Mol21, Avogadro’s number of copies mol21 is 6.02261023 [16]: concentration(ng per

Mol21, Avogadro’s number of copies mol21 is 6.02261023 [16]: concentration(ng per ml)|6:02|1023 (copies per mol) Copies length(bp)|6:6|1011 (ng per mol) Serial 10-fold dilutions spanning from 107 to 102 copies ml21 were generated for each type of standard using RT-PCR grade water and were used immediately.ngEstimated 16S rRNA gene copies based on the circular and linear standard curves were compared to the number of predicted copies and the ratio was used to assess the degree of inflation (or reduction) based on each of the standard DNA conformations.Results Comparison of Standard CurvesPlasmid DNA is routinely used to generate standards for qPCR analysis and exists primarily in the circular form [9]. A recent 256373-96-3 web report suggested that linearized plasmids were more accurate at quantifying gene estimates in eukaryotic genomes [7]. Therefore, we sought to compare two conformations of circular DNA and two linearized DNA standards in estimating numbers of 16S rRNA gene copies in genomic DNA samples from microbial strains with sequenced genomes. First, nicked circles and linearized bacterial (T. lienii) and archaeal (A. fulgidus) 16S rRNA gene plasmids and PCR amplicons were prepared from supercoiled plasmid DNA byEffect of qPCR Standards on 16S Gene Estimatesorder MNS Figure 3. Comparison of expected and estimated 16S rRNA gene copies in bacterial DNA samples. Expected bacterial 16S rRNA gene copies were calculated based on four and five 16S copies per genome for (a) P. aeruginosa and (b) 25837696 D. vulgaris, respectively. Black bars = predicted 16S copies. White bars = estimated 16S copies based on supercoiled plasmid standard. Grey bars = estimated 16S copies based on nicked-circular plasmid standard. Black and white striped bars = estimated 16S copies based on linearized plasmid standard. Black and gray striped bars = estimated 16S copies based on amplicon-based standard. Data are the average (n = 3) and error bars are 61 standard deviation among replicates. doi:10.1371/journal.pone.0051931.gNb.BtsI digest, SpeI digest, and end-point PCR, respectively. The four DNA preparations were purified, quantified using Qubit fluorometry, and analyzed by agarose gel electrophoresis (Figure 1). Propagated plasmids isolated from transformed bacterial cells were predominantly supercoiled DNAs that ran faster than their linearized counterparts (Figure 1a, compare lanes labeled S to lanes L), whereas the nicked circles ran much slower than both the linearized and supercoiled plasmids. The 16S rRNA gene amplicons that spanned the V1 2 region were approximately 350 base pairs in length (Figure 1b.). Next, to determine if the conformation of the DNA standard significantly affected amplification efficiency, the performance of qPCR reactions using serial dilutions of the four prepared standards were compared (Figure 2). Bacterial T. lienii curves spanned from 107 to 103 copies (Figure 2a and Table 2) and the performance of each standard curve is summarized in Table 3. Amplification efficiencies ranged from 85 to 89 , and an ANOVA showed that there was no significant difference between the slopes or y-intercepts of the four curves (P = 0.97). Similar results were obtained for the A. fulgidus 16S rRNA gene standards (Figure 2b and Table 2 and Table 3).Amplification efficiencies ranged from 88 to 94 and the four curves were not significantly different from one another (P = 0.99) by ANOVA. Therefore, the conformation of the standard had a negligible effect on the performance of t.Mol21, Avogadro’s number of copies mol21 is 6.02261023 [16]: concentration(ng per ml)|6:02|1023 (copies per mol) Copies length(bp)|6:6|1011 (ng per mol) Serial 10-fold dilutions spanning from 107 to 102 copies ml21 were generated for each type of standard using RT-PCR grade water and were used immediately.ngEstimated 16S rRNA gene copies based on the circular and linear standard curves were compared to the number of predicted copies and the ratio was used to assess the degree of inflation (or reduction) based on each of the standard DNA conformations.Results Comparison of Standard CurvesPlasmid DNA is routinely used to generate standards for qPCR analysis and exists primarily in the circular form [9]. A recent report suggested that linearized plasmids were more accurate at quantifying gene estimates in eukaryotic genomes [7]. Therefore, we sought to compare two conformations of circular DNA and two linearized DNA standards in estimating numbers of 16S rRNA gene copies in genomic DNA samples from microbial strains with sequenced genomes. First, nicked circles and linearized bacterial (T. lienii) and archaeal (A. fulgidus) 16S rRNA gene plasmids and PCR amplicons were prepared from supercoiled plasmid DNA byEffect of qPCR Standards on 16S Gene EstimatesFigure 3. Comparison of expected and estimated 16S rRNA gene copies in bacterial DNA samples. Expected bacterial 16S rRNA gene copies were calculated based on four and five 16S copies per genome for (a) P. aeruginosa and (b) 25837696 D. vulgaris, respectively. Black bars = predicted 16S copies. White bars = estimated 16S copies based on supercoiled plasmid standard. Grey bars = estimated 16S copies based on nicked-circular plasmid standard. Black and white striped bars = estimated 16S copies based on linearized plasmid standard. Black and gray striped bars = estimated 16S copies based on amplicon-based standard. Data are the average (n = 3) and error bars are 61 standard deviation among replicates. doi:10.1371/journal.pone.0051931.gNb.BtsI digest, SpeI digest, and end-point PCR, respectively. The four DNA preparations were purified, quantified using Qubit fluorometry, and analyzed by agarose gel electrophoresis (Figure 1). Propagated plasmids isolated from transformed bacterial cells were predominantly supercoiled DNAs that ran faster than their linearized counterparts (Figure 1a, compare lanes labeled S to lanes L), whereas the nicked circles ran much slower than both the linearized and supercoiled plasmids. The 16S rRNA gene amplicons that spanned the V1 2 region were approximately 350 base pairs in length (Figure 1b.). Next, to determine if the conformation of the DNA standard significantly affected amplification efficiency, the performance of qPCR reactions using serial dilutions of the four prepared standards were compared (Figure 2). Bacterial T. lienii curves spanned from 107 to 103 copies (Figure 2a and Table 2) and the performance of each standard curve is summarized in Table 3. Amplification efficiencies ranged from 85 to 89 , and an ANOVA showed that there was no significant difference between the slopes or y-intercepts of the four curves (P = 0.97). Similar results were obtained for the A. fulgidus 16S rRNA gene standards (Figure 2b and Table 2 and Table 3).Amplification efficiencies ranged from 88 to 94 and the four curves were not significantly different from one another (P = 0.99) by ANOVA. Therefore, the conformation of the standard had a negligible effect on the performance of t.