1
|
Gaudreault C, Salvas J, Sirois J. Savitzky-Golay smoothing and differentiation for polymerase chain reaction quantification. Biochem Cell Biol 2017; 96:380-389. [PMID: 29190123 DOI: 10.1139/bcb-2016-0194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In quantitative PCR (qPCR), replicates can minimize the impact of intra-assay variation; however, inter-assay variations must be minimized to obtain a robust quantification method. The method proposed in this study uses Savitzky-Golay smoothing and differentiation (SGSD) to identify a derivative-maximum-based cycle of quantification. It does not rely on curve modeling, as is the case with many existing techniques. PCR fluorescence data sets challenged for inter-assay variations (different thermocycler units, different reagents batches, different operators, different standard curves, and different labs) were used for the evaluation. The algorithm was compared with a four-parameter logistic model (4PLM) method, the Cy0 method, and the threshold method. The SGSD method compared favourably with all methods in terms of inter-assay variation. SGSD was statistically different from the 4PLM (P = 0.03), Cy0 (P = 0.05), and threshold (P = 0.004) methods on relative error comparison basis. For intra-assay variations, SGSD outperformed the threshold method (P = 0.005) and equalled the 4PLM and Cy0 methods (P > 0.05) on relative error basis. Our results demonstrate that the SGSD method could potentially be an alternative to sigmoid modeling based methods (4PLM and Cy0) when PCR data are challenged for inter-assay variations.
Collapse
Affiliation(s)
- Charles Gaudreault
- a Université de Sherbrooke, Engineering Faculty, 2500 boul. de l'université, QC J1K 2R1, Canada
| | - Joanny Salvas
- b Process Analytical Science Group, Pfizer Montréal, 1025 boul. Marcel-Laurin, Montréal, QC H4R 1J6, Canada
| | - Joël Sirois
- a Université de Sherbrooke, Engineering Faculty, 2500 boul. de l'université, QC J1K 2R1, Canada
| |
Collapse
|
2
|
Ribeiro EL, Oliveira AG, Laguardia-Nascimento M, Mata CPSMD, Reis JKD, Fonseca Júnior AA. Estudo comparativo e validação de três técnicas de PCR em tempo real (qPCR) para diagnóstico de Peste Suína Africana. PESQUISA VETERINARIA BRASILEIRA 2016. [DOI: 10.1590/s0100-736x2016000600003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Resumo: Este estudo verificou o desempenho de três técnicas de PCR quantitativa (Real-Time) para o diagnóstico de Peste Suína Africana, uma doença exótica no Brasil, a partir de amostras de tecidos. As três técnicas escolhidas baseiam-se na amplificação de sequências do gene da proteína viral VP72 e são preconizadas, cada uma, por laboratórios oficiais da OIE (PSA-OIE), dos Estados Unidos (PSA-USDA) e da União Europeia (PSA-EU), respectivamente. Oligonucleotídeos iniciadores e sondas de hidrólise marcadas com fluoróforos foram sintetizados conforme a literatura de referência consultada. Sequências-alvo do DNA viral foram inseridos em plasmídeo sintético, os quais serviram de controle positivo para a padronização das técnicas e otimização de reagentes, determinação dos limites de detecção e testes de verificação de desempenho. Para aferição de repetibilidade e reprodutibilidade das técnicas, as técnicas padronizadas foram repetidas em dias diferentes, por um segundo analista, com alteração no mix comercial de reagentes utilizado e em um equipamento diferente, e também por outro laboratório. Realizaram-se, ainda, provas de sensibilidade analítica com amostras de DNA viral de referência e especificidade analítica e diagnóstica, com amostras negativas. As técnicas de PSA-EU e PSA-USDA apresentaram-se mais vantajosas quanto ao consumo de iniciadores. Não houve diferenças significativas nos resultados quantitativos variando-se os dias dos ensaios, os analistas, os equipamentos e o mix de reagentes. As três técnicas apresentaram alta especificidade analítica e diagnóstica e sensibilidade diagnóstica. As três técnicas de qPCR mostraram-se eficazes para serem adotadas por um mesmo laboratório para emissão de diagnósticos oficiais de Peste Suína Africana.
Collapse
|
3
|
Inhibitory effects of neochamaejasmin B on P-glycoprotein in MDCK-hMDR1 cells and molecular docking of NCB binding in P-glycoprotein. Molecules 2015; 20:2931-48. [PMID: 25679052 PMCID: PMC6272504 DOI: 10.3390/molecules20022931] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/04/2015] [Indexed: 12/01/2022] Open
Abstract
Stellera chamaejasme L. (Thymelaeaceae) is widely distributed in Mongolia, Tibet and the northern parts of China. Its roots are commonly used as “Langdu”, which is embodied in the Pharmacopoeia of the P.R. China (2010) as a toxic Traditional Chinese Medicine. It is claimed to have antivirus, antitumor and antibacterial properties in China and other Asian countries. Studies were carried out to characterize the inhibition of neochamaejasmin B (NCB) on P-glycoprotein (P-gp, ABCB1, MDR1). Rhodamine-123 (R-123) transport and accumulation studies were performed in MDCK-hMDR1 cells. ABCB1 (MDR1) mRNA gene expression and P-gp protein expression were analyzed. Binding selectivity studies based on molecular docking were explored. R-123 transport and accumulation studies in MDCK-hMDR1 cells indicated that NCB inhibited the P-gp-mediated efflux in a concentration-dependent manner. RT-PCR and Western blot demonstrated that the P-gp expression was suppressed by NCB. To investigate the inhibition type of NCB on P-gp, Ki and Ki’ values were determined by double-reciprocal plots in R-123 accumulation studies. Since Ki was greater than Ki’, the inhibition of NCB on P-gp was likely a mixed type of competitive and non-competitive inhibition. The results were confirmed by molecular docking in our current work. The docking data indicated that NCB had higher affinity to P-gp than to Lig1 ((S)-5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one).
Collapse
|
4
|
Gensberger ET, Polt M, Konrad-Köszler M, Kinner P, Sessitsch A, Kostić T. Evaluation of quantitative PCR combined with PMA treatment for molecular assessment of microbial water quality. WATER RESEARCH 2014; 67:367-76. [PMID: 25459225 DOI: 10.1016/j.watres.2014.09.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 09/05/2014] [Accepted: 09/16/2014] [Indexed: 05/15/2023]
Abstract
Microbial water quality assessment currently relies on cultivation-based methods. Nucleic acid-based techniques such as quantitative PCR (qPCR) enable more rapid and specific detection of target organisms and propidium monoazide (PMA) treatment facilitates the exclusion of false positive results caused by DNA from dead cells. Established molecular assays (qPCR and PMA-qPCR) for legally defined microbial quality parameters (Escherichia coli, Enterococcus spp. and Pseudomonas aeruginosa) and indicator organism group of coliforms (implemented on the molecular detection of Enterobacteriaceae) were comparatively evaluated to conventional microbiological methods. The evaluation of an extended set of drinking and process water samples showed that PMA-qPCR for E. coli, Enterococcus spp. and P. aeruginosa resulted in higher specificity because substantial or complete reduction of false positive signals in comparison to qPCR were obtained. Complete compliance to reference method was achieved for E. coli PMA-qPCR and 100% specificity for Enterococcus spp. and P. aeruginosa in the evaluation of process water samples. A major challenge remained in sensitivity of the assays, exhibited through false negative results (7-23%), which is presumably due to insufficient sample preparation (i.e. concentration of bacteria and DNA extraction), rather than the qPCR limit of detection. For the detection of the indicator group of coliforms, the evaluation study revealed that the utilization of alternative molecular assays based on the taxonomic group of Enterobacteriaceae was not adequate. Given the careful optimization of the sensitivity, the highly specific PMA-qPCR could be a valuable tool for rapid detection of hygienic parameters such as E. coli, Enterococcus spp. and P. aeruginosa.
Collapse
Affiliation(s)
- Eva Theres Gensberger
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria.
| | - Marlies Polt
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Marianne Konrad-Köszler
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Paul Kinner
- AIT Austrian Institute of Technology GmbH, Environmental Resources & Technologies Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Tanja Kostić
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| |
Collapse
|
5
|
Heaney CD, Exum NG, Dufour AP, Brenner KP, Haugland RA, Chern E, Schwab KJ, Love DC, Serre ML, Noble R, Wade TJ. Water quality, weather and environmental factors associated with fecal indicator organism density in beach sand at two recreational marine beaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 497-498:440-447. [PMID: 25150738 PMCID: PMC4523396 DOI: 10.1016/j.scitotenv.2014.07.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/23/2014] [Accepted: 07/29/2014] [Indexed: 05/25/2023]
Abstract
Recent studies showing an association between fecal indicator organisms (FIOs) in sand and gastrointestinal (GI) illness among beachgoers with sand contact have important public health implications because of the large numbers of people who recreate at beaches and engage in sand contact activities. Yet, factors that influence fecal pollution in beach sand remain unclear. During the 2007 National Epidemiological and Environmental Assessment of Recreational (NEEAR) Water Study, sand samples were collected at three locations (60 m apart) on weekend days (Sat, Sun) and holidays between June and September at two marine beaches - Fairhope Beach, AL and Goddard Beach, RI - with nearby publicly-owned treatment works (POTWs) outfalls. F(+) coliphage, enterococci, Bacteroidales, fecal Bacteroides spp., and Clostridium spp. were measured in sand using culture and qPCR-based calibrator-cell equivalent methods. Water samples were also collected on the same days, times and transects as the 144 sand samples and were assayed using the same FIO measurements. Weather and environmental data were collected at the time of sample collection. Mean FIO concentrations in sand varied over time, but not space. Enterococci CFU and CCE densities in sand were not correlated, although other FIOs in sand were. The strongest correlation between FIO density in sand and water was fecal Bacteroides CCE, followed by enterococci CFU, Clostridium spp. CCE, and Bacteroidales CCE. Overall, the factors associated with FIO concentrations in sand were related to the sand-water interface (i.e., sand-wetting) and included daily average densities of FIOs in water, rainfall, and wave height. Targeted monitoring that focuses on daily trends of sand FIO variability, combined with information about specific water quality, weather, and environmental factors may inform beach monitoring and management decisions to reduce microbial burdens in beach sand. The views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency.
Collapse
Affiliation(s)
- Christopher D Heaney
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA; Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA.
| | - Natalie G Exum
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA
| | - Alfred P Dufour
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Kristen P Brenner
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Richard A Haugland
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Eunice Chern
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Kellogg J Schwab
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA
| | - David C Love
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA
| | - Marc L Serre
- Department of Environmental Sciences and Engineering, CB# 7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431, USA
| | - Rachel Noble
- Institute of Marine Sciences, CB# 3301, University of North Carolina at Chapel Hill, Morehead City, NC 28557-3301, USA
| | - Timothy J Wade
- Epidemiology Branch, Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| |
Collapse
|
6
|
Haugland RA, Siefring SD, Varma M, Dufour AP, Brenner KP, Wade TJ, Sams E, Cochran S, Braun S, Sivaganensan M. Standardization of enterococci density estimates by EPA qPCR methods and comparison of beach action value exceedances in river waters with culture methods. J Microbiol Methods 2014; 105:59-66. [DOI: 10.1016/j.mimet.2014.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/03/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
|