1
|
Aminu S, Ascandari A, Laamarti M, Safdi NEH, El Allali A, Daoud R. Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities. Crit Rev Microbiol 2023:1-25. [PMID: 38006569 DOI: 10.1080/1040841x.2023.2282447] [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: 05/22/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.
Collapse
Affiliation(s)
- Suleiman Aminu
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - AbdulAziz Ascandari
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Meriem Laamarti
- Faculty of Medical Sciences, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Nour El Houda Safdi
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| |
Collapse
|
2
|
Ultrasensitive fluorescent biosensor for detecting CaMV 35S promoter with proximity extension mediated multiple cascade strand displacement amplification and CRISPR/Cpf 1. Anal Chim Acta 2022; 1215:339973. [DOI: 10.1016/j.aca.2022.339973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/05/2022] [Accepted: 05/20/2022] [Indexed: 11/22/2022]
|
3
|
Gayathiri E, Prakash P, Selvam K, Awasthi MK, Gobinath R, Karri RR, Ragunathan MG, Jayanthi J, Mani V, Poudineh MA, Chang SW, Ravindran B. Plant microbe based remediation approaches in dye removal: A review. Bioengineered 2022; 13:7798-7828. [PMID: 35294324 PMCID: PMC9208495 DOI: 10.1080/21655979.2022.2049100] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Increased industrialization demand using synthetic dyes in the newspaper, cosmetics, textiles, food, and leather industries. As a consequence, harmful chemicals from dye industries are released into water reservoirs with numerous structural components of synthetic dyes, which are hazardous to the ecosystem, plants and humans. The discharge of synthetic dye into various aquatic environments has a detrimental effect on the balance and integrity of ecological systems. Moreover, numerous inorganic dyes exhibit tolerance to degradation and repair by natural and conventional processes. So, the present condition requires the development of efficient and effective waste management systems that do not exacerbate environmental stress or endanger other living forms. Numerous biological systems, including microbes and plants, have been studied for their ability to metabolize dyestuffs. To minimize environmental impact, bioremediation uses endophytic bacteria, which are plant beneficial bacteria that dwell within plants and may improve plant development in both normal and stressful environments. Moreover, Phytoremediation is suitable for treating dye contaminants produced from a wide range of sources. This review article proves a comprehensive evaluation of the most frequently utilized plant and microbes as dye removal technologies from dye-containing industrial effluents. Furthermore, this study examines current existing technologies and proposes a more efficient, cost-effective method for dye removal and decolorization on a big scale. This study also aims to focus on advanced degradation techniques combined with biological approaches, well regarded as extremely effective treatments for recalcitrant wastewater, with the greatest industrial potential.
Collapse
Affiliation(s)
- Ekambaram Gayathiri
- Department of Plant Biology and Plant Biotechnology, Guru Nanak College (Autonomous), Chennai - 600 042, India
| | - Palanisamy Prakash
- Department of Botany, Periyar University, Periyar Palkalai Nagar, Salem 636011, India
| | - Kuppusamy Selvam
- Department of Botany, Periyar University, Periyar Palkalai Nagar, Salem 636011, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi 712100, PR China
| | | | - Rama Rao Karri
- Faculty of Engineering, University Teknologi, Brunei, Asia
| | | | - Jayaprakash Jayanthi
- Department of Advanced Zoology and Biotechnology, Guru Nanak College, Chennai, India
| | - Vimalraj Mani
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
| | | | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon 16227, Republic of Korea
| | - Balasubramani Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University, Youngtong-Gu, Suwon 16227, Republic of Korea
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Duan L, Zhang S, Yang Y, Wang Q, Lan Q, Wang Y, Xu W, Jin W, Li L, Chen R. A feasible method for detecting unknown GMOs via a combined strategy of PCR-based suppression subtractive hybridization and next-generation sequencing. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
7
|
Takabatake R, Onishi M, Minegishi Y, Futo S, Soga K, Nakamura K, Kondo K, Mano J, Kitta K. Development of a Novel Detection Method Targeting an Ultrashort 25 bp Sequence Found in Agrobacterium-Mediated Transformed GM Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:15327-15334. [PMID: 33296196 DOI: 10.1021/acs.jafc.0c03864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Agrobacterium-mediated transformation is the most commonly used technique for plant genetic engineering. During the transformation, a T-DNA region, which is flanked by the right border (RB) and the left border, is transferred to plant nuclear chromosomes. Simultaneously, a sequence adjacent to the RB on T-DNA is frequently transferred to plant genomes together with the intentionally introduced recombinant DNA. We developed a novel polymerase chain reaction (PCR)-mediated detection method targeting this region. The conserved sequence of the region found in genetically modified (GM) crops is only 25 bp in length. To detect this ultrashort 25 bp sequence near the RB region, we designed a primer set consisting of a 12-base forward primer and a 13-base reverse primer. The predicted band was detected from GM crops by optimizing the PCR conditions. We used lateral flow DNA chromatography for rapid and inexpensive detection. The developed method would be applicable for screening the GM crops generated by Agrobacterium-mediated transformation.
Collapse
Affiliation(s)
- Reona Takabatake
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Mari Onishi
- FASMAC Co., Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Yasutaka Minegishi
- Nippon Gene Co., Ltd., 1-5, Kandanishiki-cho, Chiyoda-ku, Tokyo 101-0054, Japan
| | - Satoshi Futo
- FASMAC Co., Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Keisuke Soga
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Kosuke Nakamura
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Kazunari Kondo
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Junichi Mano
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Kazumi Kitta
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Varjani S, Rakholiya P, Ng HY, You S, Teixeira JA. Microbial degradation of dyes: An overview. BIORESOURCE TECHNOLOGY 2020; 314:123728. [PMID: 32665105 DOI: 10.1016/j.biortech.2020.123728] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 05/21/2023]
Abstract
Industrialization increases use of dyes due to its high demand in paper, cosmetic, textile, leather and food industries. This in turn would increase wastewater generation from dye industrial activities. Various dyes and its structural compounds present in dye industrial wastewater have harmful effects on plants, animals and humans. Synthetic dyes are more resistant than natural dyes to physical and chemical methods for remediation which makes them more difficult to get decolorize. Microbial degradation has been researched and reviewed largely for quicker dye degradation. Genetically engineered microorganisms (GEMs) play important role in achieving complete dye degradation. This paper provides scientific and technical information about dyes & dye intermediates and biodegradation of azo dye. It also compiles information about factors affecting dye(s) biodegradation, role of genetically modified organisms (GMOs) in process of dye(s) degradation and perspectives in this field of research.
Collapse
Affiliation(s)
- Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, Gujarat 382 010, India.
| | - Parita Rakholiya
- Gujarat Pollution Control Board, Gandhinagar, Gujarat 382 010, India; Kadi Sarva Vishwavidyalaya, Gandhinagar, Gujarat 382015, India
| | - How Yong Ng
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Siming You
- James Watt School of Engineering, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jose A Teixeira
- CEB - Centre of Biological Engineering, University of Minho, 4710057 Braga, Portugal
| |
Collapse
|
10
|
Abstract
The presence of genetically modified organisms (GMO) is commonly assessed using real-time PCR methods targeting the most common transgenic elements found in GMOs. Once the presence of GM material has been established using these screening methods, GMOs are further identified using a battery of real-time PCR methods, each being specific of one GM event and usually targeting the junction of the plant genome and of the transgenic DNA insert. If, using these specific methods, no GMO could be identified, the presence of an unauthorized GMO is suspected. In this context, the aim of this work was to develop a fast and simple method to obtain the sequence of the transgene and of its junction with plant DNA, with the presence of a screening sequence as only prior knowledge. An unauthorized GM petunia, recently found on the French market, was used as template during the development of this new molecular tool. The innovative proposed protocol is based on the circularization of fragmented DNA followed by the amplification of the transgene and of its flanking regions using long-range inverse PCR. Sequencing was performed using the Oxford Nanopore MinION technology and a bioinformatic pipeline was developed.
Collapse
|
11
|
Kersten B, Leite Montalvão AP, Hoenicka H, Vettori C, Paffetti D, Fladung M. Sequencing of two transgenic early-flowering poplar lines confirmed vector-free single-locus T-DNA integration. Transgenic Res 2020; 29:321-337. [PMID: 32356192 PMCID: PMC7283205 DOI: 10.1007/s11248-020-00203-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/18/2020] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing (NGS) approaches are attractive alternatives to the PCR-based characterisation of genetically modified plants for safety assessment and labelling since NGS is highly sensitive to the detection of T-DNA inserts as well as vector backbone sequences in transgenic plants. In this study, two independent transgenic male Populus tremula lines, T193-2 and T195-1, both carrying the FLOWERING LOCUS T gene from Arabidopsis thaliana under control of a heat-inducible promoter (pHSP::AtFT) and the non-transgenic control clone W52, were further characterised by NGS and third-generation sequencing. The results support previous findings that the T-DNA was hemizygously inserted in one genomic locus of each line. However, the T-DNA insertions consist of conglomerations of one or two T-DNA copies together with a small T-DNA fragment without AtFT parts. Based on NGS data, no additional T-DNA splinters or vector backbone sequences could be identified in the genome of the two transgenic lines. Seedlings derived from crosses between the pHSP::AtFT transgenic male parents and female wild type plants are therefore expected to be T-DNA splinter or vector backbone free. Thus, PCR analyses amplifying a partial T-DNA fragment with AtFT-specific primers are sufficient to determine whether the seedlings are transgenic or not. An analysis of 72 second generation-seedlings clearly showed that about 50% of them still reveal the presence of the T-DNA, confirming data already published. To prove if unanticipated genomic changes were induced by T-DNA integration, extended future studies using long-range sequencing technologies are required once a suitable chromosome-level P. tremula reference genome sequence is available.
Collapse
Affiliation(s)
- Birgit Kersten
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany
| | - Cristina Vettori
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry, Agricultural Genetics Section, University of Florence, P. le delle Cascine 18, 50144, Florence, Italy
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
| |
Collapse
|
12
|
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.
Collapse
|
13
|
Giraldo PA, Shinozuka H, Spangenberg GC, Cogan NO, Smith KF. Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food? FRONTIERS IN PLANT SCIENCE 2019; 10:1592. [PMID: 31921242 PMCID: PMC6918800 DOI: 10.3389/fpls.2019.01592] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.
Collapse
Affiliation(s)
- Paula A. Giraldo
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Noel O.I. Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, AgriBio, The Centre for AgriBiosciences, Melbourne, VIC, Australia
| | - Kevin F. Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, Australia
- Agriculture Victoria Research, Hamilton, VIC, Australia
| |
Collapse
|
14
|
Debode F, Hulin J, Charloteaux B, Coppieters W, Hanikenne M, Karim L, Berben G. Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies. Sci Rep 2019; 9:15595. [PMID: 31666537 PMCID: PMC6821802 DOI: 10.1038/s41598-019-51668-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
Next generation sequencing (NGS) is a promising tool for analysing the quality and safety of food and feed products. The detection and identification of genetically modified organisms (GMOs) is complex, as the diversity of transgenic events and types of structural elements introduced in plants continue to increase. In this paper, we show how a strategy that combines enrichment technologies with NGS can be used to detect a large panel of structural elements and partially or completely reconstruct the new sequence inserted into the plant genome in a single analysis, even at low GMO percentages. The strategy of enriching sequences of interest makes the approach applicable even to mixed products, which was not possible before due to insufficient coverage of the different genomes present. This approach is also the first step towards a more complete characterisation of agrifood products in a single analysis.
Collapse
Affiliation(s)
- Frédéric Debode
- Walloon Agricultural Research Center (CRA-W), Unit Traceability and Authentication, chaussée de Namur 24, 5030, Gembloux, Belgium.
| | - Julie Hulin
- Walloon Agricultural Research Center (CRA-W), Unit Traceability and Authentication, chaussée de Namur 24, 5030, Gembloux, Belgium
| | - Benoît Charloteaux
- University of Liège, GIGA - Genomics Platform, B34, 4000, Liège (Sart Tilman), Belgium
| | - Wouter Coppieters
- University of Liège, GIGA - Genomics Platform, B34, 4000, Liège (Sart Tilman), Belgium
| | - Marc Hanikenne
- University of Liège, InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, Chemin de la Vallée, 4, B22, 4000, Liège (Sart Tilman), Belgium
| | - Latifa Karim
- University of Liège, GIGA - Genomics Platform, B34, 4000, Liège (Sart Tilman), Belgium
| | - Gilbert Berben
- Walloon Agricultural Research Center (CRA-W), Unit Traceability and Authentication, chaussée de Namur 24, 5030, Gembloux, Belgium
| |
Collapse
|
15
|
Broll H, Braeuning A, Lampen A. European Court of Justice decision for genome editing: Consequences on food/feed risk assessment and detection. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
16
|
Wichert WRA, Dhummakupt ES, Zhang C, Mach PM, Bernhards RC, Glaros T, Manicke NE. Detection of Protein Toxin Simulants from Contaminated Surfaces by Paper Spray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1406-1415. [PMID: 30859394 DOI: 10.1007/s13361-019-02141-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
Proteinaceous toxins are harmful proteins derived from plants, bacteria, and other natural sources. They pose a risk to human health due to infection and also as possible biological warfare agents. Paper spray mass spectrometry (PS-MS) with wipe sampling was used to detect proteins from surfaces as a potential tool for identifying the presence of these toxins. Proteins ranging in mass between 12.4 and 66.5 kDa were tested, including a biological toxin simulant/vaccine for Staphylococcal enterotoxin B (SEBv). Various substrates were tested for these representative proteins, including a laboratory bench, a notebook cover, steel, glass, plant leaf and vinyl flooring. Carbon sputtered porous polyethylene (CSPP) was found to outperform typical chromatography paper used for paper spray, as well as carbon nanotube (CNT)-coated paper and polyethylene (PE), which have been previously shown to be well-suited for protein analysis. Low microgram quantities of the protein toxin simulant and other test proteins were successfully detected with good signal-to-noise from surfaces using a porous wipe. These applications demonstrate that PS-MS can potentially be used for rapid, sample preparation-free detection of proteins and biological warfare agents, which would be beneficial to first responders and warfighters.
Collapse
Affiliation(s)
- William R A Wichert
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN, 46202, USA
| | - Elizabeth S Dhummakupt
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, U.S. Army, 5183 Blackhawk Rd., Aberdeen Proving Ground, MD, 21010-5424, USA
| | - Chengsen Zhang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN, 46202, USA
| | - Phillip M Mach
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, U.S. Army, 5183 Blackhawk Rd., Aberdeen Proving Ground, MD, 21010-5424, USA
| | - Robert C Bernhards
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, U.S. Army, 5183 Blackhawk Rd., Aberdeen Proving Ground, MD, 21010-5424, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA, 22060, USA
| | - Trevor Glaros
- Combat Capabilities Development Command (CCDC) Chemical Biological Center, U.S. Army, 5183 Blackhawk Rd., Aberdeen Proving Ground, MD, 21010-5424, USA.
| | - Nicholas E Manicke
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN, 46202, USA.
| |
Collapse
|
17
|
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]
|
18
|
Zhu P, Fu W, Wei S, Liu X, Wang C, Lu Y, Shang Y, Wu X, Wu Y, Zhu S. A high-throughput and ultrasensitive identification methodology for unauthorized GMP component based on suspension array and logical calculator. Sci Rep 2019; 9:7311. [PMID: 31086245 PMCID: PMC6513989 DOI: 10.1038/s41598-019-43863-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/24/2019] [Indexed: 01/08/2023] Open
Abstract
To solve the problem of the unauthorized GMP components within import and export goods, the LI-US (Logic Identification of unauthorized GMP content by Universal-primer Suspension-array) system, which takes advantage of suspension array and logic calculator, was developed in the present study. Seventeen signal input channels have been optimized and validated in our research to ensure the multiplex practicality of the LI-US system. Three LI-US logic gates, including a YES gate, an OR gate and an AND gate, were designed as different detection strategies for GMP identification. The feasibility and specificity of the LI-US system were validated in the present study. Combining the optimization and evaluation of the signal input procedure, the sensitivity of this LI-US system reached 0.05% of the GMP mass concentration. The practicability evaluation of LI-US demonstrated its application within different substrates and varieties. In conclusion, the LI-US system was developed with extremely high specificity, sensitivity and practicability among different substrates and varieties, which could meet the demands of unauthorized GMP contents for both import and export goods.
Collapse
Affiliation(s)
- Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Wei Fu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Shuang Wei
- Guangdong Entry-Exit Inspection and Quarantine Bureau, Guangdong, 510000, China
| | - Xiao Liu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Chenguang Wang
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Yun Lu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Ying Shang
- Yunnan Insititute of Food Safety, Kunmming University of Science and technology, Yunnan, 650500, China
| | - Xiyang Wu
- Department of Food Science and Engineering, Jinan University, Guangzhou, 510000, China
| | - Yuping Wu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China.
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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]
|
21
|
Arulandhu AJ, van Dijk J, Staats M, Hagelaar R, Voorhuijzen M, Molenaar B, van Hoof R, Li R, Yang L, Shi J, Scholtens I, Kok E. NGS-based amplicon sequencing approach; towards a new era in GMO screening and detection. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
22
|
Dobnik D, Gruden K, Žel J, Bertheau Y, Holst-Jensen A, Bohanec M. Decision Support for the Comparative Evaluation and Selection of Analytical Methods: Detection of Genetically Modified Organisms as an Example. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1194-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
23
|
Fraiture MA, Saltykova A, Hoffman S, Winand R, Deforce D, Vanneste K, De Keersmaecker SCJ, Roosens NHC. Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO. Sci Rep 2018; 8:7903. [PMID: 29785005 PMCID: PMC5962636 DOI: 10.1038/s41598-018-26259-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region. This DNA walking is performed on transgenic elements, commonly found in GMO, that were earlier detected by real-time PCR (qPCR) screening. Previously, we have demonstrated the ability of this approach to detect unauthorized GMO via the identification of unique transgene flanking regions and the unnatural associations of elements from the transgenic cassette. In the present study, we investigate the feasibility to integrate the described workflow with the MinION Next-Generation-Sequencing (NGS). The MinION sequencing platform can provide long read-lengths and deal with heterogenic DNA libraries, allowing for rapid and efficient delivery of sequences of interest. In addition, the ability of this NGS platform to characterize unauthorized and unknown GMO without any a priori knowledge has been assessed.
Collapse
Affiliation(s)
- Marie-Alice Fraiture
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit (SBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Assia Saltykova
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Ghent University (UGent), Department of Information Technology, IMEC, Internet Technology and Data Science Lab (IDLab), Technologiepark-Zwijnaarde 15, 9052, Ghent, Belgium
| | - Stefan Hoffman
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Raf Winand
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Dieter Deforce
- Ghent University, Faculty of Pharmaceutical Sciences, Laboratory of Pharmaceutical Biotechnology, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Kevin Vanneste
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform of Biotechnology and Bioinformatics (PBB), J. Wytsmanstraat 14, 1050, Brussels, Belgium.
| |
Collapse
|
24
|
Demeke T, Dobnik D. Critical assessment of digital PCR for the detection and quantification of genetically modified organisms. Anal Bioanal Chem 2018; 410:4039-4050. [PMID: 29574561 PMCID: PMC6010488 DOI: 10.1007/s00216-018-1010-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022]
Abstract
The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing. Graphical abstract There are generally three different options for absolute quantification of genetically modified organisms (GMOs) using digital PCR: droplet- or chamber-based and droplets in chambers. All have in common the distribution of reaction mixture into several partitions, which are all subjected to PCR and scored at the end-point as positive or negative. Based on these results GMO content can be calculated.
Collapse
Affiliation(s)
- Tigst Demeke
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, MB, R3C3G8, Canada
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| |
Collapse
|
25
|
Sánchez-Paniagua López M, Manzanares-Palenzuela CL, López-Ruiz B. Biosensors for GMO Testing: Nearly 25 Years of Research. Crit Rev Anal Chem 2018; 48:391-405. [DOI: 10.1080/10408347.2018.1442708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Marta Sánchez-Paniagua López
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Beatriz López-Ruiz
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
26
|
Characterization of Plant Genetic Modifications Using Next-Generation Sequencing. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|
27
|
Nadal A, De Giacomo M, Einspanier R, Kleter G, Kok E, McFarland S, Onori R, Paris A, Toldrà M, van Dijk J, Wal JM, Pla M. Exposure of livestock to GM feeds: Detectability and measurement. Food Chem Toxicol 2017; 117:13-35. [PMID: 28847764 DOI: 10.1016/j.fct.2017.08.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/30/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022]
Abstract
This review explores the possibilities to determine livestock consumption of genetically modified (GM) feeds/ingredients including detection of genetically modified organism (GMO)-related DNA or proteins in animal samples, and the documentary system that is in place for GM feeds under EU legislation. The presence and level of GMO-related DNA and proteins can generally be readily measured in feeds, using established analytical methods such as polymerase chain reaction and immuno-assays, respectively. Various technical challenges remain, such as the simultaneous detection of multiple GMOs and the identification of unauthorized GMOs for which incomplete data on the inserted DNA may exist. Given that transfer of specific GMO-related DNA or protein from consumed feed to the animal had seldom been observed, this cannot serve as an indicator of the individual animal's prior exposure to GM feeds. To explore whether common practices, information exchange and the specific GM feed traceability system in the EU would allow to record GM feed consumption, the dairy chain in Catalonia, where GM maize is widely grown, was taken as an example. It was thus found that this system would neither enable determination of an animal's consumption of specific GM crops, nor would it allow for quantitation of the exposure.
Collapse
Affiliation(s)
- Anna Nadal
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003 Girona, Spain.
| | - Marzia De Giacomo
- Department of Veterinary Public Health and Food Safety, GMO and Mycotoxins Unit, Italian National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Ralf Einspanier
- Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Gijs Kleter
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708WB Wageningen, The Netherlands
| | - Esther Kok
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708WB Wageningen, The Netherlands
| | - Sarah McFarland
- Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Roberta Onori
- Department of Veterinary Public Health and Food Safety, GMO and Mycotoxins Unit, Italian National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Alain Paris
- Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS, UMR7245 MCAM, Paris, France
| | - Mònica Toldrà
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003 Girona, Spain
| | - Jeroen van Dijk
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708WB Wageningen, The Netherlands
| | - Jean-Michel Wal
- AgroParisTech, Institut National de la Recherche Agronomique (INRA), Paris, France
| | - Maria Pla
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003 Girona, Spain
| |
Collapse
|
28
|
Van Eenennaam AL, Young AE. Detection of dietary DNA, protein, and glyphosate in meat, milk, and eggs. J Anim Sci 2017; 95:3247-3269. [PMID: 28727079 DOI: 10.2527/jas.2016.1346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Products such as meat, milk, and eggs from animals that have consumed genetically engineered (GE) feed are not currently subject to mandatory GE labeling requirements. Some voluntary "non-genetically modified organism" labeling has been associated with such products, indicating that the animals were not fed GE crops, as there are no commercialized GE food animals. This review summarizes the available scientific literature on the detection of dietary DNA and protein in animal products and briefly discusses the implications of mandatory GE labeling for products from animals that have consumed GE feed. Because glyphosate is used on some GE crops, the available studies on glyphosate residues in animal products are also reviewed. In GE crops, recombinant DNA (rDNA) makes up a small percentage of the plant's total DNA. The final amount of DNA in food/feed depends on many factors including the variable number and density of cells in the edible parts, the DNA-containing matrix, environmental conditions, and the specific transgenic event. Processing treatments and animals' digestive systems degrade DNA into small fragments. Available reports conclude that endogenous DNA and rDNA are processed in exactly the same way in the gastrointestinal tract and that they account for a very small proportion of food intake by weight. Small pieces of high copy number endogenous plant genes have occasionally been detected in meat and milk. Similarly sized pieces of rDNA have also been identified in meat, primarily fish, although detection is inconsistent. Dietary rDNA fragments have not been detected in chicken or quail eggs or in fresh milk from cows or goats. Collectively, studies have failed to identify full-length endogenous or rDNA transcripts or recombinant proteins in meat, milk, or eggs. Similarly, because mammals do not bioaccumulate glyphosate and it is rapidly excreted, negligible levels of glyphosate in cattle, pig and poultry meat, milk, and eggs have been reported. Despite consumer concern about the presence of trace concentrations of glyphosate that might have been applied to feed crops and/or the presence of rDNA or recombinant proteins in meat, milk, and eggs, the available data do not provide evidence to suggest that products from animals that have consumed approved GE feed crops differ in any distinguishable way from those derived from animals fed conventional feed or that products from animals fed GE feedstuffs pose novel health risks.
Collapse
|
29
|
Fraiture MA, Herman P, De Loose M, Debode F, Roosens NH. How Can We Better Detect Unauthorized GMOs in Food and Feed Chains? Trends Biotechnol 2017; 35:508-517. [DOI: 10.1016/j.tibtech.2017.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/17/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022]
|
30
|
§ 64 LFGB Kick-off Meeting zu „Anwendungspotenzial moderner Analysetechniken im Bereich Lebensmittel- und Futtermittelsicherheit und deren Authentizität“. J Verbrauch Lebensm 2017. [DOI: 10.1007/s00003-017-1103-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
31
|
Li R, Quan S, Yan X, Biswas S, Zhang D, Shi J. Molecular characterization of genetically-modified crops: Challenges and strategies. Biotechnol Adv 2017; 35:302-309. [DOI: 10.1016/j.biotechadv.2017.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 12/23/2022]
|
32
|
The use of targeted genomic capture and massively parallel sequencing in diagnosis of Chinese Leukoencephalopathies. Sci Rep 2016; 6:35936. [PMID: 27779215 PMCID: PMC5078786 DOI: 10.1038/srep35936] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022] Open
Abstract
Leukoencephalopathies are diseases with high clinical heterogeneity. In clinical work, it’s difficult for doctors to make a definite etiological diagnosis. Here, we designed a custom probe library which contains the known pathogenic genes reported to be associated with Leukoencephalopathies, and performed targeted gene capture and massively parallel sequencing (MPS) among 49 Chinese patients who has white matter damage as the main imaging changes, and made the validation by Sanger sequencing for the probands’ parents. As result, a total of 40.8% (20/49) of the patients identified pathogenic mutations, including four associated with metachromatic leukodystrophy, three associated with vanishing white matter leukoencephalopathy, three associated with mitochondrial complex I deficiency, one associated with Globoid cell leukodystrophy (or Krabbe diseases), three associated with megalencephalic leukoencephalopathy with subcortical cysts, two associated with Pelizaeus-Merzbacher disease, two associated with X-linked adrenoleukodystrophy, one associated with Zellweger syndrome and one associated with Alexander disease. Targeted capture and MPS enables to identify mutations of all classes causing leukoencephalopathy. Our study combines targeted capture and MPS technology with clinical and genetic diagnosis and highlights its usefulness for rapid and comprehensive genetic testing in the clinical setting. This method will also expand our knowledge of the genetic and clinical spectra of leukoencephalopathy.
Collapse
|
33
|
Wan J, Song L, Wu Y, Brzoska P, Keys D, Chen C, Valliyodan B, Shannon JG, Nguyen HT. Application of Digital PCR in the Analysis of Transgenic Soybean Plants. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.710039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|