Effect of storage regime on the stability of DNA used as a calibration standard for real-time polymerase chain reaction

Podivinsky, Ellen; Love, John L.; Colff, Loraine Van Der; Samuel, Laly

doi:10.1016/j.ab.2009.06.024

Cited by 13 publications

(11 citation statements)

References 9 publications

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“…The relative stability of DNA extracts stored at 4 8C in the fridge is in agreement with observations from other researchers (Podivinsky et al 2009). …”

Section: Discussionsupporting

confidence: 81%

“…In addition, economic factors may persuade investigators to only analyse water samples which have levels of traditional microbial indicators above a certain value. However, several physical and chemical mechanisms could cause degradation of DNA when there is a delay between collection of a water sample and extraction of the DNA (Lindahl 1993;Podivinsky et al 2009;Rossmanith et al 2011). The aim of this study was to evaluate a range of options for storage and partial processing of water samples before PCR analysis.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Recommendations for the processing and storage of water samples before polymerase chain reaction (PCR) analysis

Gilpin

Devane

Nourozi

et al. 2013

New Zealand Journal of Marine and Freshwater Research

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A range of options for the storage and partial processing of water samples before polymerase chain reaction (PCR) analysis were evaluated. In addition, temporal storage of extracted DNA at 4 8C was investigated. Filtering the water sample and then storing that filter at (20 8C for up to six months before DNA extraction was equivalent to extracting DNA immediately. Freezing a water sample resulted in an immediate 1 log loss of PCR signal, although thereafter the sample was stable for at least three months. A rapid loss of detectable PCR product was found when storing a water sample at 4 8C for longer than one week. Extracted DNA could be stored at 4 8C for at least six months without considerable loss of PCR signal.

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“…The relative stability of DNA extracts stored at 4 8C in the fridge is in agreement with observations from other researchers (Podivinsky et al 2009). …”

Section: Discussionsupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Recommendations for the processing and storage of water samples before polymerase chain reaction (PCR) analysis

Gilpin

Devane

Nourozi

et al. 2013

New Zealand Journal of Marine and Freshwater Research

View full text Add to dashboard Cite

show abstract

“…This may be surprising to many working in the biological sciences where plasmid DNA preparations are stored for entire scientific careers; however, it is important to consider that many such research samples are usually single plasmid constructs stored at very high copy number (10 10 copies/μL − 1 μg/μL) so that recovery of the plasmid through bacterial retransformation can occur even with 99% DNA degradation. Regardless, there is strong evidence that storage at 4°C or below in aqueous or dried form would provide at least a couple of years of stability, appropriate for storing working copies of DNA-based information [31][32][33] , with lyophilized DNA showing better stability than aqueous DNA solutions 37 . One additional important caveat for DNA solutions appears to be the starting concentration of DNA, with dilute solutions of~0.02 ng/mL exhibiting substantial degradation within weeks when stored at −20°C 30 .…”

Section: Working Storage (~Accessed Multiple Times Per Year)mentioning

confidence: 99%

DNA stability: a central design consideration for DNA data storage systems

2021

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Data storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.

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“…For example, Carlsen et al showed that the Mycoplasma genitalium DNA load decreased after storage at − 20 °C for up to 18 months, which was especially notable with clinical specimens compared to frozen DNA extracts [ 44 ]. In addition, freezing aqueous solutions of DNA samples at − 20 °C might have a negative effect on DNA stability [ 45 ]. In our study, DNA was not extracted before storage, and this cannot be ruled out as having a negative effect on our test material.…”

Section: Discussionmentioning

confidence: 99%

Detection of bacterial DNA in synovial fluid in dogs with arthritis: a comparison between bacterial culture and 16S rRNA polymerase chain reaction

Vilén

Nilson

Petersson³

et al. 2021

Acta Vet Scand

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Background Septic arthritis (SA) is a serious condition in dogs that requires a prompt diagnosis and treatment to minimize long-term joint pathology. Although bacterial detection in synovial fluid (SF) through culture or cytology is often performed to confirm diagnosis, the sensitivity of these tests is low. The need for a reliable diagnostic tool to confirm the presence of bacteria in SF in humans has led to the increased use of 16S rRNA (i.e., ribosomal RNA) gene sequencing by polymerase chain reaction (16S rRNA PCR). The aim of this prospective clinical study was to compare the sensitivity and specificity of 16S rRNA PCR with bacterial culture on blood agar plates after pre-incubation of SF in paediatric blood bacterial culture bottles to identify bacteria in dogs with clinical signs of SA and to investigate the usefulness of these methods as diagnostic tools. Results Ten dogs with clinical signs of SA, nine with osteoarthritis (OA, control group) and nine with clinical signs of immune-mediated polyarthritis (IMPA, second control group) were examined. Bacterial culture was positive in seven of 10 dogs with clinical SA, of which only two were positive by 16S rRNA PCR. The sensitivity of 16S rRNA PCR and bacterial culture analysis for dogs with clinical SA were 20% and 70%, respectively. All SF samples collected from control group (n = 9) and second control group (n = 14) animals were negative on culture, and 16S rRNA PCR rendered a specificity of 100%. Conclusions Our study showed a lower sensitivity of 16S rRNA PCR than bacterial culture for dogs with clinical SA. Our findings suggest that there is currently no advantage in using 16S rRNA PCR as a diagnostic tool for dogs with clinical SA. Furthermore, our study indicates that pre-incubation in paediatric blood bacterial culture bottles before bacterial cultivation on blood agar plates might enhance bacterial culture sensitivity compared to other culture methods.

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Effect of storage regime on the stability of DNA used as a calibration standard for real-time polymerase chain reaction

Cited by 13 publications

References 9 publications

Recommendations for the processing and storage of water samples before polymerase chain reaction (PCR) analysis

Recommendations for the processing and storage of water samples before polymerase chain reaction (PCR) analysis

DNA stability: a central design consideration for DNA data storage systems

Detection of bacterial DNA in synovial fluid in dogs with arthritis: a comparison between bacterial culture and 16S rRNA polymerase chain reaction

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