1
|
Ziaei Chamgordani S, Yadegar A, Ghourchian H. C. difficile biomarkers, pathogenicity and detection. Clin Chim Acta 2024; 558:119674. [PMID: 38621586 DOI: 10.1016/j.cca.2024.119674] [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: 02/04/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is the main etiologic agent of antibiotic-associated diarrhea. CDI contributes to gut inflammation and can lead to disruption of the intestinal epithelial barrier. Recently, the rate of CDI cases has been increased. Thus, early diagnosis of C. difficile is critical for controlling the infection and guiding efficacious therapy. APPROACH A search strategy was set up using the terms C. difficile biomarkers and diagnosis. The found references were classified into two general categories; conventional and advanced methods. RESULTS The pathogenicity and biomarkers of C. difficile, and the collection manners for CDI-suspected specimens were briefly explained. Then, the conventional CDI diagnostic methods were subtly compared in terms of duration, level of difficulty, sensitivity, advantages, and disadvantages. Thereafter, an extensive review of the various newly proposed techniques available for CDI detection was conducted including nucleic acid isothermal amplification-based methods, biosensors, and gene/single-molecule microarrays. Also, the detection mechanisms, pros and cons of these methods were highlighted and compared with each other. In addition, approximately complete information on FDA-approved platforms for CDI diagnosis was collected. CONCLUSION To overcome the deficiencies of conventional methods, the potential of advanced methods for C. difficile diagnosis, their direction, perspective, and challenges ahead were discussed.
Collapse
Affiliation(s)
- Sepideh Ziaei Chamgordani
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hedayatollah Ghourchian
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
| |
Collapse
|
2
|
Marti A, Huskens J. Au Nanoparticle-Based Amplified DNA Detection on Poly-l-lysine Monolayer-Functionalized Electrodes. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:242. [PMID: 35055260 PMCID: PMC8780787 DOI: 10.3390/nano12020242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 02/06/2023]
Abstract
Affinity sensing of nucleic acids is among the most investigated areas in biosensing due to the growing importance of DNA diagnostics in healthcare research and clinical applications. Here, we report a simple electrochemical DNA detection layer, based on poly-l-lysine (PLL), in combination with gold nanoparticles (AuNPs) as a signal amplifier. The layer shows excellent reduction of non-specific binding and thereby high contrast between amplified and non-amplified signals with functionalized AuNPs; the relative change in current was 10-fold compared to the non-amplified signal. The present work may provide a general method for the detection of tumor markers based on electrochemical DNA sensing.
Collapse
Affiliation(s)
| | - Jurriaan Huskens
- Department of Molecules & Materials, MESA+ Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands;
| |
Collapse
|
3
|
Devi S, Chu PY, Wu BH, Ho YP. Mass spectrometry combined with affinity probes for the identification of CP4 EPSPS in genetically modified soybeans. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4371. [PMID: 31077490 DOI: 10.1002/jms.4371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/12/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
Sample preparation methods used for genetically modified organisms (GMOs) analysis are often time consuming, require extensive manual manipulation, and result in limited amounts of purified protein, which may complicate the detection of low-abundance GM protein. A robust sample pretreatment method prior to mass spectrometry (MS) detection of the transgenic protein (5-enolpyruvylshikimate-3-phosphate synthase [CP4 EPSPS]) present in Roundup Ready soya is investigated. Liquid chromatography-multiple reaction monitoring tandem MS (nano LC-MS/MS-MRM) was used for the detection and quantification of CP4 EPSPS. Gold nanoparticles (AuNPs) and concanavalin A (Con A)-immobilized Sepharose 4B were used as selective probes for the separation of the major storage proteins in soybeans. AuNPs that enable the capture of cysteine-containing proteins were used to reduce the complexity of the crude extract of GM soya. Con A-sepharose was used for the affinity capture of β-conglycinin and other glycoproteins of soya prior to enzymatic digestion. The methods enabled the detection of unique peptides of CP4 EPSPS at a level as low as 0.5% of GM soya in MRM mode. Stable-isotope dimethyl labeling was further applied to the quantification of GM soya. Both probes exhibited high selectivity and efficiency for the affinity capture of storage proteins, leading to the quantitative detection at 0.5% GM soya, which is a level below the current European Union's threshold for food labeling. The square correlation coefficients were greater than 0.99. The approach for sample preparation is very simple without the need for time-consuming protein prefractionation or separation procedures and thus presents a significant improvement over existing methods for the analysis of the GM soya protein.
Collapse
Affiliation(s)
- Shobha Devi
- Department of Chemistry, Rajiv Gandhi University of Knowledge Technologies, Hyderabad, India
| | - Pei-Yu Chu
- Department of Chemistry, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Bo-Hung Wu
- Department of Chemistry, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien, 97401, Taiwan
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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]
|
6
|
Chen Y, Wang Z, Liu Y, Wang X, Li Y, Ma P, Gu B, Li H. Recent advances in rapid pathogen detection method based on biosensors. Eur J Clin Microbiol Infect Dis 2018; 37:1021-1037. [DOI: 10.1007/s10096-018-3230-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/12/2018] [Indexed: 12/28/2022]
|
7
|
|
8
|
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
|
9
|
Zhou D, Wang C, Li Z, Chen Y, Gao S, Guo J, Lu W, Su Y, Xu L, Que Y. Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay. FRONTIERS IN PLANT SCIENCE 2016; 7:279. [PMID: 27014303 PMCID: PMC4782128 DOI: 10.3389/fpls.2016.00279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP) assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg(2+), 6:1 ratio of inner vs. outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was 10-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100%) by LAMP and 97/100 cases (97%) by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable, and cost-effective for detection of the bar specific transgenic sugarcane.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of AgricultureFuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of AgricultureFuzhou, China
| |
Collapse
|
10
|
Fraiture MA, Herman P, Taverniers I, De Loose M, Deforce D, Roosens NH. Current and new approaches in GMO detection: challenges and solutions. BIOMED RESEARCH INTERNATIONAL 2015; 2015:392872. [PMID: 26550567 PMCID: PMC4624882 DOI: 10.1155/2015/392872] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/07/2015] [Indexed: 11/17/2022]
Abstract
In many countries, genetically modified organisms (GMO) legislations have been established in order to guarantee the traceability of food/feed products on the market and to protect the consumer freedom of choice. Therefore, several GMO detection strategies, mainly based on DNA, have been developed to implement these legislations. Due to its numerous advantages, the quantitative PCR (qPCR) is the method of choice for the enforcement laboratories in GMO routine analysis. However, given the increasing number and diversity of GMO developed and put on the market around the world, some technical hurdles could be encountered with the qPCR technology, mainly owing to its inherent properties. To address these challenges, alternative GMO detection methods have been developed, allowing faster detections of single GM target (e.g., loop-mediated isothermal amplification), simultaneous detections of multiple GM targets (e.g., PCR capillary gel electrophoresis, microarray, and Luminex), more accurate quantification of GM targets (e.g., digital PCR), or characterization of partially known (e.g., DNA walking and Next Generation Sequencing (NGS)) or unknown (e.g., NGS) GMO. The benefits and drawbacks of these methods are discussed in this review.
Collapse
Affiliation(s)
- Marie-Alice Fraiture
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Philippe Herman
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Isabel Taverniers
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
| | - Marc De Loose
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Nancy H. Roosens
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| |
Collapse
|
11
|
Moura-Melo S, Miranda-Castro R, de-Los-Santos-Álvarez N, Miranda-Ordieres AJ, Dos Santos Junior JR, da Silva Fonseca RA, Lobo-Castañón MJ. Targeting helicase-dependent amplification products with an electrochemical genosensor for reliable and sensitive screening of genetically modified organisms. Anal Chem 2015. [PMID: 26198403 DOI: 10.1021/acs.analchem.5b02271] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cultivation of genetically modified organisms (GMOs) and their use in food and feed is constantly expanding; thus, the question of informing consumers about their presence in food has proven of significant interest. The development of sensitive, rapid, robust, and reliable methods for the detection of GMOs is crucial for proper food labeling. In response, we have experimentally characterized the helicase-dependent isothermal amplification (HDA) and sequence-specific detection of a transgene from the Cauliflower Mosaic Virus 35S Promoter (CaMV35S), inserted into most transgenic plants. HDA is one of the simplest approaches for DNA amplification, emulating the bacterial replication machinery, and resembling PCR but under isothermal conditions. However, it usually suffers from a lack of selectivity, which is due to the accumulation of spurious amplification products. To improve the selectivity of HDA, which makes the detection of amplification products more reliable, we have developed an electrochemical platform targeting the central sequence of HDA copies of the transgene. A binary monolayer architecture is built onto a thin gold film where, upon the formation of perfect nucleic acid duplexes with the amplification products, these are enzyme-labeled and electrochemically transduced. The resulting combined system increases genosensor detectability up to 10(6)-fold, allowing Yes/No detection of GMOs with a limit of detection of ∼30 copies of the CaMV35S genomic DNA. A set of general utility rules in the design of genosensors for detection of HDA amplicons, which may assist in the development of point-of-care tests, is also included. The method provides a versatile tool for detecting nucleic acids with extremely low abundance not only for food safety control but also in the diagnostics and environmental control areas.
Collapse
Affiliation(s)
- Suely Moura-Melo
- †Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain.,‡Departamento de Química, Centro de Ciências da Natureza. Universidade Federal do Piauí, Teresina, 64049-550 PI, Brasil
| | - Rebeca Miranda-Castro
- †Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain
| | | | | | - J Ribeiro Dos Santos Junior
- ‡Departamento de Química, Centro de Ciências da Natureza. Universidade Federal do Piauí, Teresina, 64049-550 PI, Brasil
| | | | | |
Collapse
|
12
|
Electrochemical genosensors as innovative tools for detection of genetically modified organisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.10.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Jung JH, Park BH, Oh SJ, Choi G, Seo TS. Integration of reverse transcriptase loop-mediated isothermal amplification with an immunochromatographic strip on a centrifugal microdevice for influenza A virus identification. LAB ON A CHIP 2015; 15:718-25. [PMID: 25426967 DOI: 10.1039/c4lc01033g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A novel centrifugal microdevice which could perform reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and immunochromatographic strip (ICS) based amplicon detection was demonstrated for simple and cost-effective influenza A virus identification. The proposed centrifugal microdevice consists of the sample and running buffer loading reservoirs, the RT-LAMP chamber, and the ICS for detecting gene expression. The entire process could be completed sequentially and automatically by simply controlling the rotation speed and by optimizing the microfluidic design. Monoplex and multiplex RT-LAMP reactions targeting H1 and/or M gene were executed at 66 °C for 40 min, and the resultant amplicons were successfully analysed on the ICS within 15 min. Influenza A H1N1 virus was subtyped by detecting H1 and M gene on the ICS even with 10 copies of viral RNAs. Highly specific and multiplex viral typing of the integrated RT-LAMP-ICS microdevice was also demonstrated. The combination of the rapid isothermal amplification with the simple colorimetric detection on a strip in a single centrifugal microdevice will provide an advanced genetic analysis platform in the field of on-site pathogen diagnostics.
Collapse
Affiliation(s)
- J H Jung
- Department of Chemical and Biomolecular Engineering (BK21 Plus program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | | | | | | | | |
Collapse
|
14
|
Li J, Macdonald J. Advances in isothermal amplification: novel strategies inspired by biological processes. Biosens Bioelectron 2015; 64:196-211. [DOI: 10.1016/j.bios.2014.08.069] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 01/02/2023]
|
15
|
Jung JH, Park BH, Oh SJ, Choi G, Seo TS. Integrated centrifugal reverse transcriptase loop-mediated isothermal amplification microdevice for influenza A virus detection. Biosens Bioelectron 2014; 68:218-224. [PMID: 25569879 PMCID: PMC7111304 DOI: 10.1016/j.bios.2014.12.043] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/12/2014] [Accepted: 12/20/2014] [Indexed: 11/29/2022]
Abstract
An integrated reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) microdevice which consists of microbead-assisted RNA purification and RT-LAMP with real-time monitoring by a miniaturized optical detector was demonstrated. The integrated RT-LAMP microdevice includes four reservoirs for a viral RNA sample (purified influenza A viral RNA or lysates), a washing solution (70% ethanol), an elution solution (RNase-free water), and an RT-LAMP cocktail, and two chambers (a waste chamber and an RT-LAMP reaction chamber). The separate reservoirs for a washing solution, an elution solution, and an RT-LAMP cocktail were designed with capillary valves for stable storage. Three influenza A virus strains (A/H1N1, A/H3N2, and A/H5N1) were used for RNA templates, and RT-LAMP primer sets were designed to detect hemagglutinin (HA) and conserved M gene. Sequential sample flow to the microbeads for RNA purification was achieved by centrifugal force with optimization of capillary valves and a siphon channel. Furthermore, the purified RNA solution was successfully isolated from the waste solution by changing the rotational direction, and combined with the RT-LAMP cocktail in the RT-LAMP reaction chamber for target gene amplification. Total process from the sample injection to the result was completed in 47 min. Influenza A H1N1 virus was confirmed on the integrated RT-LAMP microdevice even with 10 copies of viral RNAs, which revealed 10-fold higher sensitivity than that of a conventional RT-PCR. Subtyping and specificity test of influenza A H1N1 viral lysates were also performed and clinical samples were successfully genotyped to confirm influenza A virus on our proposed integrated microdevice. An integrated microdevice cosistng of RNA purification and RT-LAMP with real-time monitoring was demonstrated. Sequential sample transportation and purified RNA separation were automatically controlled by centrifugal force and optimized microchannels. Influenza viruses were isothermally amplified and the products were identified by using a miniaturized fluorescence detector. Limit of detection for influenza A H1N1 was 10 copies. Clinical samples were successfully analyzed on the microdevice.
Collapse
Affiliation(s)
- Jae Hwan Jung
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Byung Hyun Park
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Seung Jun Oh
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Goro Choi
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| |
Collapse
|
16
|
Characterization and study of transgenic cultivars by capillary and microchip electrophoresis. Int J Mol Sci 2014; 15:23851-77. [PMID: 25535077 PMCID: PMC4284794 DOI: 10.3390/ijms151223851] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 01/11/2023] Open
Abstract
Advances in biotechnology have increased the demand for suitable analytical techniques for the analysis of genetically modified organisms. Study of the substantial equivalence, discrimination between transgenic and non-transgenic cultivars, study of the unintended effects caused by a genetic modification or their response to diverse situations or stress conditions (e.g., environmental, climatic, infections) are some of the concerns that need to be addressed. Capillary electrophoresis (CE) is emerging as an alternative to conventional techniques for the study and characterization of genetically modified organisms. This article reviews the most recent applications of CE for the analysis and characterization of transgenic cultivars in the last five years. Different strategies have been described depending on the level analyzed (DNA, proteins or metabolites). Capillary gel electrophoresis (CGE) has shown to be particularly useful for the analysis of DNA fragments amplified by PCR. Metabolites and proteins have been mainly separated using capillary zone electrophoresis (CZE) using UV and MS detection. Electrophoretic chips have also proven their ability in the analysis of transgenic cultivars and a section describing the new applications is also included.
Collapse
|
17
|
Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1. PLoS One 2014; 9:e113693. [PMID: 25426953 PMCID: PMC4245218 DOI: 10.1371/journal.pone.0113693] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022] Open
Abstract
In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens.
Collapse
|
18
|
Chang PC, Reddy PM, Ho YP. Quantification of genetically modified soya using strong anion exchange chromatography and time-of-flight mass spectrometry. Anal Bioanal Chem 2014; 406:5339-46. [PMID: 24969465 DOI: 10.1007/s00216-014-7965-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/04/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
Abstract
Stable-isotope dimethyl labeling was applied to the quantification of genetically modified (GM) soya. The herbicide-resistant gene-related protein 5-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) was labeled using a dimethyl labeling reagent, formaldehyde-H2 or -D2. The identification and quantification of CP4 EPSPS was performed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The CP4 EPSPS protein was separated from high abundance proteins using strong anion exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Then, the tryptic peptides from the samples and reference were labeled with formaldehyde-H2 and formaldehyde-D2, respectively. The two labeled pools were mixed and analyzed using MALDI-MS. The data showed a good correlation between the peak ratio of the H- and D-labeled peptides and the GM soya percentages at 0.5, 1, 3, and 5 %, with R (2) of 0.99. The labeling reagents are readily available. The labeling experiments and the detection procedures are simple. The approach is useful for the quantification of GM soya at a level as low as 0.5 %.
Collapse
Affiliation(s)
- Po-Chih Chang
- Department of Chemistry, National Dong Hwa University, Hualien, 97401, Taiwan, Republic of China
| | | | | |
Collapse
|
19
|
Zhou D, Guo J, Xu L, Gao S, Lin Q, Wu Q, Wu L, Que Y. Establishment and application of a loop-mediated isothermal amplification (LAMP) system for detection of cry1Ac transgenic sugarcane. Sci Rep 2014; 4:4912. [PMID: 24810230 PMCID: PMC4014978 DOI: 10.1038/srep04912] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/14/2014] [Indexed: 11/22/2022] Open
Abstract
To meet the demand for detection of foreign genes in genetically modified (GM) sugarcane necessary for regulation of gene technology, an efficient method with high specificity and rapidity was developed for the cry1Ac gene, based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed using the sequence of cry1Ac along with optimized reaction conditions: 5.25 mM of Mg(2+), 4:1 ratio of inner primer to outer primer, 2.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. Three post-LAMP detection methods (precipitation, calcein (0.60 mM) with Mn(2+) (0.05 mM) complex and SYBR Green I visualization), were shown to be effective. The sensitivity of the LAMP method was tenfold higher than that of conventional PCR when using templates of the recombinant cry1Ac plasmid or genomic DNA from cry1Ac transgenic sugarcane plants. More importantly, this system allowed detection of the foreign gene on-site when screening GM sugarcane without complex and expensive instruments, using the naked eye. This method can not only provide technological support for detection of cry1Ac, but can also further facilitate the use of this detection technique for other transgenes in GM sugarcane.
Collapse
Affiliation(s)
- Dinggang Zhou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Qingliang Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Luguang Wu
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| |
Collapse
|
20
|
Mares P, Pokorna TJ, Sochor J, Zeman L, Baron M, Mlcek J, Balla S. The influence of feeding GMO-peas on growth of animal models. POTRAVINARSTVO 2014. [DOI: 10.5219/322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction of genetically modified (GM) food or feed into the commercial sale represents a very complicated process. One of the most important steps in approval process is the evaluation of all risks on the health status of people and animal models. Within our project the genetically modified peas was breeded that showed significant resistance against Pea seed-borne mosaic virus and Pea enation mosaic virus. Preclinical studies have been conducted to found out the effect of GMO peas on animals - rats of outbreeding line Wistar. In a total, 24 male, specific pathogen free Wistar rats were used in the experiment. At the beginning of the experiment, the animals were 28 days old. The three experimental groups with 8 individuals were created. The first group of rats was fed with GMO peas, the second group of rats consumed mix of pea cultivar Raman and the third group was control without pea addition (wheat and soya were used instead of pea). In the present study we focused our attention on health, growth and utility features of rats fed with GM pea. All characteristic were observed during the experiment lasting 35 days. Consumed feed was weighted daily and the weight of the animals was measured every seven days. The average values were compared within the groups. The aim of the experiment was to verify if resistant lines of pea influence the weight growth of animal models. The results of our experiment showed that even a high concentration (30% of GM pea) did not influence growth rate of rats to compare with both rats fed with pea of Raman cultivar and control group. We did not observe any health problems of animal models during the experiment.
Collapse
|
21
|
Non-coding RNAs in crop genetic modification: considerations and predictable environmental risk assessments (ERA). Mol Biotechnol 2014; 55:87-100. [PMID: 23381873 DOI: 10.1007/s12033-013-9648-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Of late non-coding RNAs (ncRNAs)-mediated gene silencing is an influential tool deliberately deployed to negatively regulate the expression of targeted genes. In addition to the widely employed small interfering RNA (siRNA)-mediated gene silencing approach, other variants like artificial miRNA (amiRNA), miRNA mimics, and artificial transacting siRNAs (tasiRNAs) are being explored and successfully deployed in developing non-coding RNA-based genetically modified plants. The ncRNA-based gene manipulations are typified with mobile nature of silencing signals, interference from viral genome-derived suppressor proteins, and an obligation for meticulous computational analysis to prevaricate any inadvertent effects. In a broad sense, risk assessment inquiries for genetically modified plants based on the expression of ncRNAs are competently addressed by the environmental risk assessment (ERA) models, currently in vogue, designed for the first generation transgenic plants which are based on the expression of heterologous proteins. Nevertheless, transgenic plants functioning on the foundation of ncRNAs warrant due attention with respect to their unique attributes like off-target or non-target gene silencing effects, small RNAs (sRNAs) persistence, food and feed safety assessments, problems in detection and tracking of sRNAs in food, impact of ncRNAs in plant protection measures, effect of mutations etc. The role of recent developments in sequencing techniques like next generation sequencing (NGS) and the ERA paradigm of the different countries in vogue are also discussed in the context of ncRNA-based gene manipulations.
Collapse
|
22
|
|
23
|
Kiddle G, Hardinge P, Buttigieg N, Gandelman O, Pereira C, McElgunn CJ, Rizzoli M, Jackson R, Appleton N, Moore C, Tisi LC, Murray JAH. GMO detection using a bioluminescent real time reporter (BART) of loop mediated isothermal amplification (LAMP) suitable for field use. BMC Biotechnol 2012; 12:15. [PMID: 22546148 PMCID: PMC3388468 DOI: 10.1186/1472-6750-12-15] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 04/30/2012] [Indexed: 11/12/2022] Open
Abstract
Background There is an increasing need for quantitative technologies suitable for molecular detection in a variety of settings for applications including food traceability and monitoring of genetically modified (GM) crops and their products through the food processing chain. Conventional molecular diagnostics utilising real-time polymerase chain reaction (RT-PCR) and fluorescence-based determination of amplification require temperature cycling and relatively complex optics. In contrast, isothermal amplification coupled to a bioluminescent output produced in real-time (BART) occurs at a constant temperature and only requires a simple light detection and integration device. Results Loop mediated isothermal amplification (LAMP) shows robustness to sample-derived inhibitors. Here we show the applicability of coupled LAMP and BART reactions (LAMP-BART) for determination of genetically modified (GM) maize target DNA at low levels of contamination (0.1-5.0% GM) using certified reference material, and compare this to RT-PCR. Results show that conventional DNA extraction methods developed for PCR may not be optimal for LAMP-BART quantification. Additionally, we demonstrate that LAMP is more tolerant to plant sample-derived inhibitors, and show this can be exploited to develop rapid extraction techniques suitable for simple field-based qualitative tests for GM status determination. We also assess the effect of total DNA assay load on LAMP-BART quantitation. Conclusions LAMP-BART is an effective and sensitive technique for GM detection with significant potential for quantification even at low levels of contamination and in samples derived from crops such as maize with a large genome size. The resilience of LAMP-BART to acidic polysaccharides makes it well suited to rapid sample preparation techniques and hence to both high throughput laboratory settings and to portable GM detection applications. The impact of the plant sample matrix and genome loading within a reaction must be controlled to ensure quantification at low target concentrations.
Collapse
Affiliation(s)
- Guy Kiddle
- Lumora Ltd, Bartholomew Walk, Cambridgeshire Business Park, Ely, Cambridgeshire CB7 4EA, UK.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Ujhelyi G, Dijk JPV, Prins TW, Voorhuijzen MM, Hoef AMAV, Beenen HG, Morisset D, Gruden K, Kok EJ. Comparison and transfer testing of multiplex ligation detection methods for GM plants. BMC Biotechnol 2012; 12:4. [PMID: 22257760 PMCID: PMC3271032 DOI: 10.1186/1472-6750-12-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 01/19/2012] [Indexed: 11/30/2022] Open
Abstract
Background With the increasing number of GMOs on the global market the maintenance of European GMO regulations is becoming more complex. For the analysis of a single food or feed sample it is necessary to assess the sample for the presence of many GMO-targets simultaneously at a sensitive level. Several methods have been published regarding DNA-based multidetection. Multiplex ligation detection methods have been described that use the same basic approach: i) hybridisation and ligation of specific probes, ii) amplification of the ligated probes and iii) detection and identification of the amplified products. Despite they all have this same basis, the published ligation methods differ radically. The present study investigated with real-time PCR whether these different ligation methods have any influence on the performance of the probes. Sensitivity and the specificity of the padlock probes (PLPs) with the ligation protocol with the best performance were also tested and the selected method was initially validated in a laboratory exchange study. Results Of the ligation protocols tested in this study, the best results were obtained with the PPLMD I and PPLMD II protocols and no consistent differences between these two protocols were observed. Both protocols are based on padlock probe ligation combined with microarray detection. Twenty PLPs were tested for specificity and the best probes were subjected to further evaluation. Up to 13 targets were detected specifically and simultaneously. During the interlaboratory exchange study similar results were achieved by the two participating institutes (NIB, Slovenia, and RIKILT, the Netherlands). Conclusions From the comparison of ligation protocols it can be concluded that two protocols perform equally well on the basis of the selected set of PLPs. Using the most ideal parameters the multiplicity of one of the methods was tested and 13 targets were successfully and specifically detected. In the interlaboratory exchange study it was shown that the selected method meets the 0.1% sensitivity criterion. The present study thus shows that specific and sensitive multidetection of GMO targets is now feasible.
Collapse
Affiliation(s)
- Gabriella Ujhelyi
- RIKILT-Institute of Food Safety (WUR), Akkermaalsbos 2, 6708 WB Wageningen, the Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
|
26
|
LaBarre P, Hawkins KR, Gerlach J, Wilmoth J, Beddoe A, Singleton J, Boyle D, Weigl B. A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings. PLoS One 2011; 6:e19738. [PMID: 21573065 PMCID: PMC3090398 DOI: 10.1371/journal.pone.0019738] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 04/14/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Molecular assays targeted to nucleic acid (NA) markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS) where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR) instrumentation (another is sample preparation). METHODOLOGY/PRINCIPAL FINDINGS In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented. CONCLUSIONS/SIGNIFICANCE We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA) heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes.
Collapse
Affiliation(s)
- Paul LaBarre
- PATH, Seattle, Washington, United States of America.
| | | | | | | | | | | | | | | |
Collapse
|
27
|
García-Cañas V, Simó C, León C, Ibáñez E, Cifuentes A. MS-based analytical methodologies to characterize genetically modified crops. MASS SPECTROMETRY REVIEWS 2011; 30:396-416. [PMID: 21500243 DOI: 10.1002/mas.20286] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 11/18/2009] [Accepted: 11/18/2009] [Indexed: 05/09/2023]
Abstract
The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart.
Collapse
Affiliation(s)
- Virginia García-Cañas
- Institute of Industrial Fermentations (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | | | | | | |
Collapse
|
28
|
Asiello PJ, Baeumner AJ. Miniaturized isothermal nucleic acid amplification, a review. LAB ON A CHIP 2011; 11:1420-30. [PMID: 21387067 DOI: 10.1039/c0lc00666a] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.
Collapse
Affiliation(s)
- Peter J Asiello
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | | |
Collapse
|
29
|
García-Cañas V, Mondello M, Cifuentes A. Simultaneous detection of genetically modified organisms by multiplex ligation-dependent genome amplification and capillary gel electrophoresis with laser-induced fluorescence. Electrophoresis 2010; 31:2249-59. [PMID: 20593401 DOI: 10.1002/elps.201000078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this work, an innovative method useful to simultaneously analyze multiple genetically modified organisms is described. The developed method consists in the combination of multiplex ligation-dependent genome dependent amplification (MLGA) with CGE and LIF detection using bare-fused silica capillaries. The MLGA process is based on oligonucleotide constructs, formed by a universal sequence (vector) and long specific oligonucleotides (selectors) that facilitate the circularization of specific DNA target regions. Subsequently, the circularized target sequences are simultaneously amplified with the same couple of primers and analyzed by CGE-LIF using a bare-fused silica capillary and a run electrolyte containing 2-hydroxyethyl cellulose acting as both sieving matrix and dynamic capillary coating. CGE-LIF is shown to be very useful and informative for optimizing MLGA parameters such as annealing temperature, number of ligation cycles, and selector probes concentration. We demonstrate the specificity of the method in detecting the presence of transgenic DNA in certified reference and raw commercial samples. The method developed is sensitive and allows the simultaneous detection in a single run of percentages of transgenic maize as low as 1% of GA21, 1% of MON863, and 1% of MON810 in maize samples with signal-to-noise ratios for the corresponding DNA peaks of 15, 12, and 26, respectively. These results demonstrate, to our knowledge for the first time, the great possibilities of MLGA techniques for genetically modified organisms analysis.
Collapse
Affiliation(s)
- Virginia García-Cañas
- Department of Food Analysis, Institute of Industrial Fermentations (CSIC), Madrid, Spain
| | | | | |
Collapse
|
30
|
New approaches in GMO detection. Anal Bioanal Chem 2009; 396:1991-2002. [DOI: 10.1007/s00216-009-3237-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/09/2009] [Accepted: 10/13/2009] [Indexed: 01/31/2023]
|
31
|
NAIMA as a solution for future GMO diagnostics challenges. Anal Bioanal Chem 2009; 396:2229-33. [DOI: 10.1007/s00216-009-3197-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 09/23/2009] [Accepted: 09/26/2009] [Indexed: 01/26/2023]
|
32
|
Holck AL, Drømtorp SM, Heir E. Quantitative, multiplex ligation-dependent probe amplification for the determination of eight genetically modified maize events. Eur Food Res Technol 2009. [DOI: 10.1007/s00217-009-1155-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
33
|
Holst-Jensen A. Testing for genetically modified organisms (GMOs): Past, present and future perspectives. Biotechnol Adv 2009; 27:1071-1082. [PMID: 19477261 DOI: 10.1016/j.biotechadv.2009.05.025] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This paper presents an overview of GMO testing methodologies and how these have evolved and may evolve in the next decade. Challenges and limitations for the application of the test methods as well as to the interpretation of results produced with the methods are highlighted and discussed, bearing in mind the various interests and competences of the involved stakeholders. To better understand the suitability and limitations of detection methodologies the evolution of transformation processes for creation of GMOs is briefly reviewed.
Collapse
Affiliation(s)
- Arne Holst-Jensen
- Department of Feed and Food Safety, National Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
| |
Collapse
|
34
|
Prins TW, van Dijk JP, Beenen HG, Van Hoef AMA, Voorhuijzen MM, Schoen CD, Aarts HJM, Kok EJ. Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction. BMC Genomics 2008; 9:584. [PMID: 19055784 PMCID: PMC2631584 DOI: 10.1186/1471-2164-9-584] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/04/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND To maintain EU GMO regulations, producers of new GM crop varieties need to supply an event-specific method for the new variety. As a result methods are nowadays available for EU-authorised genetically modified organisms (GMOs), but only to a limited extent for EU-non-authorised GMOs (NAGs). In the last decade the diversity of genetically modified (GM) ingredients in food and feed has increased significantly. As a result of this increase GMO laboratories currently need to apply many different methods to establish to potential presence of NAGs in raw materials and complex derived products. RESULTS In this paper we present an innovative method for detecting (approved) GMOs as well as the potential presence of NAGs in complex DNA samples containing different crop species. An optimised protocol has been developed for padlock probe ligation in combination with microarray detection (PPLMD) that can easily be scaled up. Linear padlock probes targeted against GMO-events, -elements and -species have been developed that can hybridise to their genomic target DNA and are visualised using microarray hybridisation.In a tenplex PPLMD experiment, different genomic targets in Roundup-Ready soya, MON1445 cotton and Bt176 maize were detected down to at least 1%. In single experiments, the targets were detected down to 0.1%, i.e. comparable to standard qPCR. CONCLUSION Compared to currently available methods this is a significant step forward towards multiplex detection in complex raw materials and derived products. It is shown that the PPLMD approach is suitable for large-scale detection of GMOs in real-life samples and provides the possibility to detect and/or identify NAGs that would otherwise remain undetected.
Collapse
Affiliation(s)
- Theo W Prins
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Jeroen P van Dijk
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Henriek G Beenen
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - AM Angeline Van Hoef
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Marleen M Voorhuijzen
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Cor D Schoen
- Plant Research International BV (WUR), Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Henk JM Aarts
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Esther J Kok
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| |
Collapse
|
35
|
Dobnik D, Morisset D, Gruden K. NASBA integrated multiplex amplification: A new method for multiplex and quantitative GMO detection. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
36
|
Morisset D, Dobnik D, Likar T, Gruden K. Application of NAIMA-MA for fast high throughput and quantitative GMO detection. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|