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Zhao L, Wang J, Sun XX, Wang J, Chen Z, Xu X, Dong M, Guo YN, Wang Y, Chen P, Gao W, Geng Y. Development and Evaluation of the Rapid and Sensitive RPA Assays for Specific Detection of Salmonella spp. in Food Samples. Front Cell Infect Microbiol 2021; 11:631921. [PMID: 33718280 PMCID: PMC7946851 DOI: 10.3389/fcimb.2021.631921] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella spp. is among the main foodborne pathogens which cause serious foodborne diseases. An isothermal real-time recombinase polymerase amplification (RPA) and lateral flow strip detection (LFS RPA) were used to detect Salmonella spp. targeting the conserved sequence of invasion protein A (invA). The Real-time RPA was performed in a portable florescence scanner at 39°C for 20 min. The LFS RPA was performed in an incubator block at 39°C for 15 min, under the same condition that the amplifications could be inspected by the naked eyes on the LFS within 5 min. The detection limit of Salmonella spp. DNA using real-time RPA was 1.1 × 101 fg, which was the same with real-time PCR but 10 times higher than that of LFS RPA assay. Moreover, the practicality of discovering Salmonella spp. was validated with artificially contaminated lamb, chicken, and broccoli samples. The analyzing time dropped from 60 min to proximately 5–12 min on the basis of the real-time and LFS RPA assays compared with the real-time PCR assay. Real-time and LFS RPA assays’ results were equally reliable. There was no cross-reactivity with other pathogens in both assays. In addition, the assays had good stability. All of these helped to show that the developed RPA assays were simple, rapid, sensitive, credible, and could be a potential point-of-need (PON) test required mere resources.
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Affiliation(s)
- Liwei Zhao
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Jianchang Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Xiao Xia Sun
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Jinfeng Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Zhimin Chen
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Xiangdong Xu
- School of Public Health, Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China
| | - Mengyuan Dong
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Ya-Nan Guo
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yuanyuan Wang
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Pingping Chen
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Weijuan Gao
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yunyun Geng
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
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Narayanamurthy V, Jeroish ZE, Bhuvaneshwari KS, Samsuri F. Hepatitis C virus (HCV) diagnosis via microfluidics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:740-763. [PMID: 33511975 DOI: 10.1039/d0ay02045a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Humans are subjected to various diseases; hence, proper diagnosis helps avoid further disease consequences. One such severe issue that could cause significant damage to the human liver is the hepatitis C virus (HCV). Several techniques are available to detect HCV under various categories, such as detection through antibodies, antigens, and RNA. Although immunoassays play a significant role in discovering hepatitis viruses, there is a need for point-of-care tests (POCT). Some developing strategies are required to ensure the appropriate selection of POCT for HCV detection, initiate appropriate antiviral therapy, and define associated risks, which will be critical in achieving optimal outcomes. Though molecular assays are precise, reproducible, sensitive, and specific, alternative strategies are required to enhance HCV diagnosis among the infected population. Herein, we described and assessed the potential of various microfluidic detection techniques and confirmatory approaches used in present communities. In addition, current key market players in HCV chip-based diagnosis and the future perspectives on the basis of which the diagnosis can be made easier are presented in the present review.
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Affiliation(s)
- Vigneswaran Narayanamurthy
- Fakulti Teknologi Kejuruteraan Elektrik dan Elektronik, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, 76100 Durian Tunggal, Melaka, Malaysia.
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Chaibun T, Puenpa J, Ngamdee T, Boonapatcharoen N, Athamanolap P, O'Mullane AP, Vongpunsawad S, Poovorawan Y, Lee SY, Lertanantawong B. Rapid electrochemical detection of coronavirus SARS-CoV-2. Nat Commun 2021; 12:802. [PMID: 33547323 PMCID: PMC7864991 DOI: 10.1038/s41467-021-21121-7] [Citation(s) in RCA: 240] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/μL of N and S genes, in less than 2 h. Sensor evaluation with 106 clinical samples, including 41 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.
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Affiliation(s)
- Thanyarat Chaibun
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tatchanun Ngamdee
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Nimaradee Boonapatcharoen
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pornpat Athamanolap
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand
| | - Anthony Peter O'Mullane
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Su Yin Lee
- Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Kedah, Malaysia
| | - Benchaporn Lertanantawong
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand.
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Janik M, Hamidi SV, Koba M, Perreault J, Walsh R, Bock WJ, Smietana M. Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor. LAB ON A CHIP 2021; 21:397-404. [PMID: 33331382 DOI: 10.1039/d0lc01069c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds of thousands of samples are required daily. This work presents the first research to date on direct, real-time and label-free isothermal DNA amplification monitoring using a microcavity in-line Mach-Zehnder interferometer (μIMZI) fabricated in an optical fiber. The solution based on μIMZI offers a great advantage over many other sensing concepts - making possible optical analysis in just picoliter sample volumes. The selectivity of the biosensor is determined by DNA primers immobilized on the microcavity's surface that act as selective biorecognition elements and trigger initiation of the DNA amplification process. In this study, we verified the sensing concept using circular DNA designed to target the H5N1 influenza virus. The developed biosensor exhibits an ultrahigh refractive index sensitivity reaching 14 000 nm per refractive index unit and a linear detection range between 9.4 aM and 94 pM of the target DNA sequence. Within a 30 min period, the amplification of as little as 9.4 aM DNA can be effectively detected, with a calculated limit of detection of as low as 0.2 aM DNA, suggesting that this methodology holds great promise in practical disease diagnosis applications in the future.
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Affiliation(s)
- Monika Janik
- Warsaw University of Technology, Institute of Microelectronics and Optoelectronics, Koszykowa 75, 00-662, Warszawa, Poland.
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A Novel Approach to the Bioluminescent Detection of the SARS-CoV-2 ORF1ab Gene by Coupling Isothermal RNA Reverse Transcription Amplification with a Digital PCR Approach. Int J Mol Sci 2021; 22:ijms22031017. [PMID: 33498408 PMCID: PMC7864175 DOI: 10.3390/ijms22031017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 01/17/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus, which first emerged in December 2019, represents an ongoing global public health emergency. Here, we developed an improved and highly sensitive approach to SARS-CoV-2 detection via coupling bioluminescence in real-time (BART) and reverse-transcriptase loop-mediated amplification (RT-LAMP) protocols (RT-LAMP-BART) and was also compatible with a digital LAMP system (Rainsuit), which did not allow for real-time quantification but did, nonetheless, facilitate absolute quantification with a comparable detection limit of 104 copies/mL. Through improving RNA availability in samples to ensure the target RNA present in reaction, we additionally developed a simulated digital RT-LAMP approach using this same principle to enlarge the overall reaction volume and to achieve real-time detection with a limit of detection of 10 copies/mL, and with further improvements in the overall dynamic range of this assay system being achieved through additional optimization.
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He Y, Liu Y, Cheng L, Yang Y, Qiu B, Guo L, Wang Y, Lin Z, Hong G. Highly Reproducible and Sensitive Electrochemiluminescence Biosensors for HPV Detection Based on Bovine Serum Albumin Carrier Platforms and Hyperbranched Rolling Circle Amplification. ACS APPLIED MATERIALS & INTERFACES 2021; 13:298-305. [PMID: 33382593 DOI: 10.1021/acsami.0c20742] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Most DNA-based electrochemiluminescence (ECL) biosensors are established through the self-assembly of thiolated single-stranded DNA (ssDNA) probes on the Au electrode surface. Because of this random assembly process, a significant discrepancy exists in the distribution of a modified DNA film on different electrodes, which greatly affects the reproducibility of a biosensor. In this study, a porous bovine serum albumin (BSA) layer was first modified on the electrode surface, which can improve the position distribution and spatial orientation of the self-assembly ssDNA probe. It was then coupled with hyperbranched rolling circle amplification to develop the high-reproducibility-and-sensitivity ECL biosensor for human papillomavirus 16 E6 and E7 oncogene detection. In the presence of the target DNA, the surface of the electrode accumulates abundant amplified products through reaction, which contain double-stranded DNA (dsDNA) fragments of different lengths, followed by plentiful dichlorotris (1,10-phenanthroline) ruthenium(II) hydrate (Ru(phen)32+, acting as an ECL indicator) insertion into grooves of dsDNA fragments, and a strong signal can be detected. There is a linear relationship between the signal and the target concentration range from 10 fM to 15 pM, and the detection limit is 7.6 fM (S/N = 3). After the BSA modification step, the relative standard deviation was reduced from 9.20 to 3.96%, thereby achieving good reproducibility. The proposed ECL strategy provides a new method for constructing high-reproducibility-and-sensitivity ECL biosensors.
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Affiliation(s)
- Yinghao He
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen 361003, People's Republic of China
| | - Yinhuan Liu
- Department of Laboratory Medicine, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou 350007, People's Republic of China
| | - Lingjun Cheng
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen 361003, People's Republic of China
| | - Yuanyuan Yang
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen 361003, People's Republic of China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, People's Republic of China
| | - Longhua Guo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, People's Republic of China
| | - Yan Wang
- Department of Cardiology, The Affiliated Cardiovascular Hospital of Xiamen University, Medical College of Xiamen University, Xiamen 361004, People's Republic of China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, People's Republic of China
| | - Guolin Hong
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen 361003, People's Republic of China
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Paper-Based Molecular Diagnostics. Bioanalysis 2021. [DOI: 10.1007/978-981-15-8723-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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58
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Rezaei M, Razavi Bazaz S, Zhand S, Sayyadi N, Jin D, Stewart MP, Ebrahimi Warkiani M. Point of Care Diagnostics in the Age of COVID-19. Diagnostics (Basel) 2020; 11:E9. [PMID: 33374612 PMCID: PMC7822494 DOI: 10.3390/diagnostics11010009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022] Open
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated serious respiratory disease, coronavirus disease 2019 (COVID-19), poses a major threat to global public health. Owing to the lack of vaccine and effective treatments, many countries have been overwhelmed with an exponential spread of the virus and surge in the number of confirmed COVID-19 cases. Current standard diagnostic methods are inadequate for widespread testing as they suffer from prolonged turn-around times (>12 h) and mostly rely on high-biosafety-level laboratories and well-trained technicians. Point-of-care (POC) tests have the potential to vastly improve healthcare in several ways, ranging from enabling earlier detection and easier monitoring of disease to reaching remote populations. In recent years, the field of POC diagnostics has improved markedly with the advent of micro- and nanotechnologies. Due to the COVID-19 pandemic, POC technologies have been rapidly innovated to address key limitations faced in existing standard diagnostic methods. This review summarizes and compares the latest available POC immunoassay, nucleic acid-based and clustered regularly interspaced short palindromic repeats- (CRISPR)-mediated tests for SARS-CoV-2 detection that we anticipate aiding healthcare facilities to control virus infection and prevent subsequent spread.
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Affiliation(s)
- Meysam Rezaei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
| | - Sareh Zhand
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
| | - Nima Sayyadi
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University Sydney, Sydney, NSW 2109, Australia
| | - Dayong Jin
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - Martin P. Stewart
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Molecular Medicine, Sechenov University, 119991 Moscow, Russia
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Bioluminescent detection of isothermal DNA amplification in microfluidic generated droplets and artificial cells. Sci Rep 2020; 10:21886. [PMID: 33318599 PMCID: PMC7736893 DOI: 10.1038/s41598-020-78996-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/02/2020] [Indexed: 12/02/2022] Open
Abstract
Microfluidic droplet generation affords precise, low volume, high throughput opportunities for molecular diagnostics. Isothermal DNA amplification with bioluminescent detection is a fast, low-cost, highly specific molecular diagnostic technique that is triggerable by temperature. Combining loop-mediated isothermal nucleic acid amplification (LAMP) and bioluminescent assay in real time (BART), with droplet microfluidics, should enable high-throughput, low copy, sequence-specific DNA detection by simple light emission. Stable, uniform LAMP–BART droplets are generated with low cost equipment. The composition and scale of these droplets are controllable and the bioluminescent output during DNA amplification can be imaged and quantified. Furthermore these droplets are readily incorporated into encapsulated droplet interface bilayers (eDIBs), or artificial cells, and the bioluminescence tracked in real time for accurate quantification off chip. Microfluidic LAMP–BART droplets with high stability and uniformity of scale coupled with high throughput and low cost generation are suited to digital DNA quantification at low template concentrations and volumes, where multiple measurement partitions are required. The triggerable reaction in the core of eDIBs can be used to study the interrelationship of the droplets with the environment and also used for more complex chemical processing via a self-contained network of droplets, paving the way for smart soft-matter diagnostics.
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Huang T, Li L, Liu X, Chen Q, Fang X, Kong J, Draz MS, Cao H. Loop-mediated isothermal amplification technique: principle, development and wide application in food safety. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5551-5561. [PMID: 33216073 DOI: 10.1039/d0ay01768j] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Food safety is a major and enduring challenge and has a profound impact on the quality of human life. Loop-mediated isothermal amplification (LAMP) is a relatively novel gene amplification method under isothermal conditions with rapidity, simplicity and high specificity. This review will describe the principles and development of the LAMP technique along with its advantages and disadvantages, such as LAMP integrated on classical microfluidic chips, paper-chips, electrochemical devices, nanomaterials and digital devices. Moreover, we will systematically and comprehensively review its applications in the field of food safety, such as in the detection of foodborne pathogens, allergens and organophosphorus pesticides and genetically modified organisms; finally its development trends in food safety will be discussed.
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Affiliation(s)
- Tianzeng Huang
- College of Food Science and Technology, Hainan University, 58 Renmin Avenue, Haikou 570228, China.
| | - Linzhi Li
- College of Food Science and Technology, Hainan University, 58 Renmin Avenue, Haikou 570228, China.
| | - Xing Liu
- College of Food Science and Technology, Hainan University, 58 Renmin Avenue, Haikou 570228, China. and Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China and Engineering Research Center of Utilization of Tropical Polysaccharide Resources, Haikou 570228, China and Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
| | - Qi Chen
- College of Food Science and Technology, Hainan University, 58 Renmin Avenue, Haikou 570228, China. and Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China and Engineering Research Center of Utilization of Tropical Polysaccharide Resources, Haikou 570228, China and Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
| | - Xueen Fang
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Jilie Kong
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Mohamed S Draz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA and Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Hongmei Cao
- College of Food Science and Technology, Hainan University, 58 Renmin Avenue, Haikou 570228, China. and Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China and Engineering Research Center of Utilization of Tropical Polysaccharide Resources, Haikou 570228, China and Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China
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Kumar Y, Narsaiah K. Rapid point-of-care testing methods/devices for meat species identification: A review. Compr Rev Food Sci Food Saf 2020; 20:900-923. [PMID: 33443804 DOI: 10.1111/1541-4337.12674] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/30/2020] [Accepted: 10/25/2020] [Indexed: 12/15/2022]
Abstract
The authentication of animal species is an important issue due to an increasing trend of adulteration and mislabeling of animal species in processed meat products. Polymerase chain reaction is the most sensitive and specific technique for nucleic acid-based animal species detection. However, it is a time-consuming technique that requires costly thermocyclers and sophisticated labs. In recent times, there is a need of on-site detection by point-of-care (POC) testing methods and devices under low-resource settings. These POC devices must be affordable, sensitive, specific, user-friendly, rapid and robust, equipment free, and delivered to the end users. POC devices should also confirm the concept of micro total analysis system. This review discusses POC testing methods and devices that have been developed for meat species identification. Recent developments in lateral flow assay-based devices for the identification of animal species in meat products are also reviewed. Advancements in increasing the efficiency of lateral flow detection are also discussed.
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Affiliation(s)
- Yogesh Kumar
- Department of Agricultural Structures and Environmental Control, ICAR-Central Institute of Post-Harvest Engineering and Technology (CIPHET), Ludhiana, India
| | - Kairam Narsaiah
- Department of Agricultural Structures and Environmental Control, ICAR-Central Institute of Post-Harvest Engineering and Technology (CIPHET), Ludhiana, India
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Diagnostic validation of a rapid and field-applicable PCR-lateral flow test system for point-of-care detection of cyprinid herpesvirus 3 (CyHV-3). PLoS One 2020; 15:e0241420. [PMID: 33125418 PMCID: PMC7598509 DOI: 10.1371/journal.pone.0241420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/29/2020] [Indexed: 11/19/2022] Open
Abstract
Koi herpesvirus disease (KHVD) is a highly infectious disease leading to outbreaks and mass mortality in captive and free-ranging common carp and koi carp. Outbreaks may result in high morbidity and mortality which can have a severe economic impact along the supply chain. Currently, control and prevention of KHVD relies on avoiding exposure to the virus based on efficient hygiene and biosecurity measures. An early diagnosis of the disease is crucial to prevent its spread and to minimize economic losses. Therefore, an easy-to-handle, sensitive, specific and reliable test prototype for a point-of-care detection of KHV was developed and evaluated in this study. We used a multiplex-endpoint-PCR followed by a specific probe hybridization step. PCR-products/hybridization-products were visualized with a simple and universal lateral flow immunoassay (PCR-LFA). Fifty-four gill tissue samples (KHV-positive n = 33, KHV-negative n = 21) and 46 kidney samples (KHV-positive n = 24, KHV-negative n = 22) were used to determine diagnostic sensitivity and specificity of the PCR-LFA. In addition, the usability of PCR-LFA to detect CyHV-3-DNA in gill swabs taken from 20 perished common carp during a KHVD-outbreak in a commercial carp stock was examined. This assay gave test results within approximately 60 min. It revealed a detection limit of 9 KHV gene copies/μl (95% probability), a diagnostic specificity of 100%, and diagnostic sensitivity of 94.81% if samples were tested in a single test run only. PCR inhibition was noticed when examining gill swab samples without preceding extraction of DNA or sample dilution. Test sensitivity coud be enhanced by examining samples in five replicates. Overall, our PCR-LFA proved to be a specific, easy-to-use and time-saving point-of-care-compatible test for the detection of KHV-DNA. Regarding gill swab samples, further test series using a higher number of clinical samples should be analyzed to confirm the number of replicates and the sample processing necessary to reveal a 100% diagnostic sensitivity.
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Visual detection of high-risk HPV16 and HPV18 based on loop-mediated isothermal amplification. Talanta 2020; 217:121015. [DOI: 10.1016/j.talanta.2020.121015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 11/24/2022]
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DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment. SENSORS 2020; 20:s20164648. [PMID: 32824787 PMCID: PMC7472328 DOI: 10.3390/s20164648] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022]
Abstract
Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens.
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Wang Y, Ge G, Mao R, Wang Z, Sun YZ, Du YG, Gao XH, Qi RQ, Chen HD. Genotyping of 30 kinds of cutaneous human papillomaviruses by a multiplex microfluidic loop-mediated isothermal amplification and visual detection method. Virol J 2020; 17:99. [PMID: 32646520 PMCID: PMC7345449 DOI: 10.1186/s12985-020-01373-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
Background Human papillomaviruses (HPVs), a group of non-enveloped small viruses with double-stranded circular DNA which lead to multiple skin diseases such as benign warts, are commonly seen in clinics. The current HPV detection systems aim mainly at mucosal HPVs, however, an efficient clinical approach for cutaneous HPVs detection is lacking. Objectives To establish a rapid detection system for cutaneous HPVs using a colorimetric loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue (HNB) dye in combination with microfluidic technology. Methods L1 DNA sequences of the 30 cutaneous HPVs were chemically synthesized, and LAMP primers against L1 DNA were designed with use of an online LAMP designing tool. Isothermal amplification was performed with use of a water bath and the amplification results were inspected with the naked eye. Using PCR sequencing as a control method, the specificity and sensitivity of the new detection system were obtained by detecting clinical samples. Results The lower detection limit of the LAMP assay was 107 viral DNA copies/μl when tested on synthesized L1 DNA sequences, which was better than the conventional PCR. Compared to PCR sequencing, the sensitivity of HPV27, HPV2, HPV1, HPV57, HPV3, HPV4, HPV7 and HPV75 genotypes detections were 100%, whereas the specificity was 34.55, 45.12, 95.83, 98.59 and 97.62% respectively, when tested on clinical samples. Conclusions The new cutaneous type HPV detection system is characterized by both a good sensitivity and specificity compared to conventional methods.
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Affiliation(s)
- Yining Wang
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China
| | - Ge Ge
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Rui Mao
- Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Zhuo Wang
- Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Yu-Zhe Sun
- Dermatology Hospital of Southern Medical University, No. 2 Lujing Road, Yuexiu District, Guangzhou, Guangdong Province, 510091, PR China.
| | - Yu-Guang Du
- Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA and State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.
| | - Xing-Hua Gao
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.
| | - Rui-Qun Qi
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China. .,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.
| | - Hong-Duo Chen
- Department of Dermatology, The First Hospital of China Medical University, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,NHC Key Laboratory of Immunodermatology (China Medical University), No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology, Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China.,Key Laboratory of Immunodermatology (China Medical University), Department of education of Liaoning Province, No.155 Nanjing Bei Street, Heping District, Shenyang, Liaoning Province, 110001, PR China
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Chen Z, Liu X, Liu D, Li F, Wang L, Liu S. Ultrasensitive Electrochemical DNA Biosensor Fabrication by Coupling an Integral Multifunctional Zirconia-Reduced Graphene Oxide-Thionine Nanocomposite and Exonuclease I-Assisted Cleavage. Front Chem 2020; 8:521. [PMID: 32733846 PMCID: PMC7363972 DOI: 10.3389/fchem.2020.00521] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022] Open
Abstract
In this work, a simple but sensitive electrochemical DNA biosensor for nucleic acid detection was developed by taking advantage of exonuclease (Exo) I-assisted cleavage for background reduction and zirconia-reduced graphene oxide-thionine (ZrO2-rGO-Thi) nanocomposite for integral DNA recognition, signal amplification, and reporting. The ZrO2-rGO nanocomposite was obtained by a one-step hydrothermal synthesis method. Then, thionine was adsorbed onto the rGO surface, via π-π stacking, as an excellent electrochemical probe. The biosensor fabrication is very simple, with probe DNA immobilization and hybridization recognition with the target nucleic acid. Then, the ZrO2-rGO-Thi nanocomposite was captured onto an electrode via the multicoordinative interaction of ZrO2 with the phosphate group on the DNA skeleton. The adsorbed abundant thionine molecules onto the ZrO2-rGO nanocomposite facilitated an amplified electrochemical response related with the target DNA. Since upon the interaction of the ZrO2-rGO-Thi nanocomposite with the probe DNA an immobilized electrode may also occur, an Exo I-assisted cleavage was combined to remove the unhybridized probe DNA for background reduction. With the current proposed strategy, the target DNA related with P53 gene could be sensitively assayed, with a wide linear detection range from 100 fM to 10 nM and an attractive low detection limit of 24 fM. Also, the developed DNA biosensor could differentiate the mismatched targets from complementary target DNA. Therefore, it offers a simple but effective biosensor fabrication strategy and is anticipated to show potential for applications in bioanalysis and medical diagnosis.
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Affiliation(s)
- Zhiqiang Chen
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xueqian Liu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Dengren Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Fang Li
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Li Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Shufeng Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
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67
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Yin Y, Wu Z, Li G, Huang J, Guo Q, Meng X. A DNA molecular diagnostic technology with LAMP-like sensitivity based on one pair of hairpin primers-mediated isothermal polymerization amplification. Anal Chim Acta 2020; 1134:144-149. [PMID: 33059860 DOI: 10.1016/j.aca.2020.05.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/16/2020] [Accepted: 05/23/2020] [Indexed: 11/18/2022]
Abstract
With the rapid development of isothermal amplification technology, DNA molecular diagnosis has become an important reference for clinical treatment. In this work, we have designed a DNA molecular diagnostic technology with LAMP-like sensitivity for nucleic acid analysis and detection based on only one pair of hairpin primers. This DNA molecular diagnostic technology consists of Bst DNA polymerase and one pair of hairpin primers, which are designed easily by adding a stem-loop structure to a target binding domain. When the target is present, the polymerization reaction between the hairpin primers and the target generates a specific dumbbell DNA similar to LAMP, which triggers cyclic amplification reactions to extend a series of long dsDNA products with repeated sequences by inserting fluorescent dye Eva Green observed the increase in fluorescence signal. In our method, using the hairpin primers-mediated isothermal polymerization amplification, we can specifically monitor 3-5 copies of the target nucleic acid in the system without labeling and temperature cycling in the reaction. In addition, serum samples from 13 patients with suspected schistosomiasis were targeted; we further demonstrated the ability of the technology to detect complex clinic samples, and its potentially inestimable applicability in clinic early molecular diagnostic research.
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Affiliation(s)
- Yao Yin
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Zuoci Wu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Guangping Li
- Hunan Province Institute of Schistosoma, Yueyang, 414000, China
| | - Jin Huang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
| | - Qiuping Guo
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China.
| | - Xiangxian Meng
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China.
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68
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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69
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Jiang L, Li X, Gu R, Mu D. Nanoparticles-Based Biosensor Coupled with Multiplex Loop-Mediated Isothermal Amplification for Detection of Staphylococcus aureus and Identification of Methicillin-Resistant S. aureus. Infect Drug Resist 2020; 13:1251-1262. [PMID: 32431523 PMCID: PMC7198443 DOI: 10.2147/idr.s243881] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/30/2020] [Indexed: 01/17/2023] Open
Abstract
Introduction Staphylococcus aureus (S. aureus), including methicillin-resistant S. aureus (MRSA), is a common human pathogen, which can cause a variety of infections from mild to severe. In this article, a new diagnostic method called multiplex loop-mediated isothermal amplification combined with nanoparticles-based lateral flow biosensor (mLAMP-LFB) has been developed, which was proved to be fast, reliable, and simple for detecting S. aureus, and differentiate MRSA from methicillin-susceptible S. aureus (MSSA). Materials and Methods We designed a set of six primers targeting the nuc gene of S. aureus, and a set of five primers targeting the mecA gene of MRSA. The lateral flow biosensor visually reported the S. aureus-LAMP results within 2 mins. S. aureus species and non-S. aureus species were used to identify the specificity and sensitivity of the assay. Results The best conditions for LAMP were 50 mins at 63°C, and the sensitivity was 100 fg. No cross-reactivity was shown and the specificity of this assay is 100%. This assay requires 20 mins for DNA preparation, 50 mins for isothermal amplification and 2 mins for biosensor detection. The total time is within 75 mins. Among 96 sputum samples, LAMP-LFB and traditional culture method showed the same results, 8 (8.33%) samples were MRSA-positive, and 9 (9.38%) samples were MSSA-positive. Seven (7.29%) samples were MRSA-positive and 7 (7.29%) were MSSA-positive by PCR method. Compared with the culture method, diagnostic accuracy of m-LAMP-LFB assay was 100%. The results showed that the m-LAMP-LFB method has better detection ability than the PCR method. Discussion In short, this m-LAMP-LFB assay is a specific and sensitive method that can quickly identify S. aureus stains, and distinguish MRSA from MSSA, and can be used as a new molecular method for detection of S. aureus in laboratories.
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Affiliation(s)
- Luxi Jiang
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaomeng Li
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, People's Republic of China
| | - Rumeng Gu
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, People's Republic of China
| | - Deguang Mu
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, People's Republic of China
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70
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Fan Z, Feng X, Zhang W, Zhang X, Lin JM. Rapid detection of high-risk HPV16 and HPV18 based on microchip electrophoresis. J Pharm Anal 2020; 10:329-333. [PMID: 32923006 PMCID: PMC7474136 DOI: 10.1016/j.jpha.2020.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/23/2020] [Accepted: 04/13/2020] [Indexed: 11/30/2022] Open
Abstract
Researches on detection of human papillomavirus (HPV) high-risk samples were carried out by polymerase chain reaction (PCR) coupled with microchip electrophoresis (MCE). Herein, we introduced a simple, rapid, automated method for detecting high-risk samples HPV16 and HPV18. In this research, general primers were initially selected to obtain sufficient detectable yield by PCR to verify feasibility of MCM method for HPV detection, then type-specific primers were further used to evaluate the specificity of MCE method. The results indicated MCE method was capable of specifically detecting high-risk HPV16 and HPV18, and also enabled simultaneous detection of multiplex samples. This MCE method described here has been successfully applied to HPV detection and displayed excellent reliability demonstrating by sequencing results. The inherent capability of MCE facilitated HPV detection conducted in a small chip with automated, high throughput, massive parallelized analysis. We envision that MCE method will definitely pave a way for clinical diagnosis, and even on-site screening of cervical cancer. A rapid, automatic assay was established for HPV detection. The described method exhibited the advantages of facile operation mode. The proposed method is of high sensitivity, specificity and reproducibility.
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Affiliation(s)
- Zhaoxuan Fan
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.,Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
| | - Xiao Feng
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Weifei Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.,School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong 518060, PR China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
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71
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Bialy RM, Ali MM, Li Y, Brennan JD. Protein-Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer-Containing DNA Primer. Chemistry 2020; 26:5085-5092. [PMID: 32096262 DOI: 10.1002/chem.202000245] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/21/2020] [Indexed: 12/22/2022]
Abstract
We report a method to detect proteins via suppression of rolling circle amplification (RCA) by using an appropriate aptamer as the linear primer (denoted as an aptaprimer) to initiate RCA. In the absence of a protein target, the aptaprimer is free to initiate RCA, which can produce long DNA products that are detected via binding of a fluorescent intercalating dye. Introduction of a target causes the primer region within the aptamer to become unavailable for binding to the circular template, inhibiting RCA. Using SYBR Gold or QuantiFluor dyes as fluorescent probes to bind to the RCA reaction product, it is possible to produce a generic protein-modulated RCA assay system that does not require fluorophore- or biotin-modified DNA species, substantially reducing complexity and cost of reagents. Based on this modulation of RCA, we demonstrate the ability to produce both solution and paper-based assays for rapid and quantitative detection of proteins including platelet derived growth factor and thrombin.
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Affiliation(s)
- Roger M Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Monsur M Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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Mao K, Min X, Zhang H, Zhang K, Cao H, Guo Y, Yang Z. Paper-based microfluidics for rapid diagnostics and drug delivery. J Control Release 2020; 322:187-199. [PMID: 32169536 DOI: 10.1016/j.jconrel.2020.03.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/13/2020] [Accepted: 03/07/2020] [Indexed: 02/07/2023]
Abstract
Paper is a common material that is promising for constructing microfluidic chips (lab-on-a-paper) for diagnostics and drug delivery for biomedical applications. In the past decade, extensive research on paper-based microfluidics has accumulated a large number of scientific publications in the fields of biomedical diagnosis, food safety, environmental health, drug screening and delivery. This review focuses on the recent progress on paper-based microfluidic technology with an emphasis on the design, optimization and application of the technology platform, in particular for medical diagnostics and drug delivery. Novel advances have concentrated on engineering paper devices for point-of-care (POC) diagnostics, which could be integrated with nucleic acid-based tests and isothermal amplification experiments, enabling rapid sample-to-answer assays for field testing. Among the isothermal amplification experiments, loop-mediated isothermal amplification (LAMP), an extremely sensitive nucleic acid test, specifically identifies ultralow concentrations of DNA/RNA from practical samples for diagnosing diseases. We thus mainly focus on the paper device-based LAMP assay for the rapid infectious disease diagnosis, foodborne pathogen analysis, veterinary diagnosis, plant diagnosis, and environmental public health evaluation. We also outlined progress on paper microfluidic devices for drug delivery. The paper concludes with a discussion on the challenges of this technology and our insights into how to advance science and technology towards the development of fully functional paper devices in diagnostics and drug delivery.
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Affiliation(s)
- Kang Mao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002, China
| | - Xiaocui Min
- Guangzhou Huali Science and Technology Vocational College, Guangzhou 511325, China
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002, China.
| | - Kuankuan Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002, China
| | - Haorui Cao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002, China
| | - Yongkun Guo
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, United Kingdom.
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Hong H, Sun C, Wei S, Sun X, Mutukumira A, Wu X. Development of a real-time recombinase polymerase amplification assay for rapid detection of Salmonella in powdered infant formula. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2019.104579] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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74
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Veltkamp HW, Akegawa Monteiro F, Sanders R, Wiegerink R, Lötters J. Disposable DNA Amplification Chips with Integrated Low-Cost Heaters. MICROMACHINES 2020; 11:E238. [PMID: 32106462 PMCID: PMC7143804 DOI: 10.3390/mi11030238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 01/03/2023]
Abstract
Fast point-of-use detection of, for example, early-stage zoonoses, e.g., Q-fever, bovine tuberculosis, or the Covid-19 coronavirus, is beneficial for both humans and animal husbandry as it can save lives and livestock. The latter prevents farmers from going bankrupt after a zoonoses outbreak. This paper describes the development of a fabrication process and the proof-of-principle of a disposable DNA amplification chip with an integrated heater. Based on the analysis of the milling process, metal adhesion studies, and COMSOL MultiPhysics heat transfer simulations, the first batch of chips has been fabricated and successful multiple displacement amplification reactions are performed inside these chips. This research is the first step towards the development of an early-stage zoonoses detection device. Tests with real zoonoses and DNA specific amplification reactions still need to be done.
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Affiliation(s)
- Henk-Willem Veltkamp
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Fernanda Akegawa Monteiro
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Remco Sanders
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Remco Wiegerink
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Joost Lötters
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
- Bronkhorst High-Tech BV, Nijverheidsstraat 1A, 7261 AK Ruurlo, The Netherlands
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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Zhao W, Tian S, Huang L, Liu K, Dong L. The review of Lab-on-PCB for biomedical application. Electrophoresis 2020; 41:1433-1445. [PMID: 31945803 DOI: 10.1002/elps.201900444] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 12/29/2022]
Abstract
Prevention of infectious diseases, diagnosis of diseases, and determination of treatment options all rely on biosensors to detect and analyze biomarkers, which are usually divided into four parts: cell analysis, biochemical analysis, immunoassay, and molecular diagnosis. However, traditional biosensing devices are expensive, bulky, and require a lot of time to detect, which also limited its application in resource-limited areas. In recent years, Lab-on-PCB, which combines biosensing technology and PCB technology, has been widely used in biomedical applications due to its high integration, personalized design, and easy mass production. Among these Lab-on-PCB sensing devices, the PCB circuit plays an important role. It can be directly used as a resistance sensor to count cells, and also used as a control device to automatically control the detection device. Flexible PCBs can be used to make wearable medical biosensors. In addition, due to the high degree of integration of the PCB circuit, Lab-on-PCB can perform multiple inspections on the same platform, which reduces the inspection time equivalently. Therefore, in this review paper, we discuss the application of Lab-on-PCB in four analysis methods of cell analysis, biochemical analysis, immunoassay, and molecular diagnosis, and give some suggestions for improvement and future development trends at the end.
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Affiliation(s)
- Wenhao Zhao
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Shulin Tian
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Lei Huang
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Ke Liu
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Lijuan Dong
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, P.R. China
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77
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Miao G, Zhang L, Zhang J, Ge S, Xia N, Qian S, Yu D, Qiu X. Free convective PCR: From principle study to commercial applications-A critical review. Anal Chim Acta 2020; 1108:177-197. [PMID: 32222239 DOI: 10.1016/j.aca.2020.01.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022]
Abstract
Polymerase chain reaction (PCR) is an extremely important tool for molecular diagnosis, as it can specifically amplify nucleic acid templates for sensitive detection. As another division of PCR, free convective PCR was invented in 2001, which can be performed in a capillary tube pseudo-isothermally within a significantly short time. Convective PCR thermal cycling is implemented by inducing thermal convection inside the capillary tube, which stratifies the reaction into spatially separate and stable melting, annealing, and extension zones created by the temperature gradient. Convective PCR is a promising tool that can be used for nucleic acid diagnosis as a point-of-care test (POCT) due to the significantly simplified heating strategy, reduced cost, and shortened detection time without sacrificing sensitivity and accuracy. Here, we review the history of free convective PCR from its invention to development and its commercial applications.
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Affiliation(s)
- Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Jing Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China.
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China.
| | - Shizhi Qian
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, 23529, USA.
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029, China.
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Hardinge P, Murray JAH. Full Dynamic Range Quantification using Loop-mediated Amplification (LAMP) by Combining Analysis of Amplification Timing and Variance between Replicates at Low Copy Number. Sci Rep 2020; 10:916. [PMID: 31969573 PMCID: PMC6976701 DOI: 10.1038/s41598-020-57473-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 11/09/2022] Open
Abstract
Quantification of nucleic acid targets at low copy number is problematic with the limit of detection at 95 percent confidence predicted to be 3 molecules or higher for quantitative PCR. Conversely the accuracy of digital PCR is diminished at higher concentrations of template approaching 100 percent positive partitions, with the Poisson distribution showing that an average of only 3 molecules per partition represents an amplification frequency of greater than 95 percent. Therefore a full range of template concentrations cannot be quantified accurately with these methods alone without dilution. Here we report the development of quantification metrics for use with loop-mediated amplification (LAMP) as a bridge between concentrated and dilute template concentrations. The basis for this is that real-time monitoring of LAMP reactions either by bioluminescent reporting (BART) or by fluorescent dye binding shows increasing variation in timings between replicates at low copy number due to the LAMP amplification mechanism. This effect increases with decreasing copy number, closely associated with the amplification frequency. The use of an artificial template showed that the increasing variation is not linked to the use of displacement primers during the initiation of amplification and is therefore a fundamental feature of the LAMP initiation event. Quantification between 1 and 10 copies of a template was successfully achieved with a number of methods with a low number of replicates with the strongest correlation to timing variance. These ultra-quantification methods for LAMP amplification either singularly or in combination have potential in a full dynamic range quantification strategy based on LAMP, in a closed tube, undiluted sample molecular diagnostic.
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Affiliation(s)
- Patrick Hardinge
- Cardiff School of Biosciences, Biomedical Science Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - James A H Murray
- Cardiff School of Biosciences, Biomedical Science Building, Museum Avenue, Cardiff, CF10 3AX, UK
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79
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Wu X, Song Z, Zhai X, Zuo L, Mei X, Xiang R, Kang Z, Zhou L, Wang H. Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick. Poult Sci 2020; 98:5401-5411. [PMID: 31265112 PMCID: PMC7107193 DOI: 10.3382/ps/pez372] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022] Open
Abstract
Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) are both important viruses seriously affecting poultry industry worldwide. In this study, reverse-transcription LAMP (RT-LAMP) was combined with lateral flow dipstick (LFD) forming a novel detection tool which could simultaneously detect IBV and NDV visually. Primers targeted the 5'-untranslated region (5'-UTR) of IBV genome and the conserved region of NDV large polymerase gene (LP). The specificity and sensitivity of this multiple reverse transcription-LAMP-LFD (mRT-LAMP-LFD) assay were compared with those of conventional RT-PCR, nested RT-PCR (nRT-PCR), quantification RT-PCR (qRT-PCR), and RT-LAMP monitored by electrophoresis. No non-specific amplifications were observed when the assays were tested with unrelated viruses. According to the sensitivity study, when detecting IBV or NDV alone, the lowest detection limits of mRT-LAMP-LFD were 100.8 IBV RNA copies/reaction and 100.7 NDV RNA copies/reaction. Furthermore, when detecting IBV and NDV simultaneously, the lowest detection limit was the same as that of the single detection assays. In the clinical sample study, mRT-LAMP-LFD performed the best among these assays. When tested with IBV or NDV single infected samples, the mean detection rates were 98.65% and 97.25%, respectively. In the IBV and NDV co-infected sample study, the mean detection rates of IBV and NDV were both 95%. This study showed that mRT-LAMP-LFD was a promising qualitative detection tool suitable for field single or multiple IBV and NDV detection.
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Affiliation(s)
- Xuan Wu
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Zengxu Song
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Xiwen Zhai
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Lei Zuo
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Xueran Mei
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Rong Xiang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Zhuangzhuang Kang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Long Zhou
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Hongning Wang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
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80
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Wang Y, Wang X, Gailing O, Xi D. Visual detection of Fusarium proliferatum based on dual-cycle signal amplification and T5 exonuclease. RSC Adv 2020; 10:35131-35135. [PMID: 35515665 PMCID: PMC9056896 DOI: 10.1039/d0ra06559e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/13/2020] [Indexed: 11/21/2022] Open
Abstract
A novel visual detection of Fusarium proliferatum species through recombinase polymerase amplification and rolling circle amplification was established. Single-stranded circle DNA was produced based on one strand of RPA product, which used as a template for rolling circle amplification. Schematic illustration of RPA-RCA-assisted dual amplification for visual detection of F. proliferatum.![]()
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Affiliation(s)
- Ying Wang
- College of Life Science
- Linyi University
- Linyi 276005
- People's Republic of China
- Faculty of Forest Sciences and Forest Ecology
| | - Xiaoqiang Wang
- Plant Protection Research Center
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences
- Qingdao 266101
- People's Republic of China
| | - Oliver Gailing
- Faculty of Forest Sciences and Forest Ecology
- University of Göttingen
- Göttingen 37077
- Germany
| | - Dongmei Xi
- College of Life Science
- Linyi University
- Linyi 276005
- People's Republic of China
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81
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Zhang M, Ye J, He JS, Zhang F, Ping J, Qian C, Wu J. Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review. Anal Chim Acta 2019; 1099:1-15. [PMID: 31986265 DOI: 10.1016/j.aca.2019.11.056] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022]
Abstract
Nucleic acid-based techniques could achieve highly sensitive detection by amplifying template molecules to millions of folds. It has been one of the most valued analytical methods and is applied in many detection fields, such as diagnosis of infectious diseases, food safety assurance and so on. Nucleic acid-based techniques consist of three steps: nucleic acid extraction, amplification, and product detection. Among them, the detection step plays a vital role because it shows the results directly. As the trend of detection is simple, rapid and instrument-free, it is of necessity to carry out visual detection, where the result read-out could be visible and distinguished by the naked eye. In this critical review, advanced visual detection methods are summarized and discussed in detail, aiming to promote the potential application in on-site detection.
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Affiliation(s)
- Mengyao Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Ye
- Zhijiangnan Think Tank, Zhejiang Institute of Science and Technology Information, Hangzhou, 310006, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China.
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82
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García-Bernalt Diego J, Fernández-Soto P, Crego-Vicente B, Alonso-Castrillejo S, Febrer-Sendra B, Gómez-Sánchez A, Vicente B, López-Abán J, Muro A. Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: towards a ready-to-use test. Sci Rep 2019; 9:14744. [PMID: 31611563 PMCID: PMC6791938 DOI: 10.1038/s41598-019-51342-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022] Open
Abstract
Schistosomiasis is one of the most prevalent Neglected Tropical Disease, affecting approximately 250 million people worldwide. Schistosoma mansoni is the most important species causing human intestinal schistosomiasis. Despite significant efforts in recent decades, the global disease burden of schistosomiasis remains extremely high. This could partly be attributed to the absence of accurate diagnostic tools, primarily in endemic areas. Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as a field-friendly alternative to many other complex molecular methods and it has been proposed as an ideal candidate for revolutionizing point-of-care molecular diagnostics. In a previous work, a LAMP-based method to detect S. mansoni DNA (SmMIT-LAMP) was developed by our research group for early diagnosis of active schistosomiasis in an experimental infection murine model. The SmMIT-LAMP has been further successfully evaluated in both human stool and snail samples and, recently, in human urine samples. In this study, we developed an important improvement for SmMIT-LAMP molecular assay, transforming it into a cold maintenance dry format suitable for potentially manufacturing as kit for ready-to-use for schistosomiasis diagnosis. This procedure could be applied to create dry LAMP kits for a laboratory setting and for diagnostic applications for other neglected tropical diseases.
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Affiliation(s)
- J García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - P Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain.
| | - B Crego-Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - S Alonso-Castrillejo
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - B Febrer-Sendra
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - A Gómez-Sánchez
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - B Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - J López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - A Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain.
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83
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Hardinge P, Murray JAH. Lack of specificity associated with using molecular beacons in loop mediated amplification assays. BMC Biotechnol 2019; 19:55. [PMID: 31370820 PMCID: PMC6676609 DOI: 10.1186/s12896-019-0549-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background Loop mediated isothermal amplification of nucleic acid templates is a rapid, sensitive and specific method suitable for molecular diagnostics. However the complexity of primer design and the number of primers involved can lead to false positives from non-specific primer interactions. Standard methods of LAMP detection utilise the increasing concentrations of DNA or inorganic pyrophosphate and therefore lack specificity for identifying the desired LAMP amplification. Molecular beacons used in PCR reactions are target specific and may enhance specificity with LAMP. Results We present a potential molecular beacon approach to LAMP detection targeting the single stranded region between loops, and test this for LAMP molecular beacons targeting the 35S promoter and NOS terminator sequences commonly used in GM crops. From these studies we show that molecular beacons used in LAMP, despite providing a change in fluorescent intensity with amplification, appear not to anneal to specific target sequences and therefore target specificity is not a benefit of this method. However, molecular beacons demonstrate a change in fluorescence which is indicative of LAMP amplification products. We identify the LAMP loop structure as likely to be responsible for this change in signal. Conclusions Molecular beacons can be used to detect LAMP amplification but do not provide sequence specificity. The method can be used to determine effectively LAMP amplification from other primer-driven events, but does not discriminate between different LAMP amplicons. It is therefore unsuitable for multiplex LAMP reactions due to non-specific detection of LAMP amplification. Electronic supplementary material The online version of this article (10.1186/s12896-019-0549-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Hardinge
- Cardiff School of Biosciences, Cardiff, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff, Museum Avenue, Cardiff, CF10 3AX, UK
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84
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Ding D, Gao P, Ma Q, Wang D, Xia F. Biomolecule-Functionalized Solid-State Ion Nanochannels/Nanopores: Features and Techniques. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804878. [PMID: 30756522 DOI: 10.1002/smll.201804878] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/18/2018] [Indexed: 05/12/2023]
Abstract
Solid-state ion nanochannels/nanopores, the biomimetic products of biological ion channels, are promising materials in real-world applications due to their robust mechanical and controllable chemical properties. Functionalizations of solid-state ion nanochannels/nanopores by biomolecules pave a wide way for the introduction of varied properties from biomolecules to solid-state ion nanochannels/nanopores, making them smart in response to analytes or external stimuli and regulating the transport of ions/molecules. In this review, two features for nanochannels/nanopores functionalized by biomolecules are abstracted, i.e., specificity and signal amplification. Both of the two features are demonstrated from three kinds of nanochannels/nanopores: nucleic acid-functionalized nanochannels/nanopores, protein-functionalized nanochannels/nanopores, and small biomolecule-functionalized nanochannels/nanopores, respectively. Meanwhile, the fundamental mechanisms of these combinations between biomolecules and nanochannels/nanopores are explored, providing reasonable constructs for applications in sensing, transport, and energy conversion. And then, the techniques of functionalizations and the basic principle about biomolecules onto the solid-state ion nanochannels/nanopores are summarized. Finally, some views about the future developments of the biomolecule-functionalized nanochannels/nanopores are proposed.
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Affiliation(s)
- Defang Ding
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 Lumo Road, Wuhan, 430074, P. R. China
| | - Pengcheng Gao
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 Lumo Road, Wuhan, 430074, P. R. China
| | - Qun Ma
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 Lumo Road, Wuhan, 430074, P. R. China
| | - Dagui Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 Lumo Road, Wuhan, 430074, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 Lumo Road, Wuhan, 430074, P. R. China
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
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85
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Pardy T, Sink H, Koel A, Rang T. Development of a Low-Cost, Wireless Smart Thermostat for Isothermal DNA Amplification in Lab-On-A-Chip Devices. MICROMACHINES 2019; 10:E437. [PMID: 31262090 PMCID: PMC6680506 DOI: 10.3390/mi10070437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 01/16/2023]
Abstract
Nucleic acid amplification tests (NAAT) are widely used for the detection of living organisms, recently applied in Lab-on-a-Chip (LoC) devices to make portable DNA analysis platforms. While portable LoC-NAAT can provide definitive test results on the spot, it requires specialized temperature control equipment. This work focuses on delivering a generalized low-cost, wireless smart thermostat for isothermal NAAT protocols in 2 cm × 3 cm LoC cartridges. We report on the design, prototyping, and evaluation results of our smart thermostat. The thermostat was evaluated by experimental and simulated thermal analysis using 3D printed LoC cartridges, in order to verify its applicability to various isothermal NAAT protocols. Furthermore, it was tested at the boundaries of its operating ambient temperature range as well as its battery life was evaluated. The prototype thermostat was proven functional in 20-30 °C ambient range, capable of maintaining the required reaction temperature of 12 isothermal NAAT protocols with 0.7 °C steady-state error in the worst case.
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Affiliation(s)
- Tamas Pardy
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia.
| | - Henri Sink
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia
| | - Ants Koel
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia
| | - Toomas Rang
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia
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86
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Gorgannezhad L, Stratton H, Nguyen NT. Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology. MICROMACHINES 2019; 10:E408. [PMID: 31248141 PMCID: PMC6630468 DOI: 10.3390/mi10060408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.
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Affiliation(s)
- Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Helen Stratton
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
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87
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Lee SH, Park SM, Kim BN, Kwon OS, Rho WY, Jun BH. Emerging ultrafast nucleic acid amplification technologies for next-generation molecular diagnostics. Biosens Bioelectron 2019; 141:111448. [PMID: 31252258 DOI: 10.1016/j.bios.2019.111448] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Over the last decade, nucleic acid amplification tests (NAATs) including polymerase chain reaction (PCR) were an indispensable methodology for diagnosing cancers, viral and bacterial infections owing to their high sensitivity and specificity. Because the NAATs can recognize and discriminate even a few copies of nucleic acid (NA) and species-specific NA sequences, NAATs have become the gold standard in a wide range of applications. However, limitations of NAAT approaches have recently become more apparent by reason of their lengthy run time, large reaction volume, and complex protocol. To meet the current demands of clinicians and biomedical researchers, new NAATs have developed to achieve ultrafast sample-to-answer protocols for the point-of-care testing (POCT). In this review, ultrafast NA-POCT platforms are discussed, outlining their NA amplification principles as well as delineating recent advances in ultrafast NAAT applications. The main focus is to provide an overview of NA-POCT platforms in regard to sample preparation of NA, NA amplification, NA detection process, interpretation of the analysis, and evaluation of the platform design. Increasing importance will be given to innovative, ultrafast amplification methods and tools which incorporate artificial intelligence (AI)-associated data analysis processes and mobile-healthcare networks. The future prospects of NA POCT platforms are promising as they allow absolute quantitation of NA in individuals which is essential to precision medicine.
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Affiliation(s)
- Sang Hun Lee
- Department of Bioengineering, University of California Berkeley, CA, USA
| | | | - Brian N Kim
- Department of Electrical and Computer Engineering, University of Central Florida, FL, USA
| | - Oh Seok Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea
| | - Won-Yep Rho
- School of International Engineering and Science, Chonbuk National University, Jeonju, South Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, South Korea.
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88
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Reduced False Positives and Improved Reporting of Loop-Mediated Isothermal Amplification using Quenched Fluorescent Primers. Sci Rep 2019; 9:7400. [PMID: 31089184 PMCID: PMC6517417 DOI: 10.1038/s41598-019-43817-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/30/2019] [Indexed: 11/08/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as an alternative to PCR based methods. There are numerous reported techniques to detect the LAMP amplification including turbidity, bioluminescence and intercalating fluorescent dyes. In this report we show that quenched fluorescent labels on various LAMP primers can be used to quantify and detect target DNA molecules down to single copy numbers. By selecting different fluorophores, this method can be simply multiplexed. Moreover this highly specific LAMP detection technique can reduce the incidence of false positives originating from mispriming events. Attribution of these events to particular primers will help inform and improve LAMP primer design.
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89
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Nguyen DV, Nguyen VH, Seo TS. Quantification of Colorimetric Loop-mediated Isothermal Amplification Process. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3206-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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90
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O'Sullivan S, Ali Z, Jiang X, Abdolvand R, Ünlü MS, Silva HPD, Baca JT, Kim B, Scott S, Sajid MI, Moradian S, Mansoorzare H, Holzinger A. Developments in Transduction, Connectivity and AI/Machine Learning for Point-of-Care Testing. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1917. [PMID: 31018573 PMCID: PMC6515310 DOI: 10.3390/s19081917] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/19/2022]
Abstract
We review some emerging trends in transduction, connectivity and data analytics for Point-of-Care Testing (POCT) of infectious and non-communicable diseases. The patient need for POCT is described along with developments in portable diagnostics, specifically in respect of Lab-on-chip and microfluidic systems. We describe some novel electrochemical and photonic systems and the use of mobile phones in terms of hardware components and device connectivity for POCT. Developments in data analytics that are applicable for POCT are described with an overview of data structures and recent AI/Machine learning trends. The most important methodologies of machine learning, including deep learning methods, are summarised. The potential value of trends within POCT systems for clinical diagnostics within Lower Middle Income Countries (LMICs) and the Least Developed Countries (LDCs) are highlighted.
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Affiliation(s)
- Shane O'Sullivan
- Department of Pathology, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05508-060, Brazil.
| | - Zulfiqur Ali
- Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK.
| | - Xiaoyi Jiang
- Faculty of Mathematics and Computer Science, University Münster, Münster 48149, Germany.
| | - Reza Abdolvand
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA.
| | - M Selim Ünlü
- Department of Electrical and Computer Engineering and Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | | | - Justin T Baca
- Department of Emergency Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
| | - Brian Kim
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA.
| | - Simon Scott
- Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK.
| | - Mohammed Imran Sajid
- Department of Upper GI Surgery, Wirral University Teaching Hospital, Wirral CH49 5PE, UK.
| | - Sina Moradian
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA.
| | - Hakhamanesh Mansoorzare
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA.
| | - Andreas Holzinger
- Institute for interactive Systems and Data Science, Graz University of Technology, Graz 8074, Austria.
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz 8036, Austria.
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91
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Fernández-Soto P, Gandasegui J, Carranza Rodríguez C, Pérez-Arellano JL, Crego-Vicente B, García-Bernalt Diego J, López-Abán J, Vicente B, Muro A. Detection of Schistosoma mansoni-derived DNA in human urine samples by loop-mediated isothermal amplification (LAMP). PLoS One 2019; 14:e0214125. [PMID: 30913249 PMCID: PMC6435178 DOI: 10.1371/journal.pone.0214125] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Schistosoma mansoni is the main species causing hepatic and intestinal schistosomiasis in Sub-Saharan Africa, and it is the only species in South America. Adult stages of the parasite reside in the mesenteric venous plexus of infected hosts, and eggs are shed in feces. Collecting patient stool samples for S. mansoni diagnostic purposes is difficult in large-scale field trials. Urine samples would be an alternative approach for molecular S. mansoni detection since they have several advantages over stool samples, including better handling, management and storage. Additionally, loop-mediated isothermal amplification (LAMP) technology is a powerful molecular diagnostic tool for infectious diseases, particularly under field conditions in developing countries. The present study aimed to assess the effectiveness of our previously developed LAMP assay (SmMIT-LAMP) for S. mansoni-specific detection in clinical urine samples. METHODOLOGY/PRINCIPAL FINDINGS The sensitivity of SmMIT-LAMP in urine was established in simulated fresh human urine samples artificially spiked with genomic DNA from S. mansoni. LAMP for 120 min instead of 60 min improved the sensitivity, reaching values of 0.01 fg/μL. A set of well-defined frozen stored human urine samples collected from Sub-Saharan immigrant patients was selected from a biobank to evaluate the diagnostic validity of SmMIT-LAMP. The set included urine samples from patients with microscopy-confirmed infections with S. mansoni, S. haematobium and other nonschistosome parasites, as well as urine samples from patients with microscopy-negative eosinophilia without a confirmed diagnosis. The SmMIT-LAMP was incubated for 60 and 120 min. A longer incubation time was shown to increase the LAMP-positive results in patient urine samples. We also tested urine samples from mice experimentally infected with S. mansoni, and LAMP-positive results were obtained from the third week after infection. A real-time LAMP assay was also performed with three individual urine samples. CONCLUSIONS/SIGNIFICANCE The SmMIT-LAMP could effectively detect S. mansoni DNA in mouse urine samples and produced promising results for human clinical samples. The detection of S. mansoni DNA in mouse urine samples from the third week after infection indicates that early diagnosis of active S. mansoni infection is possible using urine as a source of DNA. Further studies are still needed, but our method could be used as a promising molecular tool applicable to urine samples to diagnose human intestinal schistosomiasis caused by S. mansoni.
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Affiliation(s)
- Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
- * E-mail: (PFS); (AM)
| | - Javier Gandasegui
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Cristina Carranza Rodríguez
- Department of Medical and Surgical Sciences, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Unit of Infectious Diseases, Maternal and Child Insular University Hospital Complex, Las Palmas de Gran Canaria, Spain
| | - José Luis Pérez-Arellano
- Department of Medical and Surgical Sciences, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Unit of Infectious Diseases, Maternal and Child Insular University Hospital Complex, Las Palmas de Gran Canaria, Spain
| | - Beatriz Crego-Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Julio López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Belén Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
- * E-mail: (PFS); (AM)
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92
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Chylewska A, Ogryzek M, Makowski M. Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection. Curr Med Chem 2019; 26:121-165. [DOI: 10.2174/0929867324666171023164813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/20/2017] [Accepted: 05/20/2016] [Indexed: 11/22/2022]
Abstract
Background:Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).Methods:Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.Results:The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.Discussion:Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.
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Affiliation(s)
- Agnieszka Chylewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Małgorzata Ogryzek
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
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93
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Hu J, Huang R, Sun Y, Wei X, Wang Y, Jiang C, Geng Y, Sun X, Jing J, Gao H, Wang Z, Dong C. Sensitive and rapid visual detection of Salmonella Typhimurium in milk based on recombinase polymerase amplification with lateral flow dipsticks. J Microbiol Methods 2019; 158:25-32. [DOI: 10.1016/j.mimet.2019.01.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
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94
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Kikuchi N, Reed A, Gerasimova YV, Kolpashchikov DM. Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons. Anal Chem 2019; 91:2667-2671. [PMID: 30680988 DOI: 10.1021/acs.analchem.8b03964] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hybridization probes have been used for the detection of single nucleotide variations (SNV) in DNA and RNA sequences in the mix-and-read formats. Among the most conventional are Taqman probes, which require expensive quantitative polymerase chain reaction (qPCR) instruments with melting capabilities. More affordable isothermal amplification format requires hybridization probes that can selectively detect SNVs isothermally. Here we designed a split DNA aptamer (SDA) hybridization probe based on a recently reported DNA sequence that binds a dapoxyl dye and increases its fluorescence ( Kato, T.; Shimada, I.; Kimura, R.; Hyuga, M., Light-up fluorophore-DNA aptamer pair for label-free turn-on aptamer sensors. Chem. Commun. 2016 , 52 , 4041 - 4044 ). SDA uses two DNA strands that have low affinity to the dapoxyl dye unless hybridized to abutting positions at a specific analyte and form a dye-binding site, which is accompanied by up to a 120-fold increase in fluorescence. SDA differentiates SNV in the inhA gene of Mycobacterium tuberculosis at ambient temperatures and detects a conserved region of the Zika virus after isothermal nucleic acid sequence based amplification (NASBA) reaction. The approach reported here can be used for detection of isothermal amplification products in the mix-and-read format as an alternative to qPCR.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Adam Reed
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Yulia V Gerasimova
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Dmitry M Kolpashchikov
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States.,Burnett School of Biomedical Sciences , University of Central Florida , Orlando , 32816 , Florida United States
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95
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Zhang H, Xu Y, Fohlerova Z, Chang H, Iliescu C, Neuzil P. LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification. Trends Analyt Chem 2019; 113:44-53. [PMID: 32287531 PMCID: PMC7112807 DOI: 10.1016/j.trac.2019.01.015] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP. Introduction of loop mediated isothermal amplification (LAMP) and its principle. Classical microfluidics-based LAMP for DNA/RNA detection. Paper-based LAMP. Microfluidic-based digital LAMP. Future of microfluidic LAMP development.
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Affiliation(s)
- Haoqing Zhang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ying Xu
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerova
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic.,Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600 Brno, Czech Republic
| | - Honglong Chang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ciprian Iliescu
- Biomedical Institute for Global Health Research and Technology (BIGHEART), National University of Singapore, MD6, 14 Medical Drive #14-01, 117599, Singapore
| | - Pavel Neuzil
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China.,Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic
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96
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Kaur N, Toley BJ. Paper-based nucleic acid amplification tests for point-of-care diagnostics. Analyst 2019; 143:2213-2234. [PMID: 29683153 DOI: 10.1039/c7an01943b] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There has been a recent resurgence in the use of paper as a substrate for developing point-of-care medical diagnostic tests, possibly triggered by expiring patents published in the 1990s. A hallmark of this resurgence has been the development of advanced shapes and structures made from paper to conduct multi-step fluidic operations using the wicking action of porous materials. Such devices indicate a distinct improvement over lateral flow immunoassays, which are restricted to conducting one-step operations. New developments in paper-based diagnostic devices have triggered interest in the development of paper-based point-of-care nucleic acid amplification tests (NAATs). NAATs can identify extremely low levels of specific nucleic acid sequences from clinical samples and are the most sensitive of all available tests for infectious disease diagnosis. Because traditional PCR-based NAATs require expensive instruments, the development of portable paper-based NAAT's has become an exciting field of research. This article aims to review and analyse the current state of development of paper-based NAATs. We project paper-based NAATs as miniaturized chemical processes and shed light on various schemes of operation used for converting the multiple steps of the chemical processes into paper microfluidic devices. We conclude by elaborating on the challenges that must be overcome in the near future so that progress can be made towards the development of fully functional and commercial paper-based NAATs.
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Affiliation(s)
- Navjot Kaur
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India560012.
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97
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A Diagnostic Device for In-Situ Detection of Swine Viral Diseases: The SWINOSTICS Project. SENSORS 2019; 19:s19020407. [PMID: 30669504 PMCID: PMC6359211 DOI: 10.3390/s19020407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 02/07/2023]
Abstract
In this paper, we present the concept of a novel diagnostic device for on-site analyses, based on the use of advanced bio-sensing and photonics technologies to tackle emerging and endemic viruses causing swine epidemics and significant economic damage in farms. The device is currently under development in the framework of the EU Commission co-funded project. The overall concept behind the project is to develop a method for an early and fast on field detection of selected swine viruses by non-specialized personnel. The technology is able to detect pathogens in different types of biological samples, such as oral fluids, faeces, blood or nasal swabs. The device will allow for an immediate on-site threat assessment. In this work, we present the overall concept of the device, its architecture with the technical requirements, and all the used innovative technologies that contribute to the advancements of the current state of the art.
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98
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Oh SJ, Seo TS. Combination of a centrifugal microfluidic device with a solution-loading cartridge for fully automatic molecular diagnostics. Analyst 2019; 144:5766-5774. [DOI: 10.1039/c9an00900k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a centrifugal microfluidic device which is combined with a solution-loading cartridge for fully automatic molecular diagnostics of foodborne pathogens.
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Affiliation(s)
| | - Tae Seok Seo
- Department of Chemical Engineering
- College of Engineering
- Kyung Hee University
- Yongin-si, Gyeonggi-do
- Republic of Korea
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99
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Xu X, Wang X, Hu J, Gong Y, Wang L, Zhou W, Li X, Xu F. A smartphone-based on-site nucleic acid testing platform at point-of-care settings. Electrophoresis 2018; 40:914-921. [PMID: 30511768 DOI: 10.1002/elps.201800449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/18/2018] [Accepted: 11/20/2018] [Indexed: 11/07/2022]
Abstract
We developed a smartphone-based on-site nucleic acid testing (NAT) platform that can image and analyze lateral flow nucleic acid assays at point-of-care settings. An inexpensive add-on was devised to run lateral flow assays while providing homogeneous ambient light for imaging. In addition, an Android app with a user-friendly interface was developed for the result analysis and management. Linear color calibration is implemented inside the app to minimize the colorimetric reaction difference between smartphones. A relationship function between nucleic acid concentration and colorimetric reaction was established and evaluated by leave-one-out cross validation. The predicted concentration and true concentration showed a good agreement with an R-squared value of 0.96. This smartphone-based NAT platform can be used to diagnose infectious diseases and monitor disease progression, and assess treatment efficacy, especially for resource-limited settings.
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Affiliation(s)
- Xiayu Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, P. R. China
- Bioinspired Engineering & Biomechanics Center (BEBC), Xi'an Jiaotong University, Shaanxi, P. R. China
| | - Xuemin Wang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, P. R. China
- Bioinspired Engineering & Biomechanics Center (BEBC), Xi'an Jiaotong University, Shaanxi, P. R. China
| | - Jie Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, P. R. China
- Bioinspired Engineering & Biomechanics Center (BEBC), Xi'an Jiaotong University, Shaanxi, P. R. China
| | - Yang Gong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, P. R. China
- Bioinspired Engineering & Biomechanics Center (BEBC), Xi'an Jiaotong University, Shaanxi, P. R. China
| | - Lin Wang
- College of medicine, Xi'an International University, Shaanxi, P. R. China
| | - Wan Zhou
- Department of Chemistry and Biochemistry, Border Biomedical Research Center, & Biomedical Engineering (BME), University of Texas at El Paso, TX, USA
| | - XiuJun Li
- Department of Chemistry and Biochemistry, Border Biomedical Research Center, & Biomedical Engineering (BME), University of Texas at El Paso, TX, USA
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Shaanxi, P. R. China
- Bioinspired Engineering & Biomechanics Center (BEBC), Xi'an Jiaotong University, Shaanxi, P. R. China
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Optimised LAMP allows single copy detection of 35Sp and NOSt in transgenic maize using Bioluminescent Assay in Real Time (BART). Sci Rep 2018; 8:17590. [PMID: 30514874 PMCID: PMC6279926 DOI: 10.1038/s41598-018-36207-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/09/2018] [Indexed: 11/23/2022] Open
Abstract
Loop-mediated amplification (LAMP) has been widely used to amplify and hence detect nucleic acid target sequences from various pathogens, viruses and genetic modifications. Two distinct types of primer are required for LAMP; hairpin-forming LAMP and displacement. High specificity arises from this use of multiple primers, but without optimal conditions for LAMP, sensitivity can be poor. We confirm here the importance of LAMP primer design, concentrations and ratios for efficient LAMP amplification. We further show that displacement primers are non-essential to the LAMP reaction at certain concentrations providing accelerating loop primers are present. We investigate various methods to quantify DNA extracts from GM maize certified reference materials to calculate the target copy numbers of template presented to the LAMP reaction, and show that LAMP can amplify transgenic promoter/terminator sequences in DNA extracted from various maize GM events using primers designed to target the 35S promoter (35Sp) or NOS terminator (NOSt) sequences, detection with both bioluminescence in real-time (BART) and fluorescent methods. With prior denaturation and HPLC grade LAMP primers single copy detection was achieved, showing that optimised LAMP conditions can be combined with BART for single copy targets, with simple and cost efficient light detection electronics over fluorescent alternatives.
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