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Increasing the Efficiency of Canola and Soybean GMO Detection and Quantification Using Multiplex Droplet Digital PCR. BIOLOGY 2022; 11:biology11020201. [PMID: 35205068 PMCID: PMC8869681 DOI: 10.3390/biology11020201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary Digital PCR (dPCR) technology has been used for absolute quantification of genetically modified (GM) events. Duplex dPCR consisting of a target gene and a reference gene is mostly used for absolute quantification of GM events. We investigated the feasibility of absolute quantification of two, three, and four GM canola and soybean events at the same time using the QX200 Droplet Digital PCR (ddPCR) system. Adjustments of the probe concentrations and labels for some of the assays were needed for successful multiplex ddPCR. Absolute quantification of GM canola and soybean events was achieved for duplex, triplex, and tetraplex ddPCR at 0.1%, 1%, and 5% concentrations. Abstract The number of genetically modified (GM) events for canola, maize, and soybean has been steadily increasing. Real-time PCR is widely used for the detection and quantification of individual GM events. Digital PCR (dPCR) has also been used for absolute quantification of GM events. A duplex dPCR assay consisting of one reference gene and one GM event has been carried out in most cases. The detection of more than one GM event in a single assay will increase the efficiency of dPCR. The feasibility of detection and quantification of two, three, and four GM canola and soybean events at the same time was investigated at 0.1%, 1%, and 5% levels using the QX200 Droplet Digital PCR (ddPCR) system. The reference gene assay was carried out on the same plate but in different wells. For some of the assays, optimization of the probe concentrations and labels was needed for successful ddPCR. Results close to the expected result were achieved for duplex, triplex, and tetraplex ddPCR assays for GM canola events. Similar ddPCR results were also achieved for some GM soybean events with some exceptions. Overall, absolute quantification of up to four GM events at the same time improves the efficiency of GM detection.
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Wang X, Tang T, Miao Q, Xie S, Chen X, Tang J, Peng C, Xu X, Wei W, You Z, Xu J. Detection of transgenic rice line TT51-1 in processed foods using conventional PCR, real-time PCR, and droplet digital PCR. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.11.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Leguizamón Guerrero JE, Vela Rojas AF, Arias Cortés MM, Cifuentes Fernández LF. Panorama general de los organismos genéticamente modificados en Colombia y en el mundo: Capacidad nacional de detección. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2018. [DOI: 10.15446/rev.colomb.biote.v20n2.77080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los organismos genéticamente modificados (OGM) y en particular los cultivos genéticamente modificados (GM), son el resultado de la modificación de la información genética de una especie a partir del uso de la biotecnología moderna para proporcionar nuevas características que su contraparte no modificada no posee, tales como resistencia a insectos, tolerancia a herbicidas, contenido de nutrientes entre otros. La mayor parte de estos cultivos se concentran en cuatro productos: soya (Glycine max), maíz (Zea Mays), canola (Brassica napus) y algodón (Gossypium hirsutum); y los principales productores son Estados Unidos, Brasil, Argentina, India y Canadá. Por su parte, Colombia ocupa el puesto 18 con cultivos de maíz, algodón y claveles azules. La introducción de estas especies en cualquier mercado está limitada por la legislación propia del país destino, así como por los estudios que permiten establecer su efecto sobre el medio ambiente, la salud humana y animal; en este sentido, la precisión y confianza de las técnicas analíticas empleadas en la evaluación del contenido de OGM son un elemento importante para la toma de decisiones basadas en evidencias objetivas, especialmente frente al debate en torno a su uso. Este documento presenta una revisión de las tecnologías de análisis más importantes disponibles a nivel mundial, frente a las capacidades nacionales para su detección.
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Niu C, Xu Y, Zhang C, Zhu P, Huang K, Luo Y, Xu W. Ultrasensitive Single Fluorescence-Labeled Probe-Mediated Single Universal Primer-Multiplex-Droplet Digital Polymerase Chain Reaction for High-Throughput Genetically Modified Organism Screening. Anal Chem 2018; 90:5586-5593. [PMID: 29652133 DOI: 10.1021/acs.analchem.7b03974] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As genetically modified (GM) technology develops and genetically modified organisms (GMOs) become more available, GMOs face increasing regulations and pressure to adhere to strict labeling guidelines. A singleplex detection method cannot perform the high-throughput analysis necessary for optimal GMO detection. Combining the advantages of multiplex detection and droplet digital polymerase chain reaction (ddPCR), a single universal primer-multiplex-ddPCR (SUP-M-ddPCR) strategy was proposed for accurate broad-spectrum screening and quantification. The SUP increases efficiency of the primers in PCR and plays an important role in establishing a high-throughput, multiplex detection method. Emerging ddPCR technology has been used for accurate quantification of nucleic acid molecules without a standard curve. Using maize as a reference point, four heterologous sequences ( 35S, NOS, NPTII, and PAT) were selected to evaluate the feasibility and applicability of this strategy. Surprisingly, these four genes cover more than 93% of the transgenic maize lines and serve as preliminary screening sequences. All screening probes were labeled with FAM fluorescence, which allows the signals from the samples with GMO content and those without to be easily differentiated. This fiveplex screening method is a new development in GMO screening. Utilizing an optimal amplification assay, the specificity, limit of detection (LOD), and limit of quantitation (LOQ) were validated. The LOD and LOQ of this GMO screening method were 0.1% and 0.01%, respectively, with a relative standard deviation (RSD) < 25%. This method could serve as an important tool for the detection of GM maize from different processed, commercially available products. Further, this screening method could be applied to other fields that require reliable and sensitive detection of DNA targets.
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Affiliation(s)
- Chenqi Niu
- Laboratory of Food Safety, College of Food Science and 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.,Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China
| | - Chao Zhang
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China
| | - Pengyu Zhu
- The Institute of Plant Quarantine , Chinese Academy of Inspection and Quarantine , Beijing 100029 , 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.,Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , 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.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , Beijing 100083 , China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Laboratory of Food Safety, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing 100083 , China.,Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , Beijing 100083 , China
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Wang X, Chen X, Xu J, Wang P, Shen W. Multiplex event-specific qualitative polymerase chain reaction for detecting three transgenic rice lines and application of a standard plasmid as a quantitative reference molecule. Anal Biochem 2014; 464:1-8. [PMID: 25026190 DOI: 10.1016/j.ab.2014.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/05/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022]
Abstract
The three most well-known genetically modified (GM) rice lines in China are TT51-1, KMD1, and KF6. The purposes of this study were to establish a multiplex event-specific qualitative polymerase chain reaction (meqPCR) system for simultaneous detection of the three transgenic rice events and to construct a plasmid as the reference molecule for quantitative analysis. Event-specific primers for each event were selected or designed by focusing on the transgene borders between the inserted DNA and the flanking rice DNA. The developed meqPCR was anticipated to detect distinct amplicons as 454, 398, 301, and 250bp from KF6, KMD1, TT51-1, and the rice endogenous reference gene, respectively. The robustness of the meqPCR was tested with different levels of the three transgenic rice genomic DNAs, and the sensitivity threshold of the meqPCR was at least 50ng of 0.1% rice DNA for each event when the three transgenic rice events present and with other GM materials together. The constructed plasmid was evaluated using mixed samples with known GM contents in real-time quantitative PCR. The results indicated that the constructed plasmid was acceptable and suitable for GM rice quantitative analysis.
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Affiliation(s)
- Xiaofu Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Institute of Quality and Standard for Agricultural Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoyun Chen
- Institute of Quality and Standard for Agricultural Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Junfeng Xu
- Institute of Quality and Standard for Agricultural Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Pengfei Wang
- College of Chemistry and Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Wenbiao Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Wang X, Tang Q, Dong L, Dong Y, Su Y, Jia S, Wang Z. Construction of a standard reference plasmid containing seven target genes for the detection of transgenic cotton. Plasmid 2014; 74:39-44. [DOI: 10.1016/j.plasmid.2014.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/31/2014] [Indexed: 11/26/2022]
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Detecting authorized and unauthorized genetically modified organisms containing vip3A by real-time PCR and next-generation sequencing. Anal Bioanal Chem 2014; 406:2603-11. [PMID: 24553665 DOI: 10.1007/s00216-014-7667-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/23/2014] [Accepted: 01/27/2014] [Indexed: 11/27/2022]
Abstract
The growing number of biotech crops with novel genetic elements increasingly complicates the detection of genetically modified organisms (GMOs) in food and feed samples using conventional screening methods. Unauthorized GMOs (UGMOs) in food and feed are currently identified through combining GMO element screening with sequencing the DNA flanking these elements. In this study, a specific and sensitive qPCR assay was developed for vip3A element detection based on the vip3Aa20 coding sequences of the recently marketed MIR162 maize and COT102 cotton. Furthermore, SiteFinding-PCR in combination with Sanger, Illumina or Pacific BioSciences (PacBio) sequencing was performed targeting the flanking DNA of the vip3Aa20 element in MIR162. De novo assembly and Basic Local Alignment Search Tool searches were used to mimic UGMO identification. PacBio data resulted in relatively long contigs in the upstream (1,326 nucleotides (nt); 95 % identity) and downstream (1,135 nt; 92 % identity) regions, whereas Illumina data resulted in two smaller contigs of 858 and 1,038 nt with higher sequence identity (>99 % identity). Both approaches outperformed Sanger sequencing, underlining the potential for next-generation sequencing in UGMO identification.
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Scholtens I, Laurensse E, Molenaar B, Zaaijer S, Gaballo H, Boleij P, Bak A, Kok E. Practical experiences with an extended screening strategy for genetically modified organisms (GMOs) in real-life samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:9097-109. [PMID: 23964687 DOI: 10.1021/jf4018146] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nowadays most animal feed products imported into Europe have a GMO (genetically modified organism) label. This means that they contain European Union (EU)-authorized GMOs. For enforcement of these labeling requirements, it is necessary, with the rising number of EU-authorized GMOs, to perform an increasing number of analyses. In addition to this, it is necessary to test products for the potential presence of EU-unauthorized GMOs. Analysis for EU-authorized and -unauthorized GMOs in animal feed has thus become laborious and expensive. Initial screening steps may reduce the number of GMO identification methods that need to be applied, but with the increasing diversity also screening with GMO elements has become more complex. For the present study, the application of an informative detailed 24-element screening and subsequent identification strategy was applied in 50 animal feed samples. Almost all feed samples were labeled as containing GMO-derived materials. The main goal of the study was therefore to investigate if a detailed screening strategy would reduce the number of subsequent identification analyses. An additional goal was to test the samples in this way for the potential presence of EU-unauthorized GMOs. Finally, to test the robustness of the approach, eight of the samples were tested in a concise interlaboratory study. No significant differences were found between the results of the two laboratories.
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Affiliation(s)
- Ingrid Scholtens
- RIKILT Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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Del Gaudio S, Cirillo A, Di Bernardo G, Galderisi U, Cipollaro M. Verification of Real-Time PCR Methods for Qualitative and Quantitative Testing of Genetically Modified Organisms. J FOOD QUALITY 2012. [DOI: 10.1111/jfq.12001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- S. Del Gaudio
- Department of Experimental Medicine; Section of Biotechnology and Molecular Biology “A. Cascino”; Second University of Naples; Via Costantinopoli 16 Naples 80138 Italy
| | - A. Cirillo
- Department of Experimental Medicine; Section of Biotechnology and Molecular Biology “A. Cascino”; Second University of Naples; Via Costantinopoli 16 Naples 80138 Italy
| | - G. Di Bernardo
- Department of Experimental Medicine; Section of Biotechnology and Molecular Biology “A. Cascino”; Second University of Naples; Via Costantinopoli 16 Naples 80138 Italy
| | - U. Galderisi
- Department of Experimental Medicine; Section of Biotechnology and Molecular Biology “A. Cascino”; Second University of Naples; Via Costantinopoli 16 Naples 80138 Italy
| | - M. Cipollaro
- Department of Experimental Medicine; Section of Biotechnology and Molecular Biology “A. Cascino”; Second University of Naples; Via Costantinopoli 16 Naples 80138 Italy
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Xiao X, Wu H, Zhou X, Xu S, He J, Shen W, Zhou G, Huang M. The combination of quantitative PCR and western blot detecting CP4-EPSPS component in Roundup Ready soy plant tissues and commercial soy-related foodstuffs. J Food Sci 2012; 77:C603-8. [PMID: 22591269 DOI: 10.1111/j.1750-3841.2012.02718.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
UNLABELLED With the widespread use of Roundup Ready soy (event 40-3-2) (RRS), the comprehensive detection of genetically modified component in foodstuffs is of significant interest, but few protein-based approaches have been found useful in processed foods. In this report, the combination of quantitative PCR (qPCR) and western blot was used to detect cp4-epsps gene and its protein product in different RRS plant tissues and commercial soy-containing foodstuffs. The foods included those of plant origin produced by different processing procedures and also some products containing both meat and plant protein concentrates. The validity of the 2 methods was confirmed first. We also showed that the CP4-EPSPS protein existed in different RRS plant tissues. In certain cases, the results from the western blot and the qPCR were not consistent. To be specific, at least 2 degraded fragments of CP4-EPSPS protein (35.5 and 24.6 kDa) were observed. For dried bean curd crust and deep-fried bean curd, a degraded protein fragment with the size of 24.6 kDa appeared, while cp4-epsps gene could not be traced by qPCR. In contrast, we found a signal of cp4-epsps DNA in 3 foodstuffs, including soy-containing ham cutlet product, meat ball, and sausage by qPCR, while CP4-EPSPS protein could not be detected by western blot in such samples. Our study therefore concluded that the combination of DNA- and protein-based methods would compensate each other, thus resulting in a more comprehensive detection from nucleic acid and protein levels. PRACTICAL APPLICATION The combination of quantitative PCR (qPCR) and western blot was used to detect cp4-epsps gene and its protein product in different Roundup Ready soy (event 40-3-2) plant tissues and commercial soy-containing foodstuffs. The foods included those of plant origin produced by different processing procedures and also some products containing a combination of both meat and plant protein concentrates. This study indicated that the combination of DNA- and protein-based methods would supplement each other for genetically modified detection from nucleic acid and protein levels. Accordingly, qPCR and western blot could be used in CP4-EPSPS detection in a wide variety of soy-related foodstuffs.
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Affiliation(s)
- Xiao Xiao
- College of Life Sciences, Cooperative Demonstration Laboratory of Centrifuge Technique, Nanjing Agricultural Univ, Nanjing 210095, China
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Wang X, Teng D, Yang Y, Tian F, Guan Q, Wang J. Construction of a reference plasmid molecule containing eight targets for the detection of genetically modified crops. Appl Microbiol Biotechnol 2011; 90:721-31. [PMID: 21336925 DOI: 10.1007/s00253-011-3159-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/18/2011] [Accepted: 01/23/2011] [Indexed: 12/17/2022]
Abstract
A standard plasmid containing eight targets was developed for quantitative detection of genetically modified (GM) soybeans and cotton. These eight targets were joined in tandem to form the pTLE8 plasmid with a length of 3,680 bp. This plasmid contains part of the endogenous soybean Lec1 gene, the Cauliflower mosaic virus (CaMV) 35S promoter, the Agrobacterium tumefaciens nopaline synthase (NOS) terminator, the PAT gene of the soybean line A2704-12, the event-specific 5'-junction region of Roundup-Ready Soya (RRS, 35SG), the Cry1A(c) gene from Bacillus thuringiensis (Bt), the endogenous cotton Sad1 gene, and a part of RRS EPSPS gene. The PCR efficiencies with pTLE8 as a calibrator ranged from 99.4% to 100.2% for the standard curves of the RRS EPSPS gene and the taxon-specific Lec1 gene (R(2)≥0.996). The limits of detection and quantification were nine and 15 copies, respectively. The standard deviation (SD) and relative standard deviation (RSD) values of repeatability were from 0.09 to 0.52 and from 0.28% to 2.11%, and those for reproducibility were from 0.12 to 1.15 and 0.42% to 3.85%, respectively. The average conversion factor (Cf) for the CRMs RRS quantification was 0.91. The RSD of the mean values for known samples ranged from 3.09% to 18.53%, and the biases were from 0.5% to 40%. These results show that our method using the pTLE8 plasmid as a reference material (RM) is reliable and feasible in the identification of GM soybeans, thus paving the way for the establishment of identification management systems for various products containing GMO components.
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Affiliation(s)
- Xiumin Wang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Beijing 100081, People's Republic of China
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Dinon AZ, Prins TW, van Dijk JP, Arisi ACM, Scholtens IMJ, Kok EJ. Development and validation of real-time PCR screening methods for detection of cry1A.105 and cry2Ab2 genes in genetically modified organisms. Anal Bioanal Chem 2011; 400:1433-42. [PMID: 21445662 PMCID: PMC3081059 DOI: 10.1007/s00216-011-4875-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/04/2011] [Accepted: 03/06/2011] [Indexed: 11/28/2022]
Abstract
Primers and probes were developed for the element-specific detection of cry1A.105 and cry2Ab2 genes, based on their DNA sequence as present in GM maize MON89034. Cry genes are present in many genetically modified (GM) plants and they are important targets for developing GMO element-specific detection methods. Element-specific methods can be of use to screen for the presence of GMOs in food and feed supply chains. Moreover, a combination of GMO elements may indicate the potential presence of unapproved GMOs (UGMs). Primer-probe combinations were evaluated in terms of specificity, efficiency and limit of detection. Except for specificity, the complete experiment was performed in 9 PCR runs, on 9 different days and by testing 8 DNA concentrations. The results showed a high specificity and efficiency for cry1A.105 and cry2Ab2 detection. The limit of detection was between 0.05 and 0.01 ng DNA per PCR reaction for both assays. These data confirm the applicability of these new primer-probe combinations for element detection that can contribute to the screening for GM and UGM crops in food and feed samples.
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Affiliation(s)
- Andréia Z Dinon
- Department of Food Science and Technology, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Florianópolis, SC 880034-001, Brazil
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Development of two screening duplex PCR assays for genetically modified organism quantification using multiplex real-time PCR master mixes. Eur Food Res Technol 2010. [DOI: 10.1007/s00217-010-1394-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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