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Changtor P, Gupta YM, Yimtragool N. Optimization and application of loop-mediated isothermal amplification technique for sex identification in red-whiskered bulbul ( Pycnonotus jocosus). Ecol Evol 2022; 12:e9401. [PMID: 36225838 PMCID: PMC9534725 DOI: 10.1002/ece3.9401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022] Open
Abstract
The red‐whiskered bulbul (Pycnonotus jocosus) is a popular avian species in Thailand and many other countries. The red‐whiskered bulbul has a high economic value, but breeding is challenging since sex identification is difficult. The PCR method is now used for sex identification. However, PCR amplification and post‐PCR analysis necessitate the use of a laboratory equipped with specialized scientific instruments, which is inconvenient for field operations. This research describes a method for amplification of DNA samples using the loop‐mediated isothermal amplification (LAMP) approach, which is a molecular biology methodology for isothermal amplification that is extremely sensitive, fast, and easy for post‐LAMP product visualization. Herein, total of 23 blood samples were collected and DNA was extracted. Two sets of LAMP primers were designed for CHD‐Z and CHD‐W genes. The colorimetric assay was used to investigate the best conditions for LAMP reactions and post‐LAMP product visualization. LAMP reactions for sex identification were compared to traditional PCR in terms of sensitivity and specificity. LAMP reactions were found to be 10‐fold more sensitive than PCR at 1 ng of DNA. When compared to electrophoresis analysis, the visualization with colorimetric assay using GelRed® and SYTO™ 9 was 100% accurate. The optimal LAMP condition tested simple DNA extracted from bird feathers using the HotSHOT technique. The result showed that the optimal condition could distinguish the sex of red‐whiskered bulbuls totally and accurately. A powerful method for red‐whiskered bulbul sex identification is demonstrated in this study, which can be used in field studies because it is quick and easy to perform, has high sensitivity, and does not require advanced scientific equipment.
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Affiliation(s)
- Phanupong Changtor
- Department of Biology, Faculty of ScienceNaresuan UniversityPhitsanulokThailand
| | - Yash Munnalal Gupta
- Department of Biology, Faculty of ScienceNaresuan UniversityPhitsanulokThailand
| | - Nonglak Yimtragool
- Department of Biology, Faculty of ScienceNaresuan UniversityPhitsanulokThailand
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Cao G, Xiong Y, Nie F, Chen X, Peng L, Li Y, Yang M, Huo D, Hou C. Non-nucleic acid extraction and ultra-sensitive detection of African swine fever virus via CRISPR/Cas12a. Appl Microbiol Biotechnol 2022; 106:4695-4704. [PMID: 35715648 DOI: 10.1007/s00253-022-11999-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 12/26/2022]
Abstract
Early diagnosis of the African swine fever virus (ASFV) is the main preventive measure for ASFV. Here, we developed a fluorescent biosensor and lateral flow assay (LFA) strip based on direct PCR combined with CRISPR/Cas12a system for ASF. Direct PCR can simultaneously split samples and efficiently amplify without sacrificing sensitivity, which eliminated the steps of nucleic acid extraction. Furthermore, by the CRISPR/Cas12a, the biosensor addressed false positives caused by non-specific amplification and had high sensitivity with the actual limit of detection (LOD) of 7.6×10-4 ng·μL-1 (4 copies·μL-1). In addition, the strategy was built on the lateral flow assay (LFA) strip to achieve visual and portable detection for point-of-care testing. Moreover, the biosensor by a fluorometer and LFA strip showed a high accuracy to rival qPCR in actual sample detection. Therefore, the biosensor is an ultra-sensitive and specific tool that can replace traditional methods. KEY POINTS: • No nucleic acid extraction, direct PCR-simplified steps, and reduced time and cost • CRISPR/Cas12a solved the false positives caused by nonspecific amplification • The combination of the LFA strip and biosensor is more convenient for POC detection.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Yifan Xiong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing, 400044, People's Republic of China
| | - Xiaolong Chen
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Lan Peng
- Chongqing Medical and Pharmaceutical College Basic Department, Chongqing, 401331, People's Republic of China
| | - Yingguo Li
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing, 400044, People's Republic of China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China. .,Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China.
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Lannutti L, Mira A, Basualdo M, Rodriguez G, Erler S, Silva V, Gisder S, Genersch E, Florin-Christensen M, Schnittger L. Development of a loop-mediated isothermal amplification (LAMP) and a direct LAMP for the specific detection of Nosema ceranae, a parasite of honey bees. Parasitol Res 2020; 119:3947-3956. [DOI: 10.1007/s00436-020-06915-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/29/2020] [Indexed: 02/08/2023]
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Martzy R, Kolm C, Krska R, Mach RL, Farnleitner AH, Reischer GH. Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis. Anal Bioanal Chem 2019; 411:1695-1702. [PMID: 30617408 PMCID: PMC6453865 DOI: 10.1007/s00216-018-1553-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 12/04/2022]
Abstract
Molecular diagnostic tools in the field of food and water quality analysis are becoming increasingly widespread. Usually, based on DNA amplification techniques such as polymerase chain reaction (PCR), these methods are highly sensitive and versatile but require well-equipped laboratories and trained personnel. To reduce analysis time and avoid expensive equipment, isothermal DNA amplification methods for detecting various target organisms have been developed. However, to make molecular diagnostics suitable for low-resource settings and in-field applications, it is crucial to continuously adapt the working steps associated with DNA amplification, namely sample preparation, DNA extraction, and visualization of the results. Many novel approaches have been evaluated in recent years to tackle these challenges, e.g., the use of ionic liquids for the rapid isolation of nucleic acids from organisms relevant for food and water analysis or the integration of entire analytical workflows on microfluidic chips. In any event, the future of applications in the field of isothermal amplification will probably lie in ready-to-use cartridges combined with affordable handheld devices for on-site analysis. This trend article aims to make prospective users more familiar with this technology and its potential for moving molecular diagnostics from the laboratory to the field. Graphical abstract ᅟ.
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Affiliation(s)
- Roland Martzy
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Claudia Kolm
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Rudolf Krska
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology (IFA-Tulln), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Queen's University Belfast, Institute for Global Food Security, School of Biological Sciences, Belfast, Northern Ireland, BT71NN, UK
| | - Robert L Mach
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Synthetic Biology and Molecular Biotechnology, 1060, Vienna, Austria
| | - Andreas H Farnleitner
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Research Unit Water Quality and Health, 3500, Krems, Austria
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria.
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria.
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