scholarly journals Propidium monoazide–quantitative polymerase chain reaction (PMA-qPCR) assay for rapid detection of viable and viable but non-culturable (VBNC) Pseudomonas aeruginosa in swimming pools

2019 ◽  
Vol 17 (1) ◽  
pp. 407-416 ◽  
Author(s):  
Abdolali Golpayegani ◽  
Masoumeh Douraghi ◽  
Farhad Rezaei ◽  
Mahmood Alimohammadi ◽  
Ramin Nabizadeh Nodehi
Keyword(s):  
Polymerase Chain Reaction ◽  
Pseudomonas Aeruginosa ◽  
Rapid Detection ◽  
Quantitative Polymerase Chain Reaction ◽  
Qpcr Assay ◽  
Swimming Pools ◽  
Propidium Monoazide ◽  
Chain Reaction ◽  
Polymerase Chain

A Quantitative Polymerase Chain Reaction Assay for Rapid Detection of 9 Pathogens Directly From Stools of Travelers With Diarrhea

2013 ◽  
Vol 11 (10) ◽  
pp. 1300-1307.e3 ◽  
Author(s):  
Jenni Antikainen ◽  
Anu Kantele ◽  
Sari H. Pakkanen ◽  
Tinja Lääveri ◽  
Jukka Riutta ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Assay ◽  
Rapid Detection ◽  
Quantitative Polymerase Chain Reaction ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Clinical Validation of a Novel Commercial Reverse Transcription–Quantitative Polymerase Chain Reaction Screening Assay for Detection of ALK Translocations and Amplifications in Non–Small Cell Lung Carcinomas

2015 ◽  
Vol 140 (7) ◽  
pp. 690-693 ◽  
Author(s):  
Chunyan Liu ◽  
Kristi Pepper ◽  
Heather Hendrickson ◽  
Philip T. Cagle ◽  
Bryce P. Portier
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Quantitative Polymerase Chain Reaction ◽  
Genetic Alterations ◽  
Qpcr Assay ◽  
Egfr Mutations ◽  
Chain Reaction ◽  
Lung Cancers ◽  
Anaplastic Lymphoma ◽  
Polymerase Chain

Context.— EGFR mutations and anaplastic lymphoma kinase (ALK) translocations have significant biologic and therapeutic implications in lung cancers, particularly lung adenocarcinomas. ALK translocations are less frequent compared with EGFR mutations; interestingly, these two abnormalities are most commonly mutually exclusive. The 2013 College of American Pathologists/Association for Molecular Pathology/International Association for the Study of Lung Cancer molecular testing guideline for lung cancers recommend a testing algorithm in which detection of ALK translocations using fluorescence in situ hybridization (FISH) is to be performed following testing for EGFR mutations. Such an algorithm is cost-effective but potentially slows down turnaround time; and as a secondary test, ALK FISH assay may not be completed because it requires the use of additional tissue, and the small biopsies or cytology specimens may have been exhausted in the extraction of nucleic acid for EGFR mutation screening.Objective.—To provide efficient testing of both EGFR and ALK genetic alterations in small biopsies and cytology specimens.Design.—We validated a highly sensitive ALK reverse transcription–quantitative polymerase chain reaction (RT-qPCR) assay as a screening tool for ALK translocations and amplifications.Results.—We performed a retrospective review of cases previously tested by FISH and found that all FISH ALK translocation–positive specimens were RT-qPCR positive, and all FISH ALK translocation–negative cases were RT-qPCR negative (the sensitivity and specificity of the ALK RT-qPCR assay were 100%).Conclusion.—This assay allows rapid identification of ALK alterations, can be performed in conjunction with EGFR testing, and does not require use of valuable additional tumor tissue.

One for two: A novel and highly sensitive virulence factor-based quantitative polymerase chain reaction assay for the simultaneous detection of Rodentibacter pneumotropicus and Rodentibacter heylii in environmental sample material

2019 ◽  
Vol 54 (3) ◽  
pp. 239-250
Author(s):  
Stephanie Buchheister ◽  
Florian Roegener ◽  
Nils-Holger Zschemisch ◽  
Steven R. Talbot ◽  
Henrik Christensen ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Virulence Factor ◽  
Environmental Sample ◽  
Quantitative Polymerase Chain Reaction ◽  
Simultaneous Detection ◽  
Qpcr Assay ◽  
Environmental Sampling ◽  
Sample Material ◽  
Chain Reaction ◽  
Polymerase Chain

Hygienic monitoring of laboratory rodents has focused more and more on the analysis of environmental sample material by quantitative polymerase chain reaction (qPCR) assays. This approach requires profound knowledge of specific genetic sequences of the agents to be monitored and the assays need to be permanently adapted to take the latest research into account. [ Pasteurella] pneumotropica was recently reclassified into the new genus Rodentibacter, with Rodentibacter (R.) pneumotropicus and R. heylii as the most commonly detected species in laboratory mouse colonies. This study aimed at the development of a specific qPCR assay for the simultaneous detection of both agents. A novel primer probe set, based on detection of the specific virulence factor‚ ‘inclusion body protein A’ gene ( ibpA), was confirmed by testing the assay on currently described Rodentibacter type species and other Pasteurellaceae. Furthermore, it was validated within four different barrier units and results were compared with the cultural analysis of sentinel mice. The assay was suitable to specifically detect R. pneumotropicus and R. heylii and discriminate them from other murine Rodentibacter spp. In addition, it revealed high sensitivity for the detection of both agents in environmental sampling material including exhaust air dust in individually ventilated cage systems. Altogether, higher pathogen prevalence was detected via qPCR of environmental samples compared with cultural diagnostics of sentinel mice. This study describes a qPCR assay for the simultaneous detection of R. pneumotropicus and R. heylii. This assay was demonstrated to be beneficial during routine health monitoring, especially with regard to environmental sampling strategies.

scholarly journals Validation of a Triplex Quantitative Polymerase Chain Reaction Assay for Detection and Quantification of Traditional Protein Sources, Pisum sativum L. and Glycine max (L.) Merr., in Protein Powder Mixtures

2021 ◽  
Vol 12 ◽  
Author(s):  
Adam C. Faller ◽  
Dhivya Shanmughanandhan ◽  
Subramanyam Ragupathy ◽  
Yanjun Zhang ◽  
Zhengfei Lu ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Glycine Max ◽  
Pisum Sativum ◽  
Quantitative Polymerase Chain Reaction ◽  
Qpcr Assay ◽  
Analytical Sensitivity ◽  
Chain Reaction ◽  
Powder Mixtures ◽  
Protein Sources ◽  
Polymerase Chain

Several botanicals have been traditionally used as protein sources, including the leguminous Pisum sativum L. and Glycine max (L.) Merr. While a rich history exists of cultivating these plants for their whole, protein-rich grain, modern use as powdered supplements present a new challenge in material authentication. The absence of clear morphological identifiers of an intact plant and the existence of long, complex supply chains behoove industry to create quick, reliable analytical tools to identify the botanical source of a protein product (many of which contain multiple sources). The utility of molecular tools for plant-based protein powder authentication is gaining traction, but few validated tools exist. Multiplex quantitative polymerase chain reaction (qPCR) can provide an economical means by which sources can be identified and relative proportions quantified. We followed established guidelines for the design, optimization, and validation of qPCR assay, and developed a triplex qPCR assay that can amplify and quantify pea and soy DNA targets, normalized by a calibrator. The assay was evaluated for analytical specificity, analytical sensitivity, efficiency, precision, dynamic range, repeatability, and reproducibility. We tested the quantitative ability of the assay using pea and soy DNA mixtures, finding exceptional quantitative linearity for both targets – 0.9983 (p < 0.0001) for soy and 0.9915 (p < 0.0001) for pea. Ratios based on mass of protein powder were also tested, resulting in non-linear patterns in data that suggested the requirement of further sample preparation optimization or algorithmic correction. Variation in fragment size within different lots of commercial protein powder samples was also analyzed, revealing low SD among lots. Ultimately, this study demonstrated the utility of qPCR in the context of protein powder mixtures and highlighted key considerations to take into account for commercial implementation.

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