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Zhu L, He G, Yang G, Yang W, He Y, Chen J, Chen Y, Ji Y, Pan Z, Yao J, Chen X, Jiang D. A rapid on-site visualization platform based on RPA coupled with CRISPR-Cas12a for the detection of genetically modified papaya 'Huanong No.1'. Talanta 2024; 277:126437. [PMID: 38901194 DOI: 10.1016/j.talanta.2024.126437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
The Papaya ringspot virus (PRSV)-resistant genetically modified (GM) papaya 'Huanong No.1' has been certified as safe for consumption and widely planted in China for about 18 years. To protect consumers' rights and facilitate government supervision and monitoring, it is necessary to establish a simple, rapid, and specific detection method for 'Huanong No.1'. Herein, we developed a platform based on recombinase polymerase amplification (RPA) coupled with CRISPR-Cas12a for the detection of 'Huanong No.1'. The RPA-CRISPR-Cas12a platform was found to have high specificity, with amplification signals only present in 'Huanong No.1'. Additionally, the platform was highly sensitive, with a limit of detection (LOD) of approximately 20 copies. The detection process was fast and could be completed in less than 1 h. This novel platform enables the rapid on-site visualization detection of 'Huanong No.1', eliminating dependence on laboratory conditions and specialized instruments, and can serve as a technical reference for the rapid detection of other GM plants.
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Affiliation(s)
- Lili Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Gongwen He
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Guiqin Yang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Wenli Yang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Ying He
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Jian Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yanxin Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yi Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Zhiwen Pan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Juan Yao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Dagang Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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2
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Zhou P, Liu X, Liang J, Zhao J, Zhang Y, Xu D, Li X, Chen Z, Shi Z, Gao J. GMOIT: a tool for effective screening of genetically modified crops. BMC PLANT BIOLOGY 2024; 24:329. [PMID: 38664610 PMCID: PMC11044397 DOI: 10.1186/s12870-024-05035-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Advancement in agricultural biotechnology has resulted in increasing numbers of commercial varieties of genetically modified (GM) crops worldwide. Though several databases on GM crops are available, these databases generally focus on collecting and providing information on transgenic crops rather than on screening strategies. To overcome this, we constructed a novel tool named, Genetically Modified Organisms Identification Tool (GMOIT), designed to integrate basic and genetic information on genetic modification events and detection methods. RESULTS At present, data for each element from 118 independent genetic modification events in soybean, maize, canola, and rice were included in the database. Particularly, GMOIT allows users to customize assay ranges and thus obtain the corresponding optimized screening strategies using common elements or specific locations as the detection targets with high flexibility. Using the 118 genetic modification events currently included in GMOIT as the range and algorithm selection results, a "6 + 4" protocol (six exogenous elements and four endogenous reference genes as the detection targets) covering 108 events for the four crops was established. Plasmids pGMOIT-1 and pGMOIT-2 were constructed as positive controls or calibrators in qualitative and quantitative transgene detection. CONCLUSIONS Our study provides a simple, practical tool for selecting, detecting, and screening strategies for a sustainable and efficient application of genetic modification.
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Affiliation(s)
- Pu Zhou
- Hou Ji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
- Crops Ecological Environment Security Inspection and Supervision Center (Taiyuan), Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China
| | - Xuan Liu
- Hou Ji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
- Crops Ecological Environment Security Inspection and Supervision Center (Taiyuan), Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China
| | - Jingang Liang
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100025, China
| | - Juanli Zhao
- Hou Ji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
- Crops Ecological Environment Security Inspection and Supervision Center (Taiyuan), Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China
| | - Yuqi Zhang
- Crops Ecological Environment Security Inspection and Supervision Center (Taiyuan), Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China
| | - Dongmei Xu
- Hou Ji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
- Crops Ecological Environment Security Inspection and Supervision Center (Taiyuan), Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China
| | - Xiaying Li
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100025, China
| | - Ziyan Chen
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100025, China
| | - Zongyong Shi
- Hou Ji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China.
- Crops Ecological Environment Security Inspection and Supervision Center (Taiyuan), Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China.
| | - Jianhua Gao
- Hou Ji Laboratory in Shanxi Province, College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China.
- Crops Ecological Environment Security Inspection and Supervision Center (Taiyuan), Ministry of Agriculture and Rural Affairs, Taigu, 030801, Shanxi, China.
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3
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Wang Y, Bednarcik M, Ament C, Cheever ML, Cummings S, Geng T, Gunasekara DB, Houston N, Kouba K, Liu Z, Shippar J. Immunoassays and Mass Spectrometry for Determination of Protein Concentrations in Genetically Modified Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72. [PMID: 38607999 PMCID: PMC11046482 DOI: 10.1021/acs.jafc.3c09188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
Quantifying protein levels in genetically modified (GM) crops is crucial in every phase of development, deregulation, and seed production. Immunoassays, particularly enzyme-linked immunosorbent assay, have been the primary protein quantitation techniques for decades within the industry due to their efficiency, adaptability, and credibility. Newer immunoassay technologies like Meso Scale Discovery and Luminex offer enhanced sensitivity and multiplexing capabilities. While mass spectrometry (MS) has been widely used for small molecules and protein detection in the pharmaceutical and agricultural industries (e.g., biomarkers, endogenous allergens), its use in quantifying protein levels in GM crops has been limited. However, as trait portfolios for GM crop have expanded, MS has been increasingly adopted due to its comparable sensitivity, increased specificity, and multiplexing capabilities. This review contrasts the benefits and limitations of immunoassays and MS technologies for protein measurement in GM crops, considering factors such as cost, convenience, and specific analytical needs. Ultimately, both techniques are suitable for assessing protein concentrations in GM crops, with MS offering complementary capabilities to immunoassays. This comparison aims to provide insights into selecting between these techniques based on the user's end point needs.
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Affiliation(s)
- Yanfei Wang
- Bayer
CropScience, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Mark Bednarcik
- Syngenta
Crop Protection, Limited Liability Company, 9 Davis Drive, Post Office Box 12257, Research Triangle Park, North Carolina 27709-2257, United
States
| | - Christopher Ament
- Eurofins
Food Chemistry Testing Madison, Incorporated, 6304 Ronald Reagan Avenue, Madison, Wisconsin 53704, United States
| | - Matthew L. Cheever
- BASF
Corporation, 26 Davis Drive, Research Triangle Park, North Carolina 27709, United States
| | - Simone Cummings
- Syngenta
Crop Protection, Limited Liability Company, 9 Davis Drive, Post Office Box 12257, Research Triangle Park, North Carolina 27709-2257, United
States
| | - Tao Geng
- Bayer
CropScience, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Dulan B. Gunasekara
- BASF
Corporation, 26 Davis Drive, Research Triangle Park, North Carolina 27709, United States
| | - Norma Houston
- Corteva
Agriscience, Johnston, Iowa 50131, United States
| | - Kristen Kouba
- Corteva
Agriscience, Johnston, Iowa 50131, United States
| | - Zi Liu
- Bayer
CropScience, 700 Chesterfield
Pkwy West, Chesterfield, Missouri 63017, United
States
| | - Jeffrey Shippar
- Eurofins
Food Chemistry Testing Madison, Incorporated, 6304 Ronald Reagan Avenue, Madison, Wisconsin 53704, United States
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4
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Magembe EM, Li H, Taheri A, Zhou S, Ghislain M. Identification of T-DNA structure and insertion site in transgenic crops using targeted capture sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1156665. [PMID: 37502707 PMCID: PMC10369180 DOI: 10.3389/fpls.2023.1156665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023]
Abstract
The commercialization of GE crops requires a rigorous safety assessment, which includes a precise DNA level characterization of inserted T-DNA. In the past, several strategies have been developed for identifying T-DNA insertion sites including, Southern blot and different PCR-based methods. However, these methods are often challenging to scale up for screening of dozens of transgenic events and for crops with complex genomes, like potato. Here, we report using target capture sequencing (TCS) to characterize the T-DNA structure and insertion sites of 34 transgenic events in potato. This T-DNA is an 18 kb fragment between left and right borders and carries three resistance (R) genes (RB, Rpi-blb2 and Rpi-vnt1.1 genes) that result in complete resistance to late blight disease. Using TCS, we obtained a high sequence read coverage within the T-DNA and junction regions. We identified the T-DNA breakpoints on either ends for 85% of the transgenic events. About 74% of the transgenic events had their T-DNA with 3R gene sequences intact. The flanking sequences of the T-DNA were from the potato genome for half of the transgenic events, and about a third (11) of the transgenic events have a single T-DNA insertion mapped into the potato genome, of which five events do not interrupt an existing potato gene. The TCS results were confirmed using PCR and Sanger sequencing for 6 of the best transgenic events representing 20% of the transgenic events suitable for regulatory approval. These results demonstrate the wide applicability of TCS for the precise T-DNA insertion characterization in transgenic crops.
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Affiliation(s)
- Eric Maina Magembe
- Potato Agri-food Systems Program, International Potato Center, Nairobi, Kenya
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Hui Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Ali Taheri
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Marc Ghislain
- Potato Agri-food Systems Program, International Potato Center, Nairobi, Kenya
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5
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Wang Y, Peng C, Ding L, Su Z, Chen X, Wang X, Sun M, Xu J. An Accurate, Rapid and Cost-Effective Method for T-nos Detection Based on CRISPR/Cas12a. Foods 2023; 12:foods12030615. [PMID: 36766144 PMCID: PMC9914525 DOI: 10.3390/foods12030615] [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: 12/12/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
CRISPR/Cas12a technology is used for nucleic acid detection due to its specific recognition function and non-specific single-stranded DNA cleavage activity. Here, we developed a fluorescence visualisation detection method based on PCR and CRISPR/Cas12a approaches. The method was used to detect the nopaline synthase terminator (T-nos) of genetically modified (GM) crops, circumventing the need for expensive instruments and technicians. For enhanced sensitivity and stability of PCR-CRISPR/Cas12a detection, we separately optimised the reaction systems for PCR amplification and CRISPR/Cas12a detection. Eleven samples of soybean samples were assessed to determine the applicability of the PCR-CRISPR/Cas12a method. The method could specifically detect target gene levels as low as 60 copies in the reaction within 50 min. In addition, accurate detection of all 11 samples confirmed the applicability. The method is not limited by large-scale instruments, making it suitable for mass detection of transgenic components in plants in the field. In conclusion, we developed a new, accurate, rapid, and cost-effective method for GM detection.
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Affiliation(s)
- Yuling Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhixun Su
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Meihao Sun
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Correspondence: (M.S.); (J.X.)
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence: (M.S.); (J.X.)
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6
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Park DG, Ha ES, Kang B, Choi I, Kwak JE, Choi J, Park J, Lee W, Kim SH, Kim SH, Lee JH. Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods. J Microbiol Biotechnol 2023; 33:83-95. [PMID: 36457187 PMCID: PMC9895999 DOI: 10.4014/jmb.2211.11009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022]
Abstract
These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 108-105 CFU of target strains. However, a few false-positive results were shown at 106-105 CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.
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Affiliation(s)
- Dong-Geun Park
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Su Ha
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Byungcheol Kang
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Iseul Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Jeong-Eun Kwak
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinho Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Jeongwoong Park
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea,Corresponding author Phone: +82-2-880-4854 Fax: +82-2-873-5095 E-mail:
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7
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Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms. Foods 2023; 12:foods12030455. [PMID: 36765984 PMCID: PMC9914749 DOI: 10.3390/foods12030455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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8
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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] [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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9
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Qiu Y, You A, Zhang M, Cui H, Fu X, Wang J, Huang H, Shentu X, Ye Z, Yu X. Phage-displayed nanobody-based fluorescence-linked immunosorbent assay for the detection of Cry3Bb toxin in corn. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Quantum-Dot-Bead-Based Fluorescence-Linked Immunosorbent Assay for Sensitive Detection of Cry2A Toxin in Cereals Using Nanobodies. Foods 2022; 11:foods11182780. [PMID: 36140908 PMCID: PMC9497650 DOI: 10.3390/foods11182780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 12/29/2022] Open
Abstract
In this study, a quantum-dot-bead (QB)-based fluorescence-linked immunosorbent assay (FLISA) using nanobodies was established for sensitive determination of the Cry2A toxin in cereal. QBs were used as the fluorescent probe and conjugated with a Cry2A polyclonal antibody. An anti-Cry2A nanobody P2 was expressed and used as the capture antibody. The results revealed that the low detection limit of the developed QB-FLISA was 0.41 ng/mL, which had a 19-times higher sensitivity than the traditional colorimetric ELISA. The proposed assay exhibited a high specificity for the Cry2A toxin, and it had no evident cross-reactions with other Cry toxins. The recoveries of Cry2A from the spiked cereal sample ranged from 86.6–117.3%, with a coefficient of variation lower than 9%. Moreover, sample analysis results of the QB-FLISA and commercial ELISA kit correlated well with each other. These results indicated that the developed QB-FLISA provides a potential approach for the sensitive determination of the Cry2A toxin in cereals.
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11
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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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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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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14
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CHEN C, ZHANG Y, ZHANG R, ZHANG Y, ZHANG T, ZHANG Z, SHI G, ZHOU W. Comparison of two methods for the quantitative assessment of genetically modified soybeans. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.69921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Chen CHEN
- Hebei Food Inspection and Research Institute, China
| | - Yan ZHANG
- Hebei Food Inspection and Research Institute, China
| | - Rui ZHANG
- Hebei Food Inspection and Research Institute, China
| | - Yalun ZHANG
- Hebei Food Inspection and Research Institute, China
| | - Tao ZHANG
- Hebei Food Inspection and Research Institute, China
| | - Zilun ZHANG
- Hebei Food Inspection and Research Institute, China
| | - Guohua SHI
- Hebei Food Inspection and Research Institute, China
| | - Wei ZHOU
- Hebei Food Inspection and Research Institute, China
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15
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Chen L, Zhou J, Li T, Fang Z, Li L, Huang G, Gao L, Zhu X, Zhou X, Xiao H, Zhang J, Xiong Q, Zhang J, Ma A, Zhai W, Zhang W, Peng H. GmoDetector: An accurate and efficient GMO identification approach and its applications. Food Res Int 2021; 149:110662. [PMID: 34600664 DOI: 10.1016/j.foodres.2021.110662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
The rapid increase of genetically modified organisms (GMOs) entering the food and feed markets, and the contamination of donor (micro)organisms of transgenic elements make it more challenging for the existing GMO detection. In this study, we developed a high-throughput and contamination-removal GMO detection approach named as GmoDetector. GmoDetector targeted 64 common transgenic elements and 76 GMO-specific events collected from 251 singular GM events, and combined with next generation sequencing (NGS) and target enrichment technology to detect various GMOs. As a result, GmoDetector was able to exclude the donor (micro)organism contamination, and detect the authorized and unauthorized GMOs (UGMOs) in any forms of food or feed, such as processed or unprocessed. The sensitivity of GmoDetector is as low as 0.1% (GMO content), which has met the GMO labeling threshold for all countries. Therefore, GmoDetector is a robust tool for accurate and efficient detection of the authorized and UGMOs.
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Affiliation(s)
- Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Gang Huang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Xiaobo Zhu
- Wuhan Qingfahesheng Seed Co., Ltd., Wuhan, Hubei 430056, PR China
| | - Xusheng Zhou
- Wuhan Qingfahesheng Seed Co., Ltd., Wuhan, Hubei 430056, PR China
| | - Huafeng Xiao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Jing Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - QiJie Xiong
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China
| | - Jianan Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, PR China
| | - Aijin Ma
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China.
| | - Weixiong Zhang
- Department of Computer Science and Engineering, Department of Genetics, Washington University in St. Louis, MO 63130, USA.
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, PR China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, PR China; Mingliao Biotechnology Co., Ltd., Wuhan 430056, PR China; School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
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16
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Tay AP, Hosking B, Hosking C, Bauer DC, Wilson LO. INSIDER: alignment-free detection of foreign DNA sequences. Comput Struct Biotechnol J 2021; 19:3810-3816. [PMID: 34285780 PMCID: PMC8273350 DOI: 10.1016/j.csbj.2021.06.045] [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: 03/15/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
External DNA sequences can be inserted into an organism's genome either through natural processes such as gene transfer, or through targeted genome engineering strategies. Being able to robustly identify such foreign DNA is a crucial capability for health and biosecurity applications, such as anti-microbial resistance (AMR) detection or monitoring gene drives. This capability does not exist for poorly characterised host genomes or with limited information about the integrated sequence. To address this, we developed the INserted Sequence Information DEtectoR (INSIDER). INSIDER analyses whole genome sequencing data and identifies segments of potentially foreign origin by their significant shift in k-mer signatures. We demonstrate the power of INSIDER to separate integrated DNA sequences from normal genomic sequences on a synthetic dataset simulating the insertion of a CRISPR-Cas gene drive into wild-type yeast. As a proof-of-concept, we use INSIDER to detect the exact AMR plasmid in whole genome sequencing data from a Citrobacter freundii patient isolate. INSIDER streamlines the process of identifying integrated DNA in poorly characterised wild species or when the insert is of unknown origin, thus enhancing the monitoring of emerging biosecurity threats.
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Affiliation(s)
- Aidan P. Tay
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, New South Wales, Sydney, Australia
| | - Brendan Hosking
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney, Australia
| | - Cameron Hosking
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney, Australia
| | - Denis C. Bauer
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney, Australia
- Department of Biomedical Sciences, Macquarie University, New South Wales, Sydney, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, New South Wales, Sydney, Australia
| | - Laurence O.W. Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, New South Wales, Sydney, Australia
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17
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Smitha PK, Bathula C, Kumar AM, Chandrashekara KN, Dhar SK, Das M. Correlation of Cry1Ac mRNA and protein abundance in transgenic Gossypium hirsutum plant. 3 Biotech 2021; 11:289. [PMID: 34109092 DOI: 10.1007/s13205-021-02828-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/05/2021] [Indexed: 11/29/2022] Open
Abstract
Transcription and translation in eukaryotes are distinct processes of the molecular cascade leading to protein production from genetic material. However, establishing correlation between mRNA expression and protein abundance, the end results of the two processes of central dogma, remains a challenge. For transgenic plants, such correlation between mRNA and protein expression serves as a guide to design the transgene, in particular the choices of promoter and codon usage to ensure stable expression of the target protein in relevant tissues under various stress conditions. To elucidate level of mRNA-protein correlation in a commercial transgenic cotton plant Gossypium hirsutum, Bollgard II® (MON15985), we present the results of Cry1Ac protein expression correlating with corresponding mRNA levels. Protein was quantitated using a home-grown validated ELISA assay with a monoclonal-polyclonal antibody pair, whereas mRNA level was detected by a real-time quantitative PCR assay using standardized reference genes. Our results indicate that protein and mRNA levels are highly correlated in the leaves, but not in squares and stem. The correlations seem to be consistent between young and mature leaves and increase over time of harvesting of samples from months 1-3. These findings demonstrate that transcript level measurement could serve as a proxy to protein abundance for this commercially important cotton species, particularly for leaf tissues which are the most vulnerable organs to cotton bollworms and other pathogens. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02828-2.
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Affiliation(s)
- P K Smitha
- Tumor Immunology Program, MSMF, Mazumdar Shaw Medical Centre, Narayana Health City, 8th floor, Bommasandra, Bangalore, 560 099 Karnataka India
- Department of Biotechnology, Research and Development Centre, Bharathiar University, Coimbatore, 641 046 Tamil Nadu India
| | - Christopher Bathula
- Tumor Immunology Program, MSMF, Mazumdar Shaw Medical Centre, Narayana Health City, 8th floor, Bommasandra, Bangalore, 560 099 Karnataka India
| | - Anil M Kumar
- Incite Lab, MSMF, Mazumdar Shaw Medical Centre, Beyond Antibody, Narayana Health City, 8th floor, Bommasandra, Bangalore, 560 099 Karnataka India
| | - K N Chandrashekara
- Division of Plant Physiology and Biotechnology, UPASI Tea Research Foundation, Tea Research Institute, Nirar Dam, Valparai, Coimbatore, 642 127 Tamil Nadu India
| | - Sujan K Dhar
- Incite Lab, MSMF, Mazumdar Shaw Medical Centre, Beyond Antibody, Narayana Health City, 8th floor, Bommasandra, Bangalore, 560 099 Karnataka India
| | - Manjula Das
- Tumor Immunology Program, MSMF, Mazumdar Shaw Medical Centre, Narayana Health City, 8th floor, Bommasandra, Bangalore, 560 099 Karnataka India
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18
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Artavia G, Cortés-Herrera C, Granados-Chinchilla F. Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis. Foods 2021; 10:1081. [PMID: 34068197 PMCID: PMC8152966 DOI: 10.3390/foods10051081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/13/2021] [Accepted: 03/19/2021] [Indexed: 12/28/2022] Open
Abstract
This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.
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Affiliation(s)
- Graciela Artavia
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
| | - Carolina Cortés-Herrera
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
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19
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Yang C, Ge J, Fu X, Luo K, Xu C. Dual Reproductive Cell-Specific Promoter-Mediated Split-Cre/LoxP System Suitable for Exogenous Gene Deletion in Hybrid Progeny of Transgenic Arabidopsis. Int J Mol Sci 2021; 22:5080. [PMID: 34064885 PMCID: PMC8151399 DOI: 10.3390/ijms22105080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 01/02/2023] Open
Abstract
Genetically modified (GM) crops possess some superior characteristics, such as high yield and insect resistance, but their biosafety has aroused broad public concern. Some genetic engineering technologies have recently been proposed to remove exogenous genes from GM crops. Few approaches have been applied to maintain advantageous traits, but excising exogenous genes in seeds or fruits from these hybrid crops has led to the generation of harvested food without exogenous genes. In a previous study, split-Cre mediated by split intein could recombine its structure and restore recombination activity in hybrid plants. In the current study, the recombination efficiency of split-Cre under the control of ovule-specific or pollen-specific promoters was validated by hybridization of transgenic Arabidopsis containing the improved expression vectors. In these vectors, all exogenous genes were flanked by two loxP sites, including promoters, resistance genes, reporter genes, and split-Cre genes linked to the reporter genes via LP4/2A. A gene deletion system was designed in which NCre was driven by proDD45, and CCre was driven by proACA9 and proDLL. Transgenic lines containing NCre were used as paternal lines to hybridize with transgenic lines containing CCre. Because this hybridization method results in no co-expression of the NCre and CCre genes controlled by reproduction-specific promoters in the F1 progeny, the desirable characteristics could be retained. After self-crossing in F1 progeny, the expression level and protein activity of reporter genes were detected, and confirmed that recombination of split-Cre had occurred and the exogenous genes were partially deleted. The gene deletion efficiency represented by the quantitative measurements of GUS enzyme activity was over 59%, with the highest efficiency of 73% among variable hybrid combinations. Thus, in the present study a novel dual reproductive cell-specific promoter-mediated gene deletion system was developed that has the potential to take advantage of the merits of GM crops while alleviating biosafety concerns.
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Affiliation(s)
| | | | | | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (J.G.); (X.F.)
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (J.G.); (X.F.)
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20
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Ben-Amar A, Mliki A. Timely gene detection assay and reliable screening of genetically engineered plants using an improved direct PCR-based technology. Transgenic Res 2021; 30:263-274. [PMID: 33880718 DOI: 10.1007/s11248-021-00250-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Abstract
Engineered plants have been widely produced for fundamental and practical use. Several methods have been developed for genetically modified crop detection and quantification; however; they still laborious and expensive. Efforts are needed to set-up diagnosis-oriented techniques as alternatives to overcome DNA extraction which remains a tedious and time-consuming procedure. Here, we established a standard direct PCR workflow using a regular Taq polymerase without prior DNA purification over a wide range of plant species. Only a small amount of fresh tissue allowed direct amplification of target gene sequences. Evaluation of accuracy, sensitivity, and reproducibility of direct PCR assay was investigated for proof-of-concept, and subsequently applied to gene detection assays and rapid transgenic revealing. The newly established method achieved full success and has amplified constitutive housekeeping genes from several plant specimens in a reproducible manner with high-quality sequencing profiles. In our case, the screening of transgenic plants confirmed that both the gfp-ER reporter gene and the npt II selectable marker were integrated into the plant genome. This direct PCR approach provides a powerful tool for large-scale PCR-based gene detection making DNA purification irrelevant. It could be easily implemented for downstream applications in the field of genetic fingerprinting, plant biotechnology, and functional genomics.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia.
| | - Ahmed Mliki
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
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21
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Kaymaz SV, Elitas M. Optimization of Loop-Mediated Isothermal Amplification (LAMP) reaction mixture for biosensor applications. MethodsX 2021; 8:101282. [PMID: 34434802 PMCID: PMC8374247 DOI: 10.1016/j.mex.2021.101282] [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: 09/14/2020] [Accepted: 02/15/2021] [Indexed: 11/25/2022] Open
Abstract
Genetically Modified (GM) foods are becoming the future of agriculture on surviving global natural disasters and climate change by their enhanced production efficiency and improved functional properties. On the other hand, their adverse health and environmental effects, ample evidence on transgene leakage of Genetically Modified Organisms (GMOs) to crops have raised questions on their benefits and risks. Consequently, low-cost, reliable, rapid, and practical detection of GMOs have been important. GMO-detection platforms should be capable of stably storing detection reagents for long-delivery distances with varying ambient temperatures. In this study, we developed an event-specific, closed tube colorimetric GMO detection method based on Loop-Mediated Isothermal Amplification (LAMP) technique which can be integrated into GMO-detection platforms. The entire detection process optimized to 30 min and isothermally at 65 °C. The durability of the LAMP mixture in the test tubes showed that the LAMP reaction mixture, in which Bst polymerase and DNA sample was later included, yielded DNA amplicons for 3 days at room temperature, and for 6 days at 4 °C.•Simple, stable, and cheap storage method of LAMP reaction mixture for GMO-detection technologies.•GMO-detection platforms can stably store detection reagents for long-delivery distances with varying ambient temperatures.•Any DNA sample can be used in the field or resource-limited setting by untrained personnel.
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Affiliation(s)
- Sümeyra Vural Kaymaz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Meltem Elitas
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
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22
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Genome-Edited Plants: Opportunities and Challenges for an Anticipatory Detection and Identification Framework. Foods 2021; 10:foods10020430. [PMID: 33669278 PMCID: PMC7920036 DOI: 10.3390/foods10020430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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23
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Yang L, Chen Y, Li R, Xu W, Cui J, Zhang D, Zhang X. Universal LNA Probe-Mediated Multiplex Droplet Digital Polymerase Chain Reaction for Ultrasensitive and Accurate Quantitative Analysis of Genetically Modified Organisms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1705-1713. [PMID: 33528262 DOI: 10.1021/acs.jafc.0c06433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Multiplex and high-throughput assays are becoming the main trends in the development of new nucleic acid detection and quantification methods, such as those for genetically modified organism (GMO) analysis. Here, we report a novel universal LNA probe-mediated droplet digital polymerase chain reaction (PCR) method (ULNA-ddPCR) for multiple DNA target quantification in GMOs. In ULNA-ddPCR, only one universal LNA probe is used for multiple DNA targets instead of using one to one TaqMan probe. The specificity, sensitivity, dynamic range, and accuracy of the ULNA-ddPCR method are determined by employing GM rice analysis as an example. Simplex and triplex ULNA-ddPCR assays for three GM rice events, T2A-1, T1C-19, and G6H1, are established and evaluated. All results indicate that the developed simplex and triplex ULNA-ddPCR assays are suitable for quantitative analysis of GM rice events with high sensitivity, accuracy, and low cost. The ULNA-ddPCR method also has the potential for multiple DNA target quantification in other research fields.
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Affiliation(s)
- Litao Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Yi Chen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenting Xu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjie Cui
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiujie Zhang
- Development Center of Science and Technology, Ministry of Agriculture of People's Republic of China, Beijing 100025, China
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24
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Asif M, Siddiqui HA, Naqvi RZ, Amin I, Asad S, Mukhtar Z, Bashir A, Mansoor S. Development of event-specific detection method for identification of insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct. Sci Rep 2021; 11:3479. [PMID: 33568702 PMCID: PMC7876094 DOI: 10.1038/s41598-021-82798-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Bt cotton expressing Cry1Ac is being cultivated in Pakistan. It has been observed that pink bollworm may have developed resistance against single Bt gene (Cry1Ac). For durable resistance, insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct was developed. There was a need to characterize NIBGE-1601 event for intellectual property rights protection. The Presence of NIBGE Cry1Ac and NIBGE Cry2Ab genes was checked in NIBGE-1601 cotton plants through PCR, while there was no amplification using primers specific for Monsanto events (MON531, MON15985, MON1445). Using genome walking technology, NIBGE-601 event has been characterized. Event-specific primers of NIBGE-1601 were designed and evaluated to differentiate it from other cotton events mentioned above. NIBGE-1601 event detection primers are highly specific, therefore, can detect NIBGE 1601 event at different conditions using single or multiplex PCR. In the qualitative PCR, using NIBGE-1601 event specific primers, 0.05 ng was the limit of detection for NIBGE-1601double gene cotton genomic DNA. Thus event characterization and development of event-specific diagnostics will help in breeding new cotton varieties resistant to cotton bollworms.
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Affiliation(s)
- Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Hamid Anees Siddiqui
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Shaheen Asad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Aftab Bashir
- Department of Biological Sciences, Forman Christian College, Lahore, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan.
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25
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Duan Y, Pi Y, Li C, Jiang K. An optimized procedure for detection of genetically modified DNA in refined vegetable oils. Food Sci Biotechnol 2021; 30:129-135. [PMID: 33552624 DOI: 10.1007/s10068-020-00852-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/26/2020] [Accepted: 11/20/2020] [Indexed: 11/30/2022] Open
Abstract
In this study, the amplifiable DNA from refined vegetable oils was isolated by using commercial DNA extraction kits based on the CTAB method in combination with nucleic acid enrichment, and then the presence of genetically modified (GM) soybean and maize DNA in the oils was traced by PCR. The results showed that the duration and intensity of heating had no significant effect on the DNA stability and concentration in oils for a short period, suggesting that DNA in oils could be stably reserved for a certain time, thus making it possible to trace down refined vegetable oils reliably and effectively. The results provided a set of primers suitable for systematic GM oil detection. More importantly, this study made an important contribution to the economical and reliable detection of GM vegetable oils regarding food authenticity issues.
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Affiliation(s)
- Yuzhu Duan
- School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Yan Pi
- School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Changwen Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090 China.,School of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Keji Jiang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090 China
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26
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A novel isothermal detection method for the universal element of genetically modified soybean. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Alipour M, Jalili S, Shirzad H, Ansari Dezfouli E, Fouani MH, Sadeghan AA, Bardania H, Hosseinkhani S. Development of dual-emission cluster of Ag atoms for genetically modified organisms detection. Mikrochim Acta 2020; 187:628. [PMID: 33095319 DOI: 10.1007/s00604-020-04591-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022]
Abstract
A DNA-silver nanocluster with two distinct emissions is devised, in which this unique modality has been exploited to develop a novel nanosensor for transgenic DNA detection. TEM and fluorescence analysis revealed the formation of Ag nanoclusters with a size of around 2 nm, which exhibit dual-emissions at 550 nm (green) and 630 nm (red). Moreover, in the presence of the target sequence (CaMV 35S promoter) from the transgenic plant, the nanoclusters showed an enhancement in the green emission and a reduction in the red emission. This property provided a ratiometric-sensing platform which lacks unavoidable noises. The ratio of green to red fluorescence emission (G/R) of the nanoclusters exhibited a linear relation with the target concentration in the range 10 to 1000 nM. However, the control DNA did not affect this ratio, which clearly confirmed the selective response of the designed nanosensor. This sensing platform had a detection limit of 1.5 nM and identified the DNA of transgenic soybeans within a short time. The mechanistic evaluation of the nanoclusters further revealed the role of protonated cytosine bases in the dual emission behavior. Finally, unique features of the designed nanosensor may improve the current approaches for the development and manufacturing of GMO detection tools.
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Affiliation(s)
- Mohsen Alipour
- Department of Advanced Medical Sciences & Technologies, School of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran.
| | - Shirin Jalili
- Research Institute of Police Science & Social Studies, Tehran, Iran
| | - Hadi Shirzad
- Research Institute of Police Science & Social Studies, Tehran, Iran
| | - Ehsan Ansari Dezfouli
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohamad Hassan Fouani
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Amiri Sadeghan
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Bardania
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
- Clinical Research Development Unit, Imamsajad Hospital, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Saman Hosseinkhani
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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28
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Fraiture MA, Papazova N, Roosens NHC. DNA walking strategy to identify unauthorized genetically modified bacteria in microbial fermentation products. Int J Food Microbiol 2020; 337:108913. [PMID: 33126077 DOI: 10.1016/j.ijfoodmicro.2020.108913] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 01/07/2023]
Abstract
Recently, unexpected contaminations of unauthorized genetically modified microorganisms (GMM) carrying antimicrobial resistance (AMR) genes were reported in microbial fermentation products commercialized on the food and feed chain. To guarantee the traceability and safety of the food and feed chain, whole-genome sequencing (WGS) has played a key role to prove GMM contaminations via the characterization of unnatural associations of sequences. However, WGS requires a prior microbial isolation of the GMM strain, which can be difficult to successfully achieve. Therefore, in order to avoid such bottleneck, a culture-independent approach was proposed in this study. First, the screening for the aadD gene, an AMR gene conferring a resistance to kanamycin, and for the pUB110 shuttle vector, carrying the aadD gene and commonly used to produce GMM, is performed. In case of a positive signal, DNA walking methods anchored on the two borders of the detected pUB110 shuttle vector are applied to characterize unknown flanking regions. Following to the sequencing of the generated amplicons, unnatural associations of sequences can be identified, allowing to demonstrate the presence of unauthorized GMM. The developed culture-independent strategy was successfully applied on commercialized microbial fermentation products, allowing to prove the presence of GMM contaminations in the food and feed chain.
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Affiliation(s)
- Marie-Alice Fraiture
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nina Papazova
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Nancy H C Roosens
- Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050 Brussels, Belgium.
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29
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Ashrafi-Dehkordi E, Mazloomi SM, Hemmati F. A comparison of DNA extraction methods and PCR-based detection of GMO in textured soy protein. J Verbrauch Lebensm 2020. [DOI: 10.1007/s00003-020-01300-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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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Li Y, Hao N, Luo S, Liu Q, Sun L, Qian J, Cai J, Wang K. Simultaneous detection of TNOS and P35S in transgenic soybean based on magnetic bicolor fluorescent probes. Talanta 2020; 212:120764. [PMID: 32113537 DOI: 10.1016/j.talanta.2020.120764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/14/2020] [Accepted: 01/19/2020] [Indexed: 12/25/2022]
Abstract
A magnetic-separation-dual-targets fluorescent biosensor was fabricated to detect terminator nopaline synthase (TNOS) and promoter of cauliflower mosaic virus 35s (P35S) in transgenic soybean based on incorporation of bicolor CdTe quantum dots carried by silica nanospheres. In this protocol, the fixed probes for TNOS or P35S were magnetized firstly with Fe3O4@Au magnetic nanosphere by Au-S covalent bonding to achieve magnetized probes. Meanwhile, the capture probes for TNOS or P35S were functionalized with green or red fluorescent microspheres respectively to obtain fluorescently-labeled probes, which could emit relative strong green or red fluorescent signal. Two terminals of TNOS or P35S were recognized by magnetized probes and fluorescently-labeled probes respectively to form the sandwiched structures in the process of biosensor development subsequently, and it was separated by a magnet instantly. The fluorescence intensities of remnant supernatant were measured and analyzed accordingly to achieve simultaneous detection of TNOS and P35S. This biosensor exhibited a good dynamic range, low limit of detection and excellent selectivity in detecting transgenic soybean.
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Affiliation(s)
- Yaqi Li
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, 212003, China
| | - Nan Hao
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Shilong Luo
- Sinograin Zhenjiang Grains & Oils Quality Testing Center, Zhenjiang, 212006, China
| | - Qian Liu
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Li Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Jing Qian
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Jianrong Cai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Kun Wang
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, China; Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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32
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Bak A, Emerson JB. Cauliflower mosaic virus (CaMV) Biology, Management, and Relevance to GM Plant Detection for Sustainable Organic Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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33
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Identification of T-DNA Insertion Site and Flanking Sequence of a Genetically Modified Maize Event IE09S034 Using Next-Generation Sequencing Technology. Mol Biotechnol 2020; 61:694-702. [PMID: 31256331 DOI: 10.1007/s12033-019-00196-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular characteristics including information of insertion site, flanking sequence, and copy numbers are the base for the safety assessment and subsequent monitoring of genetically modified organisms (GMOs), which has to be revealed thoroughly in a case-by-case manner. Although both polymerase chain reaction (PCR)-based and next-generation sequencing (NGS)-based approaches are proven to be effective in the molecular characterization of most of GM events, they often fail to work with GM maize events, mainly due to the genome complexity. In this study, by using NGS, we successfully identified the 3' end T-DNA insertion site and flanking sequence of a GM maize event IE09S034, which were confirmed by PCR amplification and Sanger sequencing. Notably, insertions of unintended exogenous elements were revealed in this event although the single copy of target exogenous genes was also confirmed by digital PCR. The output of this study provides novel and important genetic evidence for the safety assessment and monitoring of GM maize event IE09S034.
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34
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Akhtar A, Rizvi Z, Irfan M, Maqbool A, Bashir A, Abdulla Malik K. Biochemical and morphological risk assessment of transgenic wheat with enhanced iron and zinc bioaccessibility. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2019.102881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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Bak A, Emerson JB. Multiplex quantitative PCR for single-reaction genetically modified (GM) plant detection and identification of false-positive GM plants linked to Cauliflower mosaic virus (CaMV) infection. BMC Biotechnol 2019; 19:73. [PMID: 31699075 PMCID: PMC6836441 DOI: 10.1186/s12896-019-0571-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 01/05/2023] Open
Abstract
Background Most genetically modified (GM) plants contain a promoter, P35S, from the plant virus, Cauliflower mosaic virus (CaMV), and many have a terminator, TNOS, derived from the bacterium, Agrobacterium tumefaciens. Assays designed to detect GM plants often target the P35S and/or TNOS DNA sequences. However, because the P35S promoter is derived from CaMV, these detection assays can yield false-positives from non-GM plants infected by this naturally-occurring virus. Results Here we report the development of an assay designed to distinguish CaMV-infected plants from GM plants in a single multiplexed quantitative PCR (qPCR) reaction. Following initial testing and optimization via PCR and singleplex-to-multiplex qPCR on both plasmid and plant DNA, TaqMan qPCR probes with different fluorescence wavelengths were designed to target actin (a positive-control plant gene), P35S, P3 (a CaMV-specific gene), and TNOS. We tested the specificity of our quadruplex qPCR assay using different DNA extracts from organic watercress and both organic and GM canola, all with and without CaMV infection, and by using commercial and industrial samples. The limit of detection (LOD) of each target was determined to be 1% for actin, 0.001% for P35S, and 0.01% for both P3 and TNOS. Conclusions This assay was able to distinguish CaMV-infected plants from GM plants in a single multiplexed qPCR reaction for all samples tested in this study, suggesting that this protocol is broadly applicable and readily transferrable to any interested parties with a qPCR platform.
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Affiliation(s)
- Aurélie Bak
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
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36
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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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37
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Identification and quantitation of genetically modified (GM) ingredients in maize, rice, soybean and wheat-containing retail foods and feeds in Turkey. Journal of Food Science and Technology 2019; 57:787-793. [PMID: 32116387 DOI: 10.1007/s13197-019-04080-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
The cultivation area and diversity of genetically modified (GM) crop varieties worldwide is increasing rapidly. Taking Turkey as an example of a country with tight restrictions on the import and use of GM crops but limited resources for product monitoring, we developed a cost-effective 3-tier screening protocol, and tested 110 retail food products and 13 animal feeds available in 2016-2017 for GM ingredients. No evidence was found for the presence of GM wheat or rice in the foodstuffs tested; however, 6 feeds and 3 food products containing soybean and/or maize were positive for one or more GM elements. GM events present in positive samples were identified by event-specific PCR and quantified by real-time PCR. We also compared the results with previous surveys in Turkey. Overall, we observed consistent use of GM animal feeds; however, these were not labelled as GM at the point of sale. Occasional food products also tested positive for GM ingredients, usually at low concentrations that could be attributed to accidental contamination.
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38
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Tu YK, Lin YC, Feng YW, Tseng YY, Chen HW. Visual, sensitive and rapid event-specific detection of genetically modified potato EH92-527-1 by loop-mediated isothermal amplification method. Biosci Biotechnol Biochem 2019; 84:43-52. [PMID: 31495297 DOI: 10.1080/09168451.2019.1661766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To date, studies on the application of loop-mediated isothermal amplification (LAMP) in the detection of genetically modified organisms (GMOs) are stably increasing and demonstrates LAMP is a potential and promising method for on spot identification of GMOs. However, little information is known for detection of GM potato events by LAMP. In this report, we developed an optimized and visual LAMP assay with high specificity and sensitivity to rapidly amplify genomic DNA of potato EH92-527-1 within 45 min. The limit of detection of LAMP in our study is 10-fold higher than the conventional PCR. Furthermore, LAMP products can be directly observed via naked eyes by addition of SYBR Green I without gel electrophoresis analysis and PCR-based equipment. Therefore, the LAMP assay developed in this paper provides an efficient, convenient and cost-effective tool for the detection of GM potato EH92-527-1.
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Affiliation(s)
- Yuan-Kai Tu
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
| | - Yen-Chun Lin
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
| | - Yu-Wei Feng
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
| | - Yeu-Yang Tseng
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Han-Wei Chen
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
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39
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Qiu Y, Li P, Liu B, Liu Y, Wang Y, Tao T, Xu J, Hammock BD, Liu X, Guan R, Zhang C. Phage-displayed nanobody based double antibody sandwich chemiluminescent immunoassay for the detection of Cry2A toxin in cereals. FOOD AGR IMMUNOL 2019. [DOI: 10.1080/09540105.2019.1642307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Yulou Qiu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
- Zhejiang Proceincial Key Laboratory of Biometrology and Inspection and Quarantine, China Jiliang University, Hangzhou, People’s Republic of China
| | - Pan Li
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Beibei Liu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Yuan Liu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Yulong Wang
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Tingting Tao
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Junli Xu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Bruce D. Hammock
- Laboratory of Pesticide and Nematology Biotechnology, Department of Entomology, University of California, Davis, CA, USA
| | - Xianjin Liu
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Rongfa Guan
- Zhejiang Proceincial Key Laboratory of Biometrology and Inspection and Quarantine, China Jiliang University, Hangzhou, People’s Republic of China
| | - Cunzheng Zhang
- Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, People’s Republic of China
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40
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Spielmann G, Ziegler S, Haszprunar G, Busch U, Huber I, Pavlovic M. Using loop-mediated isothermal amplification for fast species delimitation in eels (genus Anguilla), with special reference to the European eel (Anguilla anguilla). Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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41
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Kok EJ, Glandorf DC, Prins TW, Visser RG. Food and environmental safety assessment of new plant varieties after the European Court decision: Process-triggered or product-based? Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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42
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Boutigny AL, Barranger A, De Boisséson C, Blanchard Y, Rolland M. Targeted Next Generation Sequencing to study insert stability in genetically modified plants. Sci Rep 2019; 9:2308. [PMID: 30783176 PMCID: PMC6381221 DOI: 10.1038/s41598-019-38701-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/08/2019] [Indexed: 01/12/2023] Open
Abstract
The EU directive 2001/18/EC requires any genetically modified (GM) event to be stable. In the present work, a targeted Next-Generation Sequencing (NGS) approach using barcodes to specifically tag each individual DNA molecules during library preparation was implemented to detect mutations taking into account the background noise due to amplification and sequencing errors. The method was first showed to be efficient in detecting the mutations in synthetic samples prepared with custom-synthesized mutated or non-mutated P35S sequences mixed in different proportions. The genetic stability of a portion of the P35S promoter targeted for GM detection was then analyzed in GM flour samples. Several low frequency mutations were detected in the P35S sequences. Some mutated nucleotides were located within the primers and probes used in the P35S diagnostic test. If present not as somatic mutations but as the consensus sequence of some individuals, these mutations could influence the efficiency of the P35S real time PCR diagnostic test. This methodology could be implemented in genetic stability studies of GM inserts but also to detect single nucleotide mutant GM plants produced using "new breeding techniques".
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Affiliation(s)
- Anne-Laure Boutigny
- Anses, Plant Health Laboratory, Bacteriology Virology GMO Unit, 7 rue Jean Dixméras, 49044, Angers cedex 01, France.
| | - Audrey Barranger
- Anses, Plant Health Laboratory, Bacteriology Virology GMO Unit, 7 rue Jean Dixméras, 49044, Angers cedex 01, France
| | - Claire De Boisséson
- Anses, Ploufragan Laboratory, Viral Genetics and Biosafety Unit, BP 53, 22440, Ploufragan, France
| | - Yannick Blanchard
- Anses, Ploufragan Laboratory, Viral Genetics and Biosafety Unit, BP 53, 22440, Ploufragan, France
| | - Mathieu Rolland
- Anses, Plant Health Laboratory, Bacteriology Virology GMO Unit, 7 rue Jean Dixméras, 49044, Angers cedex 01, France
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Cottenet G, Blancpain C, Sonnard V, Chuah PF. Two FAST multiplex real-time PCR reactions to assess the presence of genetically modified organisms in food. Food Chem 2019; 274:760-765. [DOI: 10.1016/j.foodchem.2018.09.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 08/31/2018] [Accepted: 09/09/2018] [Indexed: 11/25/2022]
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Grohmann L, Keilwagen J, Duensing N, Dagand E, Hartung F, Wilhelm R, Bendiek J, Sprink T. Detection and Identification of Genome Editing in Plants: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2019; 10:236. [PMID: 30930911 PMCID: PMC6423494 DOI: 10.3389/fpls.2019.00236] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/21/2023]
Abstract
Conventional genetic engineering techniques generate modifications in the genome via stable integration of DNA elements which do not occur naturally in this combination. Therefore, the resulting organisms and (most) products thereof can unambiguously be identified with event-specific PCR-based methods targeting the insertion site. New breeding techniques such as genome editing diversify the toolbox to generate genetic variability in plants. Several of these techniques can introduce single nucleotide changes without integrating foreign DNA and thereby generate organisms with intended phenotypes. Consequently, such organisms and products thereof might be indistinguishable from naturally occurring or conventionally bred counterparts with established analytical tools. The modifications can entirely resemble random mutations regardless of being spontaneous or induced chemically or via irradiation. Therefore, if an identification of these organisms or products thereof is demanded, a new challenge will arise for (official) seed, food, and feed testing laboratories and enforcement institutions. For detailed consideration, we distinguish between the detection of sequence alterations - regardless of their origin - the identification of the process that generated a specific modification and the identification of a genotype, i.e., an organism produced by genome editing carrying a specific genetic alteration in a known background. This article briefly reviews the existing and upcoming detection and identification strategies (including the use of bioinformatics and statistical approaches) in particular for plants developed with genome editing techniques.
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Affiliation(s)
- Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
- *Correspondence: Lutz Grohmann,
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Nina Duensing
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Emilie Dagand
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Frank Hartung
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Joachim Bendiek
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Thorben Sprink
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
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45
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Qian C, Wang R, Wu H, Ping J, Wu J. Recent advances in emerging DNA-based methods for genetically modified organisms (GMOs) rapid detection. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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46
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Jacchia S, Kagkli DM, Lievens A, Angers-Loustau A, Savini C, Emons H, Mazzara M. Identification of single target taxon-specific reference assays for the most commonly genetically transformed crops using digital droplet PCR. Food Control 2018; 93:191-200. [PMID: 30393444 PMCID: PMC6058085 DOI: 10.1016/j.foodcont.2018.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 11/24/2022]
Abstract
Knowledge of the number of DNA sequences targeted by the taxon-specific reference assays is essential for correct GM quantification and is key to the harmonisation of measurement results. In the present study droplet digital PCR (ddPCR) was used to determine the number of DNA target copies of taxon-specific assays validated for real-time PCR for the four main genetically modified (GM) crops. The transferability of experimental conditions from real-time PCR to ddPCR was also explored, as well as the effect of DNA digestion. The results of this study indicate that for each crop at least one taxon-specific assay can be identified as having a single DNA target. A short list of taxon-specific reference assays is proposed as best candidates for the relative quantification of GM events for soybean, maize, cotton and oilseed rape. The investigated assays could be in most cases transferred to ddPCR without further optimisation. The use of DNA digestion did not improve ddPCR characteristics such as rain and resolution at the conditions tested.
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Affiliation(s)
- Sara Jacchia
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Dafni-Maria Kagkli
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Antoon Lievens
- European Commission, Joint Research Centre (JRC), Retieseweg 111, 2440 Geel, Belgium
| | | | - Christian Savini
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Hendrik Emons
- European Commission, Joint Research Centre (JRC), Retieseweg 111, 2440 Geel, Belgium
| | - Marco Mazzara
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
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Yamashita MSDA, Melo EO. Mucin 2 (MUC2) promoter characterization: an overview. Cell Tissue Res 2018; 374:455-463. [PMID: 30218241 DOI: 10.1007/s00441-018-2916-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 08/13/2018] [Indexed: 12/24/2022]
Abstract
Transgenic livestock have been studied with a well-known interest in improving quantitative and qualitative traits. In order to direct heterologous gene expression, it is indispensable to identify and characterize a promoter suitable for directing the expression of the gene of interest (GOI) in a tissue-specific way. The gastrointestinal tract is a desirable target for gene expression in several mammalian models. Throughout the surface of the intestinal epithelium, there is an intricate polymer network, formed by gel-forming mucins (especially MUC2 and MUC5AC, of which MUC2 is the major one), which plays a protective role due to the formation of a physical, chemical and immunological barrier between the organism and the environment. The characterization of the gel-forming mucins is difficult because of their large size and repetitive DNA sequences and domains. The main mucin in the small and large intestine, mucin 2 (MUC2), is expressed specifically in goblet cells. MUC2 plays an important role in intestinal homeostasis and its disruption is associated with several diseases and carcinomas. This mucin is also an important marker for elucidating mechanisms that regulate differentiation of the secretory cell lineage. This review presents the state of the art of MUC2 promoter structure and functional characterization.
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Affiliation(s)
| | - Eduardo O Melo
- EMBRAPA Genetic Resources and Biotechnology, PqEB Av W5 Norte, Brasilia, DF, 70770-917, Brazil
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48
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Leguizamón Guerrero JE, Vela Rojas AF, Arias Cortés MM, Cifuentes Fernández LF. Panorama general de los organismos genéticamente modificados en Colombia y en el mundo: Capacidad nacional de detección. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2018. [DOI: 10.15446/rev.colomb.biote.v20n2.77080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los organismos genéticamente modificados (OGM) y en particular los cultivos genéticamente modificados (GM), son el resultado de la modificación de la información genética de una especie a partir del uso de la biotecnología moderna para proporcionar nuevas características que su contraparte no modificada no posee, tales como resistencia a insectos, tolerancia a herbicidas, contenido de nutrientes entre otros. La mayor parte de estos cultivos se concentran en cuatro productos: soya (Glycine max), maíz (Zea Mays), canola (Brassica napus) y algodón (Gossypium hirsutum); y los principales productores son Estados Unidos, Brasil, Argentina, India y Canadá. Por su parte, Colombia ocupa el puesto 18 con cultivos de maíz, algodón y claveles azules. La introducción de estas especies en cualquier mercado está limitada por la legislación propia del país destino, así como por los estudios que permiten establecer su efecto sobre el medio ambiente, la salud humana y animal; en este sentido, la precisión y confianza de las técnicas analíticas empleadas en la evaluación del contenido de OGM son un elemento importante para la toma de decisiones basadas en evidencias objetivas, especialmente frente al debate en torno a su uso. Este documento presenta una revisión de las tecnologías de análisis más importantes disponibles a nivel mundial, frente a las capacidades nacionales para su detección.
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Fraiture MA, Vandamme J, Herman P, Roosens NHC. Development and validation of an integrated DNA walking strategy to detect GMO expressing cry genes. BMC Biotechnol 2018; 18:40. [PMID: 29945581 PMCID: PMC6020286 DOI: 10.1186/s12896-018-0446-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 05/15/2018] [Indexed: 01/09/2023] Open
Abstract
Background Recently, an integrated DNA walking strategy has been proposed to prove the presence of GMO via the characterisation of sequences of interest, including their transgene flanking regions and the unnatural associations of elements in their transgenic cassettes. To this end, the p35S, tNOS and t35S pCAMBIA elements have been selected as key targets, allowing the coverage of most of GMO, EU authorized or not. In the present study, a bidirectional DNA walking method anchored on the CryAb/c genes is proposed with the aim to cover additional GMO and additional sequences of interest. Results The performance of the proposed bidirectional DNA walking method anchored on the CryAb/c genes has been evaluated in a first time for its feasibility using several GM events possessing these CryAb/c genes. Afterwards, its sensitivity has been investigated through low concentrations of targets (as low as 20 HGE). In addition, to illustrate its applicability, the entire workflow has been tested on a sample mimicking food/feed matrices analysed in GMO routine analysis. Conclusion Given the successful assessment of its performance, the present bidirectional DNA walking method anchored on the CryAb/c genes can easily be implemented in GMO routine analysis by the enforcement laboratories and allows completing the entire DNA walking strategy in targeting an additional transgenic element frequently found in GMO. Electronic supplementary material The online version of this article (10.1186/s12896-018-0446-x) 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 Bioinformatics (PBB) by: Sciensano, Transversal & Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Julie Vandamme
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB) by: Sciensano, Transversal & Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Philippe Herman
- Scientific Institute of Public Health (WIV-ISP), Operational Direction Expertise, Service provisions & Customer relations by: Sciensano, Scientific Direction Expertise, Service provisions & Customer relations, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB) by: Sciensano, Transversal & Applied Genomics (TAG), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
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50
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Rocha-Munive MG, Soberón M, Castañeda S, Niaves E, Scheinvar E, Eguiarte LE, Mota-Sánchez D, Rosales-Robles E, Nava-Camberos U, Martínez-Carrillo JL, Blanco CA, Bravo A, Souza V. Evaluation of the Impact of Genetically Modified Cotton After 20 Years of Cultivation in Mexico. Front Bioeng Biotechnol 2018; 6:82. [PMID: 29988354 PMCID: PMC6023983 DOI: 10.3389/fbioe.2018.00082] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022] Open
Abstract
For more than 20 years cotton has been the most widely sown genetically modified (GM) crop in Mexico. Its cultivation has fulfilled all requirements and has gone through the different regulatory stages. During the last 20 years, both research-institutions and biotech-companies have generated scientific and technical information regarding GM cotton cultivation in Mexico. In this work, we collected data in order to analyze the environmental and agronomic effects of the use of GM cotton in Mexico. In 1996, the introduction of Bt cotton made it possible to reactivate this crop, which in previous years was greatly reduced due to pest problems, production costs and environmental concerns. Bt cotton is a widely accepted tool for cotton producers and has proven to be efficient for the control of lepidopteran pests. The economic benefits of its use are variable, and depend on factors such as the international cotton-prices and other costs associated with its inputs. So far, the management strategies used to prevent development of insect resistance to GM cotton has been successful, and there are no reports of insect resistance development to Bt cotton in Mexico. In addition, no effects have been observed on non-target organisms. For herbicide tolerant cotton, the prevention of herbicide resistance has also been successful since unlike other countries, the onset of resistance weeds is still slow, apparently due to cultural practices and rotation of different herbicides. Environmental benefits have been achieved with a reduction in chemical insecticide applications and the subsequent decrease in primary pest populations, so that the inclusion of other technologies—e.g., use of non-Bt cotton- can be explored. Nevertheless, control measures need to be implemented during transport of the bolls and fiber to prevent dispersal of volunteer plants and subsequent gene flow to wild relatives distributed outside the GM cotton growing areas. It is still necessary to implement national research programs, so that biotechnology and plant breeding advances can be used in the development of cotton varieties adapted to the Mexican particular environmental conditions and to control insect pests of regional importance.
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Affiliation(s)
- Martha G Rocha-Munive
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mario Soberón
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Saúl Castañeda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Esteban Niaves
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - David Mota-Sánchez
- Department of Entomology, Michigan State University, East Lansing, MI, United States
| | | | - Urbano Nava-Camberos
- Facultad de Agricultura y Zootecnia/Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Gómez Palacio, Mexico
| | | | - Carlos A Blanco
- Biology Department, University of New Mexico, Albuquerque, NM, United States
| | - Alejandra Bravo
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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