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Molecular phylogeny of mitochondrial DNA: Shrimp species identification by multiplex and real-time PCR. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106868] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Dobnik D, Gruden K, Žel J, Bertheau Y, Holst-Jensen A, Bohanec M. Decision Support for the Comparative Evaluation and Selection of Analytical Methods: Detection of Genetically Modified Organisms as an Example. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1194-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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4
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Luo J, Vogel RF, Niessen L. Rapid detection of aflatoxin producing fungi in food by real-time quantitative loop-mediated isothermal amplification. Food Microbiol 2014; 44:142-8. [DOI: 10.1016/j.fm.2014.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/10/2014] [Accepted: 06/06/2014] [Indexed: 11/30/2022]
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5
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Block A, Debode F, Grohmann L, Hulin J, Taverniers I, Kluga L, Barbau-Piednoir E, Broeders S, Huber I, Van den Bulcke M, Heinze P, Berben G, Busch U, Roosens N, Janssen E, Žel J, Gruden K, Morisset D. The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants. BMC Bioinformatics 2013; 14:256. [PMID: 23965170 PMCID: PMC3765097 DOI: 10.1186/1471-2105-14-256] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 08/06/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introduced into the host genome. Information available regarding the GMOs' molecular characterization is dispersed and not appropriately organized. For this reason, GMO testing is very challenging and requires more complex screening strategies and decision making schemes, demanding in return the use of efficient bioinformatics tools relying on reliable information. DESCRIPTION The GMOseek matrix was built as a comprehensive, online open-access tabulated database which provides a reliable, comprehensive and user-friendly overview of 328 GMO events and 247 different genetic elements (status: 18/07/2013). The GMOseek matrix is aiming to facilitate GMO detection from plant origin at different phases of the analysis. It assists in selecting the targets for a screening analysis, interpreting the screening results, checking the occurrence of a screening element in a group of selected GMOs, identifying gaps in the available pool of GMO detection methods, and designing a decision tree. The GMOseek matrix is an independent database with effective functionalities in a format facilitating transferability to other platforms. Data were collected from all available sources and experimentally tested where detection methods and certified reference materials (CRMs) were available. CONCLUSIONS The GMOseek matrix is currently a unique and very valuable tool with reliable information on GMOs from plant origin and their present genetic elements that enables further development of appropriate strategies for GMO detection. It is flexible enough to be further updated with new information and integrated in different applications and platforms.
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Affiliation(s)
- Annette Block
- Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium.
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6
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Jo IH, Bang KH, Kim YC, Lee JW, Seo AY, Seong BJ, Kim HH, Kim DH, Cha SW, Cho YG, Kim HS. Rapid Identification of Ginseng Cultivars (Panax ginseng Meyer) Using Novel SNP-Based Probes. J Ginseng Res 2013; 35:504-13. [PMID: 23717098 PMCID: PMC3659547 DOI: 10.5142/jgr.2011.35.4.504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 12/16/2011] [Accepted: 12/16/2011] [Indexed: 11/18/2022] Open
Abstract
In order to develop a novel system for the discrimination of five ginseng cultivars (Panax ginseng Meyer), single nucleotide polymorphism (SNP) genotyping assays with real-time polymerase chain reaction were conducted. Nucleotide substitution in gDNA library clones of P. ginseng cv. Yunpoong was targeted for the SNP genotyping assay. From these SNP sites, a set of modified SNP specific fluorescence probes (PGP74, PGP110, and PGP130) and novel primer sets have been developed to distinguish among five ginseng cultivars. The combination of the SNP type of the five cultivars, Chungpoong, Yunpoong, Gopoong, Kumpoong, and Sunpoong, was identified as ‘ATA’, ‘GCC’, ‘GTA’, ‘GCA’, and ‘ACC’, respectively. This study represents the first report of the identification of ginseng cultivars by fluorescence probes. An SNP genotyping assay using fluorescence probes could prove useful for the identification of ginseng cultivars and ginseng seed management systems and guarantee the purity of ginseng seed.
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Affiliation(s)
- Ick-Hyun Jo
- National Institute of Horticultural & Herbal Science, Rural Development Administration, Eumseong 369-873, Korea
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7
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Samson MC, Gullí M, Marmiroli N. Multiplex real-time PCR assays for simultaneous detection of maize MON810 and GA21 in food samples. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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8
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Debode F, Janssen E, Berben G. Development of 10 new screening PCR assays for GMO detection targeting promoters (pFMV, pNOS, pSSuAra, pTA29, pUbi, pRice actin) and terminators (t35S, tE9, tOCS, tg7). Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-1921-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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9
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Dobnik D, Baebler Š, Kogovšek P, Pompe-Novak M, Štebih D, Panter G, Janež N, Morisset D, Žel J, Gruden K. β-1,3-glucanase class III promotes spread of PVY NTN and improves in planta protein production. PLANT BIOTECHNOLOGY REPORTS 2013; 7:547-555. [PMID: 24273610 PMCID: PMC3824212 DOI: 10.1007/s11816-013-0300-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/11/2013] [Indexed: 05/18/2023]
Abstract
Glucanases are enzymes regulating the size exclusion limit and permeability of plasmodesmata and play a role in biotic stress. In plant genomes, they are encoded as relatively large gene families divided into four classes. Most studies of plant virus interactions have focused on glucanases from classes I and II. In our study, we have evaluated the role of the β-1,3-glucanase class III (Glu-III) gene in the potato-potato virus YNTN (PVYNTN) interaction and implemented the findings to plant biotechnology application. Potato cultivars Désirée and Santé, which are tolerant and extremely resistant to PVYNTN, respectively, were stably transformed with Agrobacterium tumefaciens harbouring constructs for Glu-III overexpression. Localization of Glu-III protein in patches within the cell wall was determined by tagging the Glu-III protein with green fluorescent protein. Transgenic and non-transgenic plants were challenged with PVYNTN and its multiplication and spreading was followed. Differences in viral spread were observed between transgenic lines overexpressing Glu-III and non-transgenic lines, with stronger and faster viral spread in transgenic Désirée, and some multiplication in transgenic Santé. In addition, the ability of Glu-III to improve in planta protein production after agroinfiltration was tested. The results have shown that Glu-III overexpression enables faster spreading of vectors between cells and better protein production, which could be beneficial in improving in planta protein production system using viral vectors.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Maruša Pompe-Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Dejan Štebih
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Gabriela Panter
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Nikolaja Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Velika pot 22, 5250 Solkan, Slovenia
| | - Dany Morisset
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Velika pot 22, 5250 Solkan, Slovenia
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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10
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Chuang PS, Chen MI, Shiao JC. Identification of tuna species by a real-time polymerase chain reaction technique. Food Chem 2012. [DOI: 10.1016/j.foodchem.2012.01.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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11
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Detection of genetically modified material in feed and foodstuffs containing soy and maize in Jordan. J Food Compost Anal 2012. [DOI: 10.1016/j.jfca.2012.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Terio V, Di Pinto P, Decaro N, Parisi A, Desario C, Martella V, Buonavoglia C, Tantillo MG. Identification of tuna species in commercial cans by minor groove binder probe real-time polymerase chain reaction analysis of mitochondrial DNA sequences. Mol Cell Probes 2010; 24:352-6. [DOI: 10.1016/j.mcp.2010.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 06/25/2010] [Accepted: 07/25/2010] [Indexed: 11/17/2022]
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13
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Samson MC, Gullì M, Marmiroli N. Quantitative detection method for Roundup Ready soybean in food using duplex real-time PCR MGB chemistry. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2010; 90:1437-44. [PMID: 20549794 DOI: 10.1002/jsfa.3961] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND Methodologies that enable the detection of genetically modified organisms (GMOs) (authorized and non-authorized) in food and feed strongly influence the potential for adequate updating and implementation of legislation together with labeling requirements. Quantitative polymerase chain reaction (qPCR) systems were designed to boost the sensitivity and specificity on the identification of GMOs in highly degraded DNA samples; however, such testing will become economically difficult to cope with due to increasing numbers of approved genetically modified (GM) lines. Multiplexing approaches are therefore in development to provide cost-efficient solution. RESULTS Construct-specific primers and probe were developed for quantitative analysis of Roundup Ready soybean (RRS) event glyphosate-tolerant soybean (GTS) 40-3-2. The lectin gene (Le1) was used as a reference gene, and its specificity was verified. RRS- and Le1-specific quantitative real-time PCR (qRTPCR) were optimized in a duplex platform that has been validated with respect to limit of detection (LOD) and limit of quantification (LOQ), as well as accuracy. The analysis of model processed food samples showed that the degradation of DNA has no adverse or little effects on the performance of quantification assay. CONCLUSION In this study, a duplex qRTPCR using TaqMan minor groove binder-non-fluorescent quencher (MGB-NFQ) chemistry was developed for specific detection and quantification of RRS event GTS 40-3-2 that can be used for practical monitoring in processed food products.
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Affiliation(s)
- Maria Cristina Samson
- Department of Environmental Sciences, Genetics and Environmental Biotechnology Section, University of Parma, Parma, Italy
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Branquinho MR, Ferreira RT, Cardarelli-Leite P. Survey of compliance with labeling legislation in food containing GMOs in Brazil. J Food Compost Anal 2010. [DOI: 10.1016/j.jfca.2009.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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16
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Sun Y, Kwok YC, Foo-Peng Lee P, Nguyen NT. Rapid amplification of genetically modified organisms using a circular ferrofluid-driven PCR microchip. Anal Bioanal Chem 2009; 394:1505-8. [PMID: 19399482 DOI: 10.1007/s00216-009-2808-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 04/14/2009] [Accepted: 04/16/2009] [Indexed: 10/20/2022]
Abstract
The use of genetically modified organisms (GMOs) as food and in food products is becoming more and more widespread. Polymerase chain reaction (PCR) technology is extensively used for the detection of GMOs in food products in order to verify compliance with labeling requirements. In this paper, we present a novel close-loop ferrofluid-driven PCR microchip for rapid amplification of GMOs. The microchip was fabricated in polymethyl methacrylate by CO2 laser ablation and was integrated with three temperature zones. PCR solution was contained in a circular closed microchannel and was driven by magnetic force generated by an external magnet through a small oil-based ferrofluid plug. Successful amplification of genetically modified soya and maize were achieved in less than 13 min. This PCR microchip combines advantages of cycling flexibility and quick temperature transitions associated with two existing microchip PCR techniques, and it provides a cost saving and less time-consuming way to conduct preliminary screening of GMOs.
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Affiliation(s)
- Yi Sun
- National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore
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Chaouachi M, Chupeau G, Berard A, McKhann H, Romaniuk M, Giancola S, Laval V, Bertheau Y, Brunel D. A high-throughput multiplex method adapted for GMO detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:11596-11606. [PMID: 19053386 DOI: 10.1021/jf801482r] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A high-throughput multiplex assay for the detection of genetically modified organisms (GMO) was developed on the basis of the existing SNPlex method designed for SNP genotyping. This SNPlex assay allows the simultaneous detection of up to 48 short DNA sequences (approximately 70 bp; "signature sequences") from taxa endogenous reference genes, from GMO constructions, screening targets, construct-specific, and event-specific targets, and finally from donor organisms. This assay avoids certain shortcomings of multiplex PCR-based methods already in widespread use for GMO detection. The assay demonstrated high specificity and sensitivity. The results suggest that this assay is reliable, flexible, and cost- and time-effective for high-throughput GMO detection.
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Affiliation(s)
- Maher Chaouachi
- CEA/Institut de Genomique/Centre National de Genotypage/INRA UR EPGV, 2 rue Gaston Cremieux, CP 5724, 91057 Evry cedex, France
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18
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Christianson J, McPherson M, Topinka D, Hall L, Good AG. Detecting and quantifying the adventitious presence of transgenic seeds in safflower, Carthamus tinctorius L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:5506-13. [PMID: 18578537 DOI: 10.1021/jf800683g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Safflower ( Carthamus tinctorius L.) is currently being developed as a platform for the production of novel proteins. Methods for detecting and quantifying transgenic safflower are needed to ensure seed quality and to monitor for its adventitious presence. We developed and compared three methods of assaying for transgenic safflower presence in conventional seedlots: field bioassays, enzyme-linked immunosorbent assays (ELISA), and quantitative polymerase chain reaction (Q-PCR). Limits for reliable quantification for both ELISA and Q-PCR are approximately 0.1%, although levels at least as low as 0.02% can be detected by Q-PCR. Levels of quantification for the field bioassay are limited only by space and resources available. Multiple sampling methods to detect and quantify transgenic safflower presence at levels lower than 0.1% were used on field collected samples from a pollen outcrossing experiment to quantify the adventitious presence of transgenic safflower. Taking into account the potential utility and relative advantages or disadvantages of each detection method, it is recommended that the initial testing for the adventitious presence of transgenic seed be carried out using an antibody-based test if available and that Q-PCR-based assays to quantify transgenic proportion be used when it is necessary to identify specific transgenic constructs or if antibody-based assays are not readily available.
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Affiliation(s)
- Jed Christianson
- Deparment of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Zhang H, Yang L, Guo J, Li X, Jiang L, Zhang D. Development of one novel multiple-target plasmid for duplex quantitative PCR analysis of roundup ready soybean. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:5514-20. [PMID: 18570432 DOI: 10.1021/jf800033k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To enforce the labeling regulations of genetically modified organisms (GMOs), the application of reference molecules as calibrators is becoming essential for practical quantification of GMOs. However, the reported reference molecules with tandem marker multiple targets have been proved not suitable for duplex PCR analysis. In this study, we developed one unique plasmid molecule based on one pMD-18T vector with three exogenous target DNA fragments of Roundup Ready soybean GTS 40-3-2 (RRS), that is, CaMV35S, NOS, and RRS event fragments, plus one fragment of soybean endogenous Lectin gene. This Lectin gene fragment was separated from the three exogenous target DNA fragments of RRS by inserting one 2.6 kb DNA fragment with no relatedness to RRS detection targets in this resultant plasmid. Then, we proved that this design allows the quantification of RRS using the three duplex real-time PCR assays targeting CaMV35S, NOS, and RRS events employing this reference molecule as the calibrator. In these duplex PCR assays, the limits of detection (LOD) and quantification (LOQ) were 10 and 50 copies, respectively. For the quantitative analysis of practical RRS samples, the results of accuracy and precision were similar to those of simplex PCR assays, for instance, the quantitative results were at the 1% level, the mean bias of the simplex and duplex PCR were 4.0% and 4.6%, respectively, and the statistic analysis ( t-test) showed that the quantitative data from duplex and simplex PCR had no significant discrepancy for each soybean sample. Obviously, duplex PCR analysis has the advantages of saving the costs of PCR reaction and reducing the experimental errors in simplex PCR testing. The strategy reported in the present study will be helpful for the development of new reference molecules suitable for duplex PCR quantitative assays of GMOs.
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Affiliation(s)
- Haibo Zhang
- GMO Detection Laboratory, SJTU-Bor Luh Food Safety Center, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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20
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Gryson N, Dewettinck K, Messens K. Detection of Genetically Modified Soy in Doughs and Cookies. Cereal Chem 2007. [DOI: 10.1094/cchem-84-2-0109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nicolas Gryson
- University College Ghent, Department of Food Science and Technology, Faculty of Biosciences and Landscape Architecture, Ghent University Association, Voskenslaan 270, Gent 9000
- Corresponding author. Phone: +32 9 242 42 96. Fax: +32 9 242 42 93. E-mail:
| | - Koen Dewettinck
- Ghent University, Department of Food Quality and Food Safety, Laboratory of Food Technology and Engineering
| | - Kathy Messens
- University College Ghent, Department of Food Science and Technology, Faculty of Biosciences and Landscape Architecture, Ghent University Association, Voskenslaan 270, Gent 9000
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Rønning SB, Berdal KG, Andersen CB, Holst-Jensen A. Novel reference gene, PKABA1, used in a duplex real-time polymerase chain reaction for detection and quantitation of wheat- and barley-derived DNA. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:682-7. [PMID: 16448168 DOI: 10.1021/jf052328n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We report the development of a duplex real-time Polymerase Chain Reaction (PCR) for the simultaneous detection and quantification of wheat- and barley-derived DNA. We used a single primer pair to amplify the single-copy gene PKABA1 from wheat and barley, using minor-groove-binding probes to distinguish between the two cereals. The assay was fully specific, and different wheat and barley cultivars exhibited similar Ct values, indicating stability across cultivars with respect to allelic and copy number composition. The limits of detection were 5 and 10 PCR-forming units for wheat and barley, respectively, making the duplex assay as sensitive as other singleplex reference gene systems published. We were able to detect both wheat and barley simultaneously in real food samples, and the duplex assay is considered to be suitable as an endogenous reference gene system for the detection and quantification of wheat and barley in genetically modified organisms (GMO) and other food and feed analyses.
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Affiliation(s)
- Sissel B Rønning
- Section for Feed and Food Microbiology, National Veterinary Institute, Ullevålsveien 68, Post Office Box 8156 Dep., 0033 Oslo, Norway
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Torp A, Olesen A, Sten E, Stahl Skov P, Bindslev-Jensen U, Poulsen L, Bindslev-Jensen C, Andersen S. Specific, semi-quantitative detection of the soybean allergen Gly m Bd 30K DNA by PCR. Food Control 2006. [DOI: 10.1016/j.foodcont.2004.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Moreano F, Ehlert A, Busch U, Engel KH. Ligation-dependent probe amplification for the simultaneous event-specific detection and relative quantification of DNA from two genetically modified organisms. Eur Food Res Technol 2005. [DOI: 10.1007/s00217-005-0169-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Liu YC, Lin SH, Lai HM, Jeng ST. Detection of genetically modified soybean and its product tou-kan by polymerase chain reaction with dual pairs of DNA primers. Eur Food Res Technol 2005. [DOI: 10.1007/s00217-005-0066-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Park MR, Lee HS, Kang SH. Multiplex Polymerase Chain Reaction/Microchip Electrophoresis for the Rapid Detection of GMO in Soybean. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2005. [DOI: 10.5012/jkcs.2005.49.3.255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Lopez I, Pardo MA. Application of relative quantification TaqMan real-time polymerase chain reaction technology for the identification and quantification of Thunnus alalunga and Thunnus albacares. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:4554-60. [PMID: 15913324 DOI: 10.1021/jf0500841] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A novel one-step methodology based on real-time Polymerase Chain Reaction (PCR) technology has been developed for the identification of two of the most valuable tuna species. Nowadays, species identification of seafood products has a major concern due to the importing to Europe of new species from other countries. To achieve this aim, two specific TaqMan systems were devised to identify Thunnus alalunga and Thunnus albacares. Another system specific to Scombroidei species was devised as a consensus system. In addition, a relative quantification methodology was carried out to quantify T. alalunga and T. albacares in mixtures after the relative amount of the target was compared with the consensus. This relative quantification methodology does not require a known amount of standard, allowing the analysis of many more samples together and saving costs and time. The utilization of real-time PCR does not require sample handling, preventing contamination and resulting in much faster and higher throughput results.
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Affiliation(s)
- Itziar Lopez
- Department of Food Technology, AZTI-Fisheries and Food Technological Institute, Txatxarramendi ugartea z/g, E-48395 Sukarrieta, Bizkaia, Spain
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Tani H, Noda N, Yamada K, Kurata S, Tsuneda S, Hirata A, Kanagawa T. Quantification of genetically modified soybean by quenching probe polymerase chain reaction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:2535-40. [PMID: 15796591 DOI: 10.1021/jf048031r] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Quenching probe (QProbe) polymerase chain reaction (PCR) is a simple and cost-effective real-time PCR assay in comparison with other real-time PCR assays such as the TaqMan assay. We used QProbe-PCR to quantify genetically modified (GM) soybean (Roundup Ready soybean). We designed event-specific QProbes for Le1 (soy endogenous gene) and RRS (recombinant gene), and we quantified certified reference materials containing 0.1, 0.5, 1, 2, and 5% GM soybean. The TaqMan assay was also applied to the same samples, and the results were compared. The accuracy of QProbe-PCR was similar to that of TaqMan assay. When GM soybean content was 0.5% or more, the relative standard deviations of QProbe-PCR were less than 20%. QProbe-PCR is sensitive enough to monitor labeling systems and has acceptable levels of accuracy and precision.
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Affiliation(s)
- Hidenori Tani
- Department of Chemical Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
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Yang L, Pan A, Jia J, Ding J, Chen J, Cheng H, Zhang C, Zhang D. Validation of a tomato-specific gene, LAT52, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic tomatoes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:183-190. [PMID: 15656646 DOI: 10.1021/jf0493730] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Toward the development of reliable qualitative and quantitative Polymerase Chain Reaction (PCR) detection methods of transgenic tomatoes, one tomato (Lycopersicon esculentum) species specific gene, LAT52, was selected and validated as suitable for using as an endogenous reference gene in transgenic tomato PCR detection. Both qualitative and quantitative PCR methods were assayed with 16 different tomato varieties, and identical amplified products or fluorescent signals were obtained with all of them. No amplified products and fluorescent signals were observed when DNA samples from 20 different plants such as soybean, maize, rapeseed, rice, and Arabidopsis thaliana were used as templates. These results demonstrated that the amplified LAT52 DNA sequence was specific for tomato. Furthermore, results of Southern blot showed that the LAT52 gene was a single-copy gene in the different tested tomato cultivars. In qualitative and quantitative PCR analysis, the detection sensitivities were 0.05 and 0.005 ng of tomato genomic DNA, respectively. In addition, two real-time assays employing this gene as an endogenous reference gene were established, one for the quantification of processed food samples derived from nontransgenic tomatoes that contained degraded target DNA and the other for the quantification of the junction region of CaMV35s promoter and the anti-sense ethylene-forming enzyme (EFE) gene in transgenic tomato Huafan No. 1 samples. All of these results indicated that the LAT52 gene could be successfully used as a tomato endogenous reference gene in practical qualitative and quantitative detection of transgenic tomatoes, even for some processed foods derived from transgenic and nontransgenic tomatoes.
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Affiliation(s)
- Litao Yang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
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Huang HY, Pan TM. Detection of genetically modified maize MON810 and NK603 by multiplex and real-time polymerase chain reaction methods. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2004; 52:3264-3268. [PMID: 15161180 DOI: 10.1021/jf049944o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this study, the event-specific primers for insecticide-resistant maize, MON810, and herbicide-tolerance maize, NK603, have been designed. Simplex PCR and multiplex PCR detection method have been developed. The detection limit of the multiplex PCR is 0.5% for MON810 and NK603 in 50 ng of the template for one reaction. Quantitative methods based on real-time quantitative PCR were developed for MON810 and NK603. Plasmid pMulM2 as reference molecules for the detection of MON810 and NK603 was constructed. Quantification range was from 0.5 to 100% in 100 ng of the DNA template for one reaction. The precision of real-time Q-PCR detection methods, expressed as coefficient of variation for MON810 and NK603 varied from 1.97 to 8.01% and from 3.45 to 10.94%, respectively. The range agreed with European interlaboratories test results (25%). According to the results, the methods for quantitative detection of genetically modified maize were acceptable.
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Affiliation(s)
- Hsin-Ying Huang
- Institute of Microbiology and Biochemistry, National Taiwan University, Taipei, Taiwan 106
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Hernández M, Rodríguez-Lázaro D, Esteve T, Prat S, Pla M. Development of melting temperature-based SYBR Green I polymerase chain reaction methods for multiplex genetically modified organism detection. Anal Biochem 2003; 323:164-70. [PMID: 14656521 DOI: 10.1016/j.ab.2003.07.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Commercialization of several genetically modified crops has been approved worldwide to date. Uniplex polymerase chain reaction (PCR)-based methods to identify these different insertion events have been developed, but their use in the analysis of all commercially available genetically modified organisms (GMOs) is becoming progressively insufficient. These methods require a large number of assays to detect all possible GMOs present in the sample and thereby the development of multiplex PCR systems using combined probes and primers targeted to sequences specific to various GMOs is needed for detection of this increasing number of GMOs. Here we report on the development of a multiplex real-time PCR suitable for multiple GMO identification, based on the intercalating dye SYBR Green I and the analysis of the melting curves of the amplified products. Using this method, different amplification products specific for Maximizer 176, Bt11, MON810, and GA21 maize and for GTS 40-3-2 soybean were obtained and identified by their specific Tm. We have combined amplification of these products in a number of multiplex reactions and show the suitability of the methods for identification of GMOs with a sensitivity of 0.1% in duplex reactions. The described methods offer an economic and simple alternative to real-time PCR systems based on sequence-specific probes (i.e., TaqMan chemistry). These methods can be used as selection tests and further optimized for uniplex GMO quantification.
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Affiliation(s)
- Marta Hernández
- Dpt de Genètica Molecular, Institut de Biologia Molecular de Barcelona, Centro de Investigación y Desarrollo-Consejo Superior de Investigaciones Científicas, Jordi Girona 18-26, 08034, Barcelona, Spain
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Giakoumaki E, Minunni M, Tombelli S, Tothill IE, Mascini M, Bogani P, Buiatti M. Combination of amplification and post-amplification strategies to improve optical DNA sensing. Biosens Bioelectron 2003; 19:337-44. [PMID: 14615092 DOI: 10.1016/s0956-5663(03)00193-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The work evaluated a series of approaches to optimise detection of polymerase chain reaction (PCR) amplified DNA samples by an optical sensor based on surface plasmon resonance (SPR) (BiacoreX). The optimised procedure was based on an asymmetric PCR amplification system to amplify predominantly one DNA strand, containing the sequence complementary to a specific probe. The study moved into two directions, aiming to improve the analytical performance of SPR detection in PCR amplified products. One approach concerned the application of new strategies at the level of PCR, i.e. asymmetric PCR to obtain ssDNA amplified fragments containing the target capable of hybridisation with the immobilised complementary probe. The other strategy focused on the post-PCR amplification stage. Optimised denaturing conditions were applied to both symmetrically and asymmetrically amplified fragments. The effective combination of the two strategies allowed a rapid and specific hybridisation reaction. The developed method was successfully applied in the detection of genetically modified organisms.
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Affiliation(s)
- Elsa Giakoumaki
- Cranfield Biotechnology Centre, Cranfield University, Silsoe, Bedfordshire MK45 4DT, UK
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Current awareness in phytochemical analysis. PHYTOCHEMICAL ANALYSIS : PCA 2002; 13:381-388. [PMID: 12669728 DOI: 10.1002/pca.622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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Alary R, Serin A, Duviau MP, Jourdrier P, Gautier MF. Quantification of Common Wheat Adulteration of Durum Wheat Pasta Using Real-Time Quantitative Polymerase Chain Reaction (PCR). Cereal Chem 2002. [DOI: 10.1094/cchem.2002.79.4.553] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Rémi Alary
- Unité de Biochimie et Biologie Moléculaire des Céréales, INRA, 2 Place Viala, 34060 Montpellier Cedex 01, France
- Corresponding author. Phone: +33 499612206. Fax: +33 499612348. E-mail:
| | - Arnaud Serin
- Unité de Biochimie et Biologie Moléculaire des Céréales, INRA, 2 Place Viala, 34060 Montpellier Cedex 01, France
| | - Marie-Pierre Duviau
- Unité de Biochimie et Biologie Moléculaire des Céréales, INRA, 2 Place Viala, 34060 Montpellier Cedex 01, France
| | - Philippe Jourdrier
- Unité de Biochimie et Biologie Moléculaire des Céréales, INRA, 2 Place Viala, 34060 Montpellier Cedex 01, France
| | - Marie-Françoise Gautier
- Unité de Biochimie et Biologie Moléculaire des Céréales, INRA, 2 Place Viala, 34060 Montpellier Cedex 01, France
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