 3a) but these bacteria exhibited a green color due to SYTO 9 (data not shown). In contrast, dead bacteria were stained because PMA can penetrate them (Fig. 3b).