We used EDTA tubes to collect 7 ml whole blood that was promptly centrifuged on site at 2500 rpm for 15 minutes. The buffy coat (400 μl) was transferred in a cryovial, immediately frozen in vapour phase of liquid nitrogen, and shipped in nitrogen dry shippers to the laboratory. DNA was extracted using the Wizard Genomic DNA purification kit (Promega, Madison, WI) following the manufacturer's instructions. The samples collected in the 1st and 4th day were processed using the same exact protocols.
Relative MtDNAcn (RMtDNAcn) was measured in buffy coat DNA by a quantitative real time polymerase chain reaction (PCR) assay that measure relative mitochondrial copy number by determining the ratio of mitochondrial (Mt) copy number to single copy gene (S) copy number in experimental samples relative to a reference [28 (link)]. This method is based on quantification of Mt and S quantities expressed as Cts derived from a standard curve obtained from serial dilutions of a reference DNA. The reference single copy gene used in this study was human [beta] globin (hbg). The Mt PCR mix was: iQ SYBR Green Supermix (Bio-Rad) 1×, MtF3212 500 nM, MtR3319 500 nM, EDTA 1×. The S (hbg) PCR mix was: iQ SYBR Green Supermix (Bio-Rad) 1×, hbgF 500 nM, hbgR 500 nM, EDTA 1×. 9 ng DNA was loaded in a 20 μl PCR reaction. We used pooled DNA from 20 participants randomly selected from this same study (500 ng for each sample) to create in every Mt and S PCR run a fresh standard curve, which ranged from 20 ng/μl to 0.25 ng/μl. The primers for RT Q-PCR analysis of MtDNA were: MtF3212 5'CAC CCA AGA ACA GGG TTT GT3', and MtR3319 5'TGG CCA TGG GTA TGT TGT TA3'. The primers for RT Q-PCR analysis of hbg were: hbgF 5'GCT TCT GAC ACA ACT GTG TTC ACT AGC3', and hbgR 5'CAC CAA CTT CAT CCA CGT TCA CC3'. All PCRs were performed on a DNA Engine thermal cycler Chromo4 (Bio-Rad, Hercules, California, USA). The thermal cycling conditions for MtDNA PCR were: initial 2 minutes at 50°C, and 3 minutes at 95°C to activate the hot-start iTaq DNA polymerase, followed by 40 cycles comprised of 15 s denaturation at 95°C and 49 s anneal/extend at 60°C. The thermal cycling conditions for the hbg PCR were 3 minutes at 95°C to activate the hot-start iTaq DNA polymerase, followed by 40 cycles comprised of 15 s denaturation at 95°C and 49 s anneal/extend at 58°C. Each run was completed by melting curve analysis to confirm the amplification specificity and absence of primer dimers.
All samples were run in triplicates. The average of the three Mt measurements was divided by the average of the three S measurements to calculate the Mt/S ratio for each sample. For quality control purposes, 10 blind duplicate samples were interdispersed among the test samples. The coefficient of variation for the Mt/S ratio in duplicate samples was 3.2%.
Relative MtDNAcn (RMtDNAcn) was measured in buffy coat DNA by a quantitative real time polymerase chain reaction (PCR) assay that measure relative mitochondrial copy number by determining the ratio of mitochondrial (Mt) copy number to single copy gene (S) copy number in experimental samples relative to a reference [28 (link)]. This method is based on quantification of Mt and S quantities expressed as Cts derived from a standard curve obtained from serial dilutions of a reference DNA. The reference single copy gene used in this study was human [beta] globin (hbg). The Mt PCR mix was: iQ SYBR Green Supermix (Bio-Rad) 1×, MtF3212 500 nM, MtR3319 500 nM, EDTA 1×. The S (hbg) PCR mix was: iQ SYBR Green Supermix (Bio-Rad) 1×, hbgF 500 nM, hbgR 500 nM, EDTA 1×. 9 ng DNA was loaded in a 20 μl PCR reaction. We used pooled DNA from 20 participants randomly selected from this same study (500 ng for each sample) to create in every Mt and S PCR run a fresh standard curve, which ranged from 20 ng/μl to 0.25 ng/μl. The primers for RT Q-PCR analysis of MtDNA were: MtF3212 5'CAC CCA AGA ACA GGG TTT GT3', and MtR3319 5'TGG CCA TGG GTA TGT TGT TA3'. The primers for RT Q-PCR analysis of hbg were: hbgF 5'GCT TCT GAC ACA ACT GTG TTC ACT AGC3', and hbgR 5'CAC CAA CTT CAT CCA CGT TCA CC3'. All PCRs were performed on a DNA Engine thermal cycler Chromo4 (Bio-Rad, Hercules, California, USA). The thermal cycling conditions for MtDNA PCR were: initial 2 minutes at 50°C, and 3 minutes at 95°C to activate the hot-start iTaq DNA polymerase, followed by 40 cycles comprised of 15 s denaturation at 95°C and 49 s anneal/extend at 60°C. The thermal cycling conditions for the hbg PCR were 3 minutes at 95°C to activate the hot-start iTaq DNA polymerase, followed by 40 cycles comprised of 15 s denaturation at 95°C and 49 s anneal/extend at 58°C. Each run was completed by melting curve analysis to confirm the amplification specificity and absence of primer dimers.
All samples were run in triplicates. The average of the three Mt measurements was divided by the average of the three S measurements to calculate the Mt/S ratio for each sample. For quality control purposes, 10 blind duplicate samples were interdispersed among the test samples. The coefficient of variation for the Mt/S ratio in duplicate samples was 3.2%.
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