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Alhamid G, Tombuloglu H, BenRashed HA, Almessiere MA, Rabaan AA. Ultra-sensitive colorimetric detection of SARS-CoV-2 by novel gold nanoparticle (AuNP)-assisted loop-mediated isothermal amplification (LAMP) and freezing methods. Mikrochim Acta 2024; 191:339. [PMID: 38789855 DOI: 10.1007/s00604-024-06422-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a molecular diagnosis technology with the advantages of isothermal reaction conditions and high sensitivity. However, the LAMP reactions are prone to producing false-positive results and thus are usually less reliable. This study demonstrates a gold nanoparticle (AuNP)-assisted colorimetric LAMP technique for diagnosing SARS-CoV-2, which aims to overcome the false-positive results. The AuNPs were functionalized with E gene probes, specifically tailored to bind to the amplified E-gene LAMP product, using the freezing method. Varied salt concentration and AuNP/probe combinations were tested for the highest visual performance. The experiments were conducted on synthetic SARS-CoV-2 RNA (Omicron variant), as well as on clinical samples. The assay showed an exceptional sensitivity of 8.05 fg of LAMP amplicon mixture (0.537 fg/µL). The average reaction time was ~ 30 min. In conclusion, AuNP-assisted LAMP detection will not identify any potential unspecific amplification, which helps to improve the efficiency and reliability of LAMP assays in point-of-care applications. The freezing method to functionalize the AuNPs with probes simplifies the assay, which can be utilized in further diagnostic studies.
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Affiliation(s)
- Galyah Alhamid
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia.
| | - Hajar A BenRashed
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Munirah A Almessiere
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Ali A Rabaan
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia
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2
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Lamas A, Azinheiro S, Roumani F, Prado M, Garrido-Maestu A. Evaluation of the effect of outer primer structure, and inner primer linker sequences, in the performance of Loop-mediated isothermal amplification. Talanta 2023; 260:124642. [PMID: 37167680 DOI: 10.1016/j.talanta.2023.124642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
Loop-mediated isothermal amplification, or LAMP, is nowadays the most popular isothermal nucleic acid amplification technique. This technique implements a minimum of four primers, named outer (F3/B3) and inner primers (FIP/BIP). The inner primers hybridize in two distinct regions, and some studies have reported that the usage of a linker, typically composed of four thymines, in the middle of these primers can improve assay performance. In addition to this, dual-priming oligonucleotides, DPO, have been reported to provide highly specific reducing non-specific amplifications. Considering the large number of primers implemented in LAMP assays, in the current study the suitability of DPO primers replacing regular outer primers; and their combination with different linker sequences in the inner primers were explored. The results demonstrated that replacing standard F3/B3 by DPO primers does not significantly affect that overall performance of the assay, and provides additional stability to temperature changes. This observations were consistent regardless the type of linker implemented in the inner primers, out of which in the current study a linker composed of thymines significantly outperformed the other options tested, most likely due to a combination of sequence and physical structure.
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Affiliation(s)
- Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory, Department of Analytical Chemistry, Nutrition and Bromatology, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - Sarah Azinheiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal; Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Foteini Roumani
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal; Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
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3
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Okeke ES, Chukwudozie KI, Nyaruaba R, Ita RE, Oladipo A, Ejeromedoghene O, Atakpa EO, Agu CV, Okoye CO. Antibiotic resistance in aquaculture and aquatic organisms: a review of current nanotechnology applications for sustainable management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69241-69274. [PMID: 35969340 PMCID: PMC9376131 DOI: 10.1007/s11356-022-22319-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/27/2022] [Indexed: 05/13/2023]
Abstract
Aquaculture has emerged as one of the world's fastest-growing food industries in recent years, helping food security and boosting global economic status. The indiscriminate disposal of untreated or improperly managed waste and effluents from different sources including production plants, food processing sectors, and healthcare sectors release various contaminants such as bioactive compounds and unmetabolized antibiotics, and antibiotic-resistant organisms into the environment. These emerging contaminants (ECs), especially antibiotics, have the potential to pollute the environment, particularly the aquatic ecosystem due to their widespread use in aquaculture, leading to various toxicological effects on aquatic organisms as well as long-term persistence in the environment. However, various forms of nanotechnology-based technologies are now being explored to assist other remediation technologies to boost productivity, efficiency, and sustainability. In this review, we critically highlighted several ecofriendly nanotechnological methods including nanodrug and vaccine delivery, nanoformulations, and nanosensor for their antimicrobial effects in aquaculture and aquatic organisms, potential public health risks associated with nanoparticles, and their mitigation measures for sustainable management.
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Affiliation(s)
- Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 41000, Enugu State, Nigeria
- Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, 41000, Enugu State, Nigeria
- Institute of Environmental Health and Ecological Security, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
| | - Kingsley Ikechukwu Chukwudozie
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
- Department of Clinical Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Raphael Nyaruaba
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Center for Biosafety Megascience, Wuhan Institute of Virology, CAS, Wuhan, China
| | - Richard Ekeng Ita
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Ritman University, Ikot Ekpene, Akwa Ibom State, Nigeria
| | - Abiodun Oladipo
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, Jiangsu, People's Republic of China
| | - Onome Ejeromedoghene
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- School of Chemistry and Chemical Engineering, Southeast University, Jiangning District, Nanjing, Jiangsu Province, 211189, People's Republic of China
| | - Edidiong Okokon Atakpa
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Institute of Marine Biology & Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
- Department of Animal & Environmental Biology, University of Uyo, Uyo, 1017, Akwa Ibom State, Nigeria
| | | | - Charles Obinwanne Okoye
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya.
- Department of Zoology & Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria.
- School of Environment & Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, China.
- Key Laboratory of Intelligent Agricultural Machinery Equipment, Jiangsu University, Zhenjiang, 212013, China.
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He P, Chen H, Sun J, Wang Q, Tang X, Zhang Y, Zhu F, Shen Z. Use of DNA nanosensors based on upconverting nanoparticles for detection of Nosema bombycis by fluorescence resonance energy transfer. Folia Microbiol (Praha) 2022; 67:419-425. [PMID: 35040074 DOI: 10.1007/s12223-021-00938-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022]
Abstract
In this study, NaYF4:20%Yb, 2%Er upconverting nanoparticles (UCNPs) were synthesized by solvothermal method and characterized by transmission electron microscopy and upconversion fluorescence spectrometry. The results showed that the UCNP particles present good dispersion and uniform spherical shape with a size of 29 ~ 42 nm. Hydroxyl UCNPs were converted to hydrophilic carboxylic acid-functionalized ones by ligand exchange, and the streptavidin was attached on the surface of carboxylic acid-functionalized UCNPs via amide bond. The DNA nanosensors based on UCNPs with DNA probes have been successfully developed. Only the genomic DNA of Nosema bombycis can be specifically detected by the DNA nanosensors when the DNA of Bombyx mori and its pathogens was used as target DNA. When the DNA nanosensors were used to detect the DNA of N. bombycis, a broad emission peak signal appeared at 580 nm. There is linear relationship between the signal intensity and DNA concentration of N. bombycis, I580/I545 (R2 = 0.820) and I545/I654 (R2 = 0.901). The detectable minimum concentration of genomic DNA of N. bombycis was 100 ng/μL while the tested concentrations of N. bombycis genomic DNA were 3000 ng/μL, 1500 ng/μL, 1000 ng/μL, 500 ng/μL, 250 ng/μL, and 100 ng/μL, respectively. The whole detection process for target DNA takes less than 60 min.
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Affiliation(s)
- Ping He
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Hongli Chen
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Jiancheng Sun
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Qiang Wang
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Xudong Tang
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Yiling Zhang
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Feng Zhu
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong Province, 277160, China
| | - Zhongyuan Shen
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China.
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5
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Kampeera J, Dangtip S, Suvannakad R, Khumwan P, Senapin S, Kiatpathomchai W. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with colorimetric gold nanoparticle (AuNP) probe assay for visual detection of tilapia lake virus (TiLV) in Nile and red hybrid tilapia. JOURNAL OF FISH DISEASES 2021; 44:1595-1607. [PMID: 34170523 DOI: 10.1111/jfd.13482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/11/2021] [Indexed: 05/23/2023]
Abstract
Tilapia is one of the major aquaculture species with a global economic significance. Despite a high scale of production worldwide, mortality in many tilapia cultures has recently become a problem concerned with not only intensive farming but also the prevalence of infectious pathogens. Tilapia lake virus (TiLV) has emerged as a serious single-stranded RNA disease agent that thus far has continued to cause a number of incidences across the continents. Conventional PCR-based molecular detection techniques, despite having high sensitivity for TiLV, are not best suited for the onsite identification of infected fish mainly due to their requirement of laboratory resources and extended assay turnaround time. To address this practical limitation, we have developed a novel colorimetric assay based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and gold nanoparticle (AuNP)-labelled oligonucleotide reporter probe targeting the viral genomic segment 9 that enables the assay to be completed within an hour. This technique has been shown to be compatible with a rapid nucleic extraction method that does not demand centrifugation steps or any benchtop laboratory equipment. When validated with field-acquired tilapia samples, our RT-LAMP-AuNP assay exhibited a near-perfect agreement with the semi-nested RT-PCR assay recommended by OIE with Cohen's κ coefficient of .869, yet requiring significantly less time to perform.
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Affiliation(s)
- Jantana Kampeera
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Sirintip Dangtip
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Rapheephat Suvannakad
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Pakapreud Khumwan
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Saengchan Senapin
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
- Fish and Shrimp Molecular Biology and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
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6
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Filik H, Avan AA. Nanotechnology-based Colorimetric Approaches for Pathogenic Virus Sensing: A review. Curr Med Chem 2021; 29:2691-2718. [PMID: 34269661 DOI: 10.2174/0929867328666210714154051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 11/22/2022]
Abstract
Fast and inexpensive virus identification protocols are paramount to hinder the further extent of pandemic diseases, minimize economic and social damages, and expedite proper clinical rehabilitation. Until now, various biosensors have been fabricated for the identification of pathogenic particles. But, they offer many difficulties. Nanotechnology resolves these difficulties and offers direct identification of pathogenic species in real-time. Among them, nanomaterial based-colorimetric sensing approach of pathogenic viruses by the naked eye has attracted much awareness because of their simplicity, speed, and low cost. In this review, the latest tendencies and advancements are overviewed in detecting pathogenic viruses using colorimetric concepts. We focus on and reconsider the use of distinctive nanomaterials such as metal nanoparticles, carbon nanotubes, graphene oxide, and conducting polymer to form colorimetric pathogenic virus sensors.
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Affiliation(s)
- Hayati Filik
- Istanbul University-Cerrahpaşa, Faculty of Engineering, Department of Chemistry, 34320 Avcılar, Istanbul, Turkey
| | - Asiye Aslıhan Avan
- Istanbul University-Cerrahpaşa, Faculty of Engineering, Department of Chemistry, 34320 Avcılar, Istanbul, Turkey
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7
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Jaroenram W, Hayakijkosol O, Owens L, Elliman J. Establishing a gold standard method for the detection of Cherax reovirus using reverse transcriptase, quantitative, polymerase chain reaction. J Virol Methods 2021; 293:114169. [PMID: 33887279 DOI: 10.1016/j.jviromet.2021.114169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
Cherax reovirus infects redclaw crayfish (Cherax quadricarinatus) and it may be involved in mortalities between 5-20 % and stunting of up to 40 % of survivors. The sequence of the RNA-dependent RNA polymerase was used to develop a reverse transcription, quantitative, PCR (RT-qPCR) which was specific against seven other crustacean viruses (Athtab bunyavirus, Chequa iflavirus, Macrobrachium rosenbergii nodavirus, Gill-associated virus, Taura syndrome virus, White spot syndrome virus, and Penaeus stylirostris Penstylhamaparvovirus) although GAV produced a reaction that was easily separated by melt curve analysis. A strong linear correlation (r2 = 0.9965) was obtained between viral quantities ranging from 107 to 10 viral copies/reaction with an amplification efficiency of 0.92. This RT-qPCR is 2-times faster and 100 times more sensitive than a standard RT-PCR using agarose gel electrophoresis with the potential to detect the virus down to 7.64 copies/reaction in clinical samples. In clinical crayfish samples, it was able to detect Cherax reovirus in crayfish when the traditional RT-PCR was negative. Its' measurement of uncertainty was less than 2% (0.02-1.9), similar to PCRs for other crustacean viruses. This RT-qPCR is proposed as the gold standard and should be used for the screening of populations of C. quadricarinatus for broodstock before being used in hatcheries or on farms.
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Affiliation(s)
- Wansadaj Jaroenram
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Orachun Hayakijkosol
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Leigh Owens
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Jennifer Elliman
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
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Abbas WT. Advantages and prospective challenges of nanotechnology applications in fish cultures: a comparative review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:7669-7690. [PMID: 33398757 DOI: 10.1007/s11356-020-12166-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Applications of nanotechnology in fish cultures have participated in getting over various difficulties that hinder fish productivity. They can achieve growth performance after adding some important minerals and vitamins in the form of nano-feed supplements like selenium, zinc, iron, and vitamin C. Also, they have an important role in reproduction, and fish medicine as antimicrobial, drug delivery, nano-vaccination, and rapid disease diagnosis. Moreover, their roles in water remediation and purification, and fish packaging are documented. On the other hand, some nanoparticles exhibit toxic effects on living organisms, which return to their tiny size, high reactivity, and permeability. They can alter many physiological functions and cause cytotoxicity, DNA damage, and histopathological changes. Also, nanotechnology applications cause new secondary pollutants to be introduced into the environment that can negatively affect fish health and the surrounding living organisms. So, in spite of the promising applications of nanotechnology to fulfill high growth performance and pathogen-free fish, there are a lot of debates about the potential toxicity of nanomaterials, their reactivity with the surrounding environment, and bioaccumulation. The present review aims to elucidate and discuss various advantages and challenges of nanotechnology applications in fish cultures. Also, it points to green nanotechnology as a promising alternative to chemical ones.
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Affiliation(s)
- Wafaa Tawfik Abbas
- Departmentof Hydrobiology, National Research Centre, 33 El Bohouth St. Dokki, P.O. Box 12622, Giza, Egypt.
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Wang L, He K, Sadak O, Wang X, Wang Q, Xu X. Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials. Biosens Bioelectron 2020; 169:112602. [PMID: 32947078 DOI: 10.1016/j.bios.2020.112602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022]
Abstract
The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.
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Affiliation(s)
- Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Omer Sadak
- Department of Electrical and Electronics Engineering, Ardahan University, 75000, Turkey
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Graphene-based electrochemical genosensor incorporated loop-mediated isothermal amplification for rapid on-site detection of Mycobacterium tuberculosis. J Pharm Biomed Anal 2020; 186:113333. [DOI: 10.1016/j.jpba.2020.113333] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022]
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11
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Srimongkol G, Ditmangklo B, Choopara I, Thaniyavarn J, Dean D, Kokpol S, Vilaivan T, Somboonna N. Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products. Sci Rep 2020; 10:7768. [PMID: 32385390 PMCID: PMC7211006 DOI: 10.1038/s41598-020-64710-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/17/2020] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus strains carrying enterotoxin A gene (sea) causes food poisoning and cannot be distinguished from non-pathogenic strains by the culture method. Here, we developed a rapid, specific and sensitive visual detection of sea using loop-mediated isothermal amplification (LAMP) combined with nanogold probe (AuNP) or styryl dye (STR). LAMP-AuNP and LAMP-STR can detect as low as 9.7 fg (3.2 sea copies) and 7.2 sea copies, respectively, which were lower than PCR (97 fg or 32 sea copies). The excellent performance of these new assays was demonstrated in food samples using crude DNA lysates. While the culture method detected 104 CFU/g in ground pork and 10 CFU/mL in milk in 5-7 days, LAMP-AuNP could detect down to 10 CFU/g for both samples in 27 minutes. Analyzing 80 pork and milk samples revealed that the LAMP-AuNP showed 100% sensitivity, 97-100% specificity and 97.5-100% accuracy, which were superior to the culture method, and comparable to PCR but without requirement of a thermal cycler. Furthermore, our LAMP-AuNP detect sea at a range below the food safety control (<100 CFU/g). The LAMP-STR quantitated sea in 10-1,000 CFU (7.2-720 copies). Our crude DNA lysis combined with LAMP-AuNP/STR present effective point-of-care detection and facilitate appropriate control strategies.
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Affiliation(s)
- Grittaya Srimongkol
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Boonsong Ditmangklo
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ilada Choopara
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jiraporn Thaniyavarn
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Zhao VXT, Wong TI, Zheng XT, Tan YN, Zhou X. Colorimetric biosensors for point-of-care virus detections. MATERIALS SCIENCE FOR ENERGY TECHNOLOGIES 2020; 3:237-249. [PMID: 33604529 PMCID: PMC7148662 DOI: 10.1016/j.mset.2019.10.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 05/05/2023]
Abstract
Colorimetric biosensors can be used to detect a particular analyte through color changes easily by naked eyes or simple portable optical detectors for quantitative measurement. Thus, it is highly attractive for point-of-care detections of harmful viruses to prevent potential pandemic outbreak, as antiviral medication must be administered in a timely fashion. This review paper summaries existing and emerging techniques that can be employed to detect viruses through colorimetric assay design with detailed discussion of their sensing principles, performances as well as pros and cons, with an aim to provide guideline on the selection of suitable colorimetric biosensors for detecting different species of viruses. Among the colorimetric methods for virus detections, loop-mediated isothermal amplification (LAMP) method is more favourable for its faster detection, high efficiency, cheaper cost, and more reliable with high reproducible assay results. Nanoparticle-based colorimetric biosensors, on the other hand, are most suitable to be fabricated into lateral flow or lab-on-a-chip devices, and can be coupled with LAMP or portable PCR systems for highly sensitive on-site detection of viruses, which is very critical for early diagnosis of virus infections and to prevent outbreak in a swift and controlled manner.
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Affiliation(s)
- Victoria Xin Ting Zhao
- College of Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Ten It Wong
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xin Ting Zheng
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - Xiaodong Zhou
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
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13
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Somboonna N, Choopara I, Arunrut N, Sukhonpan K, Sayasathid J, Dean D, Kiatpathomchai W. Rapid and sensitive detection of Chlamydia trachomatis sexually transmitted infections in resource-constrained settings in Thailand at the point-of-care. PLoS Negl Trop Dis 2018; 12:e0006900. [PMID: 30571705 PMCID: PMC6301561 DOI: 10.1371/journal.pntd.0006900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
| | - Ilada Choopara
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Narong Arunrut
- Bioengineering and Sensing Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Kanchapan Sukhonpan
- Department of Obstetrics and Gynecology, Buddhachinaraj Phitsanulok Hospital, Phitsanulok, Thailand
| | - Jarun Sayasathid
- Cardiac Center, Naresuan University Hospital, Phitsanulok, Thailand
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
- Joint Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
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Jaroenram W, Cecere P, Pompa PP. Xylenol orange-based loop-mediated DNA isothermal amplification for sensitive naked-eye detection of Escherichia coli. J Microbiol Methods 2018; 156:9-14. [PMID: 30502368 DOI: 10.1016/j.mimet.2018.11.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) can amplify DNA specifically and sensitively. Under minimal buffering conditions, it produces hydrogen ions that lower the pH of the solution upon DNA amplification. This characteristic was applied to visually detect amplified DNA of Escherichia coli through the use of Xylenol Orange, a pH-dependent dye. Under the optimal conditions, 120 min at 63 °C, the Xylenol orange-dependent colorimetric LAMP revealed a detection limit as low as 1 CFU, namely 100,000 times more sensitive than typical multiplex PCR, and showed no cross-reactions with other foodborne pathogens. The colorimetric assay was successfully exploited to detect E. coli contaminations in milk samples, showing high reliability and the same high sensitivity with naked-eye readout. Together with robustness, simplicity, and visual detectability of amplification, this assay can serve as an alternative tool to PCR for detecting E. coli, which is suitable for both laboratory and on-field applications.
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Affiliation(s)
- Wansadaj Jaroenram
- Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Paola Cecere
- Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Pier Paolo Pompa
- Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy.
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15
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Arunrut N, Kiatpathomchai W, Ananchaipattana C. Development and evaluation of real‐time loop mediated isothermal amplification assay for rapid and sensitive detection ofSalmonellaspp. in chicken meat products. J Food Saf 2018. [DOI: 10.1111/jfs.12564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Narong Arunrut
- Department of Biology, Faculty of Science and TechnologyRajamangala University of Technology Thanyaburi, 39 Muh1 Thanyaburi Pathum Thani Thailand
- Bioengineering and Sensing Technology Laboratory, BIOTECNational Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng Khlong Luang Pathum Thani Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, BIOTECNational Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng Khlong Luang Pathum Thani Thailand
| | - Chiraporn Ananchaipattana
- Department of Biology, Faculty of Science and TechnologyRajamangala University of Technology Thanyaburi, 39 Muh1 Thanyaburi Pathum Thani Thailand
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16
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Rapid Detection of Staphylococcus aureus via Recombinase Polymerase Amplification Combined with Lateral Flow Strip. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1200-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Manajit O, Longyant S, Sithigorngul P, Chaivisuthangkura P. Development of uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification coupled with nanogold probe (UDG-LAMP-AuNP) for specific detection of Pseudomonas aeruginosa. Mol Med Rep 2018; 17:5734-5743. [PMID: 29436623 PMCID: PMC5866016 DOI: 10.3892/mmr.2018.8557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/22/2018] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an important opportunistic pathogen that causes serious infections in humans, including keratitis in contact lens wearers. Therefore, establishing a rapid, specific and sensitive method for the identification of P. aeruginosa is imperative. In the present study, the uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification combined with nanogold labeled hybridization probe (UDG-LAMP-AuNP) was developed for the detection of P. aeruginosa. UDG-LAMP was performed to prevent carry over contamination and the LAMP reactions can be readily observed using the nanogold probe. A set of 4 primers and a hybridization probe were designed based on the ecfX gene. The UDG-LAMP reactions were performed at 65°C for 60 min using the ratio of 40% deoxyuridine triphosphate to 60% deoxythymidine triphosphate. The detection of UDG-LAMP products using the nanogold labeled hybridization probe, which appeared as a red-purple color, was examined at 65°C for 5 min with 40 mM MgSO4. The UDG-LAMP-AuNP demonstrated specificity to all tested isolates of P. aeruginosa without cross reaction to other bacteria. The sensitivity for the detection of pure culture was 1.6×103 colony-forming units (CFU) ml−1 or equivalent to 3 CFU per reaction while that of polymerase chain reaction was 30 CFU per reaction. The detection limit of spiked contact lenses was 1.1×103 CFU ml−1 or equivalent to 2 CFU per reaction. In conclusion, the UDG-LAMP-AuNP assay was rapid, simple, specific and was effective for the identification of P. aeruginosa in contaminated samples.
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Affiliation(s)
- Orapan Manajit
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Siwaporn Longyant
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Paisarn Sithigorngul
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Parin Chaivisuthangkura
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
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18
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Garrido-Maestu A, Azinheiro S, Carvalho J, Abalde-Cela S, Carbó-Argibay E, Diéguez L, Piotrowski M, Kolen’ko YV, Prado M. Combination of Microfluidic Loop-Mediated Isothermal Amplification with Gold Nanoparticles for Rapid Detection of Salmonella spp. in Food Samples. Front Microbiol 2017; 8:2159. [PMID: 29209283 PMCID: PMC5701617 DOI: 10.3389/fmicb.2017.02159] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/20/2017] [Indexed: 11/16/2022] Open
Abstract
Foodborne diseases are an important cause of morbidity and mortality. According to the World Health Organization, there are 31 main global hazards, which caused in 2010 600 million foodborne illnesses and 420000 deaths. Among them, Salmonella spp. is one of the most important human pathogens, accounting for more than 90000 cases in Europe and even more in the United States per year. In the current study we report the development, and thorough evaluation in food samples, of a microfluidic system combining loop-mediated isothermal amplification with gold nanoparticles (AuNPs). This system is intended for low-cost, in situ, detection of different pathogens, as the proposed methodology can be extrapolated to different microorganisms. A very low limit of detection (10 cfu/25 g) was obtained. Furthermore, the evaluation of spiked food samples (chicken, turkey, egg products), completely matched the expected results, as denoted by the index kappa of concordance (value of 1.00). The results obtained for the relative sensitivity, specificity and accuracy were of 100% as well as the positive and negative predictive values.
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19
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Yang HL, Qiu L, Liu Q, Wan XY, Liu S, Zhu LL, Yang B, Zhang QL, Huang J. A novel method of real-time reverse-transcription loop-mediated isothermal amplification developed for rapid and quantitative detection of a new genotype (YHV-8) of yellow head virus. Lett Appl Microbiol 2017; 63:103-10. [PMID: 27221155 DOI: 10.1111/lam.12591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 12/01/2022]
Abstract
UNLABELLED A new genotype of yellow head virus (YHV), designated as YHV-8, was found in farmed shrimp Fenneropenaeus chinensis suffering suspectedly from EMS/AHPNS (early mortality disease/acute hepatopancreatic necrosis disease) in China in 2012. In this study, a one-step, real-time reverse-transcription loop-mediated isothermal amplification (rRT-LAMP) assay was developed for better detection of both genotypes of YHV-1 and YHV-8. A set of six specific primers was successfully designed targeting a conserved region of the YHV genome. The LAMP reaction was optimized to contain 8 mmol l(-1) Mg(2+) and 1·4 mmol l(-1) dNTPs, and to be performed at 58°C for 60 min. The detection sensitivity of the rRT-LAMP method was as low as 7 × 10(0) copies per reaction. The specificity of the method was validated by the absence of any cross-reaction with the RNA samples extracted from other shrimp viruses (Taura syndrome virus, white spot syndrome virus, infectious hypodermal and haematopoietic necrosis virus, hepatopancreatic parvovirus) and specific pathogen-free (SPF) shrimp. The resulting standard curves showed high correlation coefficient values. Furthermore, the test of farm samples showed that YHV was detected in three of 111 Litopenaeus vannamei, six of eight Fenneropenaeus chinensis, five of 19 Macrobrachium rosenbergii and none of the nine Marsupenaeus japonicus. These results suggest that this assay is applicable widely as a new rapid and sensitive detection method in the research of YHV. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, we designate a new genotype of yellow head virus (YHV) as YHV genotype 8 (YHV-8) which was detected in diseased shrimp in China. A rapid, sensitive and specific rRT-LAMP detecting method for both YHV-8 and YHV-1 has been established. It is anticipated that this novel assay will be instrumental for diagnosis and surveillance of the virulent genotypes of YHV.
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Affiliation(s)
- H-L Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - L Qiu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - Q Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - X-Y Wan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - S Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - L-L Zhu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - B Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - Q-L Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - J Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
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20
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Balbin MM, Lertanantawong B, Suraruengchai W, Mingala CN. Colorimetric detection of caprine arthritis encephalitis virus (CAEV) through loop-mediated isothermal amplification (LAMP) with gold nanoprobes. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Shaalan M, Saleh M, El-Mahdy M, El-Matbouli M. Recent progress in applications of nanoparticles in fish medicine: A review. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2016; 12:701-710. [DOI: 10.1016/j.nano.2015.11.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/20/2015] [Accepted: 11/14/2015] [Indexed: 10/22/2022]
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22
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Arunrut N, Kampeera J, Sirithammajak S, Sanguanrut P, Proespraiwong P, Suebsing R, Kiatpathomchai W. Sensitive Visual Detection of AHPND Bacteria Using Loop-Mediated Isothermal Amplification Combined with DNA-Functionalized Gold Nanoparticles as Probes. PLoS One 2016; 11:e0151769. [PMID: 27003504 PMCID: PMC4803327 DOI: 10.1371/journal.pone.0151769] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/03/2016] [Indexed: 11/21/2022] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is a component cause of early mortality syndrome (EMS) of shrimp. In 2013, the causative agent was found to be unique isolates of Vibrio parahaemolyticus (VPAHPND) that contained a 69 kbp plasmid (pAP1) carrying binary Pir-like toxin genes PirvpA and PirvpB. In Thailand, AHPND was first recognized in 2012, prior to knowledge of the causative agent, and it subsequently led to a precipitous drop in shrimp production. After VPAHPND was characterized, a major focus of the AHPND control strategy was to monitor broodstock shrimp and post larvae for freedom from VPAHPND by nucleic acid amplification methods, most of which required use of expensive and sophisticated equipment not readily available in a shrimp farm setting. Here, we describe a simpler but equally sensitive approach for detection of VPAHPND based on loop-mediated isothermal amplification (LAMP) combined with unaided visual reading of positive amplification products using a DNA-functionalized, ssDNA-labled nanogold probe (AuNP). The target for the special set of six LAMP primers used was the VPAHPND PirvpA gene. The LAMP reaction was carried out at 65°C for 45 min followed by addition of the red AuNP solution and further incubation at 65°C for 5 min, allowing any PirvpA gene amplicons present to hybridize with the probe. Hybridization protected the AuNP against aggregation, so that the solution color remained red upon subsequent salt addition (positive test result) while unprotected AuNP aggregated and underwent a color change from red to blue and eventually precipitated (negative result). The total assay time was approximately 50 min. The detection limit (100 CFU) was comparable to that of other commonly-used methods for nested PCR detection of VPAHPND and 100-times more sensitive than 1-step PCR detection methods (104 CFU) that used amplicon detection by electrophoresis or spectrophotometry. There was no cross reaction with DNA templates derived from non-AHPND bacteria commonly found in shrimp ponds (including other Vibrio species). The new method significantly reduced the time, difficulty and cost for molecular detection of VPAHPND in shrimp hatchery and farm settings.
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Affiliation(s)
- Narong Arunrut
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jantana Kampeera
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sarawut Sirithammajak
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Piyachat Sanguanrut
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI road, Bangkok 10400, Thailand
| | - Porranee Proespraiwong
- Aquatic Animal Health Research Center, Charoen Pokphand Foods Pulic CO., LTD. Samutsakorn 74000, Thailand
| | - Rungkarn Suebsing
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
- * E-mail:
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Cowley J. Nidoviruses of Fish and Crustaceans. AQUACULTURE VIROLOGY 2016. [PMCID: PMC7150020 DOI: 10.1016/b978-0-12-801573-5.00032-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Viruses with diverse virion architectures demarcated into four families in the order Nidovirales have been discovered in vertebrate mammalian and fish species, as well as in invertebrate crustacean and mosquito species. The order is unified by nidoviruses sharing intermediate (12.7 kb) to very long (31.7 kb) (+) ssRNA genomes, each possessing a long 5′-terminal gene encoding overlapping ORF1a and ORF1b reading frames that contain a diversity of functionally related enzymes and that are translated in toto using a −1 ribosomal frameshift mechanism, as well as by semiconserved strategies for transcribing a nested set of 3′-coterminal subgenomic mRNAs that translate the viral proteins. The nidovirus that is most important to an aquaculture species is yellow head virus (YHV), which causes disease in shrimp farmed throughout the Eastern Hemisphere and is classified in the genus Okavirus, family Roniviridae. Fathead minnow nidovirus, genus Bafinivirus, subfamily Torovirinae, family Coronaviridae, also causes disease in minnows grown for the baitfish industry in the United States. Virions similar in morphology to okaviruses and bafiniviruses have also been detected in several crab species. Of these, however, only Eriocheir sinensis ronivirus, which causes disease in the Chinese mitten crab, an important freshwater aquaculture species in China, has been shown to possess a ~22 kb ssRNA genome that supports its being a nidovirus, but its taxonomic classification awaits genome sequence analysis. This chapter provides an overview of the structure, replication and biology of these viruses with a particular focus on YHV disease characteristics, diagnostic methods and disease prevention strategies.
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Gou H, Deng J, Wang J, Pei J, Liu W, Zhao M, Chen J. Rapid and sensitive detection of porcine epidemic diarrhea virus by reverse transcription loop-mediated isothermal amplification combined with a vertical flow visualization strip. Mol Cell Probes 2014; 29:48-53. [PMID: 25444939 DOI: 10.1016/j.mcp.2014.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 11/21/2014] [Accepted: 11/21/2014] [Indexed: 11/18/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is an important pathogen that causes vomiting, diarrhea, and dehydration, leading to serious damage to the swine industry worldwide. The establishment of effective diagnostic methods is imperative. However, traditional methods are often unsuitable. In this study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) was combined with a vertical flow (VF) nucleic acid detection strip to detect PEDV. Parameters that affect the RT-LAMP reaction were optimized. The RT-LAMP-VF assay that we established was performed at 62 °C for 40 min, and then directly evaluated on the VF visualization strip cassette. The method demonstrated high specificity for PEDV. The detection limit was 10 pg of ribonucleic acid, consistent with RT-PCR, RT-LAMP detected products on agarose gels and by direct calcein fluorescence. Application of this method to clinical samples yielded a positivity rate that was comparable to that obtained for RT-PCR. This technique saves time and is efficient, and is thus expected to be useful for the diagnosis of PEDV infection in the field.
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Affiliation(s)
- Hongchao Gou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, PR China
| | - Jieru Deng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, PR China
| | - Jiaying Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, PR China
| | - Jingjing Pei
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, PR China
| | - Wenjun Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, PR China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, PR China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, PR China.
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Jaroenram W, Owens L. Recombinase polymerase amplification combined with a lateral flow dipstick for discriminating between infectious Penaeus stylirostris densovirus and virus-related sequences in shrimp genome. J Virol Methods 2014; 208:144-51. [DOI: 10.1016/j.jviromet.2014.08.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/06/2014] [Accepted: 08/12/2014] [Indexed: 11/27/2022]
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26
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Genotyping of α-thalassemias by the colorimetric nanogold probes. Clin Chim Acta 2014; 437:197-202. [DOI: 10.1016/j.cca.2014.07.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/16/2014] [Accepted: 07/23/2014] [Indexed: 01/06/2023]
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27
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Gou H, Deng J, Pei J, Wang J, Liu W, Zhao M, Chen J. Rapid and sensitive detection of type II porcine reproductive and respiratory syndrome virus by reverse transcription loop-mediated isothermal amplification combined with a vertical flow visualization strip. J Virol Methods 2014; 209:86-94. [PMID: 25241142 DOI: 10.1016/j.jviromet.2014.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 08/30/2014] [Accepted: 09/09/2014] [Indexed: 12/01/2022]
Abstract
Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was combined with a vertical flow (VF) nucleic acid detection strip to develop a universal assay for the detection of type II porcine reproductive and respiratory syndrome virus (PRRSV). The loop primers were labeled separately with biotin and fluorescein isothiocyanate (FITC) in this assay. Using optimized parameters, the whole reaction could be completed in <50 min in a completely enclosed environment. The detection limit of this assay was found to be 1 pg RNA, 30 tissue culture infective dose 50 (TCID50) virus, or 230 copies of recombinant plasmid DNA, which is relatively higher than that of RT-LAMP analyzed by agarose gel, RT-LAMP visualized by calcein, and the conventional RT-polymerase chain reaction (PCR). No false-positive results were obtained in the specificity assay. The efficiency of the RT-LAMP method was tested by analyzing 43 clinical samples, and the results were compared with those obtained by RT-PCR analysis, with the respective positive rates of 32.56% and 27.91%. This result confirmed that the method described is a rapid, accurate, and sensitive method for universal type II PRRSV detection. Also, this method can be used for the rapid detection of type II PRRSV during the early phase of an outbreak, especially for rapid veterinary diagnosis on the spot and in rural areas.
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Affiliation(s)
- Hongchao Gou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jieru Deng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jingjing Pei
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jiaying Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenjun Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
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Loop-mediated isothermal amplification (LAMP) assays for detection and identification of aquaculture pathogens: current state and perspectives. Appl Microbiol Biotechnol 2014; 98:2881-95. [DOI: 10.1007/s00253-014-5531-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 11/26/2022]
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29
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Nikbakht H, Gill P, Tabarraei A, Niazi A. Nanomolecular detection of human influenza virus type A using reverse transcription loop-mediated isothermal amplification assisted with rod-shaped gold nanoparticles. RSC Adv 2014. [DOI: 10.1039/c3ra47398h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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30
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Chomean S, Wangmaung N, Sritongkham P, Promptmas C, Mas-oodi S, Tanyong D, Ittarat W. Molecular diagnosis of α-thalassemias by the colorimetric nanogold. Analyst 2014; 139:813-22. [DOI: 10.1039/c3an01606d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Arunrut N, Kampeera J, Suebsing R, Kiatpathomchai W. Rapid and sensitive detection of shrimp infectious myonecrosis virus using a reverse transcription loop-mediated isothermal amplification and visual colorogenic nanogold hybridization probe assay. J Virol Methods 2013; 193:542-7. [PMID: 23876366 DOI: 10.1016/j.jviromet.2013.07.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/01/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
This study reports a novel strategy for the detection of reverse transcription loop-mediated isothermal amplification (RT-LAMP) products derived from infectious myonecrosis virus (IMNV), causes a serious myonecrosis in Penaeus (Litopenaeus) vannamei, by using a ssDNA-labeled with gold nanoparticle (AuNP) probe. This technique relies on a self-aggregation method, when the AuNP aggregation is induced by an increasing of salt concentrations with visual detection. The presence of IMNV-LAMP target prevented an AuNP aggregation and a solution remained as pink color of AuNP, while non-complementary targets cannot prevent AuNP aggregation, resulting in a visible color change to purple color after addition of salt. By using the combination of LAMP and AuNP probe system, the total assay interval required approximately 50 min (exclude RNA preparation). Detection limit was 10 copies of IMNV RNA in vitro transcript that comparable to that of LAMP followed by LFD and nested RT-PCR, but it was 100-times more sensitive than RT-PCR methods. This assay can be adapted easily for rapid detection of other shrimp infectious diseases agents at low-cost with robust reagents and using a simple colorimetric detection method.
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Affiliation(s)
- Narong Arunrut
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
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32
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Jiang YS, Li B, Milligan JN, Bhadra S, Ellington AD. Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly. J Am Chem Soc 2013; 135:7430-3. [PMID: 23647466 DOI: 10.1021/ja4023978] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Catalytic hairpin assembly (CHA) is an enzyme-free amplification method that has previously proven useful in amplifying and transducing signals at the terminus of nucleic acid amplification reactions. Here, for the first time, we engineered CHA to be thermostable from 37 to 60 °C and in consequence have generalized its application to the real-time detection of isothermal amplification reactions. CHA circuits were designed and optimized for both high- and low-temperature rolling circle amplification (RCA) and strand displacement amplification (SDA). The resulting circuits not only increased the specificity of detection but also improved the sensitivity by as much as 25- to 10000-fold over comparable real-time detection methods. These methods have been condensed into a set of general rules for the design of thermostable CHA circuits with high signals and low noise.
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Affiliation(s)
- Yu Sherry Jiang
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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Suebsing R, Prombun P, Srisala J, Kiatpathomchai W. Loop-mediated isothermal amplification combined with colorimetric nanogold for detection of the microsporidian Enterocytozoon hepatopenaei in penaeid shrimp. J Appl Microbiol 2013; 114:1254-63. [PMID: 23387348 DOI: 10.1111/jam.12160] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 12/01/2022]
Abstract
AIMS Enterocytozoon hepatopenaei is an emerging microsporidian parasite that has been linked to recent losses caused by white faeces syndrome (WFS) in cultivated giant or black tiger shrimp Penaeus (Penaeus) monodon and whiteleg shrimp Penaeus (Litopenaeus) vannamei in Asia. To more accurately assess its impact on shrimp production and to determine reservoir carriers for control measures, our objective was to establish a loop-mediated isothermal amplification (LAMP) assay combined with colorimetric nanogold (AuNP) for rapid, sensitive and inexpensive detection of this parasite. METHODS AND RESULTS A set of six specific primers was designed to successfully detect the SSU rRNA gene of E. hepatopenaei by a LAMP reaction of 45 in at 65°C combined with visual detection of the amplification product via hybridization at 65°C for 5 min with a ssDNA-labelled nanogold probe, followed by salt-induced AuNP aggregation (total assay time, approximately 50 min). This method gave similar results to LAMP followed by electrophoresis or spectrophotometric detection, and it was more sensitive (0·02 fg total DNA) than a conventional nested PCR (0·2 fg total DNA). The new method gave negative results with shrimp DNA templates extracted from diseased shrimp containing other pathogens, indicating that the LAMP-AuNP assay was specific for E. hepatopenaei. CONCLUSIONS Without sacrificing sensitivity or specificity, the new LAMP-AuNP assay significantly reduced the time, ease and cost for molecular detection of E. hepatopenaei in shrimp. SIGNIFICANCE AND IMPACT OF THE STUDY The new method employs simple, inexpensive equipment and involves simple steps making it applicable for small field laboratories. Wider application of the method to screen broodstock before use in a hatchery, to screen postlarvae before stocking shrimp ponds, to test for natural carriers and to monitor shrimp in rearing ponds would help to assess and reduce the negative impact of this parasite in shrimp farming.
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Affiliation(s)
- R Suebsing
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
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