By comparison of the Ct differences of the different dilutions, it was verified that the PCR was exponential at least up to the threshold DNA concentration used for the analysis (i.e. a 10-fold dilution corresponds to a Ct difference of about 3.32). The size of the analysis product and the absence of other products were verified using analytical

agarose R788 gel electrophoresis. A standard curve was generated and used to calculate the genome copy numbers present in the dilutions of the cell extract. Together with the known cell densities (see above), this number was used to calculate the genome copy number per cell. At least three independent experiments (biologic replicates) were performed for each species, and average values and standard deviations were calculated. Dialyzed cytoplasmic extracts of Synechocystis Vismodegib clinical trial PCC6803 (see above) were used to record spectra from 220 to 340 nm. The spectra had the typical shapes of nucleic acids spectra and E260/E280 quotients typical for pure nucleic acids. The cell densities (see above) and the absorption at 260 nm were used to calculate the genome copy numbers per cell using the following parameters: absorption of one equals a DNA concentration of 50 μg mL−1, the average molecular mass of one base pair is 660 g mol−1, and the Avogadro number. The best value for the genome size is less clear, the chromosome size is 3.57 Mbp, and the genome size including

plasmids is 3.96 Mbp. The plasmid copy number is unknown and e.g. in Halobacterium salinarum, two plasmids have a copy number of five, whereas the genome has a copy number of 25 (Breuert et al., 2006). To take the unknown plasmid copy numbers into account, genome sizes of 3.96 Mbp (high plasmid copy number) and 3.65 Mbp (low plasmid copy number) were used to calculate the ploidy level of the chromosome. It should be noted that in highly polyploid species, the absorbance of RNA Buspirone HCl is much lower than that of genomic DNA and can be neglected. A short calculation should demonstrate this point: E. coli cells growing with a doubling time of 100 min. contain about 7000 ribosomes

per cell (Bremer & Dennis, 1996). If the same number is assumed for Synechocystis with a much longer doubling time, the cells would contain 3.2 × 107 nt ribosomal RNA, which makes up nearly 90% of cellular RNA. Fifty copies of a genome of 3.6 Mbp are equal to 3.6 × 108 nt. Therefore, under these conditions, DNA outnumbers RNA by more than a factor of 10. The real time PCR method for the quantification of genome copy numbers had been established for haloarchaea (Breuert et al., 2006), but, in the meantime, was also applied to methanogenic archaea and proteobacteria (Hildenbrand et al., 2011; Pecoraro et al., 2011). It has been validated against several independent methods, i.e. quantitative Southern blotting (Breuert et al., 2006), DNA isolation, and spectroscopic quantification (Hildenbrand et al., 2011), and the wealth of results published for E.