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Wang L, Chen X, Pan F, Yao G, Chen J. Development of a rapid detection method for Karenia mikimotoi by using CRISPR-Cas12a. Front Microbiol 2023; 14:1205765. [PMID: 37608945 PMCID: PMC10440436 DOI: 10.3389/fmicb.2023.1205765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
Harmful algal blooms (HABs), mainly formed by dinoflagellates, have detrimental effects on marine ecosystems and public health. Therefore, detecting HABs is crucial for early warning and prevention of HABs as well as the mitigation of their adverse effects. Although various methods, such as light microscopy, electron microscopy, real-time PCR, and microarrays, have already been established for the detection of HABs, they are still cumbersome to be exploited in the field. Therefore, rapid nucleic detection methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP)-lateral flow dipstick (LFD) have been developed for monitoring bloom-forming algae. However, the CRISPR/Cas-based detection of HABs has yet to be applied to this field. In this study, we developed a method for detecting Karenia mikimotoi (K. mikimotoi), a typical ichthyotoxic dinoflagellate responsible for global blooms. Our method utilized Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) to target and cleave the internal transcribed spacer (ITS) of K. mikimotoi, guided by RNA. We leveraged the target-activated non-specific single-stranded deoxyribonuclease cleavage activity of LbCas12a to generate signals that can be detected using fluorescence-read machines or LFDs. By combining RPA and LbCas12a with reporters, we significantly enhanced the sensitivity, enabling the detection of ITS-harboring plasmids at concentrations as low as 9.8 aM and genomic DNA of K. mikimotoi at levels as low as 3.6 × 10-5 ng/μl. Moreover, we simplified the genomic DNA extraction method using cellulose filter paper (CFP) by directly eluting the DNA into RPA reactions, reducing the extraction time to < 30 s. The entire process, from genomic DNA extraction to result reporting, takes less than an hour, enabling the identification of nearly a single cell. In conclusion, our method provided an easy, specific, and sensitive approach for detecting K. mikimotoi, offering the potential for efficient monitoring and management of K. mikimotoi blooms.
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Affiliation(s)
- Lu Wang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoyao Chen
- Fishery Resources Monitoring Center of Fujian Province, Fuzhou, China
| | - Feifei Pan
- Fishery Resources Monitoring Center of Fujian Province, Fuzhou, China
| | - Guangshan Yao
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Jianming Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
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2
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Park JW. Principles and Applications of Loop-Mediated Isothermal Amplification to Point-of-Care Tests. BIOSENSORS 2022; 12:bios12100857. [PMID: 36290994 PMCID: PMC9599884 DOI: 10.3390/bios12100857] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 05/03/2023]
Abstract
For the identification of nucleic acids, which are important biomarkers of pathogen-mediated diseases and viruses, the gold standard for NA-based diagnostic applications is polymerase chain reaction (PCR). However, the requirements of PCR limit its application as a rapid point-of-care diagnostic technique. To address the challenges associated with regular PCR, many isothermal amplification methods have been developed to accurately detect NAs. Isothermal amplification methods enable NA amplification without changes in temperature with simple devices, as well as faster amplification times compared with regular PCR. Of the isothermal amplifications, loop-mediated isothermal amplification (LAMP) is the most studied because it amplifies NAs rapidly and specifically. This review describes the principles of LAMP, the methods used to monitor the process of LAMP, and examples of biosensors that detect the amplicons of LAMP. In addition, current trends in the application of LAMP to smartphones and self-diagnosis systems for point-of-care tests are also discussed.
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Affiliation(s)
- Jee-Woong Park
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Korea
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3
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Qi L, Du Y. Diagnosis of disease relevant nucleic acid biomarkers with off-the-shelf devices. J Mater Chem B 2022; 10:3959-3973. [PMID: 35575030 DOI: 10.1039/d2tb00232a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Changes in the level of nucleic acids in blood may be correlated with some clinical disorders like cancer, stroke, trauma and autoimmune diseases, and thus, nucleic acids can serve as potential biomarkers for pathological processes. The requirement of technical equipment and operator expertise in effective information readout of modern molecular diagnostic technologies significantly restricted application outside clinical laboratories. The ability to detect nucleic acid biomarkers with off-the-shelf devices, which have the advantages of portability, simplicity, low cost and short response time, is critical to provide a prompt clinical result in circumstances where the laboratory instruments are not available. This review throws light on the current strategies and challenges for nucleic acid diagnosis with commercial portable devices, indicating the future prospect of portable diagnostic devices and making a great difference in improving the healthcare and disease surveillance in resource-limited areas.
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Affiliation(s)
- Lijuan Qi
- State key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, P. R. China. .,Department of Chemistry, University of Science and Technology of China, Anhui, P. R. China
| | - Yan Du
- State key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, P. R. China. .,Department of Chemistry, University of Science and Technology of China, Anhui, P. R. China
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Han X, Zhao T, Yan T, Yu R. Rapid and sensitive detection of Karenia mikimotoi by loop-mediated isothermal amplification combined with a lateral flow dipstick. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:24696-24703. [PMID: 34837104 DOI: 10.1007/s11356-021-17536-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Harmful algal blooms frequently occur in various coastal regions worldwide, deteriorating marine ecology and causing huge economic losses. Therefore, developing a potential method for rapid detection of harmful algae species is highly necessitated. In this study, a loop-mediated isothermal amplification (LAMP) method coupled with a lateral flow dipstick (LFD) was developed for detecting the harmful algae Karenia mikimotoi. In this method, the internal transcribed spacer (ITS) sequence of K. mikimotoi was used as the template, and the corresponding specific primers were designed by the online software PrimerExplorer V5. Biotin was labeled on the 5' end of forward inner primer (FIP), and the LAMP reaction was performed under the determined optimal conditions of 63℃ and 60 min. The lowest concentration of K. mikimotoi DNA tested using LAMP was 3.3 × 10-1 pg/μL. Additionally, a 6-FAM-labeled probe was designed and displayed on the LFD after hybridization of the amplified product with the probe. The results demonstrated that LAMP-LFD could be a promising approach for detecting and monitoring harmful algae due to its high sensitivity and specificity.
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Affiliation(s)
- Xiaotian Han
- Changjiang River Estuary Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, China.
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266100, China.
| | | | - Tian Yan
- Changjiang River Estuary Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266100, China
| | - Rencheng Yu
- Changjiang River Estuary Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266100, China
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Toldrà A, O'Sullivan CK, Diogène J, Campàs M. Detecting harmful algal blooms with nucleic acid amplification-based biotechnological tools. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141605. [PMID: 32827817 DOI: 10.1016/j.scitotenv.2020.141605] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
Harmful algal blooms (HABs) represent a growing threat to aquatic ecosystems and humans. Effective HAB management and mitigation efforts strongly rely on the availability of timely and in-situ tools for the detection of microalgae. In this sense, nucleic acid-based (molecular) methods are being considered for the unequivocal identification of microalgae as an attractive alternative to the currently used time-consuming and laboratory-based light microscopy techniques. This review provides an overview of the progress made on new molecular biotechnological tools for microalgal detection, particularly focusing on those that combine a nucleic acid (DNA or RNA) amplification step with detection. Different types of amplification processes (thermal and isothermal) and detection formats (e.g. microarrays, biosensors, lateral flows) are presented, and a comprehensive overview of their advantages and limitations is provided Although isothermal techniques are an attractive alternative to thermal amplification to reach in-situ analysis, further development is still required. Finally, current challenges, critical steps and future directions of the whole analysis process (from sample procurement to in-situ implementation) are described.
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Affiliation(s)
- Anna Toldrà
- IRTA, Ctra. Poble Nou km 5.5, 43540 Sant Carles de la Ràpita, Tarragona, Spain; Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56, 10044 Stockholm, Sweden.
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Jorge Diogène
- IRTA, Ctra. Poble Nou km 5.5, 43540 Sant Carles de la Ràpita, Tarragona, Spain
| | - Mònica Campàs
- IRTA, Ctra. Poble Nou km 5.5, 43540 Sant Carles de la Ràpita, Tarragona, Spain
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Yersinia pestis detection using biotinylated dNTPs for signal enhancement in lateral flow assays. Anal Chim Acta 2020; 1112:54-61. [PMID: 32334682 DOI: 10.1016/j.aca.2020.03.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/01/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022]
Abstract
Due to the extreme infectivity of Yersinia pestis it poses a serious threat as a potential biowarfare agent, which can be rapidly and facilely disseminated. A cost-effective and specific method for its rapid detection at extremely low levels is required, in order to facilitate a timely intervention for containment. Here, we report an ultrasensitive method exploiting a combination of isothermal nucleic acid amplification with a tailed forward primer and biotinylated dNTPs, which is performed in less than 30 min. The polymerase chain reaction (PCR) and enzyme linked oligonucleotide assay (ELONA) were used to optimise assay parameters for implementation on the LFA, and achieved detection limits of 45 pM and 940 fM using SA-HRP and SA-polyHRP, respectively. Replacing PCR with isothermal amplification, namely recombinase polymerase amplification, similar signals were obtained (314 fM), with just 15 min of amplification. The lateral flow detection of the isothermally amplified and labelled amplicon was then explored and detection limits of 7 fM and 0.63 fg achieved for synthetic and genomic DNA, respectively. The incorporation of biotinylated dNTPs and their exploitation for the ultrasensitive molecular detection of a nucleic acid target has been demonstrated and this generic platform can be exploited for a multitude of diverse real life applications.
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Xing J, Yu J, Liu Y. Improvement and evaluation of loop-mediated isothermal amplification combined with chromatographic flow dipstick assays for Vibrio parahaemolyticus. J Microbiol Methods 2020; 171:105866. [PMID: 32057897 DOI: 10.1016/j.mimet.2020.105866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 10/25/2022]
Abstract
Vibrio parahaemolyticus, a major food-borne pathogen, is a gram-negative rod-shaped halophilic bacterium which inhabits marine environments throughout the world. It can pose a threat to humans after the consumption of raw or undercooked seafood. Fast detection is crucial for hindering and controlling V. parahaemolyticus infection. Compared with traditional methods, loop-mediated isothermal amplification (LAMP) is a simple, rapid and versatile method. It can be performed at one temperature without the need for cycling. As a new method in recent years, LAMP combined with a chromatographic flow dipstick (LFD) meets the needs of point-of-care testing without the need for special instruments. It avoids the limitations of LAMP, reduces detection time and increases detection accuracy. Our previous studies have suggested that the optimized LFD method can improve the sensitivity of LAMP detection and shorten the isothermal amplification time during the detection process. In the present study, two LAMP assays were improved to LFD methods, and a LFD targeting 16S23S rRNA gene internal transcribed spacer (ITS) of V. parahaemolyticus was developed. The lower limit for tlh, toxR, ITS LFD assays were detected as 3.1 × 100, 3.1 × 101, and 3.1 × 100 CFU respectively, whether in pure cultures or artificially contaminated food samples. The shortest amplification times at the limit of each assay were determined as 20 min, 35 min and 25 min. A heating block was used to perform two (tlh and ITS) LFD assays to detect 20 food samples. Compared to a standard method (GB 4789.7-2013 National Food Safety Standards, Food Microbiology Inspection, Vibrio parahaemolyticus test), tlh and ITS LFD assays showed more MPN (most probable number) results than that of culture. It demonstrated that the improved LFD technology can provide a simple and rapid detection method with high sensitivity and specificity for detection of V. parahaemolyticus.
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Affiliation(s)
- Jiahua Xing
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Jia Yu
- College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin 300071, China.
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Wang L, Chen G, Zhang C, Wang Y, Sun R. Application of loop-mediated isothermal amplification combined with lateral flow dipstick to rapid and sensitive detection of Alexandrium catenella. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:4246-4257. [PMID: 31828710 DOI: 10.1007/s11356-019-06889-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Alexandrium catenella is one of the globally distributed toxic marine microalgae to cause paralytic shellfish poisoning that poses a great threat to marine fisheries, economy, and public health. Development of efficient and sensitive methods for accurate identification of A. catenella to minimize its damage is therefore necessary. In this study, a novel method referred to as loop-mediated isothermal amplification (LAMP) combined with lateral flow dipstick (LFD) (LAMP-LFD) was established for rapid and sensitive detection of A. catenella. The internal transcribed spacer (ITS) gene of A. catenella was cloned for sequencing and used as target for LAMP-LFD. Three sets of LAMP primers (AcLF1, AcLF2, and AcLF3) targeting the ITS were successfully designed, among which AcLF2 displaying the best performance was used in the subsequent tests. A specific LFD probe targeting the amplification region of AcLF2 was further designed. The LAMP-LFD detection system was established and the amplification conditions were optimized. Cross-reactivity tests with common marine microalgae showed that the LAMP-LFD was exclusively specific for A. catenella. The detection limits of LAMP-LFD for A. catenella genomic DNA and the plasmid containing the ITS were 4.63 × 10-4 ng μL-1 and 1.26 × 104 copies μL-1, displaying a sensitivity that is 10 times higher than that of SYBR Green I assay and 100 times higher than that of conventional PCR, respectively. Finally, the practicability of LAMP-LFD was confirmed by test with spiked samples. LAMP-LFD revealed a detection limit of approximately 0.1 cell mL-1, which was 100 times more sensitive than conventional PCR. The optimized LAMP-LFD protocol can be completed within 75 min. Therefore, the established LAMP-LFD is a specific, sensitive, and rapid method that is possibly applicable to the field monitoring of A. catenella.
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Affiliation(s)
- Liang Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China.
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Rui Sun
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
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Li Y, Lin F, Sun L, Huang A, Chen J, Hao G, Yuan X, Zhang H, Su S. Detection of cyprinid herpesvirus 2 by loop-mediated isothermal amplification in combination with a lateral flow dipstick. Mol Cell Probes 2020; 50:101507. [PMID: 31911113 DOI: 10.1016/j.mcp.2020.101507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/17/2019] [Accepted: 01/01/2020] [Indexed: 01/23/2023]
Abstract
We developed a convenient technique to detect Herpesviral haematopoietic necrosis attributed to cyprinid herpes virus 2 (CyHV-2), a serious disease of Crucian carp and goldfish related to high mortality. In the present study, we employed a lateral flow dipstick (LAMP-LFD) to present a loop-mediated isothermal amplification assay. The specificity was ascertained via other six viruses, and the sensitivity was compared using PCR method, which are the reaction conditions changes for the method improved. The results revealed that CyHV-2 performance was observable at 64 °C in a separated tube within 60 min, when the samples hybridized using an FITC-labeled probe. As the LAMP-LFD method's specificity was high, with its sensitivity identical to that of traditional PCR, the overall DNA collected revealed the lowest detection limit of 0.18 pg/μl from goldfish diseased by CyHV-2. In summary, the development of LAMP-LFD's method does not require expensive instruments, and it can be regarded as a fast, simple, and reliable method for CyHV-2 detection.
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Affiliation(s)
- Yanli Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Animal Science and Technology, Southwest University, Chongqing, 400715, PR China; Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China.
| | - Feng Lin
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China.
| | - Lihui Sun
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Aixia Huang
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Jianming Chen
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Guijie Hao
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Xuemei Yuan
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Haiqi Zhang
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China.
| | - Shengqi Su
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Animal Science and Technology, Southwest University, Chongqing, 400715, PR China.
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Molecular method for rapid detection of the red tide dinoflagellate Karenia mikimotoi in the coastal region of Xiangshan Bay, China. J Microbiol Methods 2019; 168:105801. [PMID: 31811904 DOI: 10.1016/j.mimet.2019.105801] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 11/23/2022]
Abstract
The species Karenia mikimotoi is a common nearshore red tide alga that can secrete hemolytic exotoxin and ichthyotoxin, which can induce the death of fish and shellfish, causing severe economic losses. In this study, loop-mediated isothermal amplification (LAMP) was employed in combination with the lateral flow dipstick (LFD) visual detection method to establish the LAMP-LFD rapid detection method for K. mikimotoi. The internal transcribed spacer ITS1-5.8S-ITS2 of K. mikimotoi was used as the target sequence and was amplified with specific primers designed in this study. The results indicated that the amplification optimal reaction conditions for LAMP in this paper were for 20 min at 65 °C. Moreover, LAMP had excellent specificity, showing negative results for other common red tide causing algal species. In field samples, we successfully reduced the total time, with only 23 min needed from LAMP amplification to LFD result display, which was shorter than that of conventional PCR. Consequently, LAMP-LFD should be useful for rapid field detection of low-density K. mikimotoi and for the early prevention of red tide induced by such algae.
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Zhang C, Chen G, Wang Y, Zhou J, Li C. Establishment and application of hyperbranched rolling circle amplification coupled with lateral flow dipstick for the sensitive detection of Karenia mikimotoi. HARMFUL ALGAE 2019; 84:151-160. [PMID: 31128799 DOI: 10.1016/j.hal.2019.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/23/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
The dinoflagellate Karenia mikimotoi is a noxious and harmful algal bloom (HAB)-forming microalga. Establishing a rapid, accurate, and sensitive method of detecting this harmful alga is necessary to provide warnings of imminent HABs through field monitoring. Here, an isothermal amplification technique combined with a rapid analytical method for nucleic acid-based amplified products, i.e., hyperbranched rolling circle amplification (HRCA) coupled with lateral flow dipstick (LFD), hereafter denoted as HRCA-LFD, was established to detect K. mikimotoi. The HRCA-LFD assay relied on a padlock probe (PLP) targeting DNA template and an LFD probe targeting PLP. The sequenced internal transcribed spacer of K. mikimotoi through molecular cloning was used as the target of PLP. The optimized HRCA conditions was determined to be as follows: PLP concentration, 20 pM; ligation temperature, 65 °C; ligation time, 10 min; amplification temperature, 61 °C; and amplification time, 30 min. The developed HRCA-LFD assay was specific for K. mikimotoi, displaying no cross-reactivity with other common microalgae. Sensitivity-comparison tests indicated that HRCA-LFD assay was 100-fold more sensitive than PCR, with a detection limit of 0.1 cell mL-1 when used to analyze spiked field samples. The analysis with field samples also indicated that HRCA-LFD assay was suitable for samples with a target cell density range of 1-1000 cells mL-1. All of these results suggested that HRCA-LFD assay is an alternative method for the sensitive and reliable detection of K. mikimotoi from marine water samples.
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Affiliation(s)
- Chunyun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China; School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Jin Zhou
- Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China.
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Loop-mediated isothermal amplification-lateral-flow dipstick (LAMP-LFD) to detect Mycoplasma ovipneumoniae. World J Microbiol Biotechnol 2019; 35:31. [PMID: 30701329 PMCID: PMC6353813 DOI: 10.1007/s11274-019-2601-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/18/2019] [Indexed: 11/17/2022]
Abstract
In order to establish a rapid detection method for Mycoplasma ovipneumoniae, this study used the loop-mediated isothermal amplification (LAMP) technique to carry out nucleic acid amplification and chromatographic visualization via a lateral flow dipstick (LFD) assay. The M. ovipneumoniae elongation factor TU gene (EF-TU) was detected using a set of specific primers designed for the EF-TU gene, and the EF-TU FIP was detected by biotin labeling, which was used in the LAMP amplification reaction. The digoxin-labeled probe specifically hybridized with LAMP products, which were visually detected by LFD. Here, we established the M. ovipneumoniae LAMP-LFD rapid detection method and tested the specificity, sensitivity, and clinical application of this method. Results showed that the optimized LAMP performed at 60 °C for 60 min, and LFD can specifically and visually detect M. ovipneumoniae with a minimum detectable concentration at 1.0 × 102 CFU/mL. The sensitivity of LAMP-LFD was 1000 times that of the conventional PCR detection methods, and the clinical lung tissue detection rate was 86% of 50 suspected sheep infected with M. ovipneumoniae. In conclusion, LAMP-LFD was established in this study to detect M. ovipneumoniae, a method that was highly specific, sensitive, and easy to operate, and provides a new method for the prevention and diagnosis of M. ovipneumoniae infection.
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