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Wang Y, Yang F, Fu Y, He X, Tian H, Yang L, Wu M, Cao J, Liu J. A point-of-care testing platform for on-site identification of genetically modified crops. LAB ON A CHIP 2024; 24:2622-2632. [PMID: 38644672 DOI: 10.1039/d4lc00040d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Genetically modified (GM) food is still highly controversial nowadays. Due to the disparate policies and attitudes worldwide, demands for a rapid, cost-effective and user-friendly GM crop identification method are increasingly significant for import administration, market supervision, etc. However, as the most-recognized methods, nucleic acid-based identification approaches require bulky instruments, long turn-around times and trained personnel, which are only suitable in laboratories. To fulfil the urgent needs of on-site testing, we develop a point-of-care testing platform that is able to identify 12 types of GM crops in less than 40 minutes without using laboratory settings. Our system integrates sample pre-treatment modules in a microfluidic chip, performs DNA amplification via a battery-powered portable kit, and presents results via eye-recognized colorimetric change. A paraffin-based reflow method and a slip plate-based fluid switch are developed to encapsulate and release amplification primers in individual microwells on demand, thus enabling identification of varied targets simultaneously. Our system offers an efficient, affordable and convenient tool for GM crop identification, thus it will not only benefit customs and market administration bureaus, but also satisfy demands of numerous consumers.
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Affiliation(s)
- Yangyang Wang
- State Key Laboratory of High-Performance Precision Manufacturing, Dalian University of Technology, Dalian, 116024, China.
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Furui Yang
- State Key Laboratory of High-Performance Precision Manufacturing, Dalian University of Technology, Dalian, 116024, China.
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Yingyi Fu
- State Key Laboratory of High-Performance Precision Manufacturing, Dalian University of Technology, Dalian, 116024, China.
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Xin He
- State Key Laboratory of High-Performance Precision Manufacturing, Dalian University of Technology, Dalian, 116024, China.
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Haowei Tian
- State Key Laboratory of High-Performance Precision Manufacturing, Dalian University of Technology, Dalian, 116024, China.
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Lili Yang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China.
| | - Mengxi Wu
- State Key Laboratory of High-Performance Precision Manufacturing, Dalian University of Technology, Dalian, 116024, China.
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China.
| | - Junshan Liu
- State Key Laboratory of High-Performance Precision Manufacturing, Dalian University of Technology, Dalian, 116024, China.
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, Liaoning, 116024, China
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2
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Xing Y, Liang J, Dong F, Wu J, Shi J, Xu J, Wang J. Rapid Visual LAMP Method for Detection of Genetically Modified Organisms. ACS OMEGA 2023; 8:29608-29614. [PMID: 37599972 PMCID: PMC10433496 DOI: 10.1021/acsomega.3c03567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
We developed a novel loop-mediated isothermal amplification (LAMP) method using DNA captured on polyacrylamide microparticles (PAMMPs) as templates (PAMMPs@DNA-LAMP) for rapid qualitative detection of genetically modified organisms (GMOs). Here, DNA was extracted by a fast and cost-effective method using PAMMPs. Four LAMP primers were designed for the PAMMPs@DNA-LAMP method to detect the cauliflower mosaic virus 35S (CaMV35S) promotor in GMOs. We thus developed this method for rapid extraction of DNA (5-10 min) and fast amplification of DNA within ∼30 min at a constant temperature of 63 °C. Moreover, the DNA captured by PAMMPs (PAMMPs@DNA) could be effectively detected by both conventional and quantitative PCR (qPCR) and LAMP. The PAMMPs@DNA-LAMP method was validated with high specificity, sensitivity, and performance for practical sample analysis. This assay detected 0.01% target sequences, which had a high specificity like qPCR and better than the conventional PCR (cPCR). Furthermore, PAMMPs@DNA-LAMP was successfully used to extract and detect DNA from food samples of the major crops (soybean, maize, rice, etc.). In summary, a novel PAMMPs@DNA-LAMP assay has been developed, which has higher sensitivity and spends less time than the cPCR detection using the conventional DNA extracted process. This method offers a novel approach for rapid detection of GMOs in the field.
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Affiliation(s)
- Yujun Xing
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Key Laboratory for Control/Technology
and Standard for Agro-Product Safety and Quality, Ministry of Agriculture
and Rural Affairs/Collaborative Innovation Center for Modern Grain
Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jie Liang
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Fei Dong
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Jirong Wu
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Jianrong Shi
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Jianhong Xu
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Key Laboratory for Control/Technology
and Standard for Agro-Product Safety and Quality, Ministry of Agriculture
and Rural Affairs/Collaborative Innovation Center for Modern Grain
Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jinke Wang
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering, Southeast
University, Nanjing 210096, China
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3
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Parvalbumin: A Major Fish Allergen and a Forensically Relevant Marker. Genes (Basel) 2023; 14:genes14010223. [PMID: 36672964 PMCID: PMC9858982 DOI: 10.3390/genes14010223] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Parvalbumins (PVALBs) are low molecular weight calcium-binding proteins. In addition to their role in many biological processes, PVALBs play an important role in regulating Ca2+ switching in muscles with fast-twitch fibres in addition to their role in many biological processes. The PVALB gene family is divided into two gene types, alpha (α) and beta (β), with the β gene further divided into two gene types, beta1 (β1) and beta2 (β2), carrying traces of whole genome duplication. A large variety of commonly consumed fish species contain PVALB proteins which are known to cause fish allergies. More than 95% of all fish-induced food allergies are caused by PVALB proteins. The authentication of fish species has become increasingly important as the seafood industry continues to grow and the growth brings with it many cases of food fraud. Since the PVALB gene plays an important role in the initiation of allergic reactions, it has been used for decades to develop alternate assays for fish identification. A brief review of the significance of the fish PVALB genes is presented in this article, which covers evolutionary diversity, allergic properties, and potential use as a forensic marker.
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4
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Detection and identification of authorized and unauthorized GMOs using high-throughput sequencing with the support of a sequence-based GMO database. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 4:100096. [PMID: 35415691 PMCID: PMC8991651 DOI: 10.1016/j.fochms.2022.100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/23/2022]
Abstract
Sequence-based database Nexplorer describing EU-authorized GMOs was developed. Sequences were annotated and presented in structured and extractable formats. Workflow for an efficient analysis of NGS data using Nexplorer database was designed. Method was successfully tested for various scenarios for routine GMO analysis. This paves the way for the use of NGS for routine GMO detection and identification.
The increasing number and diversity of genetically modified organisms (GMOs) for the food and feed market calls for the development of advanced methods for their detection and identification. This issue can be addressed by next generation sequencing (NGS). However, the efficiency of NGS-based strategies depends on the availability of bioinformatic methods to find sequences of the transgenic insert and junction regions, which is a challenging topic. To facilitate this task, we have developed Nexplorer, a sequence-based database in which annotated sequences of GM events are stored in a structured, searchable and extractable format. As a proof of concept, we have developed a methodology for the analysis of sequencing data of DNA walking libraries of samples containing GMOs using the database. The efficiency of the method has been tested on datasets representing various scenarios that can be encountered in routine GMO analysis. Database-guided analysis allowed obtaining detailed and reliable information with limited hands-on time. As the database allows for efficient analysis of NGS data, it paves the way for the use of NGS sequencing technology to aid routine detection and identification of GMO.
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Dong X, Raghavan V. A comprehensive overview of emerging processing techniques and detection methods for seafood allergens. Compr Rev Food Sci Food Saf 2022; 21:3540-3557. [PMID: 35676763 DOI: 10.1111/1541-4337.12987] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/21/2022]
Abstract
Seafood is rich in nutrients and plays a significant role in human health. However, seafood allergy is a worldwide health issue by inducing adverse reactions ranging from mild to life-threatening in seafood-allergic individuals. Seafood consists of fish and shellfish, with the major allergens such as parvalbumin and tropomyosin, respectively. In the food industry, effective processing techniques are applied to seafood allergens to lower the allergenicity of seafood products. Also, sensitive and rapid allergen-detection methods are developed to identify and assess allergenic ingredients at varying times. This review paper provides an overview of recent advances in processing techniques (thermal, nonthermal, combined [hybrid] treatments) and main allergen-detection methods for seafood products. The article starts with the seafood consumption and classification, proceeding with the prevalence and symptoms of seafood allergy, followed by a description of biochemical characteristics of the major seafood allergens. As the topic is multidisciplinary in scope, it is intended to provide information for further research essential for food security and safety.
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Affiliation(s)
- Xin Dong
- Department of Bioresource Engineering, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Vijaya Raghavan
- Department of Bioresource Engineering, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
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6
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Mao Z, Chen R, Wang X, Zhou Z, Peng Y, Li S, Han D, Li S, Wang Y, Han T, Liang J, Ren S, Gao Z. CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety. Trends Food Sci Technol 2022; 122:211-222. [PMID: 35250172 PMCID: PMC8885088 DOI: 10.1016/j.tifs.2022.02.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND In the context of the current pandemic caused by the novel coronavirus, molecular detection is not limited to the clinical laboratory, but also faces the challenge of the complex and variable real-time detection fields. A series of novel coronavirus events were detected in the process of food cold chain packaging and transportation, making the application of molecular diagnosis in food processing, packaging, transportation, and other links urgent. There is an urgent need for a rapid detection technology that can adapt to the diversity and complexity of food safety. SCOPE AND APPROACH This review introduces a new molecular diagnostic technology-biosensor analysis technology based on CRISPR-Cas12a. Systematic clarification of its development process and detection principles. It summarizes and systematically organizes its applications in viruses, food-borne pathogenic bacteria, small molecule detection, etc. In the past four years, which provides a brand-new and comprehensive solution for food detection. Finally, this article puts forward the challenges and the prospects for food safety. KEY FINDINGS AND CONCLUSIONS The novel coronavirus hazards infiltrated every step of the food industry, from processing to packaging to transportation. The biosensor analytical technology based on CRISPR-Cas12a has great potential in the qualitative and quantitative analysis of infectious pathogens. CRISPR-Cas12a can effectively identify the presence of the specific nucleic acid targets and the small changes in sequences, which is particularly important for nucleic acid identification and pathogen detection. In addition, the CRISPR-Cas12a method can be adjusted and reconfigured within days to detect other viruses, providing equipment for nucleic acid diagnostics in the field of food safety. The future work will focus on the development of portable microfluidic devices for multiple detection. Shao et al. employed physical separation methods to separate Cas proteins in different microfluidic channels to achieve multiple detection, and each channel simultaneously detected different targets by adding crRNA with different spacer sequences. Although CRISPR-Cas12a technology has outstanding advantages in detection, there are several technical barriers in the transformation from emerging technologies to practical applications. The newly developed CRISPR-Cas12a-based applications and methods promote the development of numerous diagnostic and detection solutions, and have great potential in medical diagnosis, environmental monitoring, and especially food detection.
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Affiliation(s)
- Zefeng Mao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaojuan Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zixuan Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Sen Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Tie Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Jun Liang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China,Corresponding author
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,Corresponding author
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,Corresponding author
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7
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Development of a Taxon-Specific Real-Time PCR Method Targeting the Bacillus subtilis Group to Strengthen the Control of Genetically Modified Bacteria in Fermentation Products. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8020078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Most of the bacteria that are used to produce fermentation products, such as enzymes, additives and flavorings, belong to the Bacillus subtilis group. Recently, unexpected contaminations with unauthorized genetically modified (GM) bacteria (viable cells and associated DNA) that were carrying antimicrobial resistance (AMR) genes was noticed in several microbial fermentation products that have been commercialized on the food and feed market. These contaminations consisted of GM Bacillus species belonging to the B. subtilis group. In order to screen for the potential presence of such contaminations, in this study we have developed a new real-time PCR method targeting the B. subtilis group, including B. subtilis, B. licheniformis, B. amyloliquefaciens and B. velezensis. The method’s performance was successfully assessed as specific and sensitive, complying with the Minimum Performance Requirements for Analytical Methods of GMO Testing that is used as a standard by the GMO enforcement laboratories. The method’s applicability was also tested on 25 commercial microbial fermentation products. In addition, this method was developed to be compatible with the PCR-based strategy that was recently developed for the detection of unauthorized GM bacteria. This taxon-specific method allows the strengthening of the set of screening markers that are targeting key sequences that are frequently found in GM bacteria (AMR genes and shuttle vector), reinforcing control over the food and feed chain in order to guarantee its safety and traceability.
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8
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Tebeje A, Tadesse H, Mengesha Y. Synthetic bio/techno/logy and its application. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1960189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Alemu Tebeje
- Department of Agricultural Biotechnology, Biotechnology Institute, University of Gondar, Gondar, Ethiopia
| | - Henok Tadesse
- Department of Biotechnology, College of Natural and Computational Science, Wolkite University, Wolkite, Ethiopia
| | - Yizengaw Mengesha
- Department of Agricultural Biotechnology, Biotechnology Institute, University of Gondar, Gondar, Ethiopia
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9
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Chhalliyil P, Ilves H, Kazakov SA, Howard SJ, Johnston BH, Fagan J. A Real-Time Quantitative PCR Method Specific for Detection and Quantification of the First Commercialized Genome-Edited Plant. Foods 2020; 9:foods9091245. [PMID: 32906573 PMCID: PMC7556030 DOI: 10.3390/foods9091245] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 11/30/2022] Open
Abstract
Discussion regarding the regulatory status of genome-edited crops has focused on precision of editing and on doubts regarding the feasibility of analytical monitoring compliant with existing GMO regulations. Effective detection methods are important, both for regulatory enforcement and traceability in case of biosafety, environmental or socio-economic impacts. Here, we approach the analysis question for the first time in the laboratory and report the successful development of a quantitative PCR detection method for the first commercialized genome-edited crop, a canola with a single base pair edit conferring herbicide tolerance. The method is highly sensitive and specific (quantification limit, 0.05%), compatible with the standards of practice, equipment and expertise typical in GMO laboratories, and readily integrable into their analytical workflows, including use of the matrix approach. The method, validated by an independent laboratory, meets all legal requirements for GMO analytical methods in jurisdictions such as the EU, is consistent with ISO17025 accreditation standards and has been placed in the public domain. Having developed a qPCR method for the most challenging class of genome edits, single-nucleotide variants, this research suggests that qPCR-based method development may be applicable to virtually any genome-edited organism. This advance resolves doubts regarding the feasibility of extending the regulatory approach currently employed for recombinant DNA-based GMOs to genome-edited organisms.
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Affiliation(s)
- Pradheep Chhalliyil
- Health Research Institute, 505 Dimick Drive, P.O. Box 370, Fairfield, IA 52556, USA;
| | - Heini Ilves
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - Sergei A. Kazakov
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - Stephanie J. Howard
- The Sustainability Council of New Zealand, P.O. Box 24304, Wellington 6142, New Zealand;
| | - Brian H. Johnston
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - John Fagan
- Health Research Institute, 505 Dimick Drive, P.O. Box 370, Fairfield, IA 52556, USA;
- Correspondence: ; Tel.: +1-641-451-5454
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10
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Hurel J, Schbath S, Bougeard S, Rolland M, Petrillo M, Touzain F. DUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples. BMC Bioinformatics 2020; 21:284. [PMID: 32631215 PMCID: PMC7336441 DOI: 10.1186/s12859-020-03611-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/17/2020] [Indexed: 11/16/2022] Open
Abstract
Background The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerated for a “GMO-free” label. In recent years, imports of undescribed GMOs have been detected. Their sequences are not described and therefore not detectable by conventional approaches, such as PCR. Results We developed DUGMO, a bioinformatics pipeline for the detection of genetically modified (GM) bacteria, including unknown GM bacteria, based on Illumina paired-end sequencing data. The method is currently focused on the detection of GM bacteria with – possibly partial – transgenes in pure bacterial samples. In the preliminary steps, coding sequences (CDSs) are aligned through two successive BLASTN against the host pangenome with relevant tuned parameters to discriminate CDSs belonging to the wild type genome (wgCDS) from potential GM coding sequences (pgmCDSs). Then, Bray-Curtis distances are calculated between the wgCDS and each pgmCDS, based on the difference of genomic vocabulary. Finally, two machine learning methods, namely the Random Forest and Generalized Linear Model, are carried out to target true GM CDS(s), based on six variables including Bray-Curtis distances and GC content. Tests carried out on a GM Bacillus subtilis showed 25 positive CDSs corresponding to the chloramphenicol resistance gene and CDSs of the inserted plasmids. On a wild type B. subtilis, no false positive sequences were detected. Conclusion DUGMO detects exogenous CDS, truncated, fused or highly mutated wild CDSs in high-throughput sequencing data, and was shown to be efficient at detecting GM sequences, but it might also be employed for the identification of recent horizontal gene transfers.
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Affiliation(s)
- Julie Hurel
- ANSES, Laboratoire de Ploufragan, GVB unit, 22440, Ploufragan, France
| | - Sophie Schbath
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Stéphanie Bougeard
- ANSES, Laboratoire de Ploufragan, EPISABE unit, 22440, Ploufragan, France
| | - Mathieu Rolland
- ANSES, Laboratoire de la santé des végétaux, 49000, Angers, France
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Fabrice Touzain
- ANSES, Laboratoire de Ploufragan, GVB unit, 22440, Ploufragan, France.
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11
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Wu H, Zhang X, Wu B, Qian C, Zhang F, Wang L, Ye Z, Wu J. Rapid on-site detection of genetically modified soybean products by real-time loop-mediated isothermal amplification coupled with a designed portable amplifier. Food Chem 2020; 323:126819. [PMID: 32334306 DOI: 10.1016/j.foodchem.2020.126819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/06/2020] [Accepted: 04/13/2020] [Indexed: 12/29/2022]
Abstract
Herein, we developed a rapid method for detection of genetically modified soybean (GTS 40-3-2) products using loop-mediated isothermal amplification (LAMP). A crude 5-minute extraction method was established for DNA extraction from soybeans and soybean products. LAMP reaction for CaMV35S promoter was optimized and the fastest threshold time (Tt) was 14 min with 4 mM magnesium ions at 63 °C. A portable instrument was designed to perform real-time LAMP in the field. As little as 0.1% GM soybean, specifically, or 0.5% GM ingredients in Chinese traditional tofu could be detected in 30 min from sampling to results. We used this method to further assess other five soybean products to determine whether they contained transgenic ingredients and compared the results with those obtained using PCR, which suggested the proposed method was applicable for rapid detection of genetically modified soybean in food products.
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Affiliation(s)
- Hui Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Xianjun Zhang
- Hangzhou An Yu Technologies Co.,Ltd., Hangzhou 310021, China
| | - Baoqiang Wu
- Hangzhou An Yu Technologies Co.,Ltd., Hangzhou 310021, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Liu Wang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, State Key Laboratory for Quality and Safety of Agro-products, Hangzhou 310021, China.
| | - Zunzhong Ye
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
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12
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Wu H, He JS, Zhang F, Ping J, Wu J. Contamination-free visual detection of CaMV35S promoter amplicon using CRISPR/Cas12a coupled with a designed reaction vessel: Rapid, specific and sensitive. Anal Chim Acta 2020; 1096:130-137. [PMID: 31883579 DOI: 10.1016/j.aca.2019.10.042] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/17/2019] [Accepted: 10/20/2019] [Indexed: 12/21/2022]
Abstract
An ultrafast and convenient method for visually detecting CaMV35S promoter amplicon (amplified products) was established by using CRISPR/Cas12a system coupled with a designed reaction vessel. Genetically modified (GM) soybean (Roundup Ready®) powders containing CaMV35S promoter were employed as detection targets, which were amplified by loop-mediated isothermal amplification (LAMP). The CRISPR/Cas12a system directly mixed with amplified products at 37 °C for 5 min and detection results could be clearly identified by the naked eye under UV light (254 nm). A designed reaction vessel was employed to make operation easier and could effectively prevent contamination at the source. The CRISPR/Cas12a detection system was optimized in our study and the concentration of magnesium ions was proved to be important for the work of CRISPR/Cas12a system. The optimized concentration range of magnesium ions was between 10 mM and 12 mM. Besides, the activated Bst DNA polymerase also had little effects on CRISPR/Cas12a system. The developed method could significantly distinguish the specific and non-specific amplification. And as low as 0.05% transgenic contents in soybean powders could be detected. It would have the potential to be complementary to instrument-based ultrahigh sensitive method and provide a new solution for on-site rapid detection.
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Affiliation(s)
- Hui Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.
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Grześkowiak BF, Tuśnio K, Woźniak A, Szalata M, Lipiński D, Jurga S, Słomski R. Transgenic Plant Detection Using an AuNPs Based SPR Biosensor. BIOSENSORS-BASEL 2019; 9:bios9040116. [PMID: 31574896 PMCID: PMC6955715 DOI: 10.3390/bios9040116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 12/04/2022]
Abstract
The intensive development and commercialization of genetically modified plants observed over the last decade has led to the development of transgenic detection methods that are rapid and sensitive. Among the strategies used for the detection/monitoring of genetically modified organisms (GMOs), surface plasmon resonance (SPR) meets the necessary criteria. This optical technique measures the changes in the refractive index in the vicinity of thin metal layers (i.e., gold) in response to biomolecular interactions occurring at a flat metal‒solution interface. Additionally, it allows the application of functionalized gold nanoparticles (AuNPs) in SPR research to enhance the signal intensity. In the present study, an SPR method, enhanced by the application of AuNPs, was developed to detect transgenic tobacco plants carrying a Streptococcus mutans antigen. The basis for the detection of the target DNA was the hybridization between the genomic DNA isolated from the leaves, stems, and roots of the transgenic tobacco and the biotinylated oligonucleotide probes immobilized onto a streptavidin (SA) sensor chip. SA-functionalized AuNPs coated with a second type of biotinylated probe were applied to increase the sensitivity of the detection method. Analysis of the results indicated that the constructed SPR-based sensor chip can potentially recognize complementary standard fragments (nonamplified genomic DNA) at concentrations as low as 1 pM. Thus, nonamplified transgenic DNA was detected using a label-free and real-time AuNPs-enhanced SPR biosensing method. This unique approach could be used to detect GMOs with high efficiency, even at a low detection limit, high repeatability, and with less time and a lower cost needed for each analysis.
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Affiliation(s)
- Bartosz F Grześkowiak
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
| | - Karol Tuśnio
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
| | - Anna Woźniak
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
| | - Marlena Szalata
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
| | - Daniel Lipiński
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
| | - Stefan Jurga
- The NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland.
| | - Ryszard Słomski
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland.
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14
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Ultrasensitive electrochemical genosensor for detection of CaMV35S gene with Fe 3O 4-Au@Ag nanoprobe. Talanta 2019; 206:120205. [PMID: 31514877 DOI: 10.1016/j.talanta.2019.120205] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/14/2022]
Abstract
We report an attomolar sensitive electrochemical genosensor for the detection of cauliflower mosaic virus 35S (CaMV35S) gene. The sandwich-type genosensor uses gold-silver core-shell (Au@Ag)-loaded iron oxide (Fe3O4) nanocomposite (Fe3O4-Au@Ag) as label of signal DNA probe (sDNA). Electrochemical sensing is accomplished at interface of electrodeposited AuNPs and carboxylated multiwalled carbon nanotubes-modified glassy carbon electrode through the specific interaction between the capture probe and target CaMV35S (tDNA), and tDNA and the labeled sDNA. The detection sensitivity was improved by the amplified reduction signal of hydrogen peroxide (H2O2), which takes advantage of the enhanced electrocatalytic activity of Fe3O4-Au@Ag. Under the optimal experimental conditions, an ultralow limit of detection was calculated to be 1.26 × 10-17 M (S/N = 3), and the blank value subtracted reduction signal of H2O2 of the sensor increased linearly with the logarithm of CaMV35S concentration over a wide range (1 × 10-16 M to 1 × 10-10 M). This genosensor displayed excellent stability, selectivity and reproducibility, and was successful in detecting the target CaMV35S in genetically modified tomato samples.
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15
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Guertler P, Grohmann L, Naumann H, Pavlovic M, Busch U. Development of event-specific qPCR detection methods for genetically modified alfalfa events J101, J163 and KK179. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100076. [PMID: 30984566 PMCID: PMC6446038 DOI: 10.1016/j.bdq.2018.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/23/2018] [Accepted: 12/04/2018] [Indexed: 11/28/2022]
Abstract
Genetically modified alfalfa is authorized for cultivation in several countries since 2005. On the other hand, cultivation in or export to the European Union is not allowed and thus neither certified reference material nor official event-specific detection methods are available. Therefore, based on patent sequence information, event-specific real-time PCR detection methods targeting the junction sequence of the alfalfa genome and the transgenic insert of the respective events J101, J163 and KK179 were developed. Newly developed plasmids were used as reference material for assay optimization and in-house validation. Plasmid standards were quantified using digital droplet PCR and LOD95%, PCR efficiency, robustness and specificity of the assays were determined using real-time PCR. A LOD95% of 10 copies per PCR reaction was observed and PCR efficiencies of 95-97 % were achieved. Different real-time PCR instruments and PCR conditions were applied to test for robustness of the assays using DNA at a concentration of 30 copies per μL for each gm alfalfa event. All replicates were positive independent of the instrument or the PCR condition. DNA from certified reference material of different genetically modified crops as well as reference materials of the three events was used to experimentally test for specificity. No unspecific amplification signal was observed for any of the assays. Validation results were in line with the "Minimum Performance Requirements for Analytical Methods of GMO Testing" of the European Network of GMO Laboratories. Furthermore, an inter-laboratory comparison study was conducted to show the transferability and applicability of the methods and to verify the assay performance parameters.
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Affiliation(s)
- Patrick Guertler
- Bavarian Health and Food Safety Authority, Veterinärstr. 2, 85764 Oberschleißheim, Germany
| | - Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety, Mauerstrasse 39-42, 10117 Berlin, Germany
| | - Heike Naumann
- Lower Saxony State Office for Consumer Protection and Food Safety, Food and Veterinary Institute, Dresdenstr. 2, 38124 Braunschweig, Germany
| | - Melanie Pavlovic
- Bavarian Health and Food Safety Authority, Veterinärstr. 2, 85764 Oberschleißheim, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Veterinärstr. 2, 85764 Oberschleißheim, Germany
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16
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Linacero R, Sanchiz A, Ballesteros I, Cuadrado C. Application of real-time PCR for tree nut allergen detection in processed foods. Crit Rev Food Sci Nutr 2019; 60:1077-1093. [PMID: 30638046 DOI: 10.1080/10408398.2018.1557103] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Currently, food allergies are an important health concern worldwide. The presence of undeclared allergenic ingredients or the presence of traces of allergens due to accidental contamination during food processing poses a great health risk to sensitized individuals. Therefore, reliable analytical methods are required to detect and identify allergenic ingredients in food products. Real-time PCR allowed a specific and accurate amplification of allergen sequences. Some processing methods could induce the fragmentation and/or degradation of genomic DNA and some studies have been performed to analyze the effect of processing on the detection of different targets, as thermal treatment, with and without applying pressure. In this review, we give an updated overview of the applications of real-time PCR for the detection of allergens of tree nut in processed food products. The different variables that contribute to the performance of PCR methodology for allergen detection are also review and discussed.
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Affiliation(s)
- Rosario Linacero
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Africa Sanchiz
- Departamento de Tecnología de Alimentos, SGIT-INIA, Madrid, Spain
| | - Isabel Ballesteros
- Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de las Américas, Quito, Ecuador
| | - Carmen Cuadrado
- Departamento de Tecnología de Alimentos, SGIT-INIA, Madrid, Spain
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17
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Andrew CI, Paul CO, Opeolu OO. Detection of genetically modified DNA in processed maize and soybean products in Nigeria. ACTA ACUST UNITED AC 2018. [DOI: 10.5897/ajb2018.16479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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18
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Fraiture MA, Saltykova A, Hoffman S, Winand R, Deforce D, Vanneste K, De Keersmaecker SCJ, Roosens NHC. Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO. Sci Rep 2018; 8:7903. [PMID: 29785005 PMCID: PMC5962636 DOI: 10.1038/s41598-018-26259-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region. This DNA walking is performed on transgenic elements, commonly found in GMO, that were earlier detected by real-time PCR (qPCR) screening. Previously, we have demonstrated the ability of this approach to detect unauthorized GMO via the identification of unique transgene flanking regions and the unnatural associations of elements from the transgenic cassette. In the present study, we investigate the feasibility to integrate the described workflow with the MinION Next-Generation-Sequencing (NGS). The MinION sequencing platform can provide long read-lengths and deal with heterogenic DNA libraries, allowing for rapid and efficient delivery of sequences of interest. In addition, the ability of this NGS platform to characterize unauthorized and unknown GMO without any a priori knowledge has been assessed.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Assia Saltykova
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Ghent University (UGent), Department of Information Technology, IMEC, Internet Technology and Data Science Lab (IDLab), Technologiepark-Zwijnaarde 15, 9052, Ghent, Belgium
| | - Stefan Hoffman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Raf Winand
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Kevin Vanneste
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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Grelewska-Nowotko K, Żurawska-Zajfert M, Żmijewska E, Sowa S. Optimization and Verification of Droplet Digital PCR Even-Specific Methods for the Quantification of GM Maize DAS1507 and NK603. Appl Biochem Biotechnol 2017; 185:207-220. [PMID: 29110175 DOI: 10.1007/s12010-017-2634-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/16/2017] [Indexed: 12/21/2022]
Abstract
In recent years, digital polymerase chain reaction (dPCR), a new molecular biology technique, has been gaining in popularity. Among many other applications, this technique can also be used for the detection and quantification of genetically modified organisms (GMOs) in food and feed. It might replace the currently widely used real-time PCR method (qPCR), by overcoming problems related to the PCR inhibition and the requirement of certified reference materials to be used as a calibrant. In theory, validated qPCR methods can be easily transferred to the dPCR platform. However, optimization of the PCR conditions might be necessary. In this study, we report the transfer of two validated qPCR methods for quantification of maize DAS1507 and NK603 events to the droplet dPCR (ddPCR) platform. After some optimization, both methods have been verified according to the guidance of the European Network of GMO Laboratories (ENGL) on analytical method verification (ENGL working group on "Method Verification." (2011) Verification of Analytical Methods for GMO Testing When Implementing Interlaboratory Validated Methods). Digital PCR methods performed equally or better than the qPCR methods. Optimized ddPCR methods confirm their suitability for GMO determination in food and feed.
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Affiliation(s)
- Katarzyna Grelewska-Nowotko
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland.
| | - Magdalena Żurawska-Zajfert
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Ewelina Żmijewska
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Sławomir Sowa
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
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20
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Salisu IB, Shahid AA, Yaqoob A, Ali Q, Bajwa KS, Rao AQ, Husnain T. Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review. FRONTIERS IN PLANT SCIENCE 2017; 8:1670. [PMID: 29085378 PMCID: PMC5650622 DOI: 10.3389/fpls.2017.01670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/11/2017] [Indexed: 06/01/2023]
Abstract
As long as the genetically modified crops are gaining attention globally, their proper approval and commercialization need accurate and reliable diagnostic methods for the transgenic content. These diagnostic techniques are mainly divided into two major groups, i.e., identification of transgenic (1) DNA and (2) proteins from GMOs and their products. Conventional methods such as PCR (polymerase chain reaction) and enzyme-linked immunosorbent assay (ELISA) were routinely employed for DNA and protein based quantification respectively. Although, these Techniques (PCR and ELISA) are considered as significantly convenient and productive, but there is need for more advance technologies that allow for high throughput detection and the quantification of GM event as the production of more complex GMO is increasing day by day. Therefore, recent approaches like microarray, capillary gel electrophoresis, digital PCR and next generation sequencing are more promising due to their accuracy and precise detection of transgenic contents. The present article is a brief comparative study of all such detection techniques on the basis of their advent, feasibility, accuracy, and cost effectiveness. However, these emerging technologies have a lot to do with detection of a specific event, contamination of different events and determination of fusion as well as stacked gene protein are the critical issues to be addressed in future.
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Affiliation(s)
- Ibrahim B. Salisu
- Department of Animal Science, Faculty of Agriculture, Federal University Dutse, Jigawa, Nigeria
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad A. Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Amina Yaqoob
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Kamran S. Bajwa
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abdul Q. Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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21
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Fraiture MA, Herman P, De Loose M, Debode F, Roosens NH. How Can We Better Detect Unauthorized GMOs in Food and Feed Chains? Trends Biotechnol 2017; 35:508-517. [DOI: 10.1016/j.tibtech.2017.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/17/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022]
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22
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Fraiture MA, Herman P, Papazova N, De Loose M, Deforce D, Ruttink T, Roosens NH. An integrated strategy combining DNA walking and NGS to detect GMOs. Food Chem 2017; 232:351-358. [PMID: 28490084 DOI: 10.1016/j.foodchem.2017.03.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 10/17/2016] [Accepted: 03/11/2017] [Indexed: 12/21/2022]
Abstract
Recently, we developed a DNA walking system for the detection and characterization of a broad spectrum of GMOs in routine analysis of food/feed matrices. Here, we present a new version with improved throughput and sensitivity by coupling the DNA walking system to Pacific Bioscience® Next-generation sequencing technology. The performance of the new strategy was thoroughly assessed through several assays. First, we tested its detection and identification capability on grains with high or low GMO content. Second, the potential impacts of food processing were investigated using rice noodle samples. Finally, GMO mixtures and a real-life sample were analyzed to illustrate the applicability of the proposed strategy in routine GMO analysis. In all tested samples, the presence of multiple GMOs was unambiguously proven by the characterization of transgene flanking regions and the combinations of elements that are typical for transgene constructs.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Institute for Agricultural, Fisheries and Food Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820 Merelbeke, Belgium; Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nina Papazova
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Marc De Loose
- Institute for Agricultural, Fisheries and Food Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820 Merelbeke, Belgium; Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium.
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Tom Ruttink
- Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium.
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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23
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Li R, Quan S, Yan X, Biswas S, Zhang D, Shi J. Molecular characterization of genetically-modified crops: Challenges and strategies. Biotechnol Adv 2017; 35:302-309. [DOI: 10.1016/j.biotechadv.2017.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 12/23/2022]
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24
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Bohanec M, Boshkoska BM, Prins TW, Kok EJ. SIGMO: A decision support System for Identification of genetically modified food or feed products. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.06.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Gao H, Yu X, Deng T, Sun M, Xiao X, Huang X, Chen Y, Li R. Event-specific detection of transgenic potato AV43-6-G7 using real-time and digital PCR methods. BMC Biotechnol 2016; 16:74. [PMID: 27784303 PMCID: PMC5081928 DOI: 10.1186/s12896-016-0303-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023] Open
Abstract
Background The isolation of unknown DNA sequences flanked by known sequences is an important task in the event-specific detection of GMOs. None of event-specific detection method was developed based on the junction sequence of an exogenous integrant in the transgenic potato AV43-6-G7. Results The flanking sequence between the exogenous fragment and recombinant chromosome of this potato was successfully acquired through exogenous gene 5′-RACE. The event-specific primers and Taqman probe were designed to amplify fragments spanning the exogenous DNA and potato genomic DNA. The specific real-time PCR and digital PCR detection methods for AV43-6-G7 potato were established based on primers designed according to the flanking sequences. The detection limit of the qualitative PCR assay was 0.01 % for AV43-6-G7 potato in 100 ng of potato genomic DNA, corresponding to approximately 11.6 copies of the potato haploid genome. The ddPCR assays for Potato AV43-6-G7 achieved a limit of quantification of approximately 58 target copies, with RSD ≤ 25 %. The aLOQ of this system was approximately 1.2 copies. Conclusions These results indicated that these event-specific methods would be useful for the identification of potato AV43-6-G7. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0303-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongwei Gao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China.
| | - Xiaofan Yu
- Qingdao University Medical College, Qingdao, China
| | - Tingting Deng
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Min Sun
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xizhi Xiao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xin Huang
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ronggui Li
- Qingdao University Medical College, Qingdao, China
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26
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Simko I. High-Resolution DNA Melting Analysis in Plant Research. TRENDS IN PLANT SCIENCE 2016; 21:528-537. [PMID: 26827247 DOI: 10.1016/j.tplants.2016.01.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/05/2015] [Accepted: 01/05/2016] [Indexed: 05/22/2023]
Abstract
Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.
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Affiliation(s)
- Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA.
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Fraiture MA, Roosens NH, Taverniers I, De Loose M, Deforce D, Herman P. Biotech rice: Current developments and future detection challenges in food and feed chain. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.03.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Salihah NT, Hossain MM, Lubis H, Ahmed MU. Trends and advances in food analysis by real-time polymerase chain reaction. Journal of Food Science and Technology 2016; 53:2196-209. [PMID: 27407185 PMCID: PMC4921084 DOI: 10.1007/s13197-016-2205-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 03/06/2016] [Accepted: 03/14/2016] [Indexed: 02/05/2023]
Abstract
Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling.
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Affiliation(s)
- Nur Thaqifah Salihah
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
| | | | - Hamadah Lubis
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
| | - Minhaz Uddin Ahmed
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
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Tsukahara K, Takabatake R, Masubuchi T, Futo S, Minegishi Y, Noguchi A, Kondo K, Nishimaki-Mogami T, Kurashima T, Mano J, Kitta K. Development and Evaluation of Event-Specific Quantitative PCR Method for Genetically Modified Soybean MON87701. SHOKUHIN EISEIGAKU ZASSHI. JOURNAL OF THE FOOD HYGIENIC SOCIETY OF JAPAN 2016; 57:187-192. [PMID: 28025452 DOI: 10.3358/shokueishi.57.187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) soybean event, MON87701. First, a standard plasmid for MON87701 quantification was constructed. The conversion factor (Cf) required to calculate the amount of genetically modified organism (GMO) was experimentally determined for a real-time PCR instrument. The determined Cf for the real-time PCR instrument was 1.24. For the evaluation of the developed method, a blind test was carried out in an inter-laboratory trial. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDr), respectively. The determined biases and the RSDr values were less than 30 and 13%, respectively, at all evaluated concentrations. The limit of quantitation of the method was 0.5%, and the developed method would thus be applicable for practical analyses for the detection and quantification of MON87701.
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Affiliation(s)
- Keita Tsukahara
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization
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Wan J, Song L, Wu Y, Brzoska P, Keys D, Chen C, Valliyodan B, Shannon JG, Nguyen HT. Application of Digital PCR in the Analysis of Transgenic Soybean Plants. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.710039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Fraiture MA, Herman P, Taverniers I, De Loose M, Deforce D, Roosens NH. Current and new approaches in GMO detection: challenges and solutions. BIOMED RESEARCH INTERNATIONAL 2015; 2015:392872. [PMID: 26550567 PMCID: PMC4624882 DOI: 10.1155/2015/392872] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/07/2015] [Indexed: 11/17/2022]
Abstract
In many countries, genetically modified organisms (GMO) legislations have been established in order to guarantee the traceability of food/feed products on the market and to protect the consumer freedom of choice. Therefore, several GMO detection strategies, mainly based on DNA, have been developed to implement these legislations. Due to its numerous advantages, the quantitative PCR (qPCR) is the method of choice for the enforcement laboratories in GMO routine analysis. However, given the increasing number and diversity of GMO developed and put on the market around the world, some technical hurdles could be encountered with the qPCR technology, mainly owing to its inherent properties. To address these challenges, alternative GMO detection methods have been developed, allowing faster detections of single GM target (e.g., loop-mediated isothermal amplification), simultaneous detections of multiple GM targets (e.g., PCR capillary gel electrophoresis, microarray, and Luminex), more accurate quantification of GM targets (e.g., digital PCR), or characterization of partially known (e.g., DNA walking and Next Generation Sequencing (NGS)) or unknown (e.g., NGS) GMO. The benefits and drawbacks of these methods are discussed in this review.
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Affiliation(s)
- Marie-Alice Fraiture
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Philippe Herman
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Isabel Taverniers
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
| | - Marc De Loose
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Nancy H. Roosens
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
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Pauwels K, De Keersmaecker SC, De Schrijver A, du Jardin P, Roosens NH, Herman P. Next-generation sequencing as a tool for the molecular characterisation and risk assessment of genetically modified plants: Added value or not? Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.07.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Fraiture MA, Herman P, Lefèvre L, Taverniers I, De Loose M, Deforce D, Roosens NH. Integrated DNA walking system to characterize a broad spectrum of GMOs in food/feed matrices. BMC Biotechnol 2015; 15:76. [PMID: 26272331 PMCID: PMC4535744 DOI: 10.1186/s12896-015-0191-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/29/2015] [Indexed: 01/28/2023] Open
Abstract
Background In order to provide a system fully integrated with qPCR screening, usually used in GMO routine analysis, as well as being able to detect, characterize and identify a broad spectrum of GMOs in food/feed matrices, two bidirectional DNA walking methods targeting p35S or tNOS, the most common transgenic elements found in GM crops, were developed. These newly developed DNA walking methods are completing the previously implemented DNA walking method targeting the t35S pCAMBIA element. Methods Food/feed matrices containing transgenic crops (Bt rice or MON863 maize) were analysed using the integrated DNA walking system. Results First, the newly developed DNA walking methods, anchored on the sequences used for the p35S or tNOS qPCR screening, were tested on Bt rice that contains these two transgenic elements. Second, the methods were assessed on a maize sample containing a low amount of the GM MON863 event, representing a more complex matrix in terms of genome size and sensitivity. Finally, to illustrate its applicability in GMO routine analysis by enforcement laboratories, the entire workflow of the integrated strategy, including qPCR screening to detect the potential presence of GMOs and the subsequent DNA walking methods to characterize and identify the detected GMOs, was applied on a GeMMA Scheme Proficiency Test matrix. Via the characterization of the transgene flanking region between the transgenic cassette and the plant genome as well as of a part of the transgenic cassette, the presence of GMOs was properly confirmed or infirmed in all tested samples. Conclusion Due to their simple procedure and their short time-frame to get results, the developed DNA walking methods proposed here can be easily implemented in GMO routine analysis by the enforcement laboratories. In providing crucial information about the transgene flanking regions and/or the transgenic cassettes, this DNA walking strategy is a key molecular tool to prove the presence of GMOs in any given food/feed matrix. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0191-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium. .,Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820, Merelbeke, Belgium. .,Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
| | - Loic Lefèvre
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
| | - Isabel Taverniers
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820, Merelbeke, Belgium.
| | - Marc De Loose
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 bus 1, 9820, Merelbeke, Belgium. .,Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052, Ghent, Belgium.
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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Datukishvili N, Kutateladze T, Gabriadze I, Bitskinashvili K, Vishnepolsky B. New multiplex PCR methods for rapid screening of genetically modified organisms in foods. Front Microbiol 2015; 6:757. [PMID: 26257724 PMCID: PMC4513241 DOI: 10.3389/fmicb.2015.00757] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/10/2015] [Indexed: 12/15/2022] Open
Abstract
We present novel multiplex PCR methods for rapid and reliable screening of genetically modified organisms (GMOs). New designed PCR primers targeting four frequently used GMO specific sequences permitted identification of new DNA markers, in particular 141 bp fragment of cauliflower mosaic virus (CaMV) 35S promoter, 224 bp fragment of Agrobacterium tumefaciens nopaline synthase (NOS) terminator, 256 bp fragment of 5-enolppyruvylshikimate-phosphate synthase (epsps) gene and 258 bp fragment of Cry1Ab delta-endotoxin (cry1Ab) gene for GMO screening. The certified reference materials containing Roundup Ready soybean (RRS) and maize MON 810 were applied for the development and optimization of uniplex and multiplex PCR systems. Evaluation of amplification products by agarose gel electrophoresis using negative and positive controls confirmed high specificity and sensitivity at 0.1% GMO for both RRS and MON 810. The fourplex PCR was developed and optimized that allows simultaneous detection of three common transgenic elements, such as: CaMV 35S promoter, NOS terminator, epsps gene together with soybean-specific lectin gene. The triplex PCR developed enables simultaneous identification of transgenic elements, such as: 35S promoter and cry1Ab gene together with maize zein gene. The analysis of different processed foods demonstrated that multiplex PCR methods developed in this study are useful for accurate and fast screening of GM food products.
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Affiliation(s)
- Nelly Datukishvili
- Ivane Beritashvili Center of Experimental Biomedicine Tbilisi, Georgia ; Faculty of Natural Sciences and Engineering, Ilia State University Tbilisi, Georgia
| | | | - Inga Gabriadze
- Ivane Beritashvili Center of Experimental Biomedicine Tbilisi, Georgia
| | - Kakha Bitskinashvili
- Faculty of Natural Sciences and Engineering, Ilia State University Tbilisi, Georgia
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Willems S, Fraiture MA, Deforce D, De Keersmaecker SCJ, De Loose M, Ruttink T, Herman P, Van Nieuwerburgh F, Roosens N. Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing. Food Chem 2015; 192:788-98. [PMID: 26304412 DOI: 10.1016/j.foodchem.2015.07.074] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 06/26/2015] [Accepted: 07/18/2015] [Indexed: 10/23/2022]
Abstract
Because the number and diversity of genetically modified (GM) crops has significantly increased, their analysis based on real-time PCR (qPCR) methods is becoming increasingly complex and laborious. While several pioneers already investigated Next Generation Sequencing (NGS) as an alternative to qPCR, its practical use has not been assessed for routine analysis. In this study a statistical framework was developed to predict the number of NGS reads needed to detect transgene sequences, to prove their integration into the host genome and to identify the specific transgene event in a sample with known composition. This framework was validated by applying it to experimental data from food matrices composed of pure GM rice, processed GM rice (noodles) or a 10% GM/non-GM rice mixture, revealing some influential factors. Finally, feasibility of NGS for routine analysis of GM crops was investigated by applying the framework to samples commonly encountered in routine analysis of GM crops.
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Affiliation(s)
- Sander Willems
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium; Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115, bus 1, 9820 Merelbeke, Belgium
| | - Dieter Deforce
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Sigrid C J De Keersmaecker
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Marc De Loose
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115, bus 1, 9820 Merelbeke, Belgium
| | - Tom Ruttink
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Caritasstraat 21, 9090 Melle, Belgium
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Filip Van Nieuwerburgh
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Nancy Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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Wang C, Li R, Quan S, Shen P, Zhang D, Shi J, Yang L. GMO detection in food and feed through screening by visual loop-mediated isothermal amplification assays. Anal Bioanal Chem 2015; 407:4829-34. [DOI: 10.1007/s00216-015-8652-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 03/05/2015] [Accepted: 03/19/2015] [Indexed: 12/22/2022]
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Turkec A, Kazan H, Baykut A, Lucas SJ. Evalution of DNA extraction methods in order to monitor genetically modified materials in soy foodstuffs and feeds commercialised in Turkey by multiplex real-time PCR. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:386-92. [PMID: 24816675 DOI: 10.1002/jsfa.6731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/22/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Soybean is one of the most important biotech crops, widely used as an ingredient in both foodstuffs and feed. DNA extraction methods have been evaluated to detect the presence of genetically modified (GM) materials in soya-containing food and feed products commercialised in Turkey. RESULTS All extraction methods performed well for the majority of soya foods and feed products analysed. However, the most successful method varied between different products; the Foodproof, Genespin and the cetyltrimethylammonium bromide (CTAB) methods each produced the highest DNA yield and purity for different soya foodstuffs and feeds. Of the samples tested, 20% were positive for the presence of at least two GM elements (35S/NOS) while 11% contained an additional GM element (35S/NOS/FMV). Of the tested products, animal feeds showed a larger prevalence of GM material (50%) than the soya-containing foodstuffs (13%). CONCLUSION The best performing extraction methods proved to be the Foodproof, Genespin and CTAB methods for soya-containing food and feed products. The results obtained herein clearly demonstrate the presence of GM soybean in the Turkish market, and that the Foodproof GMO Screening Kit provides reliable screening of soy-containing food and feed products.
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Affiliation(s)
- Aydin Turkec
- Department of Plant and Animal Production, Vocational School of Mustafakemalpasa, University of Uludag, 16500, Bursa, Turkey
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Fraiture MA, Herman P, Taverniers I, De Loose M, Van Nieuwerburgh F, Deforce D, Roosens NH. Validation of a sensitive DNA walking strategy to characterise unauthorised GMOs using model food matrices mimicking common rice products. Food Chem 2014; 173:1259-65. [PMID: 25466152 DOI: 10.1016/j.foodchem.2014.09.148] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 08/14/2014] [Accepted: 09/17/2014] [Indexed: 11/18/2022]
Abstract
To identify unauthorised GMOs in food and feed matrices, an integrated approach has recently been developed targeting pCAMBIA family vectors, highly present in transgenic plants. Their presence is first assessed by qPCR screening and is subsequently confirmed by characterising the transgene flanking regions, using DNA walking. Here, the DNA walking performance has been thoroughly tested for the first time, regarding the targeted DNA quality and quantity. Several assays, on model food matrices mimicking common rice products, have allowed to determine the limit of detection as well as the potential effects of food mixture and processing. This detection system allows the identification of transgenic insertions as low as 10 HGEs and was not affected by the presence of untargeted DNA. Moreover, despite the clear impact of food processing on DNA quality, this method was able to cope with degraded DNA. Given its specificity, sensitivity, reliability, applicability and practicability, the proposed approach is a key detection tool, easily implementable in enforcement laboratories.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 Bus 1, 9820 Merelbeke, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Isabel Taverniers
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 Bus 1, 9820 Merelbeke, Belgium
| | - Marc De Loose
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115 Bus 1, 9820 Merelbeke, Belgium; University of Gent (UGent), Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Dieter Deforce
- University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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Van Eenennaam AL, Young AE. Prevalence and impacts of genetically engineered feedstuffs on livestock populations. J Anim Sci 2014; 92:4255-78. [PMID: 25184846 DOI: 10.2527/jas.2014-8124] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Globally, food-producing animals consume 70 to 90% of genetically engineered (GE) crop biomass. This review briefly summarizes the scientific literature on performance and health of animals consuming feed containing GE ingredients and composition of products derived from them. It also discusses the field experience of feeding GE feed sources to commercial livestock populations and summarizes the suppliers of GE and non-GE animal feed in global trade. Numerous experimental studies have consistently revealed that the performance and health of GE-fed animals are comparable with those fed isogenic non-GE crop lines. United States animal agriculture produces over 9 billion food-producing animals annually, and more than 95% of these animals consume feed containing GE ingredients. Data on livestock productivity and health were collated from publicly available sources from 1983, before the introduction of GE crops in 1996, and subsequently through 2011, a period with high levels of predominately GE animal feed. These field data sets, representing over 100 billion animals following the introduction of GE crops, did not reveal unfavorable or perturbed trends in livestock health and productivity. No study has revealed any differences in the nutritional profile of animal products derived from GE-fed animals. Because DNA and protein are normal components of the diet that are digested, there are no detectable or reliably quantifiable traces of GE components in milk, meat, and eggs following consumption of GE feed. Globally, countries that are cultivating GE corn and soy are the major livestock feed exporters. Asynchronous regulatory approvals (i.e., cultivation approvals of GE varieties in exporting countries occurring before food and feed approvals in importing countries) have resulted in trade disruptions. This is likely to be increasingly problematic in the future as there are a large number of "second generation" GE crops with altered output traits for improved livestock feed in the developmental and regulatory pipelines. Additionally, advanced techniques to affect targeted genome modifications are emerging, and it is not clear whether these will be encompassed by the current GE process-based trigger for regulatory oversight. There is a pressing need for international harmonization of both regulatory frameworks for GE crops and governance of advanced breeding techniques to prevent widespread disruptions in international trade of livestock feedstuffs in the future.
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Affiliation(s)
| | - A E Young
- Department of Animal Science, University of California, Davis 95616
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Development and application of loop-mediated isothermal amplification assays for rapid visual detection of cry2Ab and cry3A genes in genetically-modified crops. Int J Mol Sci 2014; 15:15109-21. [PMID: 25167136 PMCID: PMC4200818 DOI: 10.3390/ijms150915109] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 11/17/2022] Open
Abstract
The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs) containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP) method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM) crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field.
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Development of a novel reference plasmid for accurate quantification of genetically modified Kefeng6 rice DNA in food and feed samples. BIOMED RESEARCH INTERNATIONAL 2013; 2013:134675. [PMID: 24324952 PMCID: PMC3845723 DOI: 10.1155/2013/134675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/20/2013] [Accepted: 10/04/2013] [Indexed: 12/31/2022]
Abstract
Reference plasmids are an essential tool for the quantification of genetically modified (GM) events. Quantitative real-time PCR (qPCR) is the most commonly used method to characterize and quantify reference plasmids. However, the precision of this method is often limited by calibration curves, and qPCR data can be affected by matrix differences between the standards and samples. Here, we describe a digital PCR (dPCR) approach that can be used to accurately measure the novel reference plasmid pKefeng6 and quantify the unauthorized variety of GM rice Kefeng6, eliminating the issues associated with matrix effects in calibration curves. The pKefeng6 plasmid was used as a calibrant for the quantification of Kefeng6 rice by determining the copy numbers of event- (77 bp) and taxon-specific (68 bp) fragments, their ratios, and their concentrations. The plasmid was diluted to five different concentrations. The third sample (S3) was optimized for the quantification range of dPCR according to previous reports. The ratio between the two fragments was 1.005, which closely approximated the value certified by sequencing, and the concentration was found to be 792 copies/μL. This method was precise, with an RSD of ~3%. These findings demonstrate the advantages of using the dPCR method to characterize reference materials.
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Fraiture MA, Herman P, Taverniers I, De Loose M, Deforce D, Roosens NH. An innovative and integrated approach based on DNA walking to identify unauthorised GMOs. Food Chem 2013; 147:60-9. [PMID: 24206686 DOI: 10.1016/j.foodchem.2013.09.112] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 07/12/2013] [Accepted: 09/19/2013] [Indexed: 01/23/2023]
Abstract
In the coming years, the frequency of unauthorised genetically modified organisms (GMOs) being present in the European food and feed chain will increase significantly. Therefore, we have developed a strategy to identify unauthorised GMOs containing a pCAMBIA family vector, frequently present in transgenic plants. This integrated approach is performed in two successive steps on Bt rice grains. First, the potential presence of unauthorised GMOs is assessed by the qPCR SYBR®Green technology targeting the terminator 35S pCAMBIA element. Second, its presence is confirmed via the characterisation of the junction between the transgenic cassette and the rice genome. To this end, a DNA walking strategy is applied using a first reverse primer followed by two semi-nested PCR rounds using primers that are each time nested to the previous reverse primer. This approach allows to rapidly identify the transgene flanking region and can easily be implemented by the enforcement laboratories.
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Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Molecular Biology (PBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050 Brussels, Belgium; Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Sciences Unit, Burg. Van Gansberghelaan 115, bus 1, 9820 Merelbeke, Belgium; University of Gent (UGent), Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Harelbekestraat 72, 9000 Ghent, Belgium
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