The efficiency (E) of the PCR assay was calculated using the formula, E=[10−1/slope−1] × 100, where the slope was extracted from the curve Ct=f(log Q0) and Q0 is the initial DNA or cell population in the assay. E was expressed as percentage. All values are expressed as
the mean ± SD. All MAPK Inhibitor Library cell line data were analysed using sigmastat 3.0 statistical software from Systat Inc. Differences between groups were analysed by one-way anova. Post hoc comparisons were conducted using the Holm-Sidak comparison test as suggested by Zar (1996). A P value ≤0.001 or 0.05 was considered to be statistically significant. The specificity of the primers Bc3F and Bc3R was studied by conventional PCR using B. cinerea MUCL 28920 and other genera and species of fungi potentially present on grapes. A single fragment of about 95 bp was amplified from B. cinerea genomic DNA. No product was observed with genomic DNA from isolates of the other species tested (data not shown). Specific primers for the LIP4 gene were used as described in a previous study (Tessonniere et al., 2009), in which primers were already tested against Brettanomyces but not against fungi.
So, in our study, the specificity of LIP4 primers was checked against a number of genera and species of different fungi from various origins. Apart from Yarrowia lypolitica, no amplification was observed for the tested microorganisms (data not shown).
Genomic DNA obtained from B. cinerea MUCL 28920 was used as a template for qPCR with primers MK-2206 Bc3F and Bc3R. As expected, the PCR product melting temperature was 83 ± 0.5 °C. The standard curve generated with the Bc3F/Bc3R pair in the conditions described above is shown in Fig. 1. The standard curve for B. cinerea was generated by plotting the log of DNA (pg) against the Ct value determined by qPCR. Linearity was observed across the whole range used and GPX6 the very high correlation coefficient (R2=0.99) indicated very low interassay variability. The slope of the standard curve was −3.39, which corresponds to an amplification efficiency of 97%. The limit of detection was defined as the lowest population of the microorganisms that could be detected using our SYBR Green qPCR method. Under conditions that include SYBR Green, the maximum Ct value that could be used was 30, which corresponds to a DNA concentration of 6.3 pg. Yarrowia lypolitica genomic DNA extracted from 10-fold serial dilutions of Y. lypolitica cells ranging from 8 × 103 to 8 × 107 cells mL−1 was used as a template. Ct values were plotted against the logarithm of cell concentration. Under these conditions, PCR efficiency was 93% with a correlation coefficient of 0.99. The Tm of the product was 85 ± 0.5 °C (Fig. 2).