1
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Gong L, Yao S, He Y, Liu C. Robust and Precise Quantitative Real-Time Polymerase Chain Reaction with an Amplification Efficiency-Aware Reaction Kinetics Model. Anal Chem 2023; 95:5402-5410. [PMID: 36913601 DOI: 10.1021/acs.analchem.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Quantitative real-time PCR (qPCR) is a method extensively used in nucleic acid testing for plants and animals. During the coronavirus disease 2019 (COVID-19) pandemic, high-precision qPCR analysis was urgently needed since quantitative results obtained from conventional qPCR methods were not accurate and precise, causing misdiagnoses and high rates of false-negative. To achieve more accurate results, we propose a new qPCR data analysis method with an amplification efficiency-aware reaction kinetics model (AERKM). Our reaction kinetics model (RKM) mathematically describes the tendency of the amplification efficiency during the whole qPCR process inferred by biochemical reaction dynamics. Amplification efficiency (AE) was introduced to rectify the fitted data so as to match the real reaction process for individual tests, thus reducing errors. The 5-point 10-fold gradient qPCR tests of 63 genes have been verified. The results of a 0.9% slope bias and an 8.2% ratio bias using AERKM exceed 4.1 and 39.4%, respectively, of the best performance of existing models, which demonstrates higher precision, less fluctuation, and better robustness among different nucleic acids. AERKM also provides a better understanding of the real qPCR process and gives insights into the detection, treatment, and prevention of severe diseases.
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Affiliation(s)
- Liang Gong
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Siyue Yao
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yidong He
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Chengliang Liu
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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2
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Bello JC, Higgins DS, Sakalidis ML, Quesada-Ocampo LM, Martin F, Hausbeck MK. Clade-Specific Monitoring of Airborne Pseudoperonospora spp. Sporangia Using Mitochondrial DNA Markers for Disease Management of Cucurbit Downy Mildew. PHYTOPATHOLOGY 2022; 112:2110-2125. [PMID: 35585721 DOI: 10.1094/phyto-12-21-0500-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Management of cucurbit downy mildew (CDM) caused by Pseudoperonospora cubensis, relies on an intensive fungicide program. In Michigan, CDM occurs annually due to an influx of airborne sporangia and timely alerts of airborne inoculum can assist growers in assessing the need to initiate fungicide sprays. This research aimed to improve the specific detection of airborne P. cubensis sporangia by adapting quantitative real-time polymerase chain reaction (qPCR) assays to distinguish among P. cubensis clades I and II and P. humuli in spore trap samples from commercial production sites and research plots. We also evaluated the suitability of impaction spore traps compared with Burkard traps for detection of airborne sporangia. A multiplex qPCR assay improved the specificity of P. cubensis clade II detection accelerating the assessment of field spore trap samples. After 2 years of monitoring, P. cubensis clade II DNA was detected in spore trap samples before CDM symptoms were first observed in cucumber fields (July and August), while P. cubensis clade I DNA was not detected in air samples before or after the disease onset. In some commercial cucumber fields, P. humuli DNA was detected throughout the growing season. The Burkard spore trap appeared to be better suited for recovery of sporangia at low concentrations than the impaction spore trap. This improved methodology for the monitoring of airborne Pseudoperonospora spp. sporangia could be used as part of a CDM risk advisory system to time fungicide applications that protect cucurbit crops in Michigan.
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Affiliation(s)
- Julian C Bello
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Douglas S Higgins
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Monique L Sakalidis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
- Department of Forestry, Michigan State University, East Lansing, MI 48824
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613
| | - Frank Martin
- U.S. Department of Agriculture-Agriculture Research Service, Salinas, CA 93905
| | - Mary K Hausbeck
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
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3
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Antiviral drug research for Japanese encephalitis: an updated review. Pharmacol Rep 2022; 74:273-296. [PMID: 35182390 PMCID: PMC8964565 DOI: 10.1007/s43440-022-00355-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 12/23/2022]
Abstract
Japanese encephalitis (JE) caused by the Japanese encephalitis virus (JEV) is one of Asia's most common viral encephalitis. JEV is a flavivirus, common in rural and sub-urban regions of Asian countries. Although only 1% of JEV-infected individuals develop JE, there is a 20-30% chance of death among these individuals and possible neurological sequelae post-infection. No licensed anti-JE drugs are currently available, despite extensive efforts to develop them. Literature search was performed using databases such as PubMed Central, Google Scholar, Wiley Online Library, etc. using keywords such as Japanese encephalitis virus, antiviral drugs, antiviral drug screening, antiviral drug targets, etc. From around 230 papers/abstracts and research reviews retrieved and reviewed for this study, approximately 180 most relevant and important ones have been cited. Different approaches in drug testing and various antiviral drug targets explored so far have been thoroughly searched from the literature and compiled, besides addressing the future perspectives of the antiviral drug development strategies. Although the development of effective anti-JE drugs is an urgent issue, only supportive care is currently available. Recent advancements in understanding the biology of infection and new drug targets have been promising improvements. Despite hindrances such as the unavailability of a proper drug delivery system or a treatment regimen irrespective of the stage of infection, several promising anti-JE candidate molecules are in different phases of clinical trials. Nonetheless, efficient therapy against JEV is expected to be achieved with drug combinations and a highly targeted drug delivery system soon.
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Zucha D, Kubista M, Valihrach L. Tutorial: Guidelines for Single-Cell RT-qPCR. Cells 2021; 10:cells10102607. [PMID: 34685587 PMCID: PMC8534298 DOI: 10.3390/cells10102607] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) has delivered significant insights in understanding the gene expression landscape. Thanks to its precision, sensitivity, flexibility, and cost effectiveness, RT-qPCR has also found utility in advanced single-cell analysis. Single-cell RT-qPCR now represents a well-established method, suitable for an efficient screening prior to single-cell RNA sequencing (scRNA-Seq) experiments, or, oppositely, for validation of hypotheses formulated from high-throughput approaches. Here, we aim to provide a comprehensive summary of the scRT-qPCR method by discussing the limitations of single-cell collection methods, describing the importance of reverse transcription, providing recommendations for the preamplification and primer design, and summarizing essential data processing steps. With the detailed protocol attached in the appendix, this tutorial provides a set of guidelines that allow any researcher to perform scRT-qPCR measurements of the highest standard.
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Affiliation(s)
- Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- Correspondence:
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Marongiu L, Shain EB, Martinelli M, Pagliari M, Allgayer H. maxRatio improves the detection of samples with abnormal amplification profiles on QIAgen's artus HIV-1 qPCR assay. F1000Res 2021; 9:1030. [PMID: 34557295 PMCID: PMC8442116 DOI: 10.12688/f1000research.25738.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Accurate viral load (VL) determination is paramount to determine the efficacy of anti-HIV-1 therapy. The conventional method used, fit-point (FP), assumes an equal efficiency in the polymerase chain reaction (PCR) among samples that might not hold for low-input templates. An alternative approach, maxRatio, was introduced to compensate for inhibition in PCR. Methods: Herein, we assessed whether maxRatio could improve VL quantification using 2,544 QIAgen artus HI virus-1 RT-PCR reactions. The assay’s standard dilutions were used to build external standard curves with either FP or maxRatio that re-calculated the VLs. Results: FP and maxRatio were highly comparable (Pearson’s ρ=0.994, Cohen’s κ=0.885), and the combination of the two methods identified samples (n=41) with aberrant amplification profiles. Conclusions: The combination of maxRatio and FP could improve the predictive value of the assay.
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Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery, University of Heidelberg, Medical Faculty in Mannheim, Mannheim, Baden-Wuttenberg, 68167, Germany.,Department of Biochemistry of Nutrition, University of Hohenheim, Garbenstr.30, 70599, Stuttgart, Germany
| | - Eric B Shain
- Grove Street Technology LLC, Grove Street Technology LLC, Glencoe, Illinois, 60022, USA
| | - Marianna Martinelli
- Department of Medicine and Surgery, University of Milano Bicocca, Monza, Italy, 20900, Italy
| | - Matteo Pagliari
- Department of Diagnostics in Animal Health, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Veneto, 35020, Italy
| | - Heike Allgayer
- Department of Experimental Surgery, University of Heidelberg, Medical Faculty in Mannheim, Mannheim, Baden-Wuttenberg, 68167, Germany
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6
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Green H, Wilder M, Wiedmann M, Weller D. Integrative Survey of 68 Non-overlapping Upstate New York Watersheds Reveals Stream Features Associated With Aquatic Fecal Contamination. Front Microbiol 2021; 12:684533. [PMID: 34475855 PMCID: PMC8406625 DOI: 10.3389/fmicb.2021.684533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/05/2021] [Indexed: 12/03/2022] Open
Abstract
Aquatic fecal contamination poses human health risks by introducing pathogens in water that may be used for recreation, consumption, or agriculture. Identifying fecal contaminant sources, as well as the factors that affect their transport, storage, and decay, is essential for protecting human health. However, identifying these factors is often difficult when using fecal indicator bacteria (FIB) because FIB levels in surface water are often the product of multiple contaminant sources. In contrast, microbial source-tracking (MST) techniques allow not only the identification of predominant contaminant sources but also the quantification of factors affecting the transport, storage, and decay of fecal contaminants from specific hosts. We visited 68 streams in the Finger Lakes region of Upstate New York, United States, between April and October 2018 and collected water quality data (i.e., Escherichia coli, MST markers, and physical–chemical parameters) and weather and land-use data, as well as data on other stream features (e.g., stream bed composition), to identify factors that were associated with fecal contamination at a regional scale. We then applied both generalized linear mixed models and conditional inference trees to identify factors and combinations of factors that were significantly associated with human and ruminant fecal contamination. We found that human contaminants were more likely to be identified when the developed area within the 60 m stream buffer exceeded 3.4%, the total developed area in the watershed exceeded 41%, or if stormwater outfalls were present immediately upstream of the sampling site. When these features were not present, human MST markers were more likely to be found when rainfall during the preceding day exceeded 1.5 cm. The presence of upstream campgrounds was also significantly associated with human MST marker detection. In addition to rainfall and water quality parameters associated with rainfall (e.g., turbidity), the minimum distance to upstream cattle operations, the proportion of the 60 m buffer used for cropland, and the presence of submerged aquatic vegetation at the sampling site were all associated based on univariable regression with elevated levels of ruminant markers. The identification of specific features associated with host-specific fecal contaminants may support the development of broader recommendations or policies aimed at reducing levels of aquatic fecal contamination.
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Affiliation(s)
- Hyatt Green
- Department of Environmental Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, United States
| | - Maxwell Wilder
- Department of Environmental Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Daniel Weller
- Department of Environmental Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, United States
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7
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Hsu B, Sherina V, McCall MN. Autoregressive modeling and diagnostics for qPCR amplification. Bioinformatics 2021; 36:5386-5391. [PMID: 33244594 DOI: 10.1093/bioinformatics/btaa1000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Current methods used to analyze real-time quantitative polymerase chain reaction (qPCR) data exhibit systematic deviations from the assumed model over the progression of the reaction. Slight variations in the amount of the initial target molecule or in early amplifications are likely responsible for these deviations. Commonly used 4- and 5-parameter sigmoidal models appear to be particularly susceptible to this issue, often displaying patterns of autocorrelation in the residuals. The presence of this phenomenon, even for technical replicates, suggests that these parametric models may be misspecified. Specifically, they do not account for the sequential dependent nature of the amplification process that underlies qPCR fluorescence measurements. RESULTS We demonstrate that a Smooth Transition Autoregressive (STAR) model addresses this limitation by explicitly modeling the dependence between cycles and the gradual transition between amplification regimes. In summary, application of a STAR model to qPCR amplification data improves model fit and reduces autocorrelation in the residuals. AVAILABILITY AND IMPLEMENTATION R scripts to reproduce all the analyses and results described in this manuscript can be found at: https://github.com/bhsu4/GAPDH.SO. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benjamin Hsu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Valeriia Sherina
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
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8
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Teh CSJ, Lau MY, Chong CW, Ngoi ST, Chua KH, Lee WS, Thong KL. One-step differential detection of Salmonella enterica serovar Typhi, serovar Paratyphi A and other Salmonella spp. by using a quadruplex real-time PCR assay. J Microbiol Methods 2021; 183:106184. [PMID: 33662480 DOI: 10.1016/j.mimet.2021.106184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Diseases caused by typhoidal and non-typhoidal Salmonella remain a considerable threat to both developed and developing countries. Based on the clinical symptoms and serological tests, it is sometimes difficult to differentiate the Salmonella enterica serovar Paratyphi A (S. enterica serovar Paratyphi A) from serovar Typhi (S. enterica serovar Typhi). In this study, we developed a quadruplex real-time polymerase chain reaction (PCR) assay with an internal amplification control (IAC), to simultaneously differentiate S. enterica serovar Paratyphi A from serovar Typhi and to detect other Salmonella serovars which cause salmonellosis in humans. This assay was evaluated on 155 salmonellae and non-salmonellae strains and demonstrated 100% specificity in species differentiation. Inclusion of an IAC did not affect the efficiency of the assay. Further evaluation using a blind test on spiked stool, blood and food specimens showed that the detection limit was at 103 -104 CFU/mL (or g) and a high PCR efficiency with different targets (R2 > 0.99), except for S. enterica serovar Paratyphi A in blood. This assay has been applied to clinical specimens to detect the causative agents of gastrointestinal infections and has successfully identified 6 salmonellosis patients from the 50 diarrhoea patients. The quadruplex real-time PCR developed in this study could enhance the detection and differentiation of salmonellae. This assay could be applied to stools, blood and food based on the notable performance in the simulation tests and field evaluation.
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Affiliation(s)
- Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Min Yi Lau
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor, Malaysia
| | - Soo Tein Ngoi
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Way Seah Lee
- Department of Paediatrics, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Nanotechnology & Catalysis Research Centre, Deputy Vice Chancellor (Research & Innovation), University of Malaya, 50603 Kuala Lumpur, Malaysia
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9
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Variation in Expression of Reference Genes across Life Stages of a Bee, Megachile rotundata. INSECTS 2021; 12:insects12010036. [PMID: 33418888 PMCID: PMC7825039 DOI: 10.3390/insects12010036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 01/19/2023]
Abstract
Simple Summary Reference genes are key to normalizing expression data across samples of organisms collected after different treatments are applied, but often, reference genes are not properly validated for this purpose. In this report, we screened several genes for a solitary bee, Megachile rotundata, and identified two (RPS18, and RPL8) with very stable expression levels across all life stages of the bee, and under a variety of environmental conditions, including during and after diapause. These genes should make good reference genes. We also identified other genes with stable expression, even if used only for a limited number of developmental stages. This information is important for future gene expression studies on these bees, but it also demonstrates the importance of validating reference genes in general. Abstract The alfalfa leafcutting bee, Megachile rotundata is widely used in the western United States as a pollinator for alfalfa seed production. Unfortunately, immatures experience high mortality in agriculturally managed populations. Quantified gene expression could be used to identify how this bee responds during different life stages to pathogens, environmental toxins, and other stresses, but stably expressed reference genes are needed to normalize transcription data. We evaluated twelve candidate genes for their transcription stability across different life stages, including during and after diapause. RPS18 and RPL8 were the two most stably expressed genes, followed by RPS5 and RPL27A. These genes were also very stable even during and after diapause, while the most variable genes being APN, PMIIM, NPC2, and Cr-PII had increased expression levels during larval growth and were also variable during and after diapause. The four reference genes we identified in M. rotundata may prove useful for transcriptomic studies in other bees as well, such as honey bees.
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de Puig H, Bosch I, Collins JJ, Gehrke L. Point-of-Care Devices to Detect Zika and Other Emerging Viruses. Annu Rev Biomed Eng 2020; 22:371-386. [DOI: 10.1146/annurev-bioeng-060418-052240] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rapid diagnostic tests (point-of-care devices) are critical components of informed patient care and public health monitoring (surveillance applications). We propose that among the many rapid diagnostics platforms that have been tested or are in development, lateral flow immunoassays and synthetic biology–based diagnostics (including CRISPR-based diagnostics) represent the best overall options given their ease of use, scalability for manufacturing, sensitivity, and specificity. This review describes the identification of lateral flow immunoassay monoclonal antibody pairs that detect and distinguish between closely related pathogens and that are used in combination with functionalized multicolored nanoparticles and computational methods to deconvolute data. We also highlight the promise of synthetic biology–based diagnostic tests, which use synthetic genetic circuits that activate upon recognition of a pathogen-associated nucleic acid sequence, and discuss how the combined or parallel use of lateral flow immunoassays and synthetic biology tools may represent the future of scalable rapid diagnostics.
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Affiliation(s)
- Helena de Puig
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Irene Bosch
- E25Bio Inc., Cambridge, Massachusetts 02139, USA
| | - James J. Collins
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
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11
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Panina Y, Germond A, David BG, Watanabe TM. Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay. BMC Bioinformatics 2019; 20:295. [PMID: 31146686 PMCID: PMC6543629 DOI: 10.1186/s12859-019-2911-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/21/2019] [Indexed: 11/22/2022] Open
Abstract
Background The real-time quantitative polymerase chain reaction (qPCR) is routinely used for quantification of nucleic acids and is considered the gold standard in the field of relative nucleic acid measurements. The efficiency of the qPCR reaction is one of the most important parameters in data analysis in qPCR experiments. The Minimum Information for publication of Quantitative real-time PCR Experiments (MIQE) guidelines recommends the calibration curve as the method of choice for estimation of qPCR efficiency. The precision of this method has been reported to be between SD = 0.007 (three replicates) and SD = 0.022 (no replicates). Results In this article, we present a novel approach to the analysis of qPCR data which has been obtained by running a dilution series. Unlike previously developed methods, our method, Pairwise Efficiency, involves a new formula that describes pairwise relationships between data points on separate amplification curves and thus enables extensive statistics. The comparison of Pairwise Efficiency with the calibration curve by Monte Carlo simulation shows the two-folds improvement in the precision of estimations of efficiency and gene expression ratios on the same dataset. Conclusions The Pairwise Efficiency nearly doubles the precision in qPCR efficiency determinations compared to standard calibration curve method. This paper demonstrates that applications of combinatorial treatment of data provide the improvement of the determination. Electronic supplementary material The online version of this article (10.1186/s12859-019-2911-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yulia Panina
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Arno Germond
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Brit G David
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan. .,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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Sajali N, Wong SC, Hanapi UK, Abu Bakar Jamaluddin S, Tasrip NA, Mohd Desa MN. The Challenges of DNA Extraction in Different Assorted Food Matrices: A Review. J Food Sci 2018; 83:2409-2414. [DOI: 10.1111/1750-3841.14338] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Nurhayatie Sajali
- School of Engineering and Technology; University College of Technology Sarawak; 868 Persiaran Brooke 96000 Sibu Sarawak Malaysia
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
| | - Sie Chuong Wong
- Department of Basic Science and Engineering, Faculty of Agriculture and Food Sciences; Universiti Putra Malaysia Bintulu Sarawak Campus; P.O. Box 396, Nyabau Road 97008 Bintulu Sarawak Malaysia
| | - Ummi Kalthum Hanapi
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
| | - Suhaili Abu Bakar Jamaluddin
- Department of Biomedical Science, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia; 43400, Selangor Darul Ehsan Malaysia
| | - Nor Asmara Tasrip
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
| | - Mohd Nasir Mohd Desa
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia; 43400, Selangor Darul Ehsan Malaysia
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13
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Liao J, Liu Y. Purification procedures meaningfully influence DNA quantification in milk. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Byrnes SA, Chang TC, Huynh T, Astashkina A, Weigl BH, Nichols KP. Simple Polydisperse Droplet Emulsion Polymerase Chain Reaction with Statistical Volumetric Correction Compared with Microfluidic Droplet Digital Polymerase Chain Reaction. Anal Chem 2018; 90:9374-9380. [DOI: 10.1021/acs.analchem.8b01988] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Samantha A. Byrnes
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Tim C. Chang
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Toan Huynh
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Anna Astashkina
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Bernhard H. Weigl
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
| | - Kevin P. Nichols
- Intellectual Ventures Laboratory, 14360 Southeast Eastgate Way, Bellevue, Washington 98007, United States
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15
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Žiarovská J, Kyseľ M, Cimermanová R, Knoteková Ľ. Effect of DNA extraction in the Rosa canina L. identification under different processing temperature. POTRAVINARSTVO 2017. [DOI: 10.5219/717] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rosa canina, L. is widely used for medicinal purposes as well as in food industry where it is a valuable source, bioactive compounds and natural colorants. Actually, no specific method is recommended as suitable one for DNA extraction from rose hips. The aim of the study was to compare three commercial and three non-commercial methods to extract total genomic DNA from rose hips hyphanthium. Four methods are based on the precipitation in principle and two methods are based on resin-binding. Extracted DNA was proved for the effectivity in following PCR. In total, six different DNA isolations was performed for differently heat processes rose hips - fresh hyphanthium, 2-weeks frozen hyphanthium, dried hyphanthium (50 °C) and boiled hyphanthium (100 °C). The amplification parameters of 500 bp chloroplast gene amplicon were evaluated. Obtained amounts of extracted DNA was very variable not only for every individual method used but for individual treatment of samples, too. In general, non-commercial method provided higher amount of extracted DNA, but the A260/280 ratio was lower. When regarding the processing treatment of the samples, high differences were found among the samples untreated by heat and those that were dried or boiled for three of the used extraction methods. All the samples were positive for amplification, but different amounts of amplified product were obtained. The comparison of data for concentrations of extracted DNA and concentrations of amplified product showed large differences when regarding the achieved purity of DNA in extraction.
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16
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Sidstedt M, Romsos EL, Hedell R, Ansell R, Steffen CR, Vallone PM, Rådström P, Hedman J. Accurate Digital Polymerase Chain Reaction Quantification of Challenging Samples Applying Inhibitor-Tolerant DNA Polymerases. Anal Chem 2017; 89:1642-1649. [PMID: 28118703 DOI: 10.1021/acs.analchem.6b03746] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Digital PCR (dPCR) enables absolute quantification of nucleic acids by partitioning of the sample into hundreds or thousands of minute reactions. By assuming a Poisson distribution for the number of DNA fragments present in each chamber, the DNA concentration is determined without the need for a standard curve. However, when analyzing nucleic acids from complex matrixes such as soil and blood, the dPCR quantification can be biased due to the presence of inhibitory compounds. In this study, we evaluated the impact of varying the DNA polymerase in chamber-based dPCR for both pure and impure samples using the common PCR inhibitor humic acid (HA) as a model. We compared the TaqMan Universal PCR Master Mix with two alternative DNA polymerases: ExTaq HS and Immolase. By using Bayesian modeling, we show that there is no difference among the tested DNA polymerases in terms of accuracy of absolute quantification for pure template samples, i.e., without HA present. For samples containing HA, there were great differences in performance: the TaqMan Universal PCR Master Mix failed to correctly quantify DNA with more than 13 pg/nL HA, whereas Immolase (1 U) could handle up to 375 pg/nL HA. Furthermore, we found that BSA had a moderate positive effect for the TaqMan Universal PCR Master Mix, enabling accurate quantification for 25 pg/nL HA. Increasing the amount of DNA polymerase from 1 to 5 U had a strong effect for ExTaq HS, elevating HA-tolerance four times. We also show that the average Cq values of positive reactions may be used as a measure of inhibition effects, e.g., to determine whether or not a dPCR quantification result is reliable. The statistical models developed to objectively analyze the data may also be applied in quality control. We conclude that the choice of DNA polymerase in dPCR is crucial for the accuracy of quantification when analyzing challenging samples.
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Affiliation(s)
- Maja Sidstedt
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden.,Swedish National Forensic Centre , SE-581 94 Linköping, Sweden
| | - Erica L Romsos
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Ronny Hedell
- Swedish National Forensic Centre , SE-581 94 Linköping, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Ricky Ansell
- Swedish National Forensic Centre , SE-581 94 Linköping, Sweden.,Department of Physics, Chemistry and Biology, IFM, Linköping University , SE-581 83 Linköping, Sweden
| | - Carolyn R Steffen
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Peter M Vallone
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden
| | - Johannes Hedman
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden.,Swedish National Forensic Centre , SE-581 94 Linköping, Sweden
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17
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Goldberg CS, Turner CR, Deiner K, Klymus KE, Thomsen PF, Murphy MA, Spear SF, McKee A, Oyler‐McCance SJ, Cornman RS, Laramie MB, Mahon AR, Lance RF, Pilliod DS, Strickler KM, Waits LP, Fremier AK, Takahara T, Herder JE, Taberlet P. Critical considerations for the application of environmental
DNA
methods to detect aquatic species. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12595] [Citation(s) in RCA: 497] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Caren S. Goldberg
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Cameron R. Turner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Kristy Deiner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Katy E. Klymus
- Lake Erie Center University of Toledo 6200 Bayshore Rd. Oregon OH 43616 USA
| | - Philip Francis Thomsen
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5‐7 DK‐1350 Copenhagen Denmark
| | - Melanie A. Murphy
- Department of Ecosystem Science andManagement Program in Ecology University of Wyoming Department 3354 1000 E University Ave Laramie WY 82071 USA
| | | | - Anna McKee
- U.S. Geological Survey South Atlantic Water Science Center 1770 Corporate Drive Suite 500 Norcross GA 30093 USA
| | - Sara J. Oyler‐McCance
- U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave, Building C Fort Collins CO 80526 USA
| | - Robert Scott Cornman
- U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave, Building C Fort Collins CO 80526 USA
| | - Matthew B. Laramie
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Boise ID 83706 USA
| | - Andrew R. Mahon
- Department of Biology Institute for Great Lakes Research Central Michigan University Mount Pleasant MI 48859 USA
| | - Richard F. Lance
- Environmental Laboratory US Army Engineer Research & Development Center Vicksburg MS 39180 USA
| | - David S. Pilliod
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Boise ID 83706 USA
| | - Katherine M. Strickler
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Lisette P. Waits
- Fish and Wildlife Sciences University of Idaho Moscow ID 83844‐1136 USA
| | - Alexander K. Fremier
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Teruhiko Takahara
- Faculty of Life and Environmental Science Shimane University 1060 Nishikawatsu Matsue Shimane 690‐8504 Japan
| | - Jelger E. Herder
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON) P.O. Box 1413 6501 BK Nijmegen The Netherlands
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes F‐38000 Grenoble France
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18
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Mahaffee WF, Stoll R. The Ebb and Flow of Airborne Pathogens: Monitoring and Use in Disease Management Decisions. PHYTOPATHOLOGY 2016; 106:420-431. [PMID: 27003505 DOI: 10.1094/phyto-02-16-0060-rvw] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Perhaps the earliest form of monitoring the regional spread of plant disease was a group of growers gathering together at the market and discussing what they see in their crops. This type of reporting continues to this day through regional extension blogs, by crop consultants and more formal scouting of sentential plots in the IPM PIPE network (http://www.ipmpipe.org/). As our knowledge of plant disease epidemiology has increased, we have also increased our ability to detect and monitor the presence of pathogens and use this information to make management decisions in commercial production systems. The advent of phylogenetics, next-generation sequencing, and nucleic acid amplification technologies has allowed for development of sensitive and accurate assays for pathogen inoculum detection and quantification. The application of these tools is beginning to change how we manage diseases with airborne inoculum by allowing for the detection of pathogen movement instead of assuming it and by targeting management strategies to the early phases of the epidemic development when there is the greatest opportunity to reduce the rate of disease development. While there are numerous advantages to using data on inoculum presence to aid management decisions, there are limitations in what the data represent that are often unrecognized. In addition, our understanding of where and how to effectively monitor airborne inoculum is limited. There is a strong need to improve our knowledge of the mechanisms that influence inoculum dispersion across scales as particles move from leaf to leaf, and everything in between.
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Affiliation(s)
- Walter F Mahaffee
- First author: U.S. Department of Agriculture-Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR 97330; and second author: Department of Mechanical Engineering, University of Utah, Salt Lake City 84112
| | - Rob Stoll
- First author: U.S. Department of Agriculture-Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR 97330; and second author: Department of Mechanical Engineering, University of Utah, Salt Lake City 84112
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19
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Xu W, Wang C, Zhu P, Guo T, Xu Y, Huang K, Luo Y. Real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons. Analyst 2016; 141:2542-52. [DOI: 10.1039/c6an00145a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This nicking endonuclease-mediated isothermal amplification with small molecular beacons (SMB-NEMA) method allows the simple, specific and sensitive assessment of isothermal DNA quantification.
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Affiliation(s)
- Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing 100083
- China
| | - Chenguang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing 100083
- China
| | - Pengyu Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing 100083
- China
| | - Tianxiao Guo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing 100083
- China
| | - Yuancong Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing 100083
- China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing 100083
- China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing 100083
- China
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20
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Fachmann M, Josefsen M, Hoorfar J, Nielsen M, Löfström C. Cost-effective optimization of real-time PCR-based detection of Campylobacter
and Salmonella
with inhibitor tolerant DNA polymerases. J Appl Microbiol 2015; 119:1391-402. [DOI: 10.1111/jam.12937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/03/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
Affiliation(s)
- M.S.R. Fachmann
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - M.H. Josefsen
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - J. Hoorfar
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - M.T. Nielsen
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
| | - C. Löfström
- Division of Microbiology and Production; National Food Institute; Technical University of Denmark; Søborg Denmark
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21
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Palos Ladeiro M, Bigot-Clivot A, Aubert D, Villena I, Geffard A. Assessment of Toxoplasma gondii levels in zebra mussel (Dreissena polymorpha) by real-time PCR: an organotropism study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13693-13701. [PMID: 25772876 DOI: 10.1007/s11356-015-4296-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Water quality is a public health concern that calls for relevant biomonitoring programs. Molecular tools such as polymerase chain reaction (PCR) are progressively becoming more sensitive and more specific than conventional techniques to detect pathogens in environmental samples such as water and organisms. The zebra mussel (Dreissena polymorpha) has already been demonstrated to accumulate and concentrate various human waterborne pathogens. In this study, first, a spiking experiment to evaluate detection levels of Toxoplasma gondii DNA in zebra mussel organs using real-time PCR was conducted. Overall, lower DNA levels in the hemolymph, digestive gland, and remaining tissues (gonad and foot) were detected compared to mantle, muscle, and gills. Second, an in vivo experiment with 1000 T. gondii oocysts per mussel and per day for 21 consecutive days, followed by 14 days of depuration time in protozoa-free water was performed. T. gondii DNA was detected in all organs, but greatest concentrations were observed in hemolymph and mantle tissues compared to the others organs at the end of the depuration period. These results suggest that (i) the zebra mussel is a potential new tool for measuring T. gondii concentrations and (ii) real-time PCR is a suitable method for pathogen detection in complex matrices such as tissues.
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Affiliation(s)
- M Palos Ladeiro
- Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques, UMR-I 02 (SEBIO), Université de Reims Champagne-Ardenne, Reims, France
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22
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Choosing between RT-qPCR and RNA-seq: a back-of-the-envelope estimate towards the definition of the break-even-point. Anal Bioanal Chem 2015; 406:3533-6. [PMID: 24687434 DOI: 10.1007/s00216-014-7687-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Svec D, Tichopad A, Novosadova V, Pfaffl MW, Kubista M. How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 3:9-16. [PMID: 27077029 PMCID: PMC4822216 DOI: 10.1016/j.bdq.2015.01.005] [Citation(s) in RCA: 318] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 01/24/2015] [Accepted: 01/28/2015] [Indexed: 01/22/2023]
Abstract
We have examined the imprecision in the estimation of PCR efficiency by means of standard curves based on strategic experimental design with large number of technical replicates. In particular, how robust this estimation is in terms of a commonly varying factors: the instrument used, the number of technical replicates performed and the effect of the volume transferred throughout the dilution series. We used six different qPCR instruments, we performed 1–16 qPCR replicates per concentration and we tested 2–10 μl volume of analyte transferred, respectively. We find that the estimated PCR efficiency varies significantly across different instruments. Using a Monte Carlo approach, we find the uncertainty in the PCR efficiency estimation may be as large as 42.5% (95% CI) if standard curve with only one qPCR replicate is used in 16 different plates. Based on our investigation we propose recommendations for the precise estimation of PCR efficiency: (1) one robust standard curve with at least 3–4 qPCR replicates at each concentration shall be generated, (2) the efficiency is instrument dependent, but reproducibly stable on one platform, and (3) using a larger volume when constructing serial dilution series reduces sampling error and enables calibration across a wider dynamic range.
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Key Words
- ANCOVA, analysis of covariance
- Amplification efficiency
- CLSI, Clinical and Laboratory Standards Institute
- Cq, cycle of quantification
- Dilution series
- E, PCR efficiency
- EPA, Environmental protection agency
- FDA, food and Drug Administration
- GMO, genetically modified organism
- IEC, International Electrotechnical Commission
- ISO, International Organization for Standardization
- MIQE, minimum information for publication of quantitative real-time PCR experiments
- NTC, no template control
- RIN, RNA Integrity Number
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- Real-time quantitative PCR
- Standard curve
- qPCR
- qPCR assay validation
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Affiliation(s)
- David Svec
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
| | - Ales Tichopad
- Faculty of Medicine Pilsen, Charles University, Pilsen, Czech Republic
| | - Vendula Novosadova
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
| | - Michael W Pfaffl
- Physiology Weihenstephan, TUM - Technische Universität München, Freising, Germany
| | - Mikael Kubista
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
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24
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Kalle E, Kubista M, Rensing C. Multi-template polymerase chain reaction. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 2:11-29. [PMID: 27896140 PMCID: PMC5121205 DOI: 10.1016/j.bdq.2014.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/12/2022]
Abstract
PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.
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Affiliation(s)
- Elena Kalle
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Allmas alle 5, 75007 Uppsala, Sweden
| | - Mikael Kubista
- TATAA Biocenter, Odinsgatan 28, 41103 Göteborg, Sweden; Institute of Biotechnology, Czech Academy of Sciences
| | - Christopher Rensing
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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25
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Vera-Lozada G, Scholl V, Barros MHM, Sisti D, Guescini M, Stocchi V, Stefanoff CG, Hassan R. Analysis of biological and technical variability in gene expression assays from formalin-fixed paraffin-embedded classical Hodgkin lymphomas. Exp Mol Pathol 2014; 97:433-9. [PMID: 25236575 DOI: 10.1016/j.yexmp.2014.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/09/2014] [Accepted: 09/12/2014] [Indexed: 11/16/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are invaluable sources of biological material for research and diagnostic purposes. In this study, we aimed to identify biological and technical variability in RT-qPCR TaqMan® assays performed with FFPE-RNA from lymph nodes of classical Hodgkin lymphoma samples. An ANOVA-nested 6-level design was employed to evaluate BCL2, CASP3, IRF4, LYZ and STAT1 gene expression. The most variable genes were CASP3 (low expression) and LYZ (high expression). Total variability decreased after normalization for all genes, except by LYZ. Genes with moderate and low expression were identified and suffered more the effects of the technical manipulation than high-expression genes. Pre-amplification was shown to introduce significant technical variability, which was partially alleviated by lowering to a half the amount of input RNA. Ct and Cy0 quantification methods, based on cycle-threshold and the kinetic of amplification curves, respectively, were compared. Cy0 method resulted in higher quantification values, leading to the decrease of total variability in CASP3 and LYZ genes. The mean individual noise was 0.45 (0.31 to 0.61 SD), indicating a variation of gene expression over ~1.5 folds from one case to another. We showed that total variability in RT-qPCR from FFPE-RNA is not higher than that reported for fresh complex tissues, and identified gene-, and expression level-sources of biological and technical variability, which can allow better strategies for designing RT-qPCR assays from highly degraded and inhibited samples.
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Affiliation(s)
- Gabriela Vera-Lozada
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Vanesa Scholl
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | | | - Davide Sisti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Via I Maggetti, Urbino, Italy
| | - Michele Guescini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Via I Maggetti, Urbino, Italy
| | - Vilberto Stocchi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Via I Maggetti, Urbino, Italy
| | | | - Rocio Hassan
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.
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26
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Hedman J, Knutsson R, Ansell R, Rådström P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2014; 11 Suppl 1:S87-101. [PMID: 23971826 DOI: 10.1089/bsp.2012.0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification--that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis--so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
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Affiliation(s)
- Johannes Hedman
- Johannes Hedman, PhD, is employed as a specialist at the Swedish National Laboratory of Forensic Science (SKL) and holds a research position at Applied Microbiology, Lund University. Rickard Knutsson, PhD, is Director of Security Department, National Veterinary Institute (SVA), Uppsala, Sweden . Ricky Ansell, PhD, is employed as forensic advisor and senior reporting officer at the Swedish National Laboratory of Forensic Science (SKL). Birgitta Rasmusson, PhD, is employed as research director at the Swedish National Laboratory of Forensic Science (SKL) and holds a position as adjunct professor at Applied Microbiology, Lund University. Peter Rådström, PhD, is employed as professor Applied Microbiology, Lund University
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27
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Oenological prefermentation practices strongly impact yeast population dynamics and alcoholic fermentation kinetics in Chardonnay grape must. Int J Food Microbiol 2014; 178:87-97. [PMID: 24681710 DOI: 10.1016/j.ijfoodmicro.2014.03.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 02/26/2014] [Accepted: 03/06/2014] [Indexed: 11/23/2022]
Abstract
Yeast species of Hanseniaspora and Candida genus are predominant during the early stages of winemaking, while species of Metschnikowia, Pichia, Zygoascus, Issatchenkia, Torulaspora and other genera are present at lower population levels. The impact of common oenological practices on yeast dynamics during the prefermentative stage and the early stage of alcoholic fermentation (AF) remains elusive. In this work, the effect of four prefermentative oenological practices (clarification degree, temperature, sulphite and starter yeast addition) on yeast dynamics was evaluated in a Chardonnay grape must. The growth curves of four genus or species, namely Saccharomyces spp., Hanseniaspora spp., Candida zemplinina and Torulaspora delbrueckii, were followed by quantitative PCR. The fermentation kinetics were also recorded, as well as the production of acetic acid. Variance analysis allowed determining the effect of each practice and their interaction factors, as well as their relative importance on yeast dynamics and fermentation kinetics. Our experimental design showed that the population dynamics of the four species were differently impacted by the oenological practices, with some species being more sensitive than others to the clarification degree (C. zemplinina), sulphite addition (Saccharomyces spp.), starter yeast inoculation (Hanseniaspora spp.) or prefermentation temperature (T. delbrueckii). Significant interaction effects between practices were revealed, highlighting the interest of experimental design allowing interaction analysis, as some factors may buffer the effect of other ones. Hanseniaspora genus showed atypical behaviour: growth dynamics showed a decrease during AF that we interpreted as early cellular lysis. In conclusion, this study provides new insights on the impact of common oenological practices on the dynamics of non-Saccharomyces yeast that will be useful for a better management of mixed fermentation between S. cerevisiae and non-Saccharomyces yeasts.
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28
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Chen Y, Bogema DR, Barchia IM, Herron GA. Quantification of the pirimicarb resistance allele frequency in pooled cotton aphid (Aphis gossypii Glover) samples by TaqMan SNP genotyping assay. PLoS One 2014; 9:e91104. [PMID: 24614533 PMCID: PMC3948748 DOI: 10.1371/journal.pone.0091104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/07/2014] [Indexed: 11/25/2022] Open
Abstract
Background Pesticide resistance monitoring is a crucial part to achieving sustainable integrated pest management (IPM) in agricultural production systems. Monitoring of resistance in arthropod populations is initially performed by bioassay, a method that detects a phenotypic response to pesticides. Molecular diagnostic assays, offering speed and cost improvements, can be developed when the causative mutation for resistance has been identified. However, improvements to throughput are limited as genotyping methods cannot be accurately applied to pooled DNA. Quantifying an allele frequency from pooled DNA would allow faster and cheaper monitoring of pesticide resistance. Methodology/Principal Findings We demonstrate a new method to quantify a resistance allele frequency (RAF) from pooled insects via TaqMan assay by using raw fluorescence data to calculate the transformed fluorescence ratio k’ at the inflexion point based on a four parameter sigmoid curve. Our results show that k’ is reproducible and highly correlated with RAF (r >0.99). We also demonstrate that k’ has a non-linear relationship with RAF and that five standard points are sufficient to build a prediction model. Additionally, we identified a non-linear relationship between runs for k’, allowing the combination of samples across multiple runs in a single analysis. Conclusions/Significance The transformed fluorescence ratio (k') method can be used to monitor pesticide resistance in IPM and to accurately quantify allele frequency from pooled samples. We have determined that five standards (0.0, 0.2, 0.5, 0.8, and 1.0) are sufficient for accurate prediction and are statistically-equivalent to the 13 standard points used experimentally
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Affiliation(s)
- Yizhou Chen
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Idris M Barchia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Grant A Herron
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
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Sakurai M, Watanabe T, Suzuki T, Furihata C. Time-course Comparison of Gene Expression Profiles Induced by the Genotoxic Hepatocarcinogen, Chrysene, in the Mouse Liver. Genes Environ 2014. [DOI: 10.3123/jemsge.2014.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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30
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Comparing real-time quantitative polymerase chain reaction analysis methods for precision, linearity, and accuracy of estimating amplification efficiency. Anal Biochem 2013; 449:76-82. [PMID: 24365068 DOI: 10.1016/j.ab.2013.12.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/06/2013] [Accepted: 12/15/2013] [Indexed: 11/21/2022]
Abstract
New methods are used to compare seven qPCR analysis methods for their performance in estimating the quantification cycle (Cq) and amplification efficiency (E) for a large test data set (94 samples for each of 4 dilutions) from a recent study. Precision and linearity are assessed using chi-square (χ(2)), which is the minimized quantity in least-squares (LS) fitting, equivalent to the variance in unweighted LS, and commonly used to define statistical efficiency. All methods yield Cqs that vary strongly in precision with the starting concentration N0, requiring weighted LS for proper calibration fitting of Cq vs log(N0). Then χ(2) for cubic calibration fits compares the inherent precision of the Cqs, while increases in χ(2) for quadratic and linear fits show the significance of nonlinearity. Nonlinearity is further manifested in unphysical estimates of E from the same Cq data, results which also challenge a tenet of all qPCR analysis methods - that E is constant throughout the baseline region. Constant-threshold (Ct) methods underperform the other methods when the data vary considerably in scale, as these data do.
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Schelin J, Andersson G, Vigre H, Norling B, Häggblom P, Hoorfar J, Rådström P, Löfström C. Evaluation of pre-PCR processing approaches for enumeration of Salmonella enterica
in naturally contaminated animal feed. J Appl Microbiol 2013; 116:167-78. [DOI: 10.1111/jam.12337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/09/2013] [Accepted: 08/27/2013] [Indexed: 11/29/2022]
Affiliation(s)
- J. Schelin
- Applied Microbiology; Department of Chemistry; Lund University; Lund Sweden
| | - G. Andersson
- Department of Chemistry; Environment and Feed hygiene; National Veterinary Institute (SVA); Uppsala Sweden
| | - H. Vigre
- National Food Institute; Technical University of Denmark; Søborg Denmark
| | - B. Norling
- Quintessence Research AB (QRAB); Alunda Sweden
| | - P. Häggblom
- Department of Chemistry; Environment and Feed hygiene; National Veterinary Institute (SVA); Uppsala Sweden
| | - J. Hoorfar
- National Food Institute; Technical University of Denmark; Søborg Denmark
| | - P. Rådström
- Applied Microbiology; Department of Chemistry; Lund University; Lund Sweden
| | - C. Löfström
- National Food Institute; Technical University of Denmark; Søborg Denmark
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32
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Carvalhais V, Delgado-Rastrollo M, Melo LDR, Cerca N. Controlled RNA contamination and degradation and its impact on qPCR gene expression in S. epidermidis biofilms. J Microbiol Methods 2013; 95:195-200. [PMID: 23999274 DOI: 10.1016/j.mimet.2013.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 08/14/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
Abstract
RNA quality is of utmost importance to perform gene expression quantification by qPCR. The classical methods used to determine RNA quality are based on electrophoresis and spectrophotometer assessment, namely A(260)/A(280) and A(260)/A(230) ratios. It was previously shown that due to the complex nature of Staphylococcus epidermidis biofilms, RNA extraction procedures could impact mRNA quality and thus accurate quantification. Herein, we contaminated and degraded RNA extracted from S. epidermidis biofilms, and assessed the effect on gene expression by qPCR. As expected, thermal degradation of RNA had a significant impact on gene expression on two out of the three tested genes. On the other hand, the contamination of the extracted RNA yielded an interesting result: while most contaminants did not changed the purity indicators or the integrity of RNA, significant changes on gene expression levels were found. This work confirms that poor RNA extraction has an important impact in qPCR quantification, emphasizing the consequences of carry-over contaminants on gene expression studies. Additionally, our results show that the parameters commonly used to assess the quality of extracted RNA from bacterial cultures seem to be insufficient to ensure reliable gene expression determination.
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Affiliation(s)
- Virginia Carvalhais
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Braga, Portugal
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Guescini M, Sisti D, Rocchi MBL, Panebianco R, Tibollo P, Stocchi V. Accurate and precise DNA quantification in the presence of different amplification efficiencies using an improved Cy0 method. PLoS One 2013; 8:e68481. [PMID: 23861909 PMCID: PMC3704541 DOI: 10.1371/journal.pone.0068481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/05/2013] [Indexed: 12/23/2022] Open
Abstract
Quantitative real-time PCR represents a highly sensitive and powerful technology for the quantification of DNA. Although real-time PCR is well accepted as the gold standard in nucleic acid quantification, there is a largely unexplored area of experimental conditions that limit the application of the Ct method. As an alternative, our research team has recently proposed the Cy0 method, which can compensate for small amplification variations among the samples being compared. However, when there is a marked decrease in amplification efficiency, the Cy0 is impaired, hence determining reaction efficiency is essential to achieve a reliable quantification. The proposed improvement in Cy0 is based on the use of the kinetic parameters calculated in the curve inflection point to compensate for efficiency variations. Three experimental models were used: inhibition of primer extension, non-optimal primer annealing and a very small biological sample. In all these models, the improved Cy0 method increased quantification accuracy up to about 500% without affecting precision. Furthermore, the stability of this procedure was enhanced integrating it with the SOD method. In short, the improved Cy0 method represents a simple yet powerful approach for reliable DNA quantification even in the presence of marked efficiency variations.
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Affiliation(s)
- Michele Guescini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Via I Maggetti, Urbino, Italy.
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Fishbein I, Forbes SP, Chorny M, Connolly JM, Adamo RF, Corrales RA, Alferiev IS, Levy RJ. Adenoviral vector tethering to metal surfaces via hydrolyzable cross-linkers for the modulation of vector release and transduction. Biomaterials 2013; 34:6938-48. [PMID: 23777912 DOI: 10.1016/j.biomaterials.2013.05.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 05/23/2013] [Indexed: 01/16/2023]
Abstract
The use of arterial stents and other medical implants as a delivery platform for surface immobilized gene vectors allows for safe and efficient localized expression of therapeutic transgenes. In this study we investigate the use of hydrolyzable cross-linkers with distinct kinetics of hydrolysis for delivery of gene vectors from polyallylamine bisphosphonate-modified metal surfaces. Three cross-linkers with the estimated t1/2 of ester bonds hydrolysis of 5, 12 and 50 days demonstrated a cumulative 20%, 39% and 45% vector release, respectively, after 30 days exposure to physiological buffer at 37 °C. Transgene expression in endothelial and smooth muscles cells transduced with substrate immobilized adenovirus resulted in significantly different expression profiles for each individual cross-linker. Furthermore, immobilization of adenoviral vectors effectively extended their transduction effectiveness beyond the initial phase of release. Transgene expression driven by adenovirus-tethered stents in rat carotid arteries demonstrated that a faster rate of cross-linker hydrolysis resulted in higher expression levels at day 1, which declined by day 8 after stent implantation, while inversely, slower hydrolysis was associated with increased arterial expression at day 8 in comparison with day 1. In conclusion, adjustable release of transduction-competent adenoviral vectors from metallic surfaces can be achieved, both in vitro and in vivo, through surface immobilization of adenoviral vectors using hydrolyzable cross-linkers with structure-specific release kinetics.
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Affiliation(s)
- Ilia Fishbein
- Division of Cardiology, The Children's Hospital of Philadelphia, Abramson Research Center, and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA.
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35
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Huang Y, Yin X, Zhu C, Wang W, Grierson D, Xu C, Chen K. Standard addition quantitative real-time PCR (SAQPCR): a novel approach for determination of transgene copy number avoiding PCR efficiency estimation. PLoS One 2013; 8:e53489. [PMID: 23308234 PMCID: PMC3538589 DOI: 10.1371/journal.pone.0053489] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 11/28/2012] [Indexed: 11/23/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qPCR) has been previously applied to estimate transgene copy number in transgenic plants. However, the results can be erroneous owing to inaccurate estimation of PCR efficiency. Here, a novel qPCR approach, named standard addition qPCR (SAQPCR), was devised to accurately determine transgene copy number without the necessity of obtaining PCR efficiency data. The procedures and the mathematical basis for the approach are described. A recombinant plasmid harboring both the internal reference gene and the integrated target gene was constructed to serve as the standard DNA. It was found that addition of suitable amounts of standard DNA to test samples did not affect PCR efficiency, and the guidance for selection of suitable cycle numbers for analysis was established. Samples from six individual T0 tomato (Solanum lycopersicum) plants were analyzed by SAQPCR, and the results confirmed by Southern blot analysis. The approach produced accurate results and required only small amounts of plant tissue. It can be generally applied to analysis of different plants and transgenes. In addition, it can also be applied to zygosity analysis.
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Affiliation(s)
- Yuji Huang
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, P. R. China
| | - Xueren Yin
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, P. R. China
| | - Changqing Zhu
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, P. R. China
| | - Weiwei Wang
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, P. R. China
| | - Donald Grierson
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, P. R. China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Changjie Xu
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, P. R. China
- * E-mail:
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, P. R. China
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Lievens A, Van Aelst S, Van den Bulcke M, Goetghebeur E. Simulation of between repeat variability in real time PCR reactions. PLoS One 2012; 7:e47112. [PMID: 23189123 PMCID: PMC3506646 DOI: 10.1371/journal.pone.0047112] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/12/2012] [Indexed: 11/19/2022] Open
Abstract
While many decisions rely on real time quantitative PCR (qPCR) analysis few attempts have hitherto been made to quantify bounds of precision accounting for the various sources of variation involved in the measurement process. Besides influences of more obvious factors such as camera noise and pipetting variation, changing efficiencies within and between reactions affect PCR results to a degree which is not fully recognized. Here, we develop a statistical framework that models measurement error and other sources of variation as they contribute to fluorescence observations during the amplification process and to derived parameter estimates. Evaluation of reproducibility is then based on simulations capable of generating realistic variation patterns. To this end, we start from a relatively simple statistical model for the evolution of efficiency in a single PCR reaction and introduce additional error components, one at a time, to arrive at stochastic data generation capable of simulating the variation patterns witnessed in repeated reactions (technical repeats). Most of the variation in C(q) values was adequately captured by the statistical model in terms of foreseen components. To recreate the dispersion of the repeats' plateau levels while keeping the other aspects of the PCR curves within realistic bounds, additional sources of reagent consumption (side reactions) enter into the model. Once an adequate data generating model is available, simulations can serve to evaluate various aspects of PCR under the assumptions of the model and beyond.
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Affiliation(s)
- Antoon Lievens
- Platform for Molecular Biology and Biotechnology, Scientific Institute of Public Health, Brussels, Belgium.
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37
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RT-qPCR work-flow for single-cell data analysis. Methods 2012; 59:80-8. [PMID: 23021995 DOI: 10.1016/j.ymeth.2012.09.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/21/2012] [Accepted: 09/17/2012] [Indexed: 11/22/2022] Open
Abstract
Individual cells represent the basic unit in tissues and organisms and are in many aspects unique in their properties. The introduction of new and sensitive techniques to study single-cells opens up new avenues to understand fundamental biological processes. Well established statistical tools and recommendations exist for gene expression data based on traditional cell population measurements. However, these workflows are not suitable, and some steps are even inappropriate, to apply on single-cell data. Here, we present a simple and practical workflow for preprocessing of single-cell data generated by reverse transcription quantitative real-time PCR. The approach is demonstrated on a data set based on profiling of 41 genes in 303 single-cells. For some pre-processing steps we present options and also recommendations. In particular, we demonstrate and discuss different strategies for handling missing data and scaling data for downstream multivariate analysis. The aim of this workflow is provide guide to the rapidly growing community studying single-cells by means of reverse transcription quantitative real-time PCR profiling.
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