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Natsuhara D, Miyajima A, Bussho T, Okamoto S, Nagai M, Ihira M, Shibata T. A microfluidic-based quantitative analysis system for the multiplexed genetic diagnosis of human viral infections using colorimetric loop-mediated isothermal amplification. Analyst 2024; 149:3335-3345. [PMID: 38695841 DOI: 10.1039/d4an00215f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In this study, a microfluidic-based system utilizing colorimetric loop-mediated isothermal amplification (LAMP) is introduced for the quantitative analysis of nucleic acid targets. This system offers a user-friendly and cost-effective platform for the multiplexed genetic diagnosis of various infectious diseases across multiple samples. It includes time-lapse imaging equipment for capturing images of the microfluidic device during the LAMP assay and a hue-based quantitative analysis software to analyze the LAMP reaction, streamlining diagnostic procedures. An electric pipette was used to simplify the loading of samples and LAMP reagents into the device, allowing easy operation even by untrained individuals. The hue-based analysis software employs efficient image processing and post-processing techniques to calculate DNA amplification curves based on color changes in multiple reaction chambers. This software automates several tasks, such as identifying reaction chamber areas from time-lapse images, quantifying color information within each chamber, correcting baselines of DNA amplification curves, fitting experimental data to theoretical curves, and determining the threshold time for each curve. To validate the developed system, conventional off-chip LAMP assays were conducted with a 25 μL reaction mixture in 0.2 mL polymerase chain reaction (PCR) tubes using a real-time turbidimeter. The results indicated that the threshold time obtained using the colorimetric LAMP assay in the developed system is comparable to that obtained with real-time turbidity measurements in PCR tubes, demonstrating the system's capability for quantitative analysis of target nucleic acids, including those from human herpesviruses.
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Affiliation(s)
- Daigo Natsuhara
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Akira Miyajima
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Tomoya Bussho
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Shunya Okamoto
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
- Institute for Research on Next-generation Semiconductor and Sensing Science (IRES2), Toyohashi University of Technology, Aichi 441-8580, Japan
| | - Masaru Ihira
- Faculty of Clinical Science for Biological Monitoring, Fujita Health University, Aichi 470-1192, Japan
| | - Takayuki Shibata
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
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Yang H, Zhang X, Li Y, Deng J, Liu Z, Chen Q, Zhang H. Design and application of a point-of-care testing system for triple detection of SARS-CoV-2, influenza A, and influenza B. Front Bioeng Biotechnol 2024; 12:1378709. [PMID: 38694623 PMCID: PMC11061352 DOI: 10.3389/fbioe.2024.1378709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/04/2024] [Indexed: 05/04/2024] Open
Abstract
To mitigate the continued impact of SARS-CoV-2, influenza A, and influenza B viruses on human health, a smartphone-based point-of-care testing (POCT) system was designed to detect respiratory pathogens through a nucleic acid test. This compact, light-weight, highly automated, and universal system enables the differential diagnosis of SARS-CoV-2, influenza A, and influenza B in approximately 30 min in a single-tube reaction. Numerous hospitals and disease control and prevention center assessed the triple POCT system's detection threshold, sensitivity, specificity, and stability, and have concluded that all the assessments were comparable to those of fluorescent quantitative polymerase chain reaction (PCR)-based testing. The triple POCT system is suitable as an onsite rapid-diagnosis device, as well as for pathogen screening at airports and customs.
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Affiliation(s)
- Huan Yang
- Guangzhou University of Chinese Medicine, Guangzhou, China
- General Hospital of Southern Theater Command, Guangzhou, China
| | - Xiaoming Zhang
- General Hospital of Southern Theater Command, Guangzhou, China
| | - Yating Li
- Guangzhou University of Chinese Medicine, Guangzhou, China
- General Hospital of Southern Theater Command, Guangzhou, China
| | - Jing Deng
- Beijing Genome Technology Co., Ltd., Beijing, China
| | - Zhongming Liu
- General Hospital of Southern Theater Command, Guangzhou, China
| | - Qiyue Chen
- Beijing Genome Technology Co., Ltd., Beijing, China
| | - Haiyan Zhang
- General Hospital of Southern Theater Command, Guangzhou, China
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Macchia E, Torricelli F, Caputo M, Sarcina L, Scandurra C, Bollella P, Catacchio M, Piscitelli M, Di Franco C, Scamarcio G, Torsi L. Point-Of-Care Ultra-Portable Single-Molecule Bioassays for One-Health. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309705. [PMID: 38108547 DOI: 10.1002/adma.202309705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Screening asymptomatic organisms (humans, animals, plants) with a high-diagnostic accuracy using point-of-care-testing (POCT) technologies, though still visionary holds great potential. Convenient surveillance requires easy-to-use, cost-effective, ultra-portable but highly reliable, in-vitro-diagnostic devices that are ready for use wherever they are needed. Currently, there are not yet such devices available on the market, but there are a couple more promising technologies developed at readiness-level 5: the Clustered-Regularly-Interspaced-Short-Palindromic-Repeats (CRISPR) lateral-flow-strip tests and the Single-Molecule-with-a-large-Transistor (SiMoT) bioelectronic palmar devices. They both hold key features delineated by the World-Health-Organization for POCT systems and an occurrence of false-positive and false-negative errors <1-5% resulting in diagnostic-selectivity and sensitivity >95-99%, while limit-of-detections are of few markers. CRISPR-strip is a molecular assay that, can detect down to few copies of DNA/RNA markers in blood while SiMoT immunometric and molecular test can detect down to a single oligonucleotide, protein marker, or pathogens in 0.1mL of blood, saliva, and olive-sap. These technologies can prospectively enable the systematic and reliable surveillance of asymptomatic ones prior to worsening/proliferation of illnesses allowing for timely diagnosis and swift prognosis. This could establish a proactive healthcare ecosystem that results in effective treatments for all living organisms generating diffuse and well-being at efficient costs.
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Affiliation(s)
- Eleonora Macchia
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Paolo Bollella
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Michele Catacchio
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Matteo Piscitelli
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | | | - Gaetano Scamarcio
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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Gradisteanu Pircalabioru G, Raileanu M, Dionisie MV, Lixandru-Petre IO, Iliescu C. Fast detection of bacterial gut pathogens on miniaturized devices: an overview. Expert Rev Mol Diagn 2024; 24:201-218. [PMID: 38347807 DOI: 10.1080/14737159.2024.2316756] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
INTRODUCTION Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation. AREAS COVERED Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges. EXPERT OPINION Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.
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Affiliation(s)
- Gratiela Gradisteanu Pircalabioru
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Division of Earth, Environmental and Life Sciences, The Research Institute of University of Bucharest (ICUB), Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
| | - Mina Raileanu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Department of Life and Environmental Physics, Horia Hulubei National Institute of Physics and Nuclear Engineering, Magurele, Romania
| | - Mihai Viorel Dionisie
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Irina-Oana Lixandru-Petre
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Ciprian Iliescu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Microsystems in Biomedical and Environmental Applications, National Research and Development Institute for Microtechnology, Bucharest, Romania
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Quan H, Wang S, Xi X, Zhang Y, Ding Y, Li Y, Lin J, Liu Y. Deep learning enhanced multiplex detection of viable foodborne pathogens in digital microfluidic chip. Biosens Bioelectron 2024; 245:115837. [PMID: 38000308 DOI: 10.1016/j.bios.2023.115837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/26/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023]
Abstract
Culture plating is worldwide accepted as the gold standard for quantifying viable foodborne pathogens. However, it is time-consuming (1-2 days) and requires specialized laboratory and personnel. This study reported a deep learning enhanced digital microfluidic platform for multiplex detection of viable foodborne pathogens. The new method used a Time-Lapse images driven EfficientNet-Transformer Network (TLENTNet) to type and quantify the bacteria through spatiotemporal features of bacterial growth and digital enumeration of bacterial culture. First, the bacterial sample was prepared with LB medium and injected into a pre-vacuumed microfluidic chip with an array of 800 microwells to encapsulate at most one bacterium in each well. Then, a programmed sliding microscopic platform was used to scan all microwells every 15 min, capturing time-lapse images of bacterial growth within each microwell. Finally, the TLENTNet was used to facilitate bacterial typing and quantification. Under optimal conditions, this platform was able to detect four bacterial species (S.typhimurium, E. coli O157:H7, S. aureus and B. cereus) with an average accuracy of 97.72% and a detection limit of 63 CFU/mL in 7 h.
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Affiliation(s)
- Han Quan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Siyuan Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Xinge Xi
- Key Laboratory of Smart Agriculture System Integration, Ministry of Education, China Agricultural University, Beijing, 100083, China
| | - Yingchao Zhang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Ying Ding
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Jianhan Lin
- Key Laboratory of Smart Agriculture System Integration, Ministry of Education, China Agricultural University, Beijing, 100083, China
| | - Yuanjie Liu
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China.
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Wang R, Bai B, Li D, Wang J, Huang W, Wu Y, Zhao L. Phytoplasma: A plant pathogen that cannot be ignored in agricultural production-Research progress and outlook. MOLECULAR PLANT PATHOLOGY 2024; 25:e13437. [PMID: 38393681 PMCID: PMC10887288 DOI: 10.1111/mpp.13437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024]
Abstract
Phytoplasmas are phloem-restricted plant-pathogenic bacteria transmitted by insects. They cause diseases in a wide range of host plants, resulting in significant economic and ecological losses worldwide. Research on phytoplasmas has a long history, with significant progress being made in the past 30 years. Notably, with the rapid development of phytoplasma research, scientists have identified the primary agents involved in phytoplasma transmission, established classification and detection systems for phytoplasmas, and 243 genomes have been sequenced and assembled completely or to draft quality. Multiple possible phytoplasma effectors have been investigated, elucidating the molecular mechanisms by which phytoplasmas manipulate their hosts. This review summarizes recent advances in phytoplasma research, including identification techniques, host range studies, whole- or draft-genome sequencing, effector pathogenesis and disease control methods. Additionally, future research directions in the field of phytoplasma research are discussed.
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Affiliation(s)
- Ruotong Wang
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Bixin Bai
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Danyang Li
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Jingke Wang
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Weijie Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Yunfeng Wu
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Lei Zhao
- State Key Laboratory for Crop Stress Resistance and High‐Efficiency ProductionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
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Akter J, Smith WJM, Gebrewold M, Kim I, Simpson SL, Bivins A, Ahmed W. Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167964. [PMID: 37865239 DOI: 10.1016/j.scitotenv.2023.167964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea; CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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Yu Z, Liu H, Chen Z, Shao Y, Wang Z, Cheng F, Zhang Y, Wang Z, Tu J, Song X, Qi K. LAMP assay coupled with a CRISPR/Cas12a system for the rapid and ultrasensitive detection of porcine circovirus-like virus in the field. Anal Bioanal Chem 2024; 416:363-372. [PMID: 37935845 DOI: 10.1007/s00216-023-05020-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
A recent outbreak of porcine circovirus-like virus (PCLV), a virus that may be associated with porcine diarrhea, has been reported in swine herds in China. The virus is spreading rapidly, causing huge economic losses to the swine farming industry. To achieve the rapid, inexpensive, and sensitive detection of PCLV, we combined loop-mediated isothermal amplification (LAMP) and the CRISPR/Cas12a system, whose fluorescence intensity readout can detect PCLV ORF4 gene levels as low as 10 copies. To overcome the need for sophisticated equipment, lateral flow strip reading technology was introduced for the first time in a LAMP-Cas12a-based system to detect PCLV. The lateral flow strip (LFS) results were readout by the naked eye, and the method was highly sensitive with a detection limit of 10 copies, with a detection time of about 60 min. In addition, the method is highly specific and has no cross-reactivity with other related viruses. In conclusion, LAMP-CRISPR/Cas12a-based assays have the advantages of rapidity, accuracy, portability, low cost, and visualization of the results. They therefore have great potential, especially for areas where specialized equipment is lacking, and can expect to be an ideal method for early diagnosis and on-site detection of PCLV.
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Affiliation(s)
- Zhaorong Yu
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Hua Liu
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Zhe Chen
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Ying Shao
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Zhipeng Wang
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Fanyu Cheng
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Yu Zhang
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Zhenyu Wang
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Jian Tu
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Xiangjun Song
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China.
| | - Kezong Qi
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China.
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Ndraha N, Lin HY, Wang CY, Hsiao HI, Lin HJ. Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 7:100183. [PMID: 37767229 PMCID: PMC10520789 DOI: 10.1016/j.fochms.2023.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/22/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
This article presents a review of recent advancements in the utilization of NAA-based techniques for detecting foodborne pathogens in food products, focusing on studies conducted within the past five years. This review revealed that recent research efforts have primarily aimed at enhancing sensitivity and specificity by improving sample pre-treatment/preparation, DNA isolation, and readout methods. Isothermal-based amplification methods, such as LAMP, RPA, RAA, and RCA, have emerged as promising approaches, providing rapid results within one h and often demonstrating comparable or superior sensitivity to conventional or qPCR methods. However, the attention paid to specific pathogens varies, with Salmonella spp., Listeria spp., E. coli, and V. parahaemolyticus receiving more focus than norovirus and other similar pathogens. NAA-based methods have the potential to significantly contribute to food safety and public health protection. However, further advancements are necessary to fully realize their benefits.
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Affiliation(s)
- Nodali Ndraha
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Hung-Yun Lin
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Chen-Yow Wang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Hsin-I Hsiao
- Department of Food Science, National Taiwan Ocean University, Keelung, 202301 Taiwan
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
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10
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Yang C, Gan X, Zeng Y, Xu Z, Xu L, Hu C, Ma H, Chai B, Hu S, Chai Y. Advanced design and applications of digital microfluidics in biomedical fields: An update of recent progress. Biosens Bioelectron 2023; 242:115723. [PMID: 37832347 DOI: 10.1016/j.bios.2023.115723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
Significant breakthroughs have been made in digital microfluidic (DMF)-based technologies over the past decades. DMF technology has attracted great interest in bioassays depending on automatic microscale liquid manipulations and complicated multi-step processing. In this review, the recent advances of DMF platforms in the biomedical field were summarized, focusing on the integrated design and applications of the DMF system. Firstly, the electrowetting-on-dielectric principle, fabrication of DMF chips, and commercialization of the DMF system were elaborated. Then, the updated droplets and magnetic beads manipulation strategies with DMF were explored. DMF-based biomedical applications were comprehensively discussed, including automated sample preparation strategies, immunoassays, molecular diagnosis, blood processing/testing, and microbe analysis. Emerging applications such as enzyme activity assessment and DNA storage were also explored. The performance of each bioassay was compared and discussed, providing insight into the novel design and applications of the DMF technology. Finally, the advantages, challenges, and future trends of DMF systems were systematically summarized, demonstrating new perspectives on the extensive applications of DMF in basic research and commercialization.
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Affiliation(s)
- Chengbin Yang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Xiangyu Gan
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Yuping Zeng
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Zhourui Xu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Longqian Xu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Chenxuan Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Hanbin Ma
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China; Guangdong ACXEL Micro & Nano Tech Co., Ltd, Foshan, China.
| | - Bao Chai
- Department of Dermatology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China; Department of Dermatology, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.
| | - Siyi Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Yujuan Chai
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
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11
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Zhao R, Wu R, Jin J, Ning K, Wang Z, Yi X, Kapilevich L, Liu J. Signaling pathways regulated by natural active ingredients in the fight against exercise fatigue-a review. Front Pharmacol 2023; 14:1269878. [PMID: 38155906 PMCID: PMC10752993 DOI: 10.3389/fphar.2023.1269878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023] Open
Abstract
Exercise fatigue is a normal protective mechanism of the body. However, long-term fatigue hinders normal metabolism and exercise capacity. The generation and recovery from exercise fatigue involves alterations in multiple signaling pathways, mainly AMPK, PI3K/Akt, Nrf2/ARE, NF-κB, PINK1/Parkin, and BDNF/TrkB, as well as MAPK signaling pathways that mediate energy supply, reduction of metabolites, oxidative stress homeostasis, muscle fiber type switching, and central protective effects. In recent studies, a rich variety of natural active ingredients have been identified in traditional Chinese medicines and plant extracts with anti-fatigue effects, opening up the field of research in new anti-fatigue drugs. In this review we give an overview of the signaling pathways associated with the activity of natural food active ingredients against exercise fatigue. Such a comprehensive review is necessary to understand the potential of these materials as preventive measures and treatments of exercise fatigue. We expect the findings highlighted and discussed here will help guide the development of new health products and provide a theoretical and scientific basis for future research on exercise fatigue.
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Affiliation(s)
- Rongyue Zhao
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Ruomeng Wu
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Junjie Jin
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Ke Ning
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Zhuo Wang
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
| | - Xuejie Yi
- Exercise and Health Research Center, Department of Kinesiology, Shenyang Sport University, Shenyang, Liaoning, China
| | - Leonid Kapilevich
- Faculty of Physical Education, Nаtionаl Reseаrch Tomsk Stаte University, Tomsk, Russia
| | - Jiao Liu
- College of Exercise and Health, Shenyang Sport University, Shenyang, China
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12
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Pauly MD, Weis-Torres S, Hayden TM, Ganova-Raeva LM, Kamili S. Development of simple, rapid, and sensitive methods for detection of hepatitis C virus RNA from whole blood using reverse transcription loop-mediated isothermal amplification. J Clin Microbiol 2023; 61:e0077123. [PMID: 37933990 PMCID: PMC10662345 DOI: 10.1128/jcm.00771-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an underdiagnosed global health problem. Diagnosis of current HCV infections typically requires testing for HCV RNA using high-complexity laboratory tests. Methods for the detection of HCV RNA that are simple, inexpensive, rapid, and compatible with use outside of a laboratory setting are very important in order to improve access to hepatitis C diagnostic testing and facilitate accelerated linkage to care. We developed and evaluated three simple workflows for extracting HCV RNA from small volumes of whole blood for use in a sensitive, pan-genotypic RT-LAMP assay. The water workflow uses osmotic stress to release HCV RNA and has a limit of detection of 4.3 log10(IU/mL) (95% CI 4.0-4.9). The heat workflow uses a heating step to release HCV RNA and has a limit of detection of 4.2 log10(IU/mL) (95% CI 3.8-5.1). The bead workflow, which uses chemical lysis of the sample and a streamlined paramagnetic solid phase reversible immobilization bead procedure for nucleic acid purification, has a limit of detection of 2.8 log10(IU/mL) (95% CI 2.5-3.4). When used to test whole blood spiked with HCV RNA-positive plasma samples in which most HCV levels were below 5.0 log10(IU/mL), the water, heat, and bead workflows detected HCV RNA in 69%, 75%, and 94% of samples, respectively. These workflows are compatible with visual lateral flow dipsticks, and each takes less than 60 min from sample to result. Each workflow can be performed with minimal and inexpensive equipment. With further procedural simplifications, these workflows may form the basis of assays for the point-of-care diagnosis of HCV infections.
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Affiliation(s)
- Matthew D. Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Sabrina Weis-Torres
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Tonya M. Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Lilia M. Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
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13
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Li X, Zhong Y, Qiao Y, Li H, Hu X, Imani S, Zheng S, Li J. Advances and Challenges in Cytomegalovirus Detection Methods for Liver Transplant Donors. Diagnostics (Basel) 2023; 13:3310. [PMID: 37958206 PMCID: PMC10649722 DOI: 10.3390/diagnostics13213310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
Cytomegalovirus (CMV) infection is a highly prevalent opportunistic infection among liver transplant recipients. When the liver donor is infected with CMV, there is a risk of transmission to the recipient, leading to CMV infection. To improve the postoperative outcome of liver transplantation, it is crucial to shift the focus of CMV detection to the donor and achieve early diagnosis, as well as implement effective preventative and therapeutic measures. However, the commonly used CMV detection methods in the past had limitations that prevented their early and accurate diagnosis in liver transplant donors. This review focuses on the latest advancements in CMV detection methods that can potentially be applied to liver transplant donors. The objective is to compare and evaluate their clinical utility, thereby providing guidance and support for rapid and accurate diagnosis of CMV infection in the clinic. The clustered regularly interspaced short palindromic repeats-associated proteins (CRISPR-Cas) system-based assay emerges as a promising method for detecting the virus, offering great prospects for early and expedient CMV infection diagnosis in clinical settings.
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Affiliation(s)
- Xiaoping Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
- Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yiwu Zhong
- Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yinbiao Qiao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou 310022, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
| | - Haoyu Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
| | - Xu Hu
- Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Saber Imani
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Shusen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou 310022, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
| | - Jianhui Li
- Zhejiang Chinese Medical University, Hangzhou 310053, China
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou 310022, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
- The Organ Repair and Regeneration Medicine Institute of Hangzhou, Hangzhou 310003, China
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14
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Sun X, Shan Y, Jian M, Wang Z. A Multichannel Fluorescence Isothermal Amplification Device with Integrated Internet of Medical Things for Rapid Sensing of Pathogens through Deep Learning. Anal Chem 2023; 95:15146-15152. [PMID: 37733965 DOI: 10.1021/acs.analchem.3c02973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
The landscape of diagnostic assessments has experienced a paradigm shift driven by the advent of isothermal amplification techniques on point-of-care testing (POCT). The development of compact, portable isothermal amplification devices further emphasizes their transformative influence on diagnostic approaches. However, in prioritizing portability, these devices may exhibit limitations in functionality, rendering them less effective in addressing urgent public health emergencies during sudden pathogen outbreaks. In this paper, an efficient isothermal fluorescence amplification device has been fabricated for the rapid detection of pathogens during public health crises. The device features multichannel capability for simultaneous detection of various targets, integrates with the Internet of Medical Things (IoMT) for remote control and data uploading, and includes a deep learning-based batch processing system for rapid (9.4 ms) and accurate discrimination of pathogen type with excellent accuracy. The device has been successfully employed to simultaneously detect Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus (MRSA) with limits of detection (LODs) of 18 CFU/mL (SA) and 20 CFU/mL (MRSA) within 35 min by multiplex RPA assay and CRISPR/Cas12a-mediated nucleic acid detection assay.
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Affiliation(s)
- Xudong Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yongjie Shan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Minghong Jian
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
- National Analytical Research Center of Electrochemistry and Spectroscopy, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
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15
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Rivas-Macho A, Eletxigerra U, Diez-Ahedo R, Barros Á, Merino S, Goñi-de-Cerio F, Olabarria G. Development of an Electrochemical Sensor for SARS-CoV-2 Detection Based on Loop-Mediated Isothermal Amplification. BIOSENSORS 2023; 13:924. [PMID: 37887117 PMCID: PMC10605850 DOI: 10.3390/bios13100924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused more than 6 million deaths all over the world, demonstrating the need for a simple, fast and cost-effective point-of-care (POC) test for the detection of the virus. In this work, we developed an electrochemical sensor for SARS-CoV-2 virus detection on clinical samples based on loop-mediated isothermal amplification (LAMP). With the development of this novel sensor, the time of each measurement is significantly reduced by avoiding the DNA extraction step and replacing it with inactivation of the sample by heating it at 95 °C for 10 min. To make the reaction compatible with the sample pre-treatment, an RNase inhibitor was added directly to the premix. The LAMP product was measured in a novel, easy-to-use manufactured sensor containing a custom-made screen-printed carbon electrode. Electrochemical detection was performed with a portable potentiostat, and methylene blue was used as the redox-transducing molecule. The developed sensor achieved a limit of detection of 62 viral copies and was 100% specific for the detection of the SARS-CoV-2 virus. The performance of the electrochemical sensor was validated with nasopharyngeal samples, obtaining a sensibility and specificity of 100% compared to the gold standard RT-PCR method.
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Affiliation(s)
- Ane Rivas-Macho
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
- Molecular Biology and Biomedicine PhD Program, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Unai Eletxigerra
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Ruth Diez-Ahedo
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Ángela Barros
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Santos Merino
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
- Electricity and Electronics Department, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Felipe Goñi-de-Cerio
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
| | - Garbiñe Olabarria
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
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16
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Liu CW, Tsutsui H. Sample-to-answer sensing technologies for nucleic acid preparation and detection in the field. SLAS Technol 2023; 28:302-323. [PMID: 37302751 DOI: 10.1016/j.slast.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Efficient sample preparation and accurate disease diagnosis under field conditions are of great importance for the early intervention of diseases in humans, animals, and plants. However, in-field preparation of high-quality nucleic acids from various specimens for downstream analyses, such as amplification and sequencing, is challenging. Thus, developing and adapting sample lysis and nucleic acid extraction protocols suitable for portable formats have drawn significant attention. Similarly, various nucleic acid amplification techniques and detection methods have also been explored. Combining these functions in an integrated platform has resulted in emergent sample-to-answer sensing systems that allow effective disease detection and analyses outside a laboratory. Such devices have a vast potential to improve healthcare in resource-limited settings, low-cost and distributed surveillance of diseases in food and agriculture industries, environmental monitoring, and defense against biological warfare and terrorism. This paper reviews recent advances in portable sample preparation technologies and facile detection methods that have been / or could be adopted into novel sample-to-answer devices. In addition, recent developments and challenges of commercial kits and devices targeting on-site diagnosis of various plant diseases are discussed.
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Affiliation(s)
- Chia-Wei Liu
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA
| | - Hideaki Tsutsui
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA; Department of Bioengineering, University of California, Riverside, CA 92521, USA.
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17
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Suarez GD, Bayer S, Tang YYK, Suarez DA, Cheung PPH, Nagl S. Rapid microfluidics prototyping through variotherm desktop injection molding for multiplex diagnostics. LAB ON A CHIP 2023; 23:3850-3861. [PMID: 37534874 DOI: 10.1039/d3lc00391d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
In this work, we demonstrate an inexpensive method of prototyping microfluidics using a desktop injection molding machine. A centrifugal microfluidic device with a novel central filling mechanism was developed to demonstrate the technique. We overcame the limitations of desktop machines in replicating microfluidic features by variotherm heating and cooling the mold between 50 °C and 110 °C within two minutes. Variotherm heating enabled good replication of microfeatures, with a coefficient of variation averaging only 3.6% attained for the measured widths of 100 μm wide molded channels. Using this methodology, we produced functional polystyrene centrifugal microfluidic chips, capable of aliquoting fluids into 5.0 μL reaction chambers with 97.5% accuracy. We performed allele-specific loop-mediated isothermal amplification (AS-LAMP) reactions for genotyping CYP2C19 alleles on these chips. Readouts were generated using optical pH sensors integrated onto chips, by drop-casting sensor precursor solutions into reaction chambers before final chip assembly. Positive reactions could be discerned by decreases in pH sensor fluorescence, thresholded against negative control reactions lacking the primers for nucleic acid amplification and with time-to-results averaging 38 minutes. Variotherm desktop injection molding can enable researchers to prototype microfluidic devices more cost-effectively, in an iterative fashion, due to reduced costs of smaller, in-house molds. Designs prototyped this way can be directly translated to mass production, enhancing their commercialization potential and positive impacts.
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Affiliation(s)
- Gianmarco D Suarez
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Steevanson Bayer
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Yuki Yu Kiu Tang
- Quommni Technologies Limited, Tsuen Wan, New Territories, Hong Kong
| | | | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Stefan Nagl
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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18
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Romero Deza AA, Schaumburg F, Berli CLA. Valveless On-Chip Aliquoting for Molecular Diagnosis. MICROMACHINES 2023; 14:1425. [PMID: 37512736 PMCID: PMC10386703 DOI: 10.3390/mi14071425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/09/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
The detection of nucleic acids as specific markers of infectious diseases is commonly implemented in molecular biology laboratories. The translation of these benchtop assays to a lab-on-a-chip format demands huge efforts of integration and automation. The present work is motivated by a strong requirement often posed by molecular assays that combine isothermal amplification and CRISPR/Cas-based detection: after amplification, a 2-8 microliter aliquot of the reaction products must be taken for the subsequent reaction. In order to fulfill this technical problem, we have designed and prototyped a microfluidic device that is able to meter and aliquot in the required range during the stepped assay. The operation is achieved by integrating a porous material that retains the desired amount of liquid after removing the excess reaction products, an innovative solution that avoids valving and external actuation. The prototypes were calibrated and experimentally tested to demonstrate the overall performance (general fluidics, metering, aliquoting, mixing and reaction). The proposed aliquoting method is fully compatible with additional functions, such as sample concentration or reagent storage, and could be further employed in alternative applications beyond molecular diagnosis.
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Affiliation(s)
| | - Federico Schaumburg
- Predio CCT CONICET Santa Fe, INTEC (Universidad Nacional del Litoral-CONICET), RN 168, Santa Fe 3000, Argentina
| | - Claudio L A Berli
- Predio CCT CONICET Santa Fe, INTEC (Universidad Nacional del Litoral-CONICET), RN 168, Santa Fe 3000, Argentina
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19
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Rivas-Macho A, Sorarrain A, Marimón JM, Goñi-de-Cerio F, Olabarria G. Extraction-Free Colorimetric RT-LAMP Detection of SARS-CoV-2 in Saliva. Diagnostics (Basel) 2023; 13:2344. [PMID: 37510088 PMCID: PMC10377860 DOI: 10.3390/diagnostics13142344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The pandemic situation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need of fast, simple, and cost-effective tests for the diagnosis of emerging pathogens. RT-qPCR has been established as the reference technique for the diagnosis of SARS-CoV-2 infections. This method requires a time-consuming protocol for the extraction of the nucleic acids present in the sample. A colorimetric reverse transcription loop-mediated isothermal amplification using the calcein molecule combined with a simple extraction-free method for saliva samples (calcein RT-LAMP) has been developed. Samples are heated 95 °C for 10 min before amplification at 63 °C for 40 min. The results can be observed by fluorescence or by the naked eye with a color change from orange to green. The method was compared with commercialized available colorimetric and fluorescent RT-LAMP kits. The developed method shows better sensitivity and specificity than the colorimetric commercial RT-LAMP and the same as the fluorescent RT-LAMP, without the need of a fluorescent reader. Moreover, the calcein RT-LAMP has, compared to RT-qPCR, a sensitivity of 90% and a specificity of 100% for saliva samples with a Ct ≤ 34, without the need for expensive RT-qPCR instruments, demonstrating the potential of this method for population screening.
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Affiliation(s)
- Ane Rivas-Macho
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
- Molecular Biology and Biomedicine PhD Program, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Ane Sorarrain
- Biodonostia Health Research Institute, Infectious Diseases Area, Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain
| | - José M Marimón
- Biodonostia Health Research Institute, Infectious Diseases Area, Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain
| | - Felipe Goñi-de-Cerio
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
| | - Garbiñe Olabarria
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
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20
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Mao S, Zhao J, Ding X, Vuong VA, Song J, Que L. Integrated Sensing Chip for Ultrasensitive Label-Free Detection of the Products of Loop-Mediated Isothermal Amplification. ACS Sens 2023; 8:2255-2262. [PMID: 37276452 DOI: 10.1021/acssensors.3c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that has been widely used for the detection of pathogens in many organisms. Current LAMP-based sensors usually require the LAMP products to be labeled in order for them to be detected. Here, we present a novel label-free LAMP chip, which consists of a nanopore thin-film sensor embedded inside a LAMP reaction chamber. A fraction of LAMP primers is immobilized on the sensor surface, allowing the LAMP products to be synthesized and bound to the sensor surface via immobilized primers. After the LAMP reaction components are removed from the reaction chamber, the amplified LAMP products bound to the sensor surface give rise to significantly increased transducing signals, which can be measured by a portable optical spectrometer through an optical fiber probe. As a demonstration, we used the LAMP chip to detect the causal agent of late blight, Phytophthora infestans, which is one of the most devastating plant pathogens and poses a major threat to sustainable crop production worldwide. We show that this chip can detect as low as 1 fg/μL of P. infestans DNA in 30 min, which corresponds to an attomolar level of 1.6 × 10-6 attomole/μL and is at least 10 times more sensitive than the currently available methods. This label-free sensing technology holds great promise to open up a new avenue for ultrasensitive, highly specific, rapid, and cost-effective point-of-care diagnostics of plant, animal, human, and foodborne pathogens.
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Affiliation(s)
- Subin Mao
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
| | - Jinping Zhao
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
| | - Xiaoke Ding
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
| | - Van Anh Vuong
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas 77843, United States
| | - Long Que
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
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21
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Jagannath A, Li Y, Cong H, Hassan J, Gonzalez G, Wang W, Zhang N, Gilchrist MD. UV-Assisted Hyperbranched Poly(β-amino ester) Modification of a Silica Membrane for Two-Step Microfluidic DNA Extraction from Blood. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37319124 DOI: 10.1021/acsami.3c03523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Integrating nucleic acid extraction in amplification-based point-of-care diagnostics will be a significant feature for next-generation point-of-care virus detection devices. However, extracting DNA efficiently on a microfluidic chip poses many technological and commercialization challenges, including manual steps, multiple instruments, pretreatment processes, and the use of organic solvents (ethanol, IPA) that inhibit detection, which is not viable with routine testing such as viral load monitoring of transplant patients for post-operative care. This paper presents a microfluidic system capable of two-step DNA extraction from blood using a UV-assisted hyperbranched poly(β-amino ester) (HPAE)-modified silica membrane for cytomegalovirus (CMV) detection in a rapid and instrument-free manner without the presence of amplification inhibitors. HPAEs of varying branch ratios were synthesized, screened, and coated on a silica membrane and bonded between two layers of poly(methyl methacrylate) (PMMA) substrates. Our system could selectively extract DNA from blood with an efficiency of 94% and a lower limit viral load of 300 IU/mL in 20 min. The extracted DNA was used as the template for real-time loop-mediated isothermal amplification (LAMP)-based detection of CMV and was found to produce a fluorescent signal intensity that was comparable with commercially extracted templates. This system can be integrated easily with a nucleic acid amplification system and used for routine rapid testing of viral load in patient blood samples.
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Affiliation(s)
- Akshaya Jagannath
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Yinghao Li
- The Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hengji Cong
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jaythoon Hassan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gabriel Gonzalez
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Wenxin Wang
- The Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nan Zhang
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- MiNAN Technologies Ltd., NovaUCD, Belfield, Dublin 4, Ireland
| | - Michael D Gilchrist
- School of Mechanical and Materials Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- MiNAN Technologies Ltd., NovaUCD, Belfield, Dublin 4, Ireland
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22
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Hong H, Yuan R, Ma H, Xiao L, Li B, Wang K. Accurate and ultrasensitive detection for PEDV based on photoelectrochemical sensing coupling loop-mediated isothermal amplification. Talanta 2023; 258:124476. [PMID: 36989618 DOI: 10.1016/j.talanta.2023.124476] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
Porcine epidemic diarrhea (PED) is a serious disease requiring a simple and accurate detection method. Accordingly, this study developed a novel, ultrasensitive photoelectrochemical (PEC) sensing platform using the loop-mediated isothermal amplification (LAMP) technique (LAMP-PEC). An amino (-NH2)-modified LAMP product is obtained by amplification of the PED virus gene with specially designed primers. The generated NH2-modified LAMP product is assembled on the surface of an electrode by forming imine linkages between aldehyde and amino groups based on the Schiff base reaction. A stable photocurrent is provided by a CdIn2S4 photoactive material, which possesses high photoelectric conversion efficiency. Amplified DNA assembled on the electrode surface increases steric hindrance and hinders electrons from moving from the electrode to electron acceptors, which decreases the photocurrent. This strategy can detect PEDV with a low detection limit of 0.3 fg μL-1 and a wide linear range of 1 × 10-3-1 × 102 pg/μL. The sensing platform has excellent specificity and sensitivity and can be used for the quantitative detection of many other pathogens with the assistance of LAMP.
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Affiliation(s)
- Honghong Hong
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Ruishuang Yuan
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Hanyu Ma
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Liting Xiao
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Kun Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China; School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, PR China; Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, OE, School of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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23
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Zeng Y, Khor JW, van Neel TL, Tu WC, Berthier J, Thongpang S, Berthier E, Theberge AB. Miniaturizing chemistry and biology using droplets in open systems. Nat Rev Chem 2023; 7:439-455. [PMID: 37117816 PMCID: PMC10107581 DOI: 10.1038/s41570-023-00483-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2023] [Indexed: 04/30/2023]
Abstract
Open droplet microfluidic systems manipulate droplets on the picolitre-to-microlitre scale in an open environment. They combine the compartmentalization and control offered by traditional droplet-based microfluidics with the accessibility and ease-of-use of open microfluidics, bringing unique advantages to applications such as combinatorial reactions, droplet analysis and cell culture. Open systems provide direct access to droplets and allow on-demand droplet manipulation within the system without needing pumps or tubes, which makes the systems accessible to biologists without sophisticated setups. Furthermore, these systems can be produced with simple manufacturing and assembly steps that allow for manufacturing at scale and the translation of the method into clinical research. This Review introduces the different types of open droplet microfluidic system, presents the physical concepts leveraged by these systems and highlights key applications.
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Affiliation(s)
- Yuting Zeng
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jian Wei Khor
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Tammi L van Neel
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Wan-Chen Tu
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jean Berthier
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Sanitta Thongpang
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakorn Pathom, Thailand
| | - Erwin Berthier
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - Ashleigh B Theberge
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Department of Urology, School of Medicine, University of Washington, Seattle, WA, USA.
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24
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Srivastava P, Prasad D. Isothermal nucleic acid amplification and its uses in modern diagnostic technologies. 3 Biotech 2023; 13:200. [PMID: 37215369 PMCID: PMC10193355 DOI: 10.1007/s13205-023-03628-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
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25
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Sun H, Jiang Q, Huang Y, Mo J, Xie W, Dong H, Jia Y. Integrated smart analytics of nucleic acid amplification tests via paper microfluidics and deep learning in cloud computing. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2023.104721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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26
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Rong N, Chen K, Shao J, Ouyang Q, Luo C. A 3D Scalable Chamber-Array Chip for Digital LAMP. Anal Chem 2023; 95:7830-7838. [PMID: 37115526 DOI: 10.1021/acs.analchem.2c05288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
As an absolute quantification method at the single-molecule level, digital PCR (dPCR) offers the highest accuracy. In this work, we developed a 3D scalable chamber-array chip that multiplied the number of partitions by stacking chamber-array layers and realized digital loop-mediated isothermal amplification to quantify DNA molecules. It greatly increases the number of partitions to improve the performance of dPCR without increasing the chip size, the operation workflow complicity, and operation time. For the three-chamber-array-layer chip which contains 200,000 reactors of a 0.125 nL volume, it has been proved that the reagent filling and partition were finished within 3 min, and the whole detection could be finished within 1 h. The method demonstrated that it could be scalable to a six-chamber-array layer, which contains 400,000 reactors without increasing the size of the chip and the complication of filling/partition workflow but only takes an additional hour for scanning. Due to its potential for high throughput, low cost, and simple operation, our device may significantly expand the clinical application range of dPCR.
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Affiliation(s)
- Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Kaiyue Chen
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Jiqi Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
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27
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Liu X, Wang X, Zhang H, Yan Z, Gaňová M, Lednický T, Řezníček T, Xu Y, Zeng W, Korabečná M, Neužil P. Smartphone integrated handheld (SPEED) digital polymerase chain reaction device. Biosens Bioelectron 2023; 232:115319. [PMID: 37087984 DOI: 10.1016/j.bios.2023.115319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
We demonstrate a smartphone integrated handheld (SPEED) digital polymerase chain reaction (dPCR) device for point-of-care application. The device has dimensions of ≈100 × 200 × 35 mm3 and a weight of ≈400 g. It can perform 45 PCR cycles in ≈49 min. The device also features integrated, miniaturized modules for thermal cycling, image taking, and wireless data communication. These functions are controlled by self-developed Android-based applications. The only consumable is the developed silicon-based dPCR chip, which has the potential to be recycled. The device's precision and accuracy are comparable with commercial dPCR machines. We have verified the SPEED dPCR prototype's utility in the testing of severe acute respiratory syndrome coronavirus 2, the detection of cancer-associated gene sequences, and the confirmations of Down syndrome diagnoses. Due to its low upfront capital investment, as well as its nominal running cost, we envision that the SPEED dPCR device will help to perform cancer screenings and non-invasive prenatal tests for the general population. It will also aid in the timely identification and monitoring of infectious disease testing, thereby expediting alerts with respect to potential emerging pandemics.
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Affiliation(s)
- Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Xinlu Wang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Haoqing Zhang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Ministry of Education Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Zhiqiang Yan
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, PR China
| | - Martina Gaňová
- 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
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300, Brno, Czech Republic
| | - Tomáš Řezníček
- ITD Tech s.r.o, Osvoboditelu 1005, 735 81, Bohumín, Czech Republic
| | - Ying Xu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Wen Zeng
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital of Prague, Albertov 4, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600, Brno, Czech Republic.
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28
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Lai MY, Zen LPY, Abdul Hamid MH, Jelip J, Mudin RN, Ivan VJS, Francis LNP, Saihidi I, Lau YL. Point-of-Care Diagnosis of Malaria Using a Simple, Purification-Free DNA Extraction Method Coupled with Loop-Mediated Isothermal Amplification-Lateral Flow. Trop Med Infect Dis 2023; 8:199. [PMID: 37104326 PMCID: PMC10140920 DOI: 10.3390/tropicalmed8040199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/28/2023] Open
Abstract
We propose a protocol suitable for point-of-care diagnosis of malaria utilizing a simple and purification-free DNA extraction method with the combination of loop-mediated isothermal amplification assay and lateral flow (LAMP-LF). The multiplex LAMP-LF platform developed here can simultaneously detect Plasmodium knowlesi, P. vivax, P. falciparum, and Plasmodium genus (for P. malariae and P. ovale). Through the capillary effect, the results can be observed by the red band signal on the test and control lines within 5 min. The developed multiplex LAMP-LF was tested with 86 clinical blood samples on-site at Hospital Kapit, Sarawak, Malaysia. By using microscopy as the reference method, the multiplex LAMP-LF showed 100% sensitivity (95% confidence interval (CI): 91.4 to 100.00%) and 97.8% specificity (95% CI: 88.2% to 99.9%). The high sensitivity and specificity of multiplex LAMP-LF make it ideal for use as a point-of-care diagnostic tool. The simple and purification-free DNA extraction protocol can be employed as an alternative DNA extraction method for malaria diagnosis in resource-limited settings. By combining the simple DNA extraction protocol and multiplex LAMP-LF approach, we aim to develop a simple-to-handle and easy-to-read molecular diagnostic tool for malaria in both laboratory and on-site settings.
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Affiliation(s)
- Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.Y.L.); (L.P.Y.Z.)
| | - Lee Phone Youth Zen
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.Y.L.); (L.P.Y.Z.)
| | | | - Jenarun Jelip
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62590, Malaysia
| | - Rose Nani Mudin
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62590, Malaysia
| | | | | | - Izreena Saihidi
- Hospital Kapit, Pathology Unit, Jalan Mamora, Kapit 96800, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (M.Y.L.); (L.P.Y.Z.)
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29
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Chen F, Hu Q, Li H, Xie Y, Xiu L, Zhang Y, Guo X, Yin K. Multiplex Detection of Infectious Diseases on Microfluidic Platforms. BIOSENSORS 2023; 13:bios13030410. [PMID: 36979622 PMCID: PMC10046538 DOI: 10.3390/bios13030410] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 05/31/2023]
Abstract
Infectious diseases contribute significantly to the global disease burden. Sensitive and accurate screening methods are some of the most effective means of identifying sources of infection and controlling infectivity. Conventional detecting strategies such as quantitative polymerase chain reaction (qPCR), DNA sequencing, and mass spectrometry typically require bulky equipment and well-trained personnel. Therefore, mass screening of a large population using conventional strategies during pandemic periods often requires additional manpower, resources, and time, which cannot be guaranteed in resource-limited settings. Recently, emerging microfluidic technologies have shown the potential to replace conventional methods in performing point-of-care detection because they are automated, miniaturized, and integrated. By exploiting the spatial separation of detection sites, microfluidic platforms can enable the multiplex detection of infectious diseases to reduce the possibility of misdiagnosis and incomplete diagnosis of infectious diseases with similar symptoms. This review presents the recent advances in microfluidic platforms used for multiplex detection of infectious diseases, including microfluidic immunosensors and microfluidic nucleic acid sensors. As representative microfluidic platforms, lateral flow immunoassay (LFIA) platforms, polymer-based chips, paper-based devices, and droplet-based devices will be discussed in detail. In addition, the current challenges, commercialization, and prospects are proposed to promote the application of microfluidic platforms in infectious disease detection.
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Affiliation(s)
- Fumin Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
- One Health Center, Shanghai Jiao Tong University—The University of Edinburgh, Shanghai 200025, China
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
- One Health Center, Shanghai Jiao Tong University—The University of Edinburgh, Shanghai 200025, China
| | - Huimin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
- One Health Center, Shanghai Jiao Tong University—The University of Edinburgh, Shanghai 200025, China
| | - Yi Xie
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
- One Health Center, Shanghai Jiao Tong University—The University of Edinburgh, Shanghai 200025, China
| | - Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
- One Health Center, Shanghai Jiao Tong University—The University of Edinburgh, Shanghai 200025, China
| | - Yuqian Zhang
- Department of Surgery, Division of Surgery Research, Mayo Clinic, Rochester, MN 55905, USA
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
- One Health Center, Shanghai Jiao Tong University—The University of Edinburgh, Shanghai 200025, China
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
- One Health Center, Shanghai Jiao Tong University—The University of Edinburgh, Shanghai 200025, China
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30
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Tarim EA, Anil Inevi M, Ozkan I, Kecili S, Bilgi E, Baslar MS, Ozcivici E, Oksel Karakus C, Tekin HC. Microfluidic-based technologies for diagnosis, prevention, and treatment of COVID-19: recent advances and future directions. Biomed Microdevices 2023; 25:10. [PMID: 36913137 PMCID: PMC10009869 DOI: 10.1007/s10544-023-00649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
The COVID-19 pandemic has posed significant challenges to existing healthcare systems around the world. The urgent need for the development of diagnostic and therapeutic strategies for COVID-19 has boomed the demand for new technologies that can improve current healthcare approaches, moving towards more advanced, digitalized, personalized, and patient-oriented systems. Microfluidic-based technologies involve the miniaturization of large-scale devices and laboratory-based procedures, enabling complex chemical and biological operations that are conventionally performed at the macro-scale to be carried out on the microscale or less. The advantages microfluidic systems offer such as rapid, low-cost, accurate, and on-site solutions make these tools extremely useful and effective in the fight against COVID-19. In particular, microfluidic-assisted systems are of great interest in different COVID-19-related domains, varying from direct and indirect detection of COVID-19 infections to drug and vaccine discovery and their targeted delivery. Here, we review recent advances in the use of microfluidic platforms to diagnose, treat or prevent COVID-19. We start by summarizing recent microfluidic-based diagnostic solutions applicable to COVID-19. We then highlight the key roles microfluidics play in developing COVID-19 vaccines and testing how vaccine candidates perform, with a focus on RNA-delivery technologies and nano-carriers. Next, microfluidic-based efforts devoted to assessing the efficacy of potential COVID-19 drugs, either repurposed or new, and their targeted delivery to infected sites are summarized. We conclude by providing future perspectives and research directions that are critical to effectively prevent or respond to future pandemics.
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Affiliation(s)
- E Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Muge Anil Inevi
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Ilayda Ozkan
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Seren Kecili
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Eyup Bilgi
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - M Semih Baslar
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | | | - H Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey.
- METU MEMS Center, Ankara, Turkey.
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31
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Kincses A, Vigh JP, Petrovszki D, Valkai S, Kocsis AE, Walter FR, Lin HY, Jan JS, Deli MA, Dér A. The Use of Sensors in Blood-Brain Barrier-on-a-Chip Devices: Current Practice and Future Directions. BIOSENSORS 2023; 13:bios13030357. [PMID: 36979569 PMCID: PMC10046513 DOI: 10.3390/bios13030357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 06/01/2023]
Abstract
The application of lab-on-a-chip technologies in in vitro cell culturing swiftly resulted in improved models of human organs compared to static culture insert-based ones. These chip devices provide controlled cell culture environments to mimic physiological functions and properties. Models of the blood-brain barrier (BBB) especially profited from this advanced technological approach. The BBB represents the tightest endothelial barrier within the vasculature with high electric resistance and low passive permeability, providing a controlled interface between the circulation and the brain. The multi-cell type dynamic BBB-on-chip models are in demand in several fields as alternatives to expensive animal studies or static culture inserts methods. Their combination with integrated biosensors provides real-time and noninvasive monitoring of the integrity of the BBB and of the presence and concentration of agents contributing to the physiological and metabolic functions and pathologies. In this review, we describe built-in sensors to characterize BBB models via quasi-direct current and electrical impedance measurements, as well as the different types of biosensors for the detection of metabolites, drugs, or toxic agents. We also give an outlook on the future of the field, with potential combinations of existing methods and possible improvements of current techniques.
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Affiliation(s)
- András Kincses
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
| | - Judit P. Vigh
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
- Doctoral School of Biology, University of Szeged, H-6720 Szeged, Hungary
| | - Dániel Petrovszki
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Sándor Valkai
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
| | - Anna E. Kocsis
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
| | - Fruzsina R. Walter
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
| | - Hung-Yin Lin
- Department of Chemical and Materials Engineering, National University of Kaohsiung, Kaohsiung 81148, Taiwan;
| | - Jeng-Shiung Jan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan;
| | - Mária A. Deli
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
| | - András Dér
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (A.K.); (J.P.V.); (D.P.); (S.V.); (A.E.K.); (F.R.W.)
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Zhou Z, Lan X, Zhu L, Zhang Y, Chen K, Zhang W, Xu W. Portable dual-aptamer microfluidic chip biosensor for Bacillus cereus based on aptamer tailoring and dumbbell-shaped probes. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130545. [PMID: 36493638 DOI: 10.1016/j.jhazmat.2022.130545] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
As food-borne pathogens, Bacillus cereus not only produce toxins that contaminate food and threaten human health, but also rely on spores to resist extreme environments. At present, the detection of B. cereus is still at the genome level and it is not easily distinguished from other Bacilli of the same group. Herein, we obtained the aptamers of B. cereus in different phases through Cell-SELEX technology. Then, through step-by-step tailoring and molecular docking, the two best performing aptamers were ascertained and the interaction revealed between the repeated G bases in the aptamer and the polar amino acids in the α-helix of the epiprotein. Based on these aptamers, a multifunctional dumbbell-shaped probe and an ultrasensitive microfluidic chip biosensor were designed. Tests showed that the novel sensor is able to complete detection within 1 h with a limit of detection (LOD) of 9.27 CFU/mL. Moreover, the sensor can be used in complex food environments, such as milk and rice, is able to detect both vegetative cells and spores, and it can also distinguish B. thuringiensis from the same flora. This study can provide a reference for the future development of food-borne pathogenic bacteria aptamer selecting, target interaction analysis, detection methods and equipment.
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Affiliation(s)
- Ziqi Zhou
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinyue Lan
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kehan Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wenqiang Zhang
- Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
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Shi J, Zhang Y, Yang M. Recent development of microfluidics-based platforms for respiratory virus detection. BIOMICROFLUIDICS 2023; 17:024104. [PMID: 37035101 PMCID: PMC10076069 DOI: 10.1063/5.0135778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
With the global outbreak of SARS-CoV-2, the inadequacies of current detection technology for respiratory viruses have been recognized. Rapid, portable, accurate, and sensitive assays are needed to expedite diagnosis and early intervention. Conventional methods for detection of respiratory viruses include cell culture-based assays, serological tests, nucleic acid detection (e.g., RT-PCR), and direct immunoassays. However, these traditional methods are often time-consuming, labor-intensive, and require laboratory facilities, which cannot meet the testing needs, especially during pandemics of respiratory diseases, such as COVID-19. Microfluidics-based techniques can overcome these demerits and provide simple, rapid, accurate, and cost-effective analysis of intact virus, viral antigen/antibody, and viral nucleic acids. This review aims to summarize the recent development of microfluidics-based techniques for detection of respiratory viruses. Recent advances in different types of microfluidic devices for respiratory virus diagnostics are highlighted, including paper-based microfluidics, continuous-flow microfluidics, and droplet-based microfluidics. Finally, the future development of microfluidic technologies for respiratory virus diagnostics is discussed.
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Affiliation(s)
- Jingyu Shi
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, People's Republic of China
| | - Yu Zhang
- Department of Mechanical and Automotive Engineering, Royal Melbourne Institute of Technology, Melbourne, VIC 3000, Australia
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, People's Republic of China
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34
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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35
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Marangoni JM, Ng KKS, Emadi A. Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification. MICROMACHINES 2023; 14:472. [PMID: 36838172 PMCID: PMC9960872 DOI: 10.3390/mi14020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.
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Affiliation(s)
- Jesse M. Marangoni
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Arezoo Emadi
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, ON N9B 3P4, Canada
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36
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Oberc C, Sojoudi P, Li PCH. Nucleic acid amplification test (NAAT) conducted in a microfluidic chip to differentiate between various ginseng species. Analyst 2023; 148:525-531. [PMID: 36601715 DOI: 10.1039/d2an01960d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Panax ginseng and Panax quinquefolius have different medicinal properties and market values; however, they can be difficult to distinguish from one another based on physical appearances alone. Therefore, a molecular test that can be performed in commercial settings is needed to overcome this difficulty. A locus that contains a single nucleotide polymorphism (SNP) site to differentiate between P. ginseng and P. quinquefolius has been selected. An isothermal nucleic acid amplification test (NAAT) has been developed for use in a microfluidic chip; this NAAT method, which is based on lesion-induced DNA amplification (LIDA), amplifies the extracted plant genomic samples and enhances the detection of specific SNPs. This NAAT method was used to authenticate five ginseng root samples which indicated that two of the five samples appear to be mislabeled. These authentication results were consistent with those obtained from next generation sequencing (NGS) although this molecular test is more affordable and faster than NGS.
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Affiliation(s)
- Christopher Oberc
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC, V5A 1S6, Canada.
| | - Parsa Sojoudi
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC, V5A 1S6, Canada.
| | - Paul C H Li
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC, V5A 1S6, Canada.
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Waitkus J, Chang Y, Liu L, Puttaswamy SV, Chung T, Vargas AMM, Dollery SJ, O'Connell MR, Cai H, Tobin GJ, Bhalla N, Du K. Gold Nanoparticle Enabled Localized Surface Plasmon Resonance on Unique Gold Nanomushroom Structures for On-Chip CRISPR-Cas13a Sensing. ADVANCED MATERIALS INTERFACES 2023; 10:2201261. [PMID: 37091050 PMCID: PMC10121183 DOI: 10.1002/admi.202201261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Indexed: 05/03/2023]
Abstract
A novel localized surface plasmon resonance (LSPR) system based on the coupling of gold nanomushrooms (AuNMs) and gold nanoparticles (AuNPs) is developed to enable a significant plasmonic resonant shift. The AuNP size, surface chemistry, and concentration are characterized to maximize the LSPR effect. A 31 nm redshift is achieved when the AuNMs are saturated by the AuNPs. This giant redshift also increases the full width of the spectrum and is explained by the 3D finite-difference time-domain (FDTD) calculation. In addition, this LSPR substrate is packaged in a microfluidic cell and integrated with a CRISPR-Cas13a RNA detection assay for the detection of the SARS-CoV-2 RNA targets. Once activated by the target, the AuNPs are cleaved from linker probes and randomly deposited on the AuNM substrate, demonstrating a large redshift. The novel LSPR chip using AuNP as an indicator is simple, specific, isothermal, and label-free; and thus, provides a new opportunity to achieve the next generation multiplexing and sensitive molecular diagnostic system.
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Affiliation(s)
- Jacob Waitkus
- University of California, Riverside, Riverside, CA, USA
| | - Yu Chang
- University of California, Riverside, Riverside, CA, USA
| | - Li Liu
- University of California, Riverside, Riverside, CA, USA
| | - Srinivasu Valagerahally Puttaswamy
- NIBEC School of Engineering, Ulster University, Belfast, UK
- Healthcare Technology Hub, School of Engineering, Ulster University, Belfast, UK
| | - Taerin Chung
- Tech4Health Institute and Department of Radiology, New York University Langone Health New York, USA
| | | | | | | | - Haogang Cai
- Tech4Health Institute and Department of Radiology, New York University Langone Health New York, USA
| | | | - Nikhil Bhalla
- NIBEC School of Engineering, Ulster University, Belfast, UK
- Healthcare Technology Hub, School of Engineering, Ulster University, Belfast, UK
| | - Ke Du
- University of California, Riverside, Riverside, CA, USA
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Crego-Vicente B, Fernández-Soto P, García-Bernalt Diego J, Febrer-Sendra B, Muro A. Development of a Duplex LAMP Assay with Probe-Based Readout for Simultaneous Real-Time Detection of Schistosoma mansoni and Strongyloides spp. -A Laboratory Approach to Point-Of-Care. Int J Mol Sci 2023; 24:ijms24010893. [PMID: 36614336 PMCID: PMC9821331 DOI: 10.3390/ijms24010893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is the most popular technology for point-of-care testing applications due its rapid, sensitive and specific detection with simple instrumentation compared to PCR-based methods. Many systems for reading the results of LAMP amplifications exist, including real-time fluorescence detection using fluorophore-labelled probes attached to oligonucleotide sequences complementary to the target nucleic acid. This methodology allows the simultaneous detection of multiple targets (multiplexing) in one LAMP assay. A method for multiplexing LAMP is the amplification by release of quenching (DARQ) technique by using a 5'-quencher modified LAMP primer annealed to 3'-fluorophore-labelled acting as detection oligonucleotide. The main application of multiplex LAMP is the rapid and accurate diagnosis of infectious diseases, allowing differentiation of co-infecting pathogens in a single reaction. Schistosomiasis, caused among other species by Schistosoma mansoni and strongyloidiasis, caused by Strongyloides stercoralis, are the most common helminth-parasite infections worldwide with overlapping distribution areas and high possibility of coinfections in the human population. It would be of great interest to develop a duplex LAMP to detect both pathogens in the same reaction. In this study, we investigate the use of our two previously developed and well-stablished LAMP assays for S. mansoni and Strongyloides spp. DNA detection in a new duplex real-time eight-primer system based on a modified DARQ probe method that can be performed in a portable isothermal fluorimeter with minimal laboratory resources. We also applied a strategy to stabilize the duplexed DARQ-LAMP mixtures at room temperature for use as ready-to-use formats facilitating analysis in field settings as point-of-care diagnostics for schistosomiasis and strongyloidiasis.
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39
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Li Q, An Z, Sun T, Ji S, Wang W, Peng Y, Wang Z, Salentijn GIJ, Gao Z, Han D. Sensitive colorimetric detection of antibiotic resistant Staphylococcus aureus on dairy farms using LAMP with pH-responsive polydiacetylene. Biosens Bioelectron 2023; 219:114824. [PMID: 36327562 DOI: 10.1016/j.bios.2022.114824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/29/2022] [Accepted: 10/16/2022] [Indexed: 11/19/2022]
Abstract
Rapidly and accurately detecting antibiotic-resistant pathogens in agriculture and husbandry is important since these represent a major threat to public health. While much attention has been dedicated to detecting now-common resistant bacteria, such as methicillin-resistant Staphylococcus aureus, fewer methods have been developed to assess resistance against macrolides in Staphylococcus aureus (SA). Here, we report a visual on-site detection system for macrolide resistant SA in dairy products. First, metagenomic sequencing in raw milk, cow manure, water and aerosol deposit collected from dairy farms around Tianjin was used to identify the most abundant macrolide resistance gene, which was found to be the macB gene. In parallel, SA housekeeping genes were screened to allow selective identification of SA, which resulted in the selection of the SAOUHSC_01275 gene. Next, LAMP assays targeting the above-mentioned genes were developed and interpreted by agarose gel electrophoresis. For on-site application, different pH-sensitive colorimetric LAMP indicators were compared, which resulted in selection of polydiacetylene (PDA) as the most sensitive candidate. Additionally, a semi-quantitative detection could be realized by analyzing the RGB information via smartphone with a LOD of 1.344 × 10-7 ng/μL of genomic DNA from a milk sample. Finally, the proposed method was successfully carried out at a real farm within 1 h from sample to result by using freeze-dried reagents and portable devices. This is the first instance in which PDA is used to detect LAMP products, and this generic read-out system can be expanded to other antibiotic resistant genes and bacteria.
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Affiliation(s)
- Qiaofeng Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Wageningen Food Safety Research, Wageningen University & Research, P.O. Box 230, 6700, AE, Wageningen, the Netherlands
| | - Zhaoxia An
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Tieqiang Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shuaifeng Ji
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Weiya Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Gert I J Salentijn
- Wageningen Food Safety Research, Wageningen University & Research, P.O. Box 230, 6700, AE, Wageningen, the Netherlands; Laboratory of Organic Chemistry, Wageningen University, Wageningen, 6708, WE, the Netherlands.
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
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40
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Li M, Ge H, Sun Z, Fu J, Cao L, Feng X, Meng G, Peng Y, Liu Y, Zhao C. A loop-mediated isothermal amplification-enabled analytical assay for the detection of SARS-CoV-2: A review. Front Cell Infect Microbiol 2022; 12:1068015. [PMID: 36619749 PMCID: PMC9816412 DOI: 10.3389/fcimb.2022.1068015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The number of words: 4645, the number of figures: 4, the number of tables: 1The outbreak of COVID-19 in December 2019 caused a global pandemic of acute respiratory disease, and with the increasing virulence of mutant strains and the number of confirmed cases, this has resulted in a tremendous threat to global public health. Therefore, an accurate diagnosis of COVID-19 is urgently needed for rapid control of SARS-CoV-2 transmission. As a new molecular biology technology, loop-mediated isothermal amplification (LAMP) has the advantages of convenient operation, speed, low cost and high sensitivity and specificity. In the past two years, rampant COVID-19 and the continuous variation in the virus strains have demanded higher requirements for the rapid detection of pathogens. Compared with conventional RT-PCR and real-time RT-PCR methods, genotyping RT-LAMP method and LAMP plus peptide nucleic acid (PNA) probe detection methods have been developed to correctly identified SARS-CoV-2 variants, which is also why LAMP technology has attracted much attention. LAMP detection technology combined with lateral flow assay, microfluidic technology and other sensing technologies can effectively enhance signals by nucleic acid amplification and help to give the resulting output in a faster, more convenient and user-friendly way. At present, LAMP plays an important role in the detection of SARS-CoV-2.
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Affiliation(s)
- Mingna Li
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Hongjuan Ge
- College of public health, Jilin Medical University, Jilin, China
| | - Zhe Sun
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Jangshan Fu
- College of public health, Jilin Medical University, Jilin, China
| | - Lele Cao
- College of public health, Jilin Medical University, Jilin, China
| | - Xinrui Feng
- College of public health, Jilin Medical University, Jilin, China,Medical college, Yanbian University, Jilin, China
| | - Guixian Meng
- College of medical laboratory, Jilin Medical University, Jilin, China
| | - Yubo Peng
- Business School, The University of Adelaide, Adelaide, SA, Australia
| | - Yan Liu
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
| | - Chen Zhao
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
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41
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Wei S, Wang L, Shi M, Li J, Sun C, Liu Y, Zhang Z, Wu Y, Huang L, Tang F, Lv L, Mu X, Tian W, Lin C, Lu J, Sun B, Dai B, Xiong H, Nie X, Ding W, Ouyang Y, Lin L, Liu X. Rapid, accurate, and novel diagnostic technique for respiratory pathogens: Clinical application of loop-mediated isothermal amplification assay in older patients with pneumonia, a multicenter prospective observational study. Front Microbiol 2022; 13:1048997. [PMID: 36601400 PMCID: PMC9806167 DOI: 10.3389/fmicb.2022.1048997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Background Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method using only one type of enzyme that can amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. Chips for Complicated Infection Detection (CCID) is based on LAMP. This study translate CCID into clinical application and evaluate its diagnostic value for pneumonia. Methods Eighty one older patients with pneumonia were prospectively enrolled from January 1 to July 23, 2021, and 57 sputum/airway secretion and 35 bronchoalveolar lavage fluid samples were collected and analyzed by CCID and conventional microbiological tests (CMTs). Samples were collected, transported, monitored, and managed by a multidisciplinary team using a sample management information system. Results CCID turnaround time was 50 min, and the detection limit was 500 copies/reaction. The percentage of positive samples was significantly higher using CCID than CMTs, especially for Klebsiella pneumoniae (odds ratio [OR], 9.0; 95% confidence interval [CI], 1.1-70.5; p < 0.05), Enterococcus faecalis (OR, ∞; p < 0.01), Stenotrophomonas maltophilia (OR, ∞; p < 0.01), fungi (OR, 26.0; 95% CI, 3.6-190.0; p < 0.01), and viruses (CCID only; p < 0.01). In addition, the percentage of positive results was significantly higher using CCID than CMTs in patients who used antibiotics for more than 3 days (91.9% vs. 64.9%; p < 0.01). Analyzing clinical impact, 55 cases (59.8%) benefited from CCID. Conclusion CCID allows the rapid and accurate detection of pneumonia in older patients. Moreover, this technique is less affected by previous antibiotic treatment and can improve patient care.
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Affiliation(s)
- Shanchen Wei
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Lina Wang
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Mingwei Shi
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Jun Li
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Chunping Sun
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | | | - Zhi Zhang
- Bio Biological Group Co., Ltd, Beijing, China
| | - Yiqun Wu
- School of Public Health, Peking University Health Science Center, Beijing, China
| | - Lei Huang
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Fei Tang
- Department of Respiratory, Anhui Chest Hospital, Hefei, China
| | - Liping Lv
- Department of Respiratory, Anhui Chest Hospital, Hefei, China
| | - Xiangdong Mu
- Department of Respiratory, Tsinghua ChangGung Hospital, Beijing, China
| | - Wei Tian
- Department of Geriatrics, Jishuitan Hospital, Beijing, China
| | - Caiwei Lin
- Department of Emergency, Aerospace Center Hospital, Beijing, China
| | - Jianrong Lu
- Department of Emergency, Jingmei Group General Hospital, Beijing, China
| | - Baojun Sun
- Department of Respiratory, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Bin Dai
- Department of Neurosurgery, Shijitan Hospital, Beijing, China
| | - Hui Xiong
- Department of Emergency, Peking University First Hospital, Beijing, China
| | - Xiuhong Nie
- Department of Respiratory, Xuanwu Hospital, Beijing, China
| | - Weimin Ding
- Department of Respiratory Endoscopy, Beijing Chest Hospital, Beijing, China
| | - Yuqing Ouyang
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Lianjun Lin
- Department of Geriatrics, Peking University First Hospital, Beijing, China,*Correspondence: Lianjun Lin,
| | - Xinmin Liu
- Department of Geriatrics, Peking University First Hospital, Beijing, China,Xinmin Liu,
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42
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Sugano Y, Sakata K, Nakamura K, Hosokawa A, Kouguchi H, Suzuki T, Kondo K. Loop-mediated isothermal amplification (LAMP) for rapid and easy identification of Omphalotus japonicus. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 5:100115. [PMID: 35800296 PMCID: PMC9253582 DOI: 10.1016/j.fochms.2022.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/04/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022]
Abstract
We constructed a LAMP to specifically detect toxic Omphalotus japonicus mushrooms. The process took less than 2 h from DNA extraction to detection. Results were determined visually using fluorescent detection reagents. This method can be used to identify food poisoning caused by O. japonicus.
Omphalotus japonicus is a major toxic mushroom in Japan. When food poisoning caused by O. japonicus occurs, quick and accurate identification using a method that does not rely on morphological discrimination is required. Because the loop-mediated isothermal amplification (LAMP) method meets these requirements, we developed a LAMP method for detecting O. japonicus. Amplification occurred within 60 min, and the presence or absence of O. japonicus was confirmed within 2 h, including the DNA extraction protocol. The LAMP method did not show cross-reactivity with 13 species of edible mushrooms, had high specificity toward O. japonicus, and had sufficient detection sensitivity even in a mixed mushroom sample containing 1% O. japonicus. Additionally, O. japonicus could be detected in simulated food poisoning samples of heated and digested mushrooms, and in actual food poisoning residual samples.
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Affiliation(s)
- Yohei Sugano
- Department of Food Hygiene, Hokkaido Institute of Public Health, Kita-ku, 0600819 Sapporo, Japan
- Corresponding author.
| | - Kozue Sakata
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-ku, 2109501 Kawasaki, Japan
| | - Kosuke Nakamura
- Division of Foods, National Institute of Health Sciences, Kawasaki-ku, 2109501 Kawasaki, Japan
| | - Aoi Hosokawa
- Department of Food Hygiene, Hokkaido Institute of Public Health, Kita-ku, 0600819 Sapporo, Japan
| | - Hirokazu Kouguchi
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Kita-ku, 0600819 Sapporo, Japan
| | - Tomohiro Suzuki
- Department of General Affairs and Planning, Hokkaido Institute of Public Health, Kita-ku, 0600819 Sapporo, Japan
| | - Kazunari Kondo
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-ku, 2109501 Kawasaki, Japan
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43
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McCloskey D, Boza J, Mason CE, Erickson D. MINI: A high-throughput point-of-care device for performing hundreds of nucleic acid tests per day. Biosens Bioelectron 2022; 216:114654. [PMID: 36084523 PMCID: PMC10960951 DOI: 10.1016/j.bios.2022.114654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022]
Abstract
There are a variety of infectious diseases with a high incidence and mortality in limited resource settings that could benefit from rapid point of care molecular diagnosis. Global health efforts have sought to implement mass-screening programs to provide earlier detection and subsequent treatment in an effort to control transmission and improve health outcomes. However, many of the current diagnostic technologies under development are limited to fewer than 10 samples per run, which inherently restricts the screening throughput of these devices. We have developed a high throughput device called "MINI" that is capable of testing hundreds of samples per day at the point-of-care. MINI can utilize multiple energy sources - electricity, flame, or solar - to perform loop-mediated isothermal amplification (LAMP) in a portable and robust device which is ideal for use in limited resource settings. The unique opto-electronic design of MINI minimizes the energy and space requirements of the device and maximizes the optical isolation and signal clarity, enabling point-of-care analysis of 96 unique samples at once. We show comparable performance to a commercial instrument using two different LAMP assays for Kaposi's sarcoma-associated herpesvirus and a common housekeeping gene, GAPDH. With a single device capable of running hundreds of samples per day, increased access to modern molecular diagnostics could improve health outcomes for a variety of diseases common in limited resource settings.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Juan Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher E Mason
- Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - David Erickson
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA; Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
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44
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Feng J, Neuzil J, Manz A, Iliescu C, Neuzil P. Microfluidic trends in drug screening and drug delivery. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Xiao B, Zhao R, Wang N, Zhang J, Sun X, Chen A. Recent advances in centrifugal microfluidic chip-based loop-mediated isothermal amplification. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Huang T, Zhang R, Li J. CRISPR-Cas-based techniques for pathogen detection: Retrospect, recent advances, and future perspectives. J Adv Res 2022:S2090-1232(22)00240-5. [PMID: 36367481 PMCID: PMC10403697 DOI: 10.1016/j.jare.2022.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements. AIM OF REVIEW This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation. KEY SCIENTIFIC CONCEPTS OF REVIEW Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.
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47
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Toldrà A, Ainla A, Khaliliazar S, Landin R, Chondrogiannis G, Hanze M, Réu P, Hamedi MM. Portable electroanalytical nucleic acid amplification tests using printed circuit boards and open-source electronics. Analyst 2022; 147:4249-4256. [PMID: 35993403 PMCID: PMC9511072 DOI: 10.1039/d2an00923d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/10/2022] [Indexed: 09/19/2023]
Abstract
The realization of electrochemical nucleic acid amplification tests (NAATs) at the point of care (POC) is highly desirable, but it remains a challenge given their high cost and lack of true portability/miniaturization. Here we show that mass-produced, industrial standardized, printed circuit boards (PCBs) can be repurposed to act as near-zero cost electrodes for self-assembled monolayer-based DNA biosensing, and further integration with a custom-designed and low-cost portable potentiostat. To show the analytical capability of this system, we developed a NAAT using isothermal recombinase polymerase amplification, bypassing the need of thermal cyclers, followed by an electrochemical readout relying on a sandwich hybridization assay. We used our sensor and device for analytical detection of the toxic microalgae Ostreopsis cf. ovata as a proof of concept. This work shows the potential of PCBs and open-source electronics to be used as powerful POC DNA biosensors at a low-cost.
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Affiliation(s)
- Anna Toldrà
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Alar Ainla
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Shirin Khaliliazar
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Roman Landin
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Georgios Chondrogiannis
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Martin Hanze
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Mahiar M Hamedi
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
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48
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Torezin Mendonça G, Cassaboni Stracke M, de Oliveira Coelho B, Bruna Soligo Sanchuki H, Klassen de Oliveira V, Klerynton Marchini F, Lucíola Zanette D, Nóbrega Aoki M, Ribeiro Viana E, Blanes L. A new RT-LAMP-on-a-Chip Instrument for SARS-CoV-2 diagnostics. Microchem J 2022; 180:107600. [PMID: 35620142 PMCID: PMC9121651 DOI: 10.1016/j.microc.2022.107600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 02/08/2023]
Abstract
This work describes the development of a Point-of-Care (POC) Lab-on-a-Chip (LOC) instrument for diagnosis of SARS-CoV-2 by Reverse-Transcription Loop-mediated isothermal amplification (RT-LAMP). The hardware is based on a Raspberry Pi computer ($35), a video camera, an Arduino Nano microcontroller, a printed circuit board as a heater and a 3D printed housing. The chips were manufactured in polymethyl methacrylate (PMMA) using a CO2 laser cutting machine and sealed with a PCR optic plastic film. The chip temperature is precisely controlled by a proportional-integral-derivative (PID) algorithm. During the RT-LAMP amplifications the chip was maintained at ∼ (65.0 ± 0.1) °C for 25 minutes and 5 minutes cooling down, totaling a 30 minutes of reaction .The software interpretation occurs in less than a second. The chip design has four 25 µL chambers, two for clinical samples and two for positive and negative control-samples. The RT-LAMP master mix solution added in the chip chambers contains the pH indicator Phenol Red, that is pink (for pH ∼ 8.0) before amplification and becomes yellow (pH ∼ 6.0) if the genetic material is amplified. The RT-LAMP SARS-CoV-2 diagnostic was made by color image recognition using the OpenCV machine vision software library. The software was programmed to automatically distinguish the HSV color parameter distribution in each one of the four chip chambers. The instrument was successfully tested for SARS-CoV-2 diagnosis, in 22 clinic samples, 11 positives and 11 negatives, achieving an assertiveness of 86% when compared to the results obtained by RT-LAMP standard reactions performed in conventional PCR equipment.
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Affiliation(s)
- Geovani Torezin Mendonça
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Bruna de Oliveira Coelho
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | | | - Fabricio Klerynton Marchini
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Dalila Lucíola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Emilson Ribeiro Viana
- Research and Characterization of Nanomaterials and Nanodevices Laboratory (LPCA-NN), Physics Department, Federal University of Technology - Paraná, 7 de setembro 3165 Avenue, Curitiba, Paraná, Brazil
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Corresponding author
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49
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Das D, Lin CW, Kwon JS, Chuang HS. Rotational diffusometric sensor with isothermal amplification for ultra-sensitive and rapid detection of SARS-CoV-2 nsp2 cDNA. Biosens Bioelectron 2022; 210:114293. [PMID: 35477152 PMCID: PMC9020650 DOI: 10.1016/j.bios.2022.114293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022]
Abstract
In the wake of a pandemic, the development of rapid, simple, and accurate molecular diagnostic tests can significantly aid in reducing the spread of infections. By combining particle imaging with molecular assays, a quick and highly sensitive biosensor can readily identify a pathogen at low concentrations. Here, we implement functionalized particle-enabled rotational diffusometry in combination with loop-mediated isothermal amplification for the rapid detection of the SARS-CoV-2 nsp2 gene in the recombinant plasmid as a proof of concept for COVID-19 diagnostics. By analyzing the images of blinking signals generated by these modified particles, the change in micro-level viscosity due to nucleic acid amplification was measured. The high sensitivity of rotational diffusometry enabled facile detection within 10 min, with a limit of detection of 70 ag/μL and a sample volume of 2 μL. Tenfold higher detection sensitivity was observed for rotational diffusometry in comparison with real-time PCR. In addition, the system stability and the effect of temperature on rotational diffusometric measurements were studied and reported. These results demonstrated the utility of a rotational diffusometric platform for the rapid and sensitive detection of SARS-CoV-2 cDNA fragments.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung 413, Taiwan
| | - Jae-Sung Kwon
- Department of Mechanical Engineering, Incheon National University, Incheon, Republic of Korea.
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, 701, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, 701, Taiwan; Core Facility Center, National Cheng Kung University, Tainan, 701, Taiwan.
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50
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Natsuhara D, Misawa S, Saito R, Shirai K, Okamoto S, Nagai M, Kitamura M, Shibata T. A microfluidic diagnostic device with air plug-in valves for the simultaneous genetic detection of various food allergens. Sci Rep 2022; 12:12852. [PMID: 35896785 PMCID: PMC9329328 DOI: 10.1038/s41598-022-16945-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/19/2022] [Indexed: 01/12/2023] Open
Abstract
The identification of accidental allergen contamination in processed foods is crucial for risk management strategies in the food processing industry to effectively prevent food allergy incidents. Here, we propose a newly designed passive stop valve with high pressure resistance performance termed an “air plug-in valve” to further improve microfluidic devices for the detection of target nucleic acids. By implementing the air plug-in valve as a permanent stop valve, a maximal allowable flow rate of 70 µL/min could be achieved for sequential liquid dispensing into an array of 10 microchambers, which is 14 times higher than that achieved with the previous valve arrangement using single-faced stop valves. Additionally, we demonstrate the simultaneous detection of multiple food allergens (wheat, buckwheat, and peanut) based on the colorimetric loop-mediated isothermal amplification assay using our diagnostic device with 10 microchambers compactly arranged in a 20-mm-diameter circle. After running the assays at 60 °C for 60 min, any combination of the three types of food allergens and tea plant, which were used as positive and negative control samples, respectively, yielded correct test results, without any cross-contamination among the microchambers. Thus, our diagnostic device will provide a rapid and easy sample-to-answer platform for ensuring food safety and security.
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Affiliation(s)
- Daigo Natsuhara
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan.
| | - Sae Misawa
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, 350-0295, Japan
| | - Ryogo Saito
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan
| | - Koki Shirai
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan
| | - Shunya Okamoto
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan
| | - Masashi Kitamura
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, 350-0295, Japan
| | - Takayuki Shibata
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan.
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