TY - JOUR
AU1 - Asvapathanagul, Pitiporn
AU2 - Garrido-Baserba, Manel
AU3 - Olson, Betty H.
AU4 - Park, Hee-Deung
AU5 - Chen, Deqiang
AU6 - Rosso, Diego
AB - An existing bead-beating DNA extraction protocol was employed to compare the DNA extraction recovery and fragment quality of 6 different aeration diffuser biofilms. Escherichia coli, Gordonia amarae, and mixed liquor were used as controls. The fraction of total DNA<sub>biofilm</sub> decreased monotonically with increasing number of beat beatings (BB) when the amount of DNA present was sufficient (>4 μg<sub>DNA</sub>/cm<sup>2</sup>), excluding the ceramic disk. While controls required only 2 BBs, 3 out of 5 BBs achieved ≥70% of total DNA (70.3 ± 1.7%) for 5 out of 6 biofilms. Quantitative polymerase chain reaction (PCR) analyses of 353 and 1,505 basepair (bp) amplicons from pure culture extracts showed target copy numbers were not degraded for the first 2 BBs, but the third BB decreased amplicon concentrations by 0.65 and 1.12 log for E. coli, and 0.39 and 0.40 log for G. amarae, respectively. The 353 bp fragment amplification from biofilm samples showed minimal degradation for the first 3 BBs. PCR and gel electrophoresis confirmed integrity of amplified 1,505 bp DNA fragments over the 5 BBs, except in the EDPM (75 mm diameter, tube) diffuser biofilm (4.98 ± 0.62 μg<sub>DNA</sub>/cm<sup>2</sup>). Taken together, this study showed type of diffuser membrane biofilms had no effects on extraction efficiency, but low DNA concentrations reduced extraction performance.
TI - Comparison of DNA Extraction Efficiency and Reproducibility of Different Aeration Diffuser Biofilms Using Bead-Beating Protocol
JF - Microbial Physiology
DO - 10.1159/000500875
DA - 2019-01-01
UR - https://www.deepdyve.com/lp/karger/comparison-of-dna-extraction-efficiency-and-reproducibility-of-05r8Cz8jq2
SP - 293
EP - 304
VL - 28
IS - 6
DP - DeepDyve
ER -