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A New Reference Plasmid “pGMT27” Provides an Efficient Transgenic Detection Method for Flue-Cured Tobacco. J FOOD QUALITY 2021. [DOI: 10.1155/2021/3220013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Owing to the economic value of its foliage, tobacco (Nicotiana tabacum) is cultivated all across the world. For the detection of genetically modified (GM) tobacco, there is a lack of universal standard material which ultimately limits the detection methods because the accuracy and comparability of the results cannot be ensured. Here, we prepared a reference plasmid “pGMT27” for the detection of GM tobacco, which was 18,296 bp in length harboring two of the tobacco endogenous and seven exogenous genes. By using qualitative PCR test for the nine genes, 10 copies were used for plasmid sensitivity. In the quantitative real-time PCR (qPCR) assays with pGMT27 as a calibrator, the reaction efficiencies for P-35S and NR were 101.427% and 98.036%, respectively, whereas the limit of detection (LOD) and limit of quantification (LOQ) were 5 copies and 10 copies per reaction. For standard deviation (SD) and relative standard deviation (RSD) of the Ct values, the repeatability values were from 0.04 to 0.42 and from 0.18% to 1.29%, respectively; and the reproducibility values were from 0.04 to 0.39 and from 0.18% to 1.14%, respectively. For the unknown sample test, the average conversion factor (Cf) was 0.39, and the accuracy bias was from −15.55% to 1.93%; for precision, the SD values ranged from 0.02 to 0.62, while RSD values were from 1.34% to 10.6%. We concluded that using the pGMT27 plasmid as a calibrator provided a highly efficient transgenic detection method for flue-cured tobacco.
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Deng T, Huang W, Ren J, Ma X, Ge Y, Chen Y. Verification and applicability of endogenous reference genes for quantifying GM rice by digital PCR. Anal Biochem 2019; 587:113442. [DOI: 10.1016/j.ab.2019.113442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/16/2019] [Accepted: 09/16/2019] [Indexed: 11/28/2022]
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3
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Analysis of Genetically Modified Organisms by Pyrosequencing on a Portable Photodiode-Based Bioluminescence Sequencer. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-1-4939-3308-2_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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4
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Milavec M, Dobnik D, Yang L, Zhang D, Gruden K, Zel J. GMO quantification: valuable experience and insights for the future. Anal Bioanal Chem 2014; 406:6485-97. [PMID: 25182968 DOI: 10.1007/s00216-014-8077-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/23/2014] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
Abstract
Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.
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Affiliation(s)
- Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia,
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5
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Morisset D, Novak PK, Zupanič D, Gruden K, Lavrač N, Žel J. GMOseek: a user friendly tool for optimized GMO testing. BMC Bioinformatics 2014; 15:258. [PMID: 25084968 PMCID: PMC4138379 DOI: 10.1186/1471-2105-15-258] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 07/19/2014] [Indexed: 12/21/2022] Open
Abstract
Background With the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or seed samples with their relevant regulations became difficult and costly. Many of them have already adopted the so called "matrix approach" to rationalize the resources and efforts used to increase their efficiency within a limited budget. Most of the time, the "matrix approach" is implemented using limited information and some proprietary (if any) computational tool to efficiently use the available data. Results The developed GMOseek software is designed to support decision making in all the phases of routine GMO laboratory testing, including the interpretation of wet-lab results. The tool makes use of a tabulated matrix of GM events and their genetic elements, of the laboratory analysis history and the available information about the sample at hand. The tool uses an optimization approach to suggest the most suited screening assays for the given sample. The practical GMOseek user interface allows the user to customize the search for a cost-efficient combination of screening assays to be employed on a given sample. It further guides the user to select appropriate analyses to determine the presence of individual GM events in the analyzed sample, and it helps taking a final decision regarding the GMO composition in the sample. GMOseek can also be used to evaluate new, previously unused GMO screening targets and to estimate the profitability of developing new GMO screening methods. Conclusion The presented freely available software tool offers the GMO testing laboratories the possibility to select combinations of assays (e.g. quantitative real-time PCR tests) needed for their task, by allowing the expert to express his/her preferences in terms of multiplexing and cost. The utility of GMOseek is exemplified by analyzing selected food, feed and seed samples from a national reference laboratory for GMO testing and by comparing its performance to existing tools which use the matrix approach. GMOseek proves superior when tested on real samples in terms of GMO coverage and cost efficiency of its screening strategies, including its capacity of simple interpretation of the testing results. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-258) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dany Morisset
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia.
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6
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Song Q, Wei G, Zhou G. Analysis of genetically modified organisms by pyrosequencing on a portable photodiode-based bioluminescence sequencer. Food Chem 2014; 154:78-83. [PMID: 24518318 DOI: 10.1016/j.foodchem.2014.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 05/23/2013] [Accepted: 01/01/2014] [Indexed: 10/25/2022]
Abstract
A portable bioluminescence analyser for detecting the DNA sequence of genetically modified organisms (GMOs) was developed by using a photodiode (PD) array. Pyrosequencing on eight genes (zSSIIb, Bt11 and Bt176 gene of genetically modified maize; Lectin, 35S-CTP4, CP4EPSPS, CaMV35S promoter and NOS terminator of the genetically modified Roundup ready soya) was successfully detected with this instrument. The corresponding limit of detection (LOD) was 0.01% with 35 PCR cycles. The maize and soya available from three different provenances in China were detected. The results indicate that pyrosequencing using the small size of the detector is a simple, inexpensive, and reliable way in a farm/field test of GMO analysis.
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Affiliation(s)
- Qinxin Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China
| | - Guijiang Wei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Guohua Zhou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China.
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7
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Detection of the genetically modified organisms from food products/ Detecţia organismelor modificate genetic din produse alimentare. REV ROMANA MED LAB 2014. [DOI: 10.2478/rrlm-2014-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Spalinskas R, Van den Bulcke M, Milcamps A. Efficient retrieval of recombinant sequences of GM plants by Cauliflower Mosaic Virus 35S promoter-based bidirectional LT-RADE. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-2078-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Morisset D, Štebih D, Milavec M, Gruden K, Žel J. Quantitative analysis of food and feed samples with droplet digital PCR. PLoS One 2013; 8:e62583. [PMID: 23658750 PMCID: PMC3642186 DOI: 10.1371/journal.pone.0062583] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/22/2013] [Indexed: 01/08/2023] Open
Abstract
In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed.
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Affiliation(s)
- Dany Morisset
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
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10
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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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11
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Ballari RV, Martin A, Gowda LR. Detection and identification of genetically modified EE-1 brinjal (Solanum melongena) by single, multiplex and SYBR® real-time PCR. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:340-347. [PMID: 22729745 DOI: 10.1002/jsfa.5764] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/28/2012] [Accepted: 05/14/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Brinjal is an important vegetable crop. Major crop loss of brinjal is due to insect attack. Insect-resistant EE-1 brinjal has been developed and is awaiting approval for commercial release. Consumer health concerns and implementation of international labelling legislation demand reliable analytical detection methods for genetically modified (GM) varieties. RESULTS End-point and real-time polymerase chain reaction (PCR) methods were used to detect EE-1 brinjal. In end-point PCR, primer pairs specific to 35S CaMV promoter, NOS terminator and nptII gene common to other GM crops were used. Based on the revealed 3' transgene integration sequence, primers specific for the event EE-1 brinjal were designed. These primers were used for end-point single, multiplex and SYBR-based real-time PCR. End-point single PCR showed that the designed primers were highly specific to event EE-1 with a sensitivity of 20 pg of genomic DNA, corresponding to 20 copies of haploid EE-1 brinjal genomic DNA. The limits of detection and quantification for SYBR-based real-time PCR assay were 10 and 100 copies respectively. CONCLUSION The prior development of detection methods for this important vegetable crop will facilitate compliance with any forthcoming labelling regulations.
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MESH Headings
- Bacillus thuringiensis Toxins
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Benzothiazoles
- Crops, Agricultural/genetics
- Crops, Agricultural/metabolism
- Diamines
- Endotoxins/genetics
- Endotoxins/metabolism
- Fluorescent Dyes/chemistry
- Food Inspection/methods
- Food Inspection/standards
- Food Labeling/legislation & jurisprudence
- Food, Genetically Modified/adverse effects
- Hemolysin Proteins/genetics
- Hemolysin Proteins/metabolism
- India
- Legislation, Food
- Limit of Detection
- Multiplex Polymerase Chain Reaction
- Organic Chemicals/chemistry
- Pest Control, Biological
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Proteins, Dietary/genetics
- Plant Proteins, Dietary/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Promoter Regions, Genetic
- Quinolines
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Solanum melongena/genetics
- Solanum melongena/metabolism
- Terminator Regions, Genetic
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Affiliation(s)
- Rajashekhar V Ballari
- Department of Food Safety and Analytical Quality Control Laboratory, CSIR-Central Food Technological Research Institute, Mysore 570 020, India
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12
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Holst-Jensen A, Bertheau Y, de Loose M, Grohmann L, Hamels S, Hougs L, Morisset D, Pecoraro S, Pla M, den Bulcke MV, Wulff D. Detecting un-authorized genetically modified organisms (GMOs) and derived materials. Biotechnol Adv 2012; 30:1318-35. [DOI: 10.1016/j.biotechadv.2012.01.024] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/06/2012] [Accepted: 01/25/2012] [Indexed: 01/25/2023]
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13
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Dinon AZ, Brod FCA, Mello CS, Oliveira EMM, Faria JC, Arisi ACM. Primers and probes development for specific PCR detection of genetically modified common bean (Phaseolus vulgaris) Embrapa 5.1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:4672-4677. [PMID: 22506690 DOI: 10.1021/jf3011257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genetically modified common bean Embrapa 5.1, developed by Brazilian Agricultural Research Corporation (Embrapa), is the first commercial GM plant produced in Latin America. It presents high resistance to the Bean golden mosaic virus. In this work, primers and probes targeting a taxon-specific reference DNA sequence for the common bean (Phaseolus vulgaris L.) and a construct-specific DNA sequence of Embrapa 5.1 GM common bean were successfully developed. The primers and probes showed high specificity for the target detection. Both methods showed suitable efficiency and performance to be used as an endogenous target for detection of common bean DNA and for construct-specific detection of GM common bean Embrapa 5.1, respectively. Both real-time PCR assays proved to be valuable for future assessment of interlaboratory studies.
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Affiliation(s)
- Andréia Z Dinon
- Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346, 88034-001, Florianópolis, Santa Catarina, Brazil
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14
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Kluga L, Folloni S, Van den Bulcke M, Van den Eede G, Querci M. Applicability of the “Real-Time PCR-Based Ready-to-Use Multi-Target Analytical System for GMO Detection” in processed maize matrices. Eur Food Res Technol 2011. [DOI: 10.1007/s00217-011-1615-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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15
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Holck A, Pedersen BO, Heir E. Detection of five novel GMO maize events by qualitative, multiplex PCR and fluorescence capillary gel electrophoresis. Eur Food Res Technol 2010. [DOI: 10.1007/s00217-010-1302-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Busch U, Block A, Meißner E. Gentechnisch veränderte Lebensmittel. Nutzpflanzen nach Maß. CHEM UNSERER ZEIT 2010. [DOI: 10.1002/ciuz.201000506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Van den Bulcke M, Lievens A, Barbau-Piednoir E, MbongoloMbella G, Roosens N, Sneyers M, Casi AL. A theoretical introduction to "combinatory SYBRGreen qPCR screening", a matrix-based approach for the detection of materials derived from genetically modified plants. Anal Bioanal Chem 2010; 396:2113-23. [PMID: 19960341 PMCID: PMC2836468 DOI: 10.1007/s00216-009-3286-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 10/20/2009] [Accepted: 11/03/2009] [Indexed: 11/20/2022]
Abstract
The detection of genetically modified (GM) materials in food and feed products is a complex multi-step analytical process invoking screening, identification, and often quantification of the genetically modified organisms (GMO) present in a sample. "Combinatory qPCR SYBRGreen screening" (CoSYPS) is a matrix-based approach for determining the presence of GM plant materials in products. The CoSYPS decision-support system (DSS) interprets the analytical results of SYBRGREEN qPCR analysis based on four values: the C(t)- and T(m) values and the LOD and LOQ for each method. A theoretical explanation of the different concepts applied in CoSYPS analysis is given (GMO Universe, "Prime number tracing", matrix/combinatory approach) and documented using the RoundUp Ready soy GTS40-3-2 as an example. By applying a limited set of SYBRGREEN qPCR methods and through application of a newly developed "prime number"-based algorithm, the nature of subsets of corresponding GMO in a sample can be determined. Together, these analyses provide guidance for semi-quantitative estimation of GMO presence in a food and feed product.
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Affiliation(s)
- Marc Van den Bulcke
- Division of Biosafety and Biotechnology, Scientific Institute of Public Health, J. Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Antoon Lievens
- Division of Biosafety and Biotechnology, Scientific Institute of Public Health, J. Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Elodie Barbau-Piednoir
- Division of Biosafety and Biotechnology, Scientific Institute of Public Health, J. Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Guillaume MbongoloMbella
- Division of Biosafety and Biotechnology, Scientific Institute of Public Health, J. Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Nancy Roosens
- Division of Biosafety and Biotechnology, Scientific Institute of Public Health, J. Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Myriam Sneyers
- Division of Biosafety and Biotechnology, Scientific Institute of Public Health, J. Wytsmanstreet 14, 1050 Brussels, Belgium
| | - Amaya Leunda Casi
- Division of Biosafety and Biotechnology, Scientific Institute of Public Health, J. Wytsmanstreet 14, 1050 Brussels, Belgium
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Alderborn A, Sundström J, Soeria-Atmadja D, Sandberg M, Andersson HC, Hammerling U. Genetically modified plants for non-food or non-feed purposes: straightforward screening for their appearance in food and feed. Food Chem Toxicol 2009; 48:453-64. [PMID: 20004226 DOI: 10.1016/j.fct.2009.10.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 10/06/2009] [Accepted: 10/30/2009] [Indexed: 01/17/2023]
Abstract
Genetically modified (GM) plants aimed at producing food/feed are part of regular agriculture in many areas of the World. Commodity plants have also found application as bioreactors, designated non-food/non-feed GM (NFGM) plants, thereby making raw material for further refinement to industrial, diagnostic or pharmaceutical preparations. Many among them may pose health challenge to consumers or livestock animals, if occurring in food/feed. NFGM plants are typically released into the environment, but are grown under special oversight and any among several containment practices, none of which provide full protection against accidental dispersal. Adventitious admixture with food or feed can occur either through distributional mismanagement or as a consequence of gene flow to plant relatives. To facilitate NFGM surveillance we propose a new mandatory tagging of essentially all such plants, prior to cultivation or marketing in the European Union. The suggested tag--Plant-Made Industrial or Pharmaceutical Products Tag (PMIP-T)--is envisaged to occur as a transgenic silent DNA identifier in host plants and designed to enable technically simple identification and characterisation of any NFGM. Implementation of PMIP-T would permit inexpensive, reliable and high-throughput screening for NFGM specifically. The paper outlines key NFGM prospects and challenges as well as the PMIP-T concept.
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Affiliation(s)
- A Alderborn
- Dept. of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
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19
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Molecular toolbox for the identification of unknown genetically modified organisms. Anal Bioanal Chem 2009; 396:2073-89. [DOI: 10.1007/s00216-009-3287-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 10/23/2009] [Accepted: 11/03/2009] [Indexed: 12/18/2022]
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20
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Knowledge-technology-based discovery of unauthorized genetically modified organisms. Anal Bioanal Chem 2009; 396:1951-9. [DOI: 10.1007/s00216-009-3218-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Shi R, Wang Y, Hu Y, Chen L, Wan QH. Preparation of magnetite-loaded silica microspheres for solid-phase extraction of genomic DNA from soy-based foodstuffs. J Chromatogr A 2009; 1216:6382-6. [PMID: 19632684 DOI: 10.1016/j.chroma.2009.07.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/06/2009] [Accepted: 07/10/2009] [Indexed: 11/27/2022]
Abstract
Solid-phase extraction has been widely employed for the preparation of DNA templates for polymerase chain reaction (PCR)-based analytical methods. Among the variety of adsorbents studied, magnetically responsive silica particles are particularly attractive due to their potential to simplify, expedite, and automate the extraction process. Here we report a facile method for the preparation of such magnetic particles, which entails impregnation of porous silica microspheres with iron salts, followed by calcination and reduction treatments. The samples were characterized using powder X-ray diffractometry (XRD), scanning electron microscopy (SEM), nitrogen adsorption/desorption isotherms, and vibrating sample magnetometry (VSM). XRD data show that magnetite nanocrystals of about 27.2 nm are produced within the pore channels of the silica support after reduction. SEM images show that the as-synthesized particles exhibit spherical shape and uniform particle size of about 3 microm as determined by the silica support. Nitrogen sorption data confirm that the magnetite-loaded silica particles possess typical mesopore structure with BET surface area of about 183 m(2)/g. VSM data show that the particles display paramagnetic behavior with saturation magnetization of 11.37 emu/g. The magnetic silica microspheres coated with silica shells were tested as adsorbents for rapid extraction of genomic DNA from soybean-derived products. The purified DNA templates were amplified by PCR for screening of genetically modified organisms (GMOs). The preliminary results confirm that the DNA extraction protocols using magnetite-loaded silica microspheres are capable of producing DNA templates which are inhibitor-free and ready for downstream analysis.
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Affiliation(s)
- Ruobing Shi
- School of Pharmaceutical Science & Technology, Tianjin University, Tianjin 300072, China
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22
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Holst-Jensen A. Testing for genetically modified organisms (GMOs): Past, present and future perspectives. Biotechnol Adv 2009; 27:1071-1082. [PMID: 19477261 DOI: 10.1016/j.biotechadv.2009.05.025] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This paper presents an overview of GMO testing methodologies and how these have evolved and may evolve in the next decade. Challenges and limitations for the application of the test methods as well as to the interpretation of results produced with the methods are highlighted and discussed, bearing in mind the various interests and competences of the involved stakeholders. To better understand the suitability and limitations of detection methodologies the evolution of transformation processes for creation of GMOs is briefly reviewed.
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Affiliation(s)
- Arne Holst-Jensen
- Department of Feed and Food Safety, National Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
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Li Y, Xing D, Zhang C. Rapid detection of genetically modified organisms on a continuous-flow polymerase chain reaction microfluidics. Anal Biochem 2009; 385:42-9. [PMID: 19010299 DOI: 10.1016/j.ab.2008.10.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 10/21/2008] [Accepted: 10/21/2008] [Indexed: 02/07/2023]
Abstract
The ability to perform DNA amplification on a microfluidic device is very appealing. In this study, a compact continuous-flow polymerase chain reaction (PCR) microfluidics was developed for rapid analysis of genetically modified organisms (GMOs) in genetically modified soybeans. The device consists of three pieces of copper and a transparent polytetrafluoroethylene capillary tube embedded in the spiral channel fabricated on the copper. On this device, the P35S and Tnos sequences were successfully amplified within 9min, and the limit of detection of the DNA sample was estimated to be 0.005 ng microl(-1). Furthermore, a duplex continuous-flow PCR was also reported for the detection of the P35S and Tnos sequences in GMOs simultaneously. This method was coupled with the intercalating dye SYBR Green I and the melting curve analysis of the amplified products. Using this method, temperature differences were identified by the specific melting temperature values of two sequences, and the limit of detection of the DNA sample was assessed to be 0.01 ng microl(-1). Therefore, our results demonstrated that the continuous-flow PCR assay could discriminate the GMOs in a cost-saving and less time-consuming way.
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Affiliation(s)
- Yuyuan Li
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, South China Normal University, No. 55 Zhongshan Avenue West, Tianhe District, Guangzhou 510631, People's Republic of China
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Mano J, Shigemitsu N, Futo S, Akiyama H, Teshima R, Hino A, Furui S, Kitta K. Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:26-37. [PMID: 19072282 DOI: 10.1021/jf802551h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .
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Affiliation(s)
- Junichi Mano
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki, Japan
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25
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OGUCHI T, ONISHI M, MINEGISHI Y, KUROSAWA Y, KASAHARA M, AKIYAMA H, TESHIMA R, FUTO S, FURUI S, HINO A, KITTA K. Development of Quantitative Duplex Real-Time PCR Method for Screening Analysis of Genetically Modified Maize. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2009; 50:117-25. [DOI: 10.3358/shokueishi.50.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Akiyama H, Nakamura F, Yamada C, Nakamura K, Nakajima O, Kawakami H, Harikai N, Furui S, Kitta K, Teshima R. A Screening Method for the Detection of the 35S Promoter and the Nopaline Synthase Terminator in Genetically Modified Organisms in a Real-Time Multiplex Polymerase Chain Reaction Using High-Resolution Melting-Curve Analysis. Biol Pharm Bull 2009; 32:1824-9. [DOI: 10.1248/bpb.32.1824] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Chihiro Yamada
- Department of Food Science & Nutrition, Kyoritsu Women's University
| | | | | | - Hiroshi Kawakami
- Department of Food Science & Nutrition, Kyoritsu Women's University
| | - Naoki Harikai
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University
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Prins TW, van Dijk JP, Beenen HG, Van Hoef AMA, Voorhuijzen MM, Schoen CD, Aarts HJM, Kok EJ. Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction. BMC Genomics 2008; 9:584. [PMID: 19055784 PMCID: PMC2631584 DOI: 10.1186/1471-2164-9-584] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/04/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND To maintain EU GMO regulations, producers of new GM crop varieties need to supply an event-specific method for the new variety. As a result methods are nowadays available for EU-authorised genetically modified organisms (GMOs), but only to a limited extent for EU-non-authorised GMOs (NAGs). In the last decade the diversity of genetically modified (GM) ingredients in food and feed has increased significantly. As a result of this increase GMO laboratories currently need to apply many different methods to establish to potential presence of NAGs in raw materials and complex derived products. RESULTS In this paper we present an innovative method for detecting (approved) GMOs as well as the potential presence of NAGs in complex DNA samples containing different crop species. An optimised protocol has been developed for padlock probe ligation in combination with microarray detection (PPLMD) that can easily be scaled up. Linear padlock probes targeted against GMO-events, -elements and -species have been developed that can hybridise to their genomic target DNA and are visualised using microarray hybridisation.In a tenplex PPLMD experiment, different genomic targets in Roundup-Ready soya, MON1445 cotton and Bt176 maize were detected down to at least 1%. In single experiments, the targets were detected down to 0.1%, i.e. comparable to standard qPCR. CONCLUSION Compared to currently available methods this is a significant step forward towards multiplex detection in complex raw materials and derived products. It is shown that the PPLMD approach is suitable for large-scale detection of GMOs in real-life samples and provides the possibility to detect and/or identify NAGs that would otherwise remain undetected.
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Affiliation(s)
- Theo W Prins
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Jeroen P van Dijk
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Henriek G Beenen
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - AM Angeline Van Hoef
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Marleen M Voorhuijzen
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Cor D Schoen
- Plant Research International BV (WUR), Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Henk JM Aarts
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Esther J Kok
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
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Current awareness in phytochemical analysis. PHYTOCHEMICAL ANALYSIS : PCA 2008; 19:568-575. [PMID: 18988322 DOI: 10.1002/pca.1041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Holst-Jensen A. GMO testing: Past, present and future perspectives. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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