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Ding L, Xu X, Wang X, Chen X, Lu Y, Xu J, Peng C. Qualitative and Quantitative Detection of CRISPR-Associated Cas Gene in Gene-Edited Foods. Foods 2023; 12:3681. [PMID: 37835336 PMCID: PMC10572612 DOI: 10.3390/foods12193681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Effective regulation of gene-edited products and resolution of public concerns are the prerequisites for the industrialization of gene-edited crops and their derived foods. CRISPR-associated protein, the core element of the CRISPR system, requires to be regulated. Thus, there is an urgent need to establish qualitative and quantitative detection methods for the Cas gene. In the present study, the primers and probes were designed and screened for Cas12a (Cpf1), which is the most commonly used target site in gene editing; we performed PCR system optimization, determined the optimal primer concentration and annealing temperature, and established qualitative PCR and quantitative PCR (qPCR) assays for detecting Cpf1 in gene editing by specificity and sensitivity tests. In specificity testing, qualitative PCR and qPCR methods could 100% detect samples containing Cpf1 DNA, while the detection rate of other samples without Cpf1 was 0%. In the assay sensitivity test, the limit of detection of qualitative PCR was 0.1% (approximately 44 copies), and the limit of detection of the qPCR method was 14 copies. In the stability test, both the qualitative PCR and qPCR methods were repeated 60 times at their corresponding lowest detection limit concentrations, and the results were positive. Thus, the qualitative and quantitative assays for Cpf1 are specific, sensitive, and stable. The method provides technical support for the effective monitoring of gene-edited products and their derived foods in the future.
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Affiliation(s)
- Lin Ding
- 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
| | - Xiaoli Xu
- 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
| | - Xiaofu Wang
- 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
| | - 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
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Junfeng Xu
- 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
| | - Cheng Peng
- 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
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Li Y, Xiao F, Zhai C, Li X, Wu Y, Gao H, Li J, Zhai S, Liu B, Wu G. Qualitative and Quantitative Real-Time PCR Methods for Assessing False-Positive Rates in Genetically Modified Organisms Based on the Microbial-Infection-Linked HPT Gene. Int J Mol Sci 2022; 23:10000. [PMID: 36077399 DOI: 10.3390/ijms231710000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The hygromycin phosphotransferase (HPT) gene as a selective marker is normally used in screening tests as a first step in detecting and quantifying genetically modified organisms (GMOs) in seeds, food, and feed materials. Nevertheless, if researchers only focus on the HPT gene, it is difficult to distinguish genetically modified (GM) crops from microbial infection, leading to miscalculation of the rate of GM materials in a given sample set. Here, we cloned the 7259 bp sequence carrying the HPT gene from soybean sprouts using the genome walking strategy. BLAST analysis revealed that this sequence was derived from plasmids naturally occurring in microorganisms, such as Escherichia coli, Klebsiella pneumoniae or Salmonella sp. Using the reconstructed plasmid pFP-hpt, qualitative PCR and quantitative real-time PCR (qPCR) methods were established, and 261 bp and 156 bp products were produced. The specificity of these assays was assessed against related pFP-hpt plasmids, plant species with important agronomic traits, and GM crops containing the HPT gene. No unexpected results were observed between samples using these qualitative PCR and qPCR methods. The sensitivity of this qualitative PCR assay was determined at 20 copies, while the limit of detection (LOD) and limit of quantification (LOQ) of qPCR were both 5 copies per reaction. Our in-house validation indicated that the amplification efficiency, linearity, and repeatability of this qPCR assay were in line with performance requirements. Furthermore, a qualitative and quantitative duplex PCR showed high reliability for the simultaneous detection of the HPT gene in a plant sample and environmental micro-organisms harboring the HPT gene in one PCR reaction. These qualitative PCR and qPCR assays were able to differentiate between plants infected with E. coli harboring the HPT gene from GM plants, indicating that these two methods are broadly applicable for routine GMO testing.
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Chiappa G, Cafiso A, Monza E, Serra V, Olivieri E, Romeo C, Bazzocchi C. Development of a PCR for Borrelia burgdorferi sensu lato, targeted on the groEL gene. Folia Parasitol (Praha) 2020; 67. [PMID: 33043891 DOI: 10.14411/fp.2020.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/09/2020] [Indexed: 11/19/2022]
Abstract
Borrelia burgdorferi sensu lato (s.l.) is the etiological agent of Lyme disease, transmitted by ticks of the genus Ixodes Latreille. Diagnosis of Lyme disease in humans is often difficult and a detailed knowledge of the circulation of B. burgdorferi s.l. in tick hosts is therefore fundamental to support clinical procedures. Here we developed a molecular approach for the detection of B. burgdorferi s.l. in North Italian Ixodes ricinus (Linnaeus). The method is based on the amplification of a fragment of the groEL gene, which encodes a heat-shock protein highly conserved among B. burgdorferi s.l. species. The tool was applied in both qualitative and Real-time PCR approaches testing ticks collected in a North Italian area. The obtained results suggest that this new molecular tool could represent a sensitive and specific method for epidemiological studies aimed at defining the distribution of B. burgdorferi s.l. in I. ricinus and, consequently, the exposure risk for humans.
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Affiliation(s)
- Giulia Chiappa
- Department of Veterinary Medicine, University of Milan, Lodi, Italy
| | | | - Elisa Monza
- Department of Veterinary Medicine, University of Milan, Lodi, Italy
| | - Valentina Serra
- Department of Veterinary Medicine, University of Milan, Lodi, Italy
| | - Emanuela Olivieri
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Claudia Romeo
- Department of Veterinary Medicine, University of Milan, Lodi, Italy
| | - Chiara Bazzocchi
- Department of Veterinary Medicine, University of Milan, Lodi, Italy.,Pediatric Clinical Research Centre "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy.,Coordinated Research Centre "EpiSoMi", University of Milan, Milan, Italy
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Accetta R, Elli L, Libera L, Siracusa C, Cassavia F, Orsini F, Orlandi L, Passamonti F, Casalone R, Pallotti F. Analysis of three screening methods for the detection of calreticulin gene mutations. Int J Lab Hematol 2019; 42:e76-e79. [PMID: 31693300 DOI: 10.1111/ijlh.13117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/01/2019] [Accepted: 10/09/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Raffaella Accetta
- SSD Laboratorio Analisi-SMEL Specializzato in Citogenetica e Genetica Medica, ASST Settelaghi-Ospedale di Circolo-Fondazione Macchi, Varese, Italy
| | - Lorenzo Elli
- SSD Laboratorio Analisi-SMEL Specializzato in Citogenetica e Genetica Medica, ASST Settelaghi-Ospedale di Circolo-Fondazione Macchi, Varese, Italy
| | - Laura Libera
- UO Ematologia, ASST Settelaghi- Ospedale di Circolo-Fondazione Macchi, Varese, Italy
| | - Claudia Siracusa
- UO Ematologia, ASST Settelaghi- Ospedale di Circolo-Fondazione Macchi, Varese, Italy
| | | | | | | | - Francesco Passamonti
- UO Ematologia, ASST Settelaghi- Ospedale di Circolo-Fondazione Macchi, Varese, Italy.,Dipartimento di Medicina e Chirurgia, Università degli Studi dell'Insubria, Varese, Italy
| | - Rosario Casalone
- SSD Laboratorio Analisi-SMEL Specializzato in Citogenetica e Genetica Medica, ASST Settelaghi-Ospedale di Circolo-Fondazione Macchi, Varese, Italy
| | - Francesco Pallotti
- SSD Laboratorio Analisi-SMEL Specializzato in Citogenetica e Genetica Medica, ASST Settelaghi-Ospedale di Circolo-Fondazione Macchi, Varese, Italy.,Dipartimento di Medicina e Chirurgia, Università degli Studi dell'Insubria, Varese, Italy
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Li Z, Li X, Wang C, Song G, Pi L, Zheng L, Zhang D, Yang L. One Novel Multiple-Target Plasmid Reference Molecule Targeting Eight Genetically Modified Canola Events for Genetically Modified Canola Detection. J Agric Food Chem 2017; 65:8489-8500. [PMID: 28844131 DOI: 10.1021/acs.jafc.7b02453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Multiple-target plasmid DNA reference materials have been generated and utilized as good substitutes of matrix-based reference materials in the analysis of genetically modified organisms (GMOs). Herein, we report the construction of one multiple-target plasmid reference molecule, pCAN, which harbors eight GM canola event-specific sequences (RF1, RF2, MS1, MS8, Topas 19/2, Oxy235, RT73, and T45) and a partial sequence of the canola endogenous reference gene PEP. The applicability of this plasmid reference material in qualitative and quantitative PCR assays of the eight GM canola events was evaluated, including the analysis of specificity, limit of detection (LOD), limit of quantification (LOQ), and performance of pCAN in the analysis of various canola samples, etc. The LODs are 15 copies for RF2, MS1, and RT73 assays using pCAN as the calibrator and 10 genome copies for the other events. The LOQ in each event-specific real-time PCR assay is 20 copies. In quantitative real-time PCR analysis, the PCR efficiencies of all event-specific and PEP assays are between 91% and 97%, and the squared regression coefficients (R2) are all higher than 0.99. The quantification bias values varied from 0.47% to 20.68% with relative standard deviation (RSD) from 1.06% to 24.61% in the quantification of simulated samples. Furthermore, 10 practical canola samples sampled from imported shipments in the port of Shanghai, China, were analyzed employing pCAN as the calibrator, and the results were comparable with those assays using commercial certified materials as the calibrator. Concluding from these results, we believe that this newly developed pCAN plasmid is one good candidate for being a plasmid DNA reference material in the detection and quantification of the eight GM canola events in routine analysis.
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Affiliation(s)
- Zhuqing Li
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Xiang Li
- Shanghai Entry-Exit Inspection and Quarantine Bureau, GMO Detection Laboratory , 1208 Minheng Road, Shanghai 200135, P. R. China
| | - Canhua Wang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Guiwen Song
- Development Center of Science and Technology, Ministry of Agriculture of People's Republic of China , Beijing 100025, China
| | - Liqun Pi
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Lan Zheng
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Dabing Zhang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection , Huaian 223300, China
| | - Litao Yang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
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Yuan J, Chang H, Zhao J, Tang Z, Shi Z, Wang J. [Detection of transgenic components in animal feeds on Shanxi markets]. Sheng Wu Gong Cheng Xue Bao 2016; 32:1576-1589. [PMID: 29034627 DOI: 10.13345/j.cjb.160117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To assess the presence of genetically modified (GM) maize and soybean in a range of commercialized feed in Shanxi province of China in 2015, improved hexadecyltrimethy ammonium bromide (CTAB) method was used to extract DNA. The screening of packed feeds was carried out by qualitative PCR. Then positive feeds were unpacked and detected by the CaMV 35S promoter, NOS terminator, zSSIIb, Lectin and CryIA (b) genes. The identified maize and soybean events were confirmed by event-specific MON810 and GTS40-3-2. Results showed that 83.3% of the feeds was tested positive for GMOs, in which positive rates of maize, soybean, pig and layer feeds were 6.67%, 100%, 93.3% and 73.3%, respectively. The results of real-time PCR were consistent with qualitative PCR. These results indicated that commercialized GM feed had a wide positive product scope in Shanxi province of China. Further studies are necessary to study effects of feeding livestock and poultry with feed containing GM ingredients on animals and their products.
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Affiliation(s)
- Jianqin Yuan
- College of Life Science, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Hong Chang
- College of Life Science, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Jianghe Zhao
- College of Life Science, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Zhongwei Tang
- College of Life Science, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Zongyong Shi
- College of Life Science, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Jundong Wang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, Shanxi, China
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