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Hu H, Liu L, Wei XY, Duan JJ, Deng JY, Pei DS. Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172414. [PMID: 38631624 DOI: 10.1016/j.scitotenv.2024.172414] [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: 12/14/2023] [Revised: 03/15/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 109 copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R2 = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R2 = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Li Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Jin-Jing Duan
- Chongqing Miankai Biotechnology Research Institute Co., Ltd., Chongqing 400025, China; School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jiao-Yun Deng
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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Jiang JZ, Fang YF, Wei HY, Zhu P, Liu M, Yuan WG, Yang LL, Guo YX, Jin T, Shi M, Yao T, Lu J, Ye LT, Shi SK, Wang M, Duan M, Zhang DC. A remarkably diverse and well-organized virus community in a filter-feeding oyster. MICROBIOME 2023; 11:2. [PMID: 36611217 PMCID: PMC9825006 DOI: 10.1186/s40168-022-01431-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Viruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation. RESULTS Here, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oyster Crassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels. CONCLUSIONS In this study, we generated a first "knowledge landscape" of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems. Video Abstract.
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Affiliation(s)
- Jing-Zhe Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China.
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China.
- Tianjin Agricultural University, Tianjin, 300384, China.
| | - Yi-Fei Fang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Majorbio Bio-Pharm Technology Co Ltd, Shanghai, 201203, China
| | - Hong-Ying Wei
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
- Guangdong Magigene Biotechnology Co Ltd, Guangzhou, 510000, Guangdong, China
| | - Peng Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Min Liu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Wen-Guang Yuan
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China
| | - Li-Ling Yang
- Tianjin Agricultural University, Tianjin, 300384, China
| | | | - Tao Jin
- Guangdong Magigene Biotechnology Co Ltd, Guangzhou, 510000, Guangdong, China
| | - Mang Shi
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Tuo Yao
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China
| | - Jie Lu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China
| | - Ling-Tong Ye
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China
| | - Shao-Kun Shi
- Shenzhen Fisheries Development Research Center, Shenzhen, 518067, Guangdong, China
| | - Meng Wang
- Bureau of Agriculture and Rural Affairs of Conghua District, Guangzhou, 510925, Guangdong, China
| | - Ming Duan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Hubei.
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China.
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Feng Z, Chu X, Han M, Yu C, Jiang Y, Wang H, Lu L, Xu D. Rapid visual detection of Micropterus salmoides rhabdovirus using recombinase polymerase amplification combined with lateral flow dipsticks. JOURNAL OF FISH DISEASES 2022; 45:461-469. [PMID: 34984680 DOI: 10.1111/jfd.13575] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Largemouth bass (Micropterus salmoides) is an important freshwater-cultured species in China. Recently, a lethal and epidemic disease caused by Micropterus salmoides rhabdovirus (MSRV) results in huge economic losses to the largemouth bass industry. Current diagnostics for detecting MSRV are limited in sensitivity and speed and are inconvenient to be used for non-laboratory detection. In this study, three rapid and convenient detection assays of MSRV by recombinase polymerase amplification (RPA) and lateral flow dipsticks (LFD), targeting the conserved sequences of the MSRV-SS N gene, are described. With these RPA methods, the detection could achieve within 50 min at 38°C. Both methods of RPA-AGE and RPA-LFD could detect the viral DNA as low as 170 copies/μl of the MSRV standard plasmid and were 100-fold more sensitive than that in the method of routine PCR. Meanwhile, these RPA methods were highly specific for the detection of MSRV and can be feasibly applied to the diagnostic of MSRV infection. In brief, RPA-AGE, RPA-LFD and RT-RPA-LFD provide convenient, rapid, sensitive and reliable methods that could improve field diagnosis of MSRV with limited machine resources, and would enhance the production of largemouth bass.
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Affiliation(s)
- Zizhao Feng
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Xin Chu
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Minzhen Han
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Chenwei Yu
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Yousheng Jiang
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, China
| | - Hao Wang
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, China
| | - Liqun Lu
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, China
| | - Dan Xu
- College of Fisheries and life science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, China
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Morga B, Jacquot M, Pelletier C, Chevignon G, Dégremont L, Biétry A, Pepin JF, Heurtebise S, Escoubas JM, Bean TP, Rosani U, Bai CM, Renault T, Lamy JB. Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species. Front Microbiol 2021; 12:711377. [PMID: 34326830 PMCID: PMC8313985 DOI: 10.3389/fmicb.2021.711377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.
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Affiliation(s)
| | | | | | | | | | | | - Jean-François Pepin
- Ifremer, ODE-Littoral-Laboratoire Environnement Ressources des Pertuis Charentais (LER-PC), La Tremblade, France
| | | | - Jean-Michel Escoubas
- IHPE, CNRS, Ifremer, Université de Montpellier - Université de Perpignan Via Domitia, Montpellier, France
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Umberto Rosani
- Department of Biology, University of Padua, Padua, Italy
| | - Chang-Ming Bai
- Yellow Sea Fisheries Research Institute, CAFS, Qingdao, China
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Zaczek-Moczydłowska MA, Mohamed-Smith L, Toldrà A, Hooper C, Campàs M, Furones MD, Bean TP, Campbell K. A Single-Tube HNB-Based Loop-Mediated Isothermal Amplification for the Robust Detection of the Ostreid herpesvirus 1. Int J Mol Sci 2020; 21:E6605. [PMID: 32917059 PMCID: PMC7555478 DOI: 10.3390/ijms21186605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 01/05/2023] Open
Abstract
The Ostreid herpesvirus 1 species affects shellfish, contributing significantly to high economic losses during production. To counteract the threat related to mortality, there is a need for the development of novel point-of-care testing (POCT) that can be implemented in aquaculture production to prevent disease outbreaks. In this study, a simple, rapid and specific colorimetric loop-mediated isothermal amplification (LAMP) assay has been developed for the detection of Ostreid herpesvirus1 (OsHV-1) and its variants infecting Crassostrea gigas (C. gigas). The LAMP assay has been optimized to use hydroxynaphthol blue (HNB) for visual colorimetric distinction of positive and negative templates. The effect of an additional Tte UvrD helicase enzyme used in the reaction was also evaluated with an improved reaction time of 10 min. Additionally, this study provides a robust workflow for optimization of primers for uncultured viruses using designed target plasmid when DNA availability is limited.
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Affiliation(s)
- Maja A. Zaczek-Moczydłowska
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
| | - Letitia Mohamed-Smith
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
| | - Anna Toldrà
- IRTA, 43540 Sant Carles de la Ràpita, Spain; (A.T.); (M.C.); (M.D.F.)
| | - Chantelle Hooper
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth DT4 8UB, UK;
| | - Mònica Campàs
- IRTA, 43540 Sant Carles de la Ràpita, Spain; (A.T.); (M.C.); (M.D.F.)
| | - M. Dolors Furones
- IRTA, 43540 Sant Carles de la Ràpita, Spain; (A.T.); (M.C.); (M.D.F.)
| | - Tim P. Bean
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK;
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
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Detection of isothermally amplified ostreid herpesvirus 1 DNA in Pacific oyster (Crassostrea gigas) using a miniaturised electrochemical biosensor. Talanta 2020; 207:120308. [DOI: 10.1016/j.talanta.2019.120308] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 01/10/2023]
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