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Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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2
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Nai YH, Doeven EH, Guijt RM. An improved nucleic acid sequence-based amplification method mediated by T4 gene 32 protein. PLoS One 2022; 17:e0265391. [PMID: 35324960 PMCID: PMC8947125 DOI: 10.1371/journal.pone.0265391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/01/2022] [Indexed: 01/06/2023] Open
Abstract
The uptake of Nucleic Acid Sequence-Based Amplification (NASBA) for point of care testing may be hindered by a complexity in the workflow due the requirement of a thermal denaturation step to initiate the cyclic isothermal amplification before the addition of the amplification enzymes. Despite reports of successful enhancement of other DNA and RNA amplification methods using DNA and RNA binding proteins, this has not been reported for NASBA. Here, three single-stranded binding proteins, RecA, Extreme Thermostable Single-stranded binding protein (ET SSB) and T4 gene gp32 protein (gp32), were incorporated in NASBA protocol and used for single pot, one-step NASBA at 41 °C. Indeed, all SSBs showed significantly improved amplifications compared with the 2-step process, but only gp32 showed no non-specific aberrant amplification, and slightly improved the time-to-positivity in comparison with the conventional NASBA. For synthetic HIV-1 RNA, gp32 was found to improve the time-to-positivity (ttp) by average of 13.6% of one-step NASBA and 6.7% of conventional NASBA for the detection of HIV-1 RNA, showing its potential for simplifying the workflow as desirable for point of care applications of NASBA.
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Affiliation(s)
- Yi Heng Nai
- Centre for Regional and Rural Futures, Deakin University, Geelong, Victoria, Australia
- * E-mail: (YHN); (RMG)
| | - Egan H. Doeven
- Centre for Regional and Rural Futures, Deakin University, Geelong, Victoria, Australia
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures, Deakin University, Geelong, Victoria, Australia
- * E-mail: (YHN); (RMG)
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Zou Y, Mason MG, Botella JR. Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics. PLoS One 2020; 15:e0235216. [PMID: 32598374 PMCID: PMC7323990 DOI: 10.1371/journal.pone.0235216] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
A number of isothermal DNA amplification technologies claim to be ideal for point-of-need (PON) applications as they enable reactions to be performed using a single-temperature heat source (e.g. water bath). Thus, we examined several isothermal amplification methods focusing on simplicity, cost, sensitivity and reproducibility to identify the most suitable method(s) for low resource PON applications. A number of methods were found unsuitable as they either involved multiple temperature incubations, were relatively expensive or required relatively large amounts target DNA for amplification. Among the methods examined, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) were found to be the most suitable for PON applications as they are both single step methods that provide highly sensitive and reproducible amplifications. The speed of LAMP reactions was greatly enhanced, up to 76%, with the addition of loop primers while the presence of swarm primers and the sequestration of free magnesium ions with nucleotides also enhanced the amplification speed. In contrast, we were unable to enhance RPA's performance from the original published literature. While both RPA and LAMP have some drawbacks, either isothermal technology can reliably be used for on-site diagnostics with minimal equipment.
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Affiliation(s)
- Yiping Zou
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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Yang X, Qi YJ, Al-Attala MN, Gao ZH, Yi XK, Zhang AF, Zang HY, Gu CY, Gao TC, Chen Y. Rapid Detection of Alternaria Species Involved in Pear Black Spot Using Loop-Mediated Isothermal Amplification. Plant Dis 2019; 103:3002-3008. [PMID: 31573432 DOI: 10.1094/pdis-01-19-0149-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alternaria species are the most important fungal pathogens that attack various crops as well as fruit trees such as pear and cause black spot disease. Here, a loop-mediated isothermal amplification (LAMP) assay is developed for the detection of Alternaria species. A. alternata cytochrome b (cyt-b) gene was used to design two pairs of primers and amplified a 229-bp segment of Aacyt-b gene. The results showed that LAMP assay is faster and simpler than polymerase chain reaction (PCR). LAMP assay is highly sensitive method for the detection of about 1 pg of genomic DNA of A. alternata by using optimized concentration of MgCl2 (4 mM) in final LAMP reaction. In contrast, the limit of detection was 1 ng of target DNA via conventional PCR. Among the genomic DNA of 46 fungal species, only the tubes containing DNA of Alternaria spp. except A. porri, A. solani, and A. infectoria changed color from orange to yellowish green with SYBR Green I including the main pathogens of pear black spot. The yellowish green color was indicative of DNA amplification. Moreover, LAMP assay was used for testing infected tissues among 22 healthy and diseased pear tissues; the orange color changed to yellowish green for infected tissues only. Altogether, we conclude that cyt-b gene can be used for the detection of Alternaria spp. via LAMP assay, which is involved in pear black spot disease.
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Affiliation(s)
- Xue Yang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Yong-Jie Qi
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, China
| | - Mohamed N Al-Attala
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Plant Pathology Unit, Plant Protection Department, Desert Research Center, Cairo 11753, Egypt
| | - Zheng-Hui Gao
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, China
| | - Xing-Kai Yi
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, China
| | - Ai-Fang Zhang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Hao-Yu Zang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Tong-Chun Gao
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Yu Chen
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
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Sharafdarkolaee SH, Gill P, Motovali-Bashi M, Sharafdarkolaee FH. Isothermal Amplification Methods for the SNP Genotyping. Curr Mol Med 2019; 19:461-472. [PMID: 31131752 DOI: 10.2174/1566524019666190527083947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/30/2018] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
The demands for genotyping techniques with acceptable precision, accuracy, cost-effectiveness in high throughput formats made driving forces for continuous development of novel technologies. A wide range of mutation detection techniques based on polymerase chain reaction (PCR) have been introduced. The best alternatives were the isothermal amplification technologies that those did not require a thermal cycler. In this review, we aimed to describe the most known isothermal amplification techniques for SNP genotyping.
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Affiliation(s)
| | - Pooria Gill
- Nanomedicine Group, Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Motovali-Bashi
- Department of Genetics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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Fan Q, Xie Z, Xie Z, Xie L, Huang J, Zhang Y, Zeng T, Zhang M, Wan S, Luo S, Liu J, Deng X. Development of duplex fluorescence-based loop-mediated isothermal amplification assay for detection of Mycoplasma bovis and bovine herpes virus 1. J Virol Methods 2018; 261:132-138. [PMID: 30142375 DOI: 10.1016/j.jviromet.2018.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/03/2018] [Accepted: 08/20/2018] [Indexed: 12/16/2022]
Abstract
Mycoplasma bovis (MB) and bovine herpes virus 1 (BHV-1) are two important pathogens that cause bovine respiratory disease in the beef feedlot and dairy industries. The aim of this study was to develop and validate a duplex fluorescence-based loop-mediated isothermal amplification (DLAMP) assay for simultaneous detection of MB and BHV-1. Two sets of specific primers for each pathogen were designed to target the unique sequences of the MB uvrC gene and the BHV-1 gB gene. The inner primer for BHV-1 was synthesized with the fluorophore FAM at the 5' end to detect the BHV-1 gB gene, and the inner primer for MB was synthesized with the fluorophore CY5 at the 5' end to detect the MB uvrC gene. The DLAMP reaction conditions were optimized for rapid and specific detection of MB and BHV-1. The DLAMP assay developed here could specifically detect MB and BHV-1 without cross-reaction with other known non-target bovine pathogens. The sensitivity of this DLAMP assay was as low as 2 × 102 copies for recombinant plasmids containing the MB and BHV-1 target genes. In a detection test of 125 clinical samples, the positive rates for MB, BHV-1 and co-infection were 44.8%, 13.6% and 1.6%, respectively. Furthermore, the sensitivity and specificity of DLAMP were determined as 95%-96.6% and 100%, respectively, of those of field sample detection by the real-time polymerase chain reaction (PCR) assay recommended by the World Organisation for Animal Health. Overall, DLAMP provides a rapid, sensitive and specific assay for the identification of MB and BHV-1 in clinical specimens and for epidemiological surveillance.
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Affiliation(s)
- Qing Fan
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Zhixun Xie
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Zhiqin Xie
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Liji Xie
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Jiaoling Huang
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Yanfan Zhang
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Tingting Zeng
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Minxiu Zhang
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Sheng Wan
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Sisi Luo
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Jiabo Liu
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
| | - Xianwen Deng
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning 530001, PR China.
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Rivero R, Bisio M, Velázquez EB, Esteva MI, Scollo K, González NL, Altcheh J, Ruiz AM. Rapid detection of Trypanosoma cruzi by colorimetric loop-mediated isothermal amplification (LAMP): A potential novel tool for the detection of congenital Chagas infection. Diagn Microbiol Infect Dis 2017; 89:26-28. [DOI: 10.1016/j.diagmicrobio.2017.06.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/10/2017] [Accepted: 06/12/2017] [Indexed: 02/07/2023]
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Abstract
While DNA circuits are becoming increasingly useful as signal transducers, their utility is inhibited by their slow catalytic rate. Here, we demonstrate how RecA, a recombination enzyme that catalyzes sequence specific strand exchange, can be used to increase circuit rates up to 9-fold. We also show how the introduction of RNA into DNA circuits further controls the specificity of RecA strand exchange, improving signal-to-noise.
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Affiliation(s)
- J N Milligan
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway, Austin, TX, USA.
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