Real-Time PCR Determination of Escherichia coli Genomic DNA Contamination in Plasmid Preparations

2002 ◽  
Vol 301 (1) ◽  
pp. 151-153 ◽  
Author(s):  
Adrián Vilalta ◽  
Vanessa Whitlow ◽  
Terrie Martin
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Real Time Pcr ◽  
Genomic Dna ◽  
Dna Contamination

scholarly journals LEM-PCR: a method for determining relative transcript isoform proportions using real-time PCR without a standard curve

Genome ◽  
2010 ◽  
Vol 53 (8) ◽  
pp. 637-642 ◽  
Author(s):  
S. Virtue ◽  
M. Dale ◽  
J. K. Sethi ◽  
A. Vidal-Puig
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Genomic Dna ◽  
Linear Equations ◽  
Large Change ◽  
Standard Curve ◽  
Relative Expression Level ◽  
Small Change ◽  
Abundant Transcript

Many genes express multiple transcript isoforms generated by alternative splicing of mRNA. Using real-time PCR, it is straightforward to determine the relative expression level of each isoform independently. However, it is less trivial to determine the relative proportions of different isoforms in a cDNA sample. The relative proportions of different isoforms can be important, as a small change in a highly abundant transcript may be more relevant than a large change in a minimally expressed transcript. Currently, determining the relative proportions of isoforms requires the construction of a standard curve using recombinant plasmid DNA or genomic DNA. As recombinant or genomic DNA standards often amplify with different efficiencies to cDNA samples, they may give under- or overestimations of isoform abundances. The method described in this article uses a titration curve generated from the same cDNA samples measured in the experiment. By using samples with different levels of separate isoforms, it is possible to derive linear equations which, when solved, allow the determination of the proportion of each isoform within the samples under study.

scholarly journals Association of Ct Values from Real-Time PCR with Culture in Microbiological Clearance Samples for Shiga Toxin-Producing Escherichia coli (STEC)

2020 ◽  
Vol 8 (11) ◽  
pp. 1801
Author(s):  
Michael Bording-Jorgensen ◽  
Brendon D. Parsons ◽  
Gillian A.M. Tarr ◽  
Binal Shah-Gandhi ◽  
Colin Lloyd ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Shiga Toxin ◽  
Real Time Pcr ◽  
Gene Detection ◽  
Culture Positivity ◽  
Hands On ◽  
Culture Independent ◽  
Chromogenic Agar ◽  
Stool Samples

Shiga toxin-producing Escherichia coli (STEC) are associated with acute gastroenteritis worldwide, which induces a high economic burden on both healthcare and individuals. Culture-independent diagnostic tests (CIDT) in frontline microbiology laboratories have been implemented in Alberta since 2019. The objectives of this study were to determine the association between gene detection and culture positivity over time using STEC microbiological clearance samples and also to establish the frequency of specimen submission. Both stx genes’ amplification by real-time PCR was performed with DNA extracted from stool samples using the easyMAG system. Stools were inoculated onto chromogenic agar for culture. An association between gene detection and culture positivity was found to be independent of which stx gene was present. CIDT can provide rapid reporting with less hands-on time and technical expertise. However, culture is still important for surveillance and early cluster detection. In addition, stool submissions could be reduced from daily to every 3–5 days until a sample is negative by culture.

Real-time PCR for differentiation of F18 variants among enterotoxigenic and Shiga toxin-producing Escherichia coli from piglets with diarrhoea and oedema disease

2013 ◽  
Vol 198 (2) ◽  
pp. 538-540 ◽  
Author(s):  
Jae-Won Byun ◽  
Byeong Yeal Jung ◽  
Ha-Young Kim ◽  
John M. Fairbrother ◽  
Myoung-Heon Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Shiga Toxin ◽  
Real Time Pcr ◽  
Oedema Disease

scholarly journals Application of quantitative real-time PCR compared to filtration methods for the enumeration of Escherichia coli in surface waters within Vietnam

2016 ◽  
Vol 15 (1) ◽  
pp. 155-162 ◽  
Author(s):  
Pierangeli G. Vital ◽  
Nguyen Thi Van Ha ◽  
Le Thi Hong Tuyet ◽  
Kenneth W. Widmer
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Surface Waters ◽  
Real Time Pcr ◽  
Membrane Filtration ◽  
Quantitative Real Time Pcr ◽  
Wet Season ◽  
Culture Methods ◽  
Fecal Indicator ◽  
Filtration Method

Surface water samples in Vietnam were collected from the Saigon River, rural and suburban canals, and urban runoff canals in Ho Chi Minh City, Vietnam, and were processed to enumerate Escherichia coli. Quantification was done through membrane filtration and quantitative real-time polymerase chain reaction (PCR). Mean log colony-forming unit (CFU)/100 ml E. coli counts in the dry season for river/suburban canals and urban canals were log 2.8 and 3.7, respectively, using a membrane filtration method, while using Taqman quantitative real-time PCR they were log 2.4 and 2.8 for river/suburban canals and urban canals, respectively. For the wet season, data determined by the membrane filtration method in river/suburban canals and urban canals samples had mean counts of log 3.7 and 4.1, respectively. While mean log CFU/100 ml counts in the wet season using quantitative PCR were log 3 and 2, respectively. Additionally, the urban canal samples were significantly lower than those determined by conventional culture methods for the wet season. These results show that while quantitative real-time PCR can be used to determine levels of fecal indicator bacteria in surface waters, there are some limitations to its application and it may be impacted by sources of runoff based on surveyed samples.

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