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Zanatta CB, Hoepers AM, Nodari RO, Agapito-Tenfen SZ. Specificity Testing for NGT PCR-Based Detection Methods in the Context of the EU GMO Regulations. Foods 2023; 12:4298. [PMID: 38231759 DOI: 10.3390/foods12234298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
The term new genomic techniques (NGTs) is an umbrella term used to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework used to detect GMOs in Europe is an established single harmonized procedure that is mandatory for the authorization of GM food and feed, thus generating a reliable, transparent, and effective labeling scheme for GMO products. However, NGT products can challenge the implementation and enforcement of the current regulatory system in the EU, relating in particular to the detection of NGT products that contain no foreign genetic material. Consequently, the current detection methods might fail to meet the minimum performance requirements. Although existing detection methods may be able to detect and quantify even small alterations in the genome, this does not necessarily confirm the distinction between products resulting from NGTs subject to the GMO legislation and other products. Therefore, this study provides a stepwise approach for the in silico prediction of PCR systems' specificity by testing a bioinformatics pipeline for amplicon and primer set searches in current genomic databases. In addition, it also empirically tested the PCR system evaluated during the in silico analysis. Two mutant genotypes produced by CRISPR-Cas9 in Arabidopsis thaliana were used as a case study. Overall, our results demonstrate that the single PCR system developed for identifying a nucleotide insertion in the grf1-3 genotype has multiple matches in the databases, which do not enable the discrimination of this mutated event. Empirical assays further support this demonstration. In contrast, the second mutated genotype, grf8-61, which contains a -3 bp deletion, did not yield any matches in the sequence variant database. However, the primer sequences were not efficient during the empirical assay. Our approach represents a first step in decision making for analytical methods for NGT detection, identification, and quantification in light of the European labeling regulations.
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Affiliation(s)
- Caroline Bedin Zanatta
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Aline Martins Hoepers
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Rubens Onofre Nodari
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
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Badai SS, Rasid OA, Masani MYA, Chan KL, Chan PL, Shaharuddin NA, Abdullah MP, Parveez GKA, Ho CL. Functional characterization of the MSP-C6 promoter as a potential tool for mesocarp-preferential expression of transgenes. J Plant Physiol 2023; 289:154080. [PMID: 37699261 DOI: 10.1016/j.jplph.2023.154080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Modification of lipid composition in the mesocarp tissue of oil palm involves genetic manipulation of multiple genes. More than one mesocarp-preferential promoter is necessary for the expression of individual transgenes in the same plant to obviate transcriptional gene silencing. This study aimed to identify genes that are preferentially expressed in the mesocarp tissue and characterize selected candidate mesocarp-preferential promoters. Ten transcripts that were preferentially expressed in the mesocarp tissue were identified from the analysis of 82 transcriptome datasets of 12 different oil palm tissues. The expression of two candidate genes, MSP-C1 and MSP-C6, was verified to be preferentially expressed in the mesocarp tissues and shown to have a low expression level in non-mesocarp tissues by reverse transcription quantitative real-time PCR (RT-qPCR). MSP-C6 promoter fragments of different lengths were transformed into tomato plants for further characterization. Both unripe and ripe fruits of transgenic tomato plants transformed with a construct harboring the MSP-C6-F1 (2014 bp) promoter were shown to have high beta-glucuronidase (GUS) activities. The findings of this study suggest the potential applications of the MSP-C6 promoter as a molecular tool for genetic engineering of novel traits in fruit crops.
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Affiliation(s)
- Siti Suriawati Badai
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Omar Abd Rasid
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Mat Yunus Abdul Masani
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Kuang Lim Chan
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Pek Lan Chan
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Chai Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
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Fraiture MA, D'aes J, Guiderdoni E, Meunier AC, Delcourt T, Hoffman S, Vandermassen E, De Keersmaecker SCJ, Vanneste K, Roosens NHC. Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms. Foods 2023; 12. [PMID: 36765984 DOI: 10.3390/foods12030455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in OsMADS26 were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs.
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Strobbe S, Wesana J, Van Der Straeten D, De Steur H. Public acceptance and stakeholder views of gene edited foods: a global overview. Trends Biotechnol 2023; 41:736-740. [PMID: 36658005 DOI: 10.1016/j.tibtech.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/09/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023]
Abstract
The increasing popularity of gene editing in plants has prompted research on stakeholder views. Gene edited foods are often more accepted than genetically modified foods, though differences occur within target groups, regions, and products. Nevertheless, marketing challenges related to a lack of familiarity with the technology, labeling, and risk perception remain.
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Affiliation(s)
- Simon Strobbe
- Ghent University, Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, Belgium
| | - Joshua Wesana
- Ghent University, Department of Agricultural Economics, Ghent University, Coupure Links 653, Ghent, Belgium; Food and Markets Department, Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, UK; Faculty of Agriculture and Environmental Sciences, Mountains of the Moon University, Kasindikwa Village, Lake Saaka, Fort Portal, Uganda
| | - Dominique Van Der Straeten
- Ghent University, Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, Belgium
| | - Hans De Steur
- Ghent University, Department of Agricultural Economics, Ghent University, Coupure Links 653, Ghent, Belgium.
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Pascher K, Hainz-Renetzeder C, Jagersberger M, Kneissl K, Gollmann G, Schneeweiss GM. Contamination of imported kernels by unapproved genome-edited varieties poses a major challenge for monitoring and traceability during transport and handling on a global scale: inferences from a study on feral oilseed rape in Austria. Front Genome Ed 2023; 5:1176290. [PMID: 37153078 PMCID: PMC10156978 DOI: 10.3389/fgeed.2023.1176290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Novel techniques such as CRISPR/Cas are increasingly being applied for the development of modern crops. However, the regulatory framework for production, labelling and handling of genome-edited organisms varies worldwide. Currently, the European Commission is raising the question whether genome-edited organisms should still be regulated as genetically modified organisms in the future or whether a deregulation should be implemented. In our paper, based on the outcome of a 2-year case study on oilseed rape in Austria, we show that seed spillage during import and subsequent transport and handling activities is a key factor for the unintended dispersal of seeds into the environment, the subsequent emergence of feral oilseed rape populations and their establishment and long-term persistence in natural habitats. These facts must likewise be considered in case of genome-edited oilseed rape contaminants that might be accidentally introduced with conventional kernels. We provide evidence that in Austria a high diversity of oilseed rape genotypes, including some with alleles not known from cultivated oilseed rape in Austria, exists at sites with high seed spillage and low weed management, rendering these sites of primary concern with respect to possible escape of genome-edited oilseed rape varieties into the environment. Since appropriate detection methods for single genome-edited oilseed rape events have only recently started to be successfully developed and the adverse effects of these artificial punctate DNA exchanges remain largely unknown, tracing the transmission and spread of these genetic modifications places high requirements on their monitoring, identification, and traceability.
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Affiliation(s)
- Kathrin Pascher
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Institute of Zoology, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Austria
- *Correspondence: Kathrin Pascher,
| | - Christa Hainz-Renetzeder
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Institute of Landscape Development, Recreation and Conservation Planning (ILEN), Department of Landscape, Spatial and Infrastructure Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michaela Jagersberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Katharina Kneissl
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Günter Gollmann
- Department of Evolutionary Biology, Unit for Theoretical Biology, University of Vienna, Vienna, Austria
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Artika IM, Dewi YP, Nainggolan IM, Siregar JE, Antonjaya U. Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis. Genes (Basel) 2022; 13:genes13122387. [PMID: 36553654 PMCID: PMC9778061 DOI: 10.3390/genes13122387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Successful detection of the first SARS-CoV-2 cases using the real-time polymerase chain reaction (real-time PCR) method reflects the power and usefulness of this technique. Real-time PCR is a variation of the PCR assay to allow monitoring of the PCR progress in actual time. PCR itself is a molecular process used to enzymatically synthesize copies in multiple amounts of a selected DNA region for various purposes. Real-time PCR is currently one of the most powerful molecular approaches and is widely used in biological sciences and medicine because it is quantitative, accurate, sensitive, and rapid. Current applications of real-time PCR include gene expression analysis, mutation detection, detection and quantification of pathogens, detection of genetically modified organisms, detection of allergens, monitoring of microbial degradation, species identification, and determination of parasite fitness. The technique has been used as a gold standard for COVID-19 diagnosis. Modifications of the standard real-time PCR methods have also been developed for particular applications. This review aims to provide an overview of the current applications of the real-time PCR technique, including its role in detecting emerging viruses such as SARS-CoV-2.
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Affiliation(s)
- I Made Artika
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor 16680, Indonesia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
- Correspondence:
| | - Yora Permata Dewi
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Ita Margaretha Nainggolan
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Josephine Elizabeth Siregar
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Ungke Antonjaya
- Eijkman Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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Wang J, Hu X, Wang Y, Zeng H, Liu X, Liu H. Rapid detection of genetically modified products based on CRISPR-Cas12a combined with recombinase polymerase amplification. Curr Res Food Sci 2022; 5:2281-2286. [DOI: 10.1016/j.crfs.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/22/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
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Fraiture MA, Guiderdoni E, Meunier AC, Papazova N, Roosens NH. ddPCR strategy to detect a gene-edited plant carrying a single variation point: Technical feasibility and interpretation issues. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Weidner C, Edelmann S, Moor D, Lieske K, Savini C, Jacchia S, Sacco MG, Mazzara M, Lämke J, Eckermann KN, Emons H, Mankertz J, Grohmann L. Assessment of the Real-Time PCR Method Claiming to be Specific for Detection and Quantification of the First Commercialised Genome-Edited Plant. FOOD ANAL METHOD. [DOI: 10.1007/s12161-022-02237-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Abstract
A real-time PCR method was recently published with a claim to be specific for the detection and identification of some genome-edited oilseed rape (OSR) lines commercialised in North America. The method was designed to detect a single base mutation in the AHAS1C gene, which confers herbicide tolerance. The authors claim that the method is event-specific for the genome-edited OSR line 5715 and fulfils all requirements for GMO analytical methods according to EU regulations. We have thoroughly assessed the method in relation to the minimum performance requirements (MPR) established by the European Network of GMO Laboratories (ENGL). The method was found to be sufficiently sensitive and robust when tested with pure genomic DNA of the OSR line 40 K. However, our results show that the method is not event-specific and detects also OSR lines carrying the same point mutation caused by somaclonal variation. Moreover, impaired robustness was observed using non-modified genomic DNA at the amount specified in the original protocol. Significant non-specific PCR amplifications with PCR products as non-target template DNA and with genomic DNA from numerous OSR varieties as well as from wild radish were found by three ISO/IEC 17025 accredited reference laboratories in tests using different master mixes and PCR cycler models. The assessment shows that the method does not meet the MPR for qualitative PCR methods and therefore is not fit-for-purpose for official controls of genetically modified products in the EU. Suggestions are provided for conditions under which analytical methods for genome-edited organisms should be validated.
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Chhalliyil P, Ilves H, Kazakov SA, Howard SJ, Johnston BH, Fagan J. Correction: Chhalliyil et al. A Real-Time Quantitative PCR Method Specific for Detection and Quantification of the First Commercialized Genome-Edited Plant. Foods 2020, 9, 1245. Foods 2022; 11:585. [PMID: 35206099 DOI: 10.3390/foods11040585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/07/2022] [Indexed: 01/25/2023] Open
Abstract
The stated objective of the paper was to provide regulatory laboratories and industry laboratories a complete, legally robust method for the quantitative detection of SU canola [...].
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Ding S, Hu H, Yue X, Feng K, Gao X, Dong Q, Yang M, Tamer U, Huang G, Zhang J. A fluorescent biosensor based on quantum dot-labeled streptavidin and poly-l-lysine for the rapid detection of Salmonella in milk. J Dairy Sci 2022; 105:2895-2907. [PMID: 35181133 DOI: 10.3168/jds.2021-21229] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023]
Abstract
Salmonella, as a common foodborne pathogen in dairy products, poses a great threat to human health. We studied a new detection method based on quantum dots (QD). A fluorescent biosensor with multiple fluorescent signal amplification based on a streptavidin (SA) biotin system and the polyamino linear polymer poly-l-lysine (PLL) were established to detect Salmonella in milk. First, Salmonella was captured on a black 96-well plate with paired Salmonella mAb to form a double-antibody sandwich. Second, SA was immobilized on biotin-modified mAb by SA-biotin specific bond. Then, the biotin-modified polylysine (BT-PLL) was bound on SA and specifically bonded again through the SA-biotin system. Finally, water-soluble CdSe/ZnS QD-labeled SA was added to a black 96-well plate for covalent coupling with BT-PLL. The fluorescent signal was amplified in a dendritic manner by the layer-by-layer overlap of SA and biotin and the covalent coupling of biotinylated PLL. Under optimal conditions, the detection limit was 4.9 × 103 cfu/mL in PBS. The detection limit was 10 times better than that of the conventional sandwich ELISA. In addition, the proposed biosensor was well specific and could be used for detecting Salmonella in milk samples.
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Affiliation(s)
- Shuangyan Ding
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Hailiang Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Xianglin Yue
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Kaiwen Feng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Xiaoyu Gao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Qiuling Dong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Mingqi Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Ugur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06500, Ankara, Turkey
| | - Ganhui Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Jinsheng Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China.
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Harshitha R, Arunraj DR. Real-time quantitative PCR: A tool for absolute and relative quantification. Biochem Mol Biol Educ 2021; 49:800-812. [PMID: 34132460 DOI: 10.1002/bmb.21552] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 04/08/2021] [Accepted: 05/27/2021] [Indexed: 05/26/2023]
Abstract
Real-time quantitative PCR is a technique used to monitor the PCR reaction in real time. RT-qPCR is broadly classified into two types based on its purpose: absolute and relative quantification. Absolute quantification is used in a wide array of fields such as microbiology, food technology, and biotechnology to quantify the microbiological load/adulterants in a commodity/copy numbers respectively, whereas Relative quantification is used in the field of genomics and functional transcriptomics to perform gene expression analysis in biological experiments. A laboratory work that covers the basic principles involved in RT-qPCR and data analysis using the manual as well as the software methods are incorporated. The laboratory experiment was designed to provide insights on certain important principles such as primer characteristics, PCR efficiency, and melt curve analysis. This laboratory exercise provides all the significant components of RT-qPCR, which can be useful while performing an experiment in an undergraduate and graduate laboratory.
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Affiliation(s)
- Ravikumar Harshitha
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, India
| | - Duraipandian Rex Arunraj
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, India
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Zhang H, Li J, Zhao S, Yan X, Si N, Gao H, Li Y, Zhai S, Xiao F, Wu G, Wu Y. An Editing-Site-Specific PCR Method for Detection and Quantification of CAO1-Edited Rice. Foods 2021; 10:foods10061209. [PMID: 34071965 PMCID: PMC8226746 DOI: 10.3390/foods10061209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/03/2022] Open
Abstract
Genome-edited plants created by genome editing technology have been approved for commercialization. Due to molecular characteristics that differ from classic genetically modified organisms (GMOs), establishing regulation-compliant analytical methods for identification and quantification of genome-edited plants has always been regarded as a challenging task. An editing-site-specific PCR method was developed based on the unique edited sequence in CAO1-edited rice plants. Test results of seven primer/probe sets indicated that this method can identify specific CAO1-edited rice from other CAO1-edited rice and wild types of rice with high specificity and sensitivity. The use of LNA (locked nucleic acid) in a probe can efficiently increase the specificity of the editing-site-specific PCR method at increased annealing temperature which can eliminate non-specific amplification of the non-target. The genome-edited ingredient content in blinded samples at the level of 0.1% to 5.0% was accurately quantified by this method on the ddPCR platform with RSD of <15% and bias in the range of ±17%, meeting the performance requirements for GMO detection method. The developed editing-site-specific PCR method presents a promising detection and quantification technique for genome-edited plants with known edited sequence.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yuhua Wu
- Correspondence: ; Tel.: +86-27-86711573
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14
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Ribarits A, Eckerstorfer M, Simon S, Stepanek W. Genome-Edited Plants: Opportunities and Challenges for an Anticipatory Detection and Identification Framework. Foods 2021; 10:430. [PMID: 33669278 DOI: 10.3390/foods10020430] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/28/2022] Open
Abstract
It is difficult to trace and identify genome-edited food and feed products if relevant information is not made available to competent authorities. This results in major challenges, as genetically modified organism (GMO) regulatory frameworks for food and feed that apply to countries such as the member states of the European Union (EU) require enforcement based on detection. An international anticipatory detection and identification framework for voluntary collaboration and collation of disclosed information on genome-edited plants could be a valuable tool to address these challenges caused by data gaps. Scrutinizing different information sources and establishing a level of information that is sufficient to unambiguously conclude on the application of genome editing in the plant breeding process can support the identification of genome-edited products by complementing the results of analytical detection. International coordination to set up an appropriate state-of-the-art database is recommended to overcome the difficulty caused by the non-harmonized bio-safety regulation requirements of genome-edited food and feed products in various countries. This approach helps to avoid trade disruptions and to facilitate GMO/non-GMO labeling schemes. Implementation of the legal requirements for genome-edited food and feed products in the EU and elsewhere would substantially benefit from such an anticipatory framework.
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