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Liu Y, Tang Y, Bao Y, Cai K, Lu B, Zhao R, Yu C, Du Y, Li B. Iso-E-Codelock: A Rebuilding-free Electrochemical Chip with a Customizable Decoding Probe for Real-Time and Portable Pathogen Diagnostics. Angew Chem Int Ed Engl 2024; 63:e202400340. [PMID: 38497899 DOI: 10.1002/anie.202400340] [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: 01/05/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/19/2024]
Abstract
In order to realize portable pathogen diagnostics with easier quantitation, digitization and integration, we develop a ready-to-use electrochemical sensing strategy (Iso-E-Codelock) for real-time detection of isothermal nucleic acid amplification. Bridged by a branched DNA as codelock, the isothermal amplicon is transduced into increased current of an electrochemical probe, holding multiple advantages of high sensitivity, high selectivity, signal-on response, "zero" background and one-pot operation. Through a self-designed portable instrument (BioAlex PHE-T), the detection can be implemented on a multichannel microchip and output real-time amplification curves just like an expensive commercial PCR machine. The microchip is a rebuilding-free and disposable component. The branch codelock probe can be customized for different targets and designs. Such high performance and flexibility have been demonstrated utilizing four virus (SARS-CoV-2, African swine fever, FluA and FluB) genes as targets, and two branch (3-way and 4-way) DNAs as codelock probes.
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Affiliation(s)
- Yichen Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yidan Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yin Bao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Kaiwei Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Rujian Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Chunxu Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
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2
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Burrow DT, Heggestad JT, Kinnamon DS, Chilkoti A. Engineering Innovative Interfaces for Point-of-Care Diagnostics. Curr Opin Colloid Interface Sci 2023; 66:101718. [PMID: 37359425 PMCID: PMC10247612 DOI: 10.1016/j.cocis.2023.101718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023]
Abstract
The ongoing Coronavirus disease 2019 (COVID-19) pandemic illustrates the need for sensitive and reliable tools to diagnose and monitor diseases. Traditional diagnostic approaches rely on centralized laboratory tests that result in long wait times to results and reduce the number of tests that can be given. Point-of-care tests (POCTs) are a group of technologies that miniaturize clinical assays into portable form factors that can be run both in clinical areas --in place of traditional tests-- and outside of traditional clinical settings --to enable new testing paradigms. Hallmark examples of POCTs are the pregnancy test lateral flow assay and the blood glucose meter. Other uses for POCTs include diagnostic assays for diseases like COVID-19, HIV, and malaria but despite some successes, there are still unsolved challenges for fully translating these lower cost and more versatile solutions. To overcome these challenges, researchers have exploited innovations in colloid and interface science to develop various designs of POCTs for clinical applications. Herein, we provide a review of recent advancements in lateral flow assays, other paper based POCTs, protein microarray assays, microbead flow assays, and nucleic acid amplification assays. Features that are desirable to integrate into future POCTs, including simplified sample collection, end-to-end connectivity, and machine learning, are also discussed in this review.
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Affiliation(s)
- Damon T Burrow
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
| | - Jacob T Heggestad
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
| | - David S Kinnamon
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
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3
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Das D, Lin CW, Chuang HS. LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection. BIOSENSORS 2022; 12:bios12121068. [PMID: 36551035 PMCID: PMC9775414 DOI: 10.3390/bios12121068] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.
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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 404, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung 413, Taiwan
| | - 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
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4
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Lim RRX, Ang WL, Ambrosi A, Sofer Z, Bonanni A. Electroactive nanocarbon materials as signaling tags for electrochemical PCR. Talanta 2022; 245:123479. [DOI: 10.1016/j.talanta.2022.123479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/15/2022]
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5
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Yaghoobi A, Abiri R, Alvandi A, Arkan E, Jalalvand AR. A novel electrochemical biosensor as an efficient electronic device for impedimetric and amperometric quantification of the pneumococcus. SENSING AND BIO-SENSING RESEARCH 2022. [DOI: 10.1016/j.sbsr.2022.100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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6
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Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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7
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Yaghoobi A, Abiri R, Alvandi A, Arkan E, Jalalvand AR. A novel and highly selective aptamer-based sandwich-type biosensor assisted by second-order calibration methods for efficient biosensing of Streptococcus pneumoniae. SENSORS INTERNATIONAL 2022. [DOI: 10.1016/j.sintl.2022.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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8
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Tzepos RG, Raman E, Toote LE, Wright DW, Gerdon AE. Signal Amplification with Co(III) Protoporphyrin IX Nanoparticles and Anodic Stripping Voltammetry. ELECTROANAL 2021. [DOI: 10.1002/elan.202100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Robert G. Tzepos
- Emmanuel College Department of Chemistry and Physics 400 Fenway Boston MA 02115
| | - Easwer Raman
- Emmanuel College Department of Chemistry and Physics 400 Fenway Boston MA 02115
| | - Lauren E. Toote
- Elizabethtown College Department of Chemistry and Biochemistry 1 Alpha Drive Elizabethtown PA 17022
| | - David W. Wright
- Vanderbilt University Department of Chemistry 7330 Stevenson Center Nashville TN 37235
| | - Aren E. Gerdon
- Emmanuel College Department of Chemistry and Physics 400 Fenway Boston MA 02115
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9
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Yadav AK, Verma D, Kumar A, Kumar P, Solanki PR. The perspectives of biomarker-based electrochemical immunosensors, artificial intelligence and the Internet of Medical Things toward COVID-19 diagnosis and management. MATERIALS TODAY. CHEMISTRY 2021; 20:100443. [PMID: 33615086 PMCID: PMC7877231 DOI: 10.1016/j.mtchem.2021.100443] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 05/08/2023]
Abstract
The World Health Organization (WHO) has declared the COVID-19 an international health emergency due to the severity of infection progression, which became more severe due to its continuous spread globally and the unavailability of appropriate therapy and diagnostics systems. Thus, there is a need for efficient devices to detect SARS-CoV-2 infection at an early stage. Nowadays, the reverse transcription polymerase chain reaction (RT-PCR) technique is being applied for detecting this virus around the globe; however, factors such as stringent expertise, long diagnostic times, invasive and painful screening, and high costs have restricted the use of RT-PCR methods for rapid diagnostics. Therefore, the development of cost-effective, portable, sensitive, prompt and selective sensing systems to detect SARS-CoV-2 in biofluids at fM/pM/nM concentrations would be a breakthrough in diagnostics. Immunosensors that show increased specificity and sensitivity are considerably fast and do not imply costly reagents or instruments, reducing the cost for COVID-19 detection. The current developments in immunosensors perhaps signify the most significant opportunity for a rapid assay to detect COVID-19, without the need of highly skilled professionals and specialized tools to interpret results. Artificial intelligence (AI) and the Internet of Medical Things (IoMT) can also be equipped with this immunosensing approach to investigate useful networking through database management, sharing, and analytics to prevent and manage COVID-19. Herein, we represent the collective concepts of biomarker-based immunosensors along with AI and IoMT as smart sensing strategies with bioinformatics approach to monitor non-invasive early stage SARS-CoV-2 development, with fast point-of-care (POC) diagnostics as the crucial goal. This approach should be implemented quickly and verified practicality for clinical samples before being set in the present times for mass-diagnostic research.
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Affiliation(s)
- A K Yadav
- Special Center for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
| | - D Verma
- Special Center for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
- Amity Institute of Applied Sciences, Amity University, Noida, Uttar Pradesh, 201301, India
| | - A Kumar
- National Institute of Immunology, New Delhi, 110067, India
| | - P Kumar
- Sri Aurobindo College, Delhi University, New Delhi, 110017, India
| | - P R Solanki
- Special Center for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
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10
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Gupta N, Augustine S, Narayan T, O’Riordan A, Das A, Kumar D, Luong JHT, Malhotra BD. Point-of-Care PCR Assays for COVID-19 Detection. BIOSENSORS 2021; 11:141. [PMID: 34062874 PMCID: PMC8147281 DOI: 10.3390/bios11050141] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Abstract
Molecular diagnostics has been the front runner in the world's response to the COVID-19 pandemic. Particularly, reverse transcriptase-polymerase chain reaction (RT-PCR) and the quantitative variant (qRT-PCR) have been the gold standard for COVID-19 diagnosis. However, faster antigen tests and other point-of-care (POC) devices have also played a significant role in containing the spread of SARS-CoV-2 by facilitating mass screening and delivering results in less time. Thus, despite the higher sensitivity and specificity of the RT-PCR assays, the impact of POC tests cannot be ignored. As a consequence, there has been an increased interest in the development of miniaturized, high-throughput, and automated PCR systems, many of which can be used at point-of-care. This review summarizes the recent advances in the development of miniaturized PCR systems with an emphasis on COVID-19 detection. The distinct features of digital PCR and electrochemical PCR are detailed along with the challenges. The potential of CRISPR/Cas technology for POC diagnostics is also highlighted. Commercial RT-PCR POC systems approved by various agencies for COVID-19 detection are discussed.
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Affiliation(s)
- Niharika Gupta
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi 110042, India; (N.G.); (S.A.); (A.D.)
| | - Shine Augustine
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi 110042, India; (N.G.); (S.A.); (A.D.)
| | - Tarun Narayan
- Nanotechnology Group, Tyndall National Institute, University College Cork, T12 K8AF Cork, Ireland; (T.N.); (A.O.)
| | - Alan O’Riordan
- Nanotechnology Group, Tyndall National Institute, University College Cork, T12 K8AF Cork, Ireland; (T.N.); (A.O.)
| | - Asmita Das
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi 110042, India; (N.G.); (S.A.); (A.D.)
| | - D. Kumar
- Department of Applied Chemistry, Delhi Technological University, Shahbad Daulatpur, New Delhi 110042, India;
| | - John H. T. Luong
- School of Chemistry, University College Cork, T12 K8AF Cork, Ireland
| | - Bansi D. Malhotra
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi 110042, India; (N.G.); (S.A.); (A.D.)
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11
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Stem-loop-primer assisted isothermal amplification enabling high-specific and ultrasensitive nucleic acid detection. Biosens Bioelectron 2021; 184:113239. [PMID: 33857727 DOI: 10.1016/j.bios.2021.113239] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 11/20/2022]
Abstract
It is highly desired to perform accurate and rapid nucleic acid detections for disease diagnosis at resource-limited setting, such as small clinics, remote areas and home. However, the challenges in sample handling, expensive equipment and complicated operation make canonical polymerase chain reaction (PCR) impossible to run the point-of-care testing (POCT). Herein we report a novel nucleic acid detection method, named stem-loop-primer assisted isothermal amplification (SPA), which specifically and sensitively amplifies target nucleic acid by using Bst DNA polymerase, a pair of canonical PCR primers and their stem-loop derivatives. The stem-loop-primers are easily designed by adding a stem-loop sequence to the canonical PCR primers at 5'-ends. In contrast to loop-mediated isothermal amplification (LAMP), which is a widespread isothermal amplification technology, our SPA is more specific and convenient to design and run. Further, we have demonstrated that SPA can specifically detect type 16, 18, 52 and 58 Human Papilloma viruses (HPV) in cervical samples, suggesting its specificity and robustness for nucleic acid detection. Moreover, pH indicator based colorimetric SPA was developed, which offered 100% accuracy for HPV16 detection in cervical samples, thereby demonstrating its great potential for POCT nucleic acid testing.
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12
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Zhang X, Li G, Chen G, Zhu N, Wu D, Wu Y, James TD. Recent progresses and remaining challenges for the detection of Zika virus. Med Res Rev 2021; 41:2039-2108. [PMID: 33559917 DOI: 10.1002/med.21786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
Abstract
Zika virus (ZIKV) has emerged as a particularly notorious mosquito-borne flavivirus, which can lead to a devastating congenital syndrome in the fetuses of pregnant mothers (e.g., microcephaly, spasticity, craniofacial disproportion, miscarriage, and ocular abnormalities) and cause the autoimmune disorder Guillain-Barre' syndrome of adults. Due to its severity and rapid dispersal over several continents, ZIKV has been acknowledged to be a global health concern by the World Health Organization. Unfortunately, the ZIKV has recently resurged in India with the potential for devastating effects. Researchers from all around the world have worked tirelessly to develop effective detection strategies and vaccines for the prevention and control of ZIKV infection. In this review, we comprehensively summarize the most recent research into ZIKV, including the structural biology and evolution, historical overview, pathogenesis, symptoms, and transmission. We then focus on the detection strategies for ZIKV, including viral isolation, serological assays, molecular assays, sensing methods, reverse transcription loop mediated isothermal amplification, transcription-mediated amplification technology, reverse transcription strand invasion based amplification, bioplasmonic paper-based device, and reverse transcription isothermal recombinase polymerase amplification. To conclude, we examine the limitations of currently available strategies for the detection of ZIKV, and outline future opportunities and research challenges.
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Affiliation(s)
- Xianlong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Guang Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Niu Zhu
- Department of Public Health, Xi'an Medical University, Xi'an, China
| | - Di Wu
- Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Yongning Wu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath, UK.,School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, China
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13
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Nunez-Bajo E, Silva Pinto Collins A, Kasimatis M, Cotur Y, Asfour T, Tanriverdi U, Grell M, Kaisti M, Senesi G, Stevenson K, Güder F. Disposable silicon-based all-in-one micro-qPCR for rapid on-site detection of pathogens. Nat Commun 2020; 11:6176. [PMID: 33268779 PMCID: PMC7710731 DOI: 10.1038/s41467-020-19911-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022] Open
Abstract
Rapid screening and low-cost diagnosis play a crucial role in choosing the correct course of intervention when dealing with highly infectious pathogens. This is especially important if the disease-causing agent has no effective treatment, such as the novel coronavirus SARS-CoV-2, and shows no or similar symptoms to other common infections. Here, we report a disposable silicon-based integrated Point-of-Need transducer (TriSilix) for real-time quantitative detection of pathogen-specific sequences of nucleic acids. TriSilix can be produced at wafer-scale in a standard laboratory (37 chips of 10 × 10 × 0.65 mm in size can be produced in 7 h, costing ~0.35 USD per device). We are able to quantitatively detect a 563 bp fragment of genomic DNA of Mycobacterium avium subspecies paratuberculosis through real-time PCR with a limit-of-detection of 20 fg, equivalent to a single bacterium, at the 35th cycle. Using TriSilix, we also detect the cDNA from SARS-CoV-2 (1 pg) with high specificity against SARS-CoV (2003).
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Affiliation(s)
| | | | - Michael Kasimatis
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Yasin Cotur
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Tarek Asfour
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Ugur Tanriverdi
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Max Grell
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Matti Kaisti
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
- Department of Future Technologies, University of Turku, 20500, Turku, Finland
| | - Guglielmo Senesi
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Karen Stevenson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Scotland, EH26 0PZ, UK
| | - Firat Güder
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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14
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Goyal G, Ammanath G, Palaniappan A, Liedberg B. Stoichiometric Tuning of PNA Probes to Au 0.8Ag 0.2 Alloy Nanoparticles for Visual Detection of Nucleic Acids in Plasma. ACS Sens 2020; 5:2476-2485. [PMID: 32700531 DOI: 10.1021/acssensors.0c00667] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Standard detection methods for nucleic acids, an important class of diagnostic biomarkers, are often laborious and cumbersome. In need for development of facile methodologies, localized surface plasmon resonance (LSPR) assays have been widely explored for both spectroscopic and visual detection of nucleic acids. Our sensing approach is based on monitoring changes in the LSPR band due to interaction between peptide nucleic acid (PNA) and plasmonic nanoparticles (NPs) in the presence/absence of target nucleic acid. We have investigated the importance of tuning the stoichiometry of PNA to NPs to enable "naked-eye" detection of nucleic acids at clinically relevant concentration ranges. Assaying in plasma is achieved by incorporation of silver in gold NPs (AuNPs) via an alloying process. The synthesized gold/silver alloy NPs reduce nonspecific adsorption of proteinaceous interferents in plasma. Furthermore, the gold/silver alloy NPs absorb in the most sensitive cyan to green transition zone (∼500 nm) yielding highly competitive visual limits of detection (LODs). The visual LOD (calculated objectively using the ΔE algorithm) for a model microRNA (mir21) using a productive combination of stoichiometric tuning of the PNA to NP ratio and compositional tuning of the NPs in buffer and plasma extract equals 200 pM (∼250 times lower than existing reports) and 3 nM, respectively. We envision that the proposed LSPR assay based on Au0.8Ag0.2NPs offers an avenue for rapid and sensitive on-site detection of nucleic acids in complex matrixes in combination with efficient target extraction kits.
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Affiliation(s)
- Garima Goyal
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore 639798
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Gopal Ammanath
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Alagappan Palaniappan
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Bo Liedberg
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore 639798
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
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15
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Yi TT, Zhang HY, Liang H, Gong GZ, Cai Y. Betaine-assisted recombinase polymerase assay for rapid hepatitis B virus detection. Biotechnol Appl Biochem 2020; 68:469-475. [PMID: 32388885 PMCID: PMC8411421 DOI: 10.1002/bab.1940] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/07/2020] [Indexed: 12/31/2022]
Abstract
Hepatitis B virus (HBV) is a worldwide epidemic pathogen that causes hepatitis B. On‐site screening the HBV infection is of critical importance for preventing and diagnosing HBV infection. In this paper, a simple, visual, and rapid method for on‐site detection of HBV‐DNA has been developed. This method is based on betaine‐assisted recombinase polymerase assay and followed with naked‐eye detection via lateral flow assay (BRPA‐LF). Result show that nonspecific amplification is prone to occur in recombinase polymerase amplification (RPA) if the assay was performed with serum sample without purification. This problem has been addressed by adding 0.8 M of betaine to the RPA reactions. It was demonstrated that BRPA‐LF can detect 1,000 copies of HBV‐DNA in 50 μL mixture, and achieved 90% sensitivity and 100% specificity for serum sample detection. These results demonstrated that BRPA‐LF can resist serum interference and has great potential for on‐site screening of HBV infection.
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Affiliation(s)
- Ting-Ting Yi
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China.,Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Han-Yun Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hua Liang
- Sichuan CellMed Clinical Laboratory Co., Ltd, Nanchong, Sichuan, People's Republic of China
| | - Guo-Zhong Gong
- Department of Laboratory Medicine, Suining First People's Hospital, Suining, People's Republic of China
| | - Yan Cai
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China.,Prenatal diagnosis center, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
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16
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Leung KK, Martens I, Yu HZ, Bizzotto D. Measuring and Controlling the Local Environment of Surface-Bound DNA in Self-Assembled Monolayers on Gold When Prepared Using Potential-Assisted Deposition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6837-6847. [PMID: 32484684 DOI: 10.1021/acs.langmuir.9b03970] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
DNA self-assembled monolayers (SAMs) were prepared using potential-assisted deposition on clean gold single-crystal bead electrodes under a number of conditions (constant or square-wave potential perturbations in TRIS or phosphate immobilization buffers with and without Cl-). The local environment around the fluorophore-labeled DNA tethered to the electrode surface was characterized using in situ fluorescence microscopy during electrochemical measurements as a function of the underlying surface crystallography. Potential-assisted deposition from a TRIS buffer containing Cl- created DNA SAMs that were uniformly distributed on the surface with little preference to the underlying crystallography. A constant (+0.4 V/SCE) or a square-wave potential perturbation (+0.4 to -0.3 V/SCE, 50 Hz) resulted in similar DNA-modified surfaces in TRIS immobilization buffer. Deposition using a square-wave potential without Cl- resulted in lower DNA surface coverage. Despite this, the local environment around the DNA in the SAM appears to be densely packed. This implies the formation of clusters of densely packed DNA in the SAM. This effect was also demonstrated when depositing from a phosphate buffer. DNA clusters were significantly reduced when Cl- was present in the buffer. Clusters were most prevalent on the low-index plane surfaces (e.g., {111} and {100}) and less on the higher-index planes (e.g., {210} or {311}). A mechanism is proposed to rationalize the formation of DNA-clustered regions for deposition using a square-wave potential perturbation. The conditions for creating clusters of DNA in a SAM or for preventing these clusters from forming provide an approach for tailoring the surfaces used for biosensing.
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Affiliation(s)
- Kaylyn K Leung
- AMPEL, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Isaac Martens
- AMPEL, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Hua-Zhong Yu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dan Bizzotto
- AMPEL, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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17
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Chen Y, Liu Y, Shi Y, Ping J, Wu J, Chen H. Magnetic particles for integrated nucleic acid purification, amplification and detection without pipetting. Trends Analyt Chem 2020; 127:115912. [PMID: 32382202 PMCID: PMC7202819 DOI: 10.1016/j.trac.2020.115912] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid amplification based detection plays an important role in food safety, environmental monitoring and clinical diagnosis. However, traditional nucleic acid detection process involves transferring liquid from one tube to another by pipetting. It requires trained persons, equipped labs and consumes lots of time. The ideal nucleic acid detection is integrated, closed, simplified and automated. Magnetic particles actuated by magnetic fields can efficiently adsorb nucleic acids and promote integrated nucleic acid assays without pipetting driven by pumps and centrifuges. We will comprehensively review magnetic particles assisted integrated system for nucleic acid detection and hope it can inspire further related study.
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Key Words
- ATP, adenosine triphosphate
- DLS, dynamic light scattering
- FMR, ferromagnetic resonance
- GTC, guanidinium thiocyanate
- ICP-AES, inductively coupled plasma atomic emission spectroscopy
- IFAST, immiscible filtration assisted by surface tension
- Immiscible interface
- Integrated detection
- LAMP, loop-mediated isothermal amplification
- Magnetic particles
- Nucleic acid
- PCR, polymerase chain reaction
- PEG, polyethylene glycol
- POCT, point-of-care testing
- RPA, recombinase polymerase amplification
- SQUID, superconducting quantum interference device magnetometer
- TEM, transmission electron microscopy
- XRD, X-Ray diffraction
- qPCR, quantitative PCR
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Affiliation(s)
- Yanju Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Liu
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Ya Shi
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China
| | - Huan Chen
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
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18
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Trotter M, Borst N, Thewes R, von Stetten F. Review: Electrochemical DNA sensing – Principles, commercial systems, and applications. Biosens Bioelectron 2020; 154:112069. [DOI: 10.1016/j.bios.2020.112069] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 02/06/2023]
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19
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20
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Kubota R, Sasaki Y, Minamiki T, Minami T. Chemical Sensing Platforms Based on Organic Thin-Film Transistors Functionalized with Artificial Receptors. ACS Sens 2019; 4:2571-2587. [PMID: 31475522 DOI: 10.1021/acssensors.9b01114] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organic thin-film transistors (OTFTs) have attracted intense attention as promising electronic devices owing to their various applications such as rollable active-matrix displays, flexible nonvolatile memories, and radiofrequency identification (RFID) tags. To further broaden the scope of the application of OTFTs, we focus on the host-guest chemistry combined with the electronic devices. Extended-gate types of OTFTs functionalized with artificial receptors were fabricated to achieve chemical sensing of targets in complete aqueous media. Organic and inorganic ions (cations and anions), neutral molecules, and proteins, which are regarded as target analytes in the field of host-guest chemistry, were electrically detected by artificial receptors. Molecular recognition phenomena on the extended-gate electrode were evaluated by several analytical methods such as photoemission yield spectroscopy in the air, contact angle goniometry, and X-ray photoelectron spectroscopy. Interestingly, the electrical responses of the OTFTs were highly sensitive to the chemical structures of the guests. Thus, the OTFTs will facilitate the selective sensing of target analytes and the understanding of chemical conversions in biological and environmental systems. Furthermore, such cross-reactive responses observed in our studies will provide some important insights into next-generation sensing systems such as OTFT arrays. We strongly believe that our approach will enable the development of new intriguing sensor platforms in the field of host-guest chemistry, analytical chemistry, and organic electronics.
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Affiliation(s)
- Riku Kubota
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153−8505, Japan
| | - Yui Sasaki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153−8505, Japan
| | - Tsukuru Minamiki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153−8505, Japan
| | - Tsuyoshi Minami
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153−8505, Japan
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21
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Grell M, Dincer C, Le T, Lauri A, Nunez Bajo E, Kasimatis M, Barandun G, Maier SA, Cass AEG, Güder F. Autocatalytic Metallization of Fabrics Using Si Ink, for Biosensors, Batteries and Energy Harvesting. ADVANCED FUNCTIONAL MATERIALS 2019; 29:1804798. [PMID: 32733177 PMCID: PMC7384005 DOI: 10.1002/adfm.201804798] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/21/2018] [Indexed: 05/20/2023]
Abstract
Commercially available metal inks are mainly designed for planar substrates (for example, polyethylene terephthalate foils or ceramics), and they contain hydrophobic polymer binders that fill the pores in fabrics when printed, thus resulting in hydrophobic electrodes. Here, a low-cost binder-free method for the metallization of woven and nonwoven fabrics is presented that preserves the 3D structure and hydrophilicity of the substrate. Metals such as Au, Ag, and Pt are grown autocatalytically, using metal salts, inside the fibrous network of fabrics at room temperature in a two-step process, with a water-based silicon particle ink acting as precursor. Using this method, (patterned) metallized fabrics are being enabled to be produced with low electrical resistance (less than 3.5 Ω sq-1). In addition to fabrics, the method is also compatible with other 3D hydrophilic substrates such as nitrocellulose membranes. The versatility of this method is demonstrated by producing coil antennas for wireless energy harvesting, Ag-Zn batteries for energy storage, electrochemical biosensors for the detection of DNA/proteins, and as a substrate for optical sensing by surface enhanced Raman spectroscopy. In the future, this method of metallization may pave the way for new classes of high-performance devices using low-cost fabrics.
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Affiliation(s)
- Max Grell
- Department of BioengineeringImperial College LondonLondonSW7 2AZUK
| | - Can Dincer
- Department of BioengineeringImperial College LondonLondonSW7 2AZUK
- Laboratory for SensorsDepartment of Microsystems Engineering‐IMTEKUniversity of Freiburg79110FreiburgGermany
| | - Thao Le
- Department of ChemistryImperial College LondonLondonSW7 2AZUK
| | - Alberto Lauri
- Department of PhysicsImperial College LondonLondonSW7 2AZUK
| | | | | | | | - Stefan A. Maier
- Department of PhysicsImperial College LondonLondonSW7 2AZUK
- Chair in Hybrid NanosystemsNanoinstitute MunichFaculty of PhysicsLudwig‐Maximilians‐Universität München80539MünchenGermany
| | | | - Firat Güder
- Department of BioengineeringImperial College LondonLondonSW7 2AZUK
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22
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Verhaven A, Doneux T, Bizzotto D. Application of FRET Microscopy to the Study of the Local Environment and Dynamics of DNA SAMs on Au Electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14802-14810. [PMID: 30189138 DOI: 10.1021/acs.langmuir.8b02131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Immobilized DNA probe strands self-assembled on an electrode surface are the bases of many electrochemically based biosensors. Control or measurement of the local environment around each DNA molecule tethered to the electrode surface is needed because the local environment can influence the binding or hybridization efficiency of the target in solution. Measurement of this local environment in buffer or under electrochemical control can be challenging. Here we demonstrate the use of fluorescence microscopy and a Förster resonance energy transfer (FRET) methodology to characterize multicomponent DNA SAMs. The DNA SAMs that were studied were composed of a series of mole fraction ratios of alkylthiol-modified DNA which was labeled with either AlexaFluor488 or AlexaFluor647, a FRET donor and acceptor, respectively. The DNA SAMs were hybridized before assembly onto the electrode surface. Wide-field filter-based FRET microscopy was used to study the assembly of DNA SAMs onto gold bead electrodes. These single-crystal gold bead electrodes contain many surface crystallographic regions which enable the comparison of the adsorbed DNA local environment. These surfaces show that most surface modifications are uniformly prepared, and the FRET efficiency can be explained through simple surface density considerations. The FRET efficiency for different compositions of the donor and acceptor for these regions is also explained through 2D FRET modeling. Not all surfaces were similar to the (111) and (110) regions showing deviations from the expected FRET behavior. Also demonstrated is FRET imaging using a confocal microscope. This approach proves useful in the analysis of a more dynamic system, such as the analysis of reductive desorption of the mixed-component DNA SAM. FRET microscopy is useful for surface analysis of the DNA local environment, enabling a measure of the surface modification, local density, and clustering and eventually a new detection modality.
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Affiliation(s)
- Alexandra Verhaven
- Chimie Analytique et Chimie des Interfaces, Faculté des Sciences , Université Libre de Bruxelles (ULB) , Bruxelles 1050 , Belgium
| | - T Doneux
- Chimie Analytique et Chimie des Interfaces, Faculté des Sciences , Université Libre de Bruxelles (ULB) , Bruxelles 1050 , Belgium
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23
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Chen BJ, Mani V, Huang ST, Hu YC, Shan HCP. Bisintercalating DNA redox reporters for real-time electrochemical qLAMP. Biosens Bioelectron 2018; 129:277-283. [PMID: 30266426 DOI: 10.1016/j.bios.2018.09.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/30/2018] [Accepted: 09/16/2018] [Indexed: 11/19/2022]
Abstract
The electrochemical detection methods have emerged as a potential alternative to the bench-top optical systems in monitoring nucleic acid amplification. DNA intercalating redox reporters play a crucial role in such monitoring schemes. Here, a series of bisintercalating redox probes have been tailor-made to meet specific requirements of electrochemical quantitative loop-mediated isothermal amplification (qLAMP). The probes composed of two naphthoquinone-imidazole (NQIM) derivatives as signal motifs that are covalently bridged by different linkers (R). They are bis-NQIM-R; R = Alkane (Ak), ethylene glycol (EG) and phenyl (Ph). The linkers allow the probes to be fine-tuned for securing ideal redox reporter. DNA binding studies via electrochemical and fluorescence techniques demonstrate that the bis-NQIM-R probes possess better ds-DNA bisintercalating ability compared to their mono-analogs. The bis-NQIM-Ph was implemented in a real-time electrochemical qLAMP, for which a prototype custom-made device that can perform fully automated multiplexed analyses is devised. A single copy of Salmonella DNA was quantified in just 10 min and the performance is comparable to the benchtop fluorescence method. Thus, the bisintercalating redox reporters incorporated electrochemical detection schemes hold great promise in qLAMP.
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Affiliation(s)
- Bo-Jun Chen
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan, ROC
| | - Veerappan Mani
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan, ROC; Graduate Institute of Biomedical and Biochemical Engineering, National Taipei University of Technology, Taipei, Taiwan, ROC
| | - Sheng-Tung Huang
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan, ROC; Graduate Institute of Biomedical and Biochemical Engineering, National Taipei University of Technology, Taipei, Taiwan, ROC.
| | - Yi-Chiuen Hu
- National Applied Research Lab, Hsinchu, Taiwan, ROC
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24
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Papadakis G, Murasova P, Hamiot A, Tsougeni K, Kaprou G, Eck M, Rabus D, Bilkova Z, Dupuy B, Jobst G, Tserepi A, Gogolides E, Gizeli E. Micro-nano-bio acoustic system for the detection of foodborne pathogens in real samples. Biosens Bioelectron 2018; 111:52-58. [DOI: 10.1016/j.bios.2018.03.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/21/2018] [Accepted: 03/26/2018] [Indexed: 01/30/2023]
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25
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Barreda-García S, Miranda-Castro R, de-Los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Solid-phase helicase dependent amplification and electrochemical detection of Salmonella on highly stable oligonucleotide-modified ITO electrodes. Chem Commun (Camb) 2018; 53:9721-9724. [PMID: 28782763 DOI: 10.1039/c7cc05128j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An on-surface isothermal helicase-dependent amplification is devised for simple, point-of-need quantification of bacterial genomes. The method relies on the enzyme-extension of a thiol-modified reverse primer anchored to indium tin oxide electrodes, which shows strikingly high thermal and storage stability. Amplification and electrochemical detection of only 10 genomes are thus performed on the same platform without thermal cycling.
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Affiliation(s)
- S Barreda-García
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, Oviedo, Spain.
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26
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Tsaloglou MN, Nemiroski A, Camci-Unal G, Christodouleas DC, Murray LP, Connelly JT, Whitesides GM. Handheld isothermal amplification and electrochemical detection of DNA in resource-limited settings. Anal Biochem 2017; 543:116-121. [PMID: 29224732 DOI: 10.1016/j.ab.2017.11.025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 01/09/2023]
Abstract
This paper demonstrates a new method for electrochemical detection of specific sequences of DNA present in trace amounts in serum or blood. This method is designed for use at the point-of-care (particularly in resource-limited settings). By combining recombinase polymerase amplification (RPA)- an isothermal alternative to the polymerase chain reaction - with an electroactive mediator, this electrochemical methodology enables accurate detection of DNA in the field using a low-cost, portable electrochemical analyzer (specifically designed for this type of analysis). This handheld device has four attributes: (1) It uses disposable, paper-based strips that incorporate screen-printed carbon electrodes; (2) It accomplishes thermoregulation with ±0.1 °C temperature accuracy; (3) It enables electrochemical detection using a variety of pulse sequences, including square-wave and cyclic voltammetry, and coulometry; (4) It is operationally simple to use. Detection of genomic DNA from Mycobacterium smegmatis (a surrogate for M. tuberculosis-the main cause of tuberculosis), and from M. tuberculosis itself down to ∼0.040 ng/μL provides a proof-of-concept for the applicability of this method of screening for disease using molecular diagnostics. With minor modifications to the reagents, this method will also enable field monitoring of food and water quality.
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Affiliation(s)
- Maria-Nefeli Tsaloglou
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, MA 02138, United States; Diagnostics for All Inc., 4 Technology Way, Salem, MA 01970, United States
| | - Alex Nemiroski
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, MA 02138, United States
| | - Gulden Camci-Unal
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, MA 02138, United States
| | - Dionysios C Christodouleas
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, MA 02138, United States
| | - Lara P Murray
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, MA 02138, United States
| | - John T Connelly
- Diagnostics for All Inc., 4 Technology Way, Salem, MA 01970, United States
| | - George M Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, MA 02138, United States; Kavli Institute for Bionano Inspired Science and Technology, School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, MA 02138, United States.
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27
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Preliminary evaluation for a novel voltammetric analysis of targeted nucleic acid by combining electrochemical DNA chip and digital loop-mediated isothermal amplification. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.11.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Hashimoto K, Inada M, Ito K. A novel voltammetric approach for real-time electrochemical detection of targeted nucleic acid sequences using LAMP. Anal Biochem 2017; 539:113-117. [DOI: 10.1016/j.ab.2017.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 11/29/2022]
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29
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Chen W, Yu H, Sun F, Ornob A, Brisbin R, Ganguli A, Vemuri V, Strzebonski P, Cui G, Allen KJ, Desai SA, Lin W, Nash DM, Hirschberg DL, Brooks I, Bashir R, Cunningham BT. Mobile Platform for Multiplexed Detection and Differentiation of Disease-Specific Nucleic Acid Sequences, Using Microfluidic Loop-Mediated Isothermal Amplification and Smartphone Detection. Anal Chem 2017; 89:11219-11226. [PMID: 28819973 DOI: 10.1021/acs.analchem.7b02478] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
New tools are needed to enable rapid detection, identification, and reporting of infectious viral and microbial pathogens in a wide variety of point-of-care applications that impact human and animal health. We report the design, construction, and characterization of a platform for multiplexed analysis of disease-specific DNA sequences that utilizes a smartphone camera as the sensor in conjunction with a hand-held "cradle" that interfaces the phone with a silicon-based microfluidic chip embedded within a credit-card-sized cartridge. Utilizing specific nucleic acid sequences for four equine respiratory pathogens as representative examples, we demonstrated the ability of the system to utilize a single 15 μL droplet of test sample to perform selective positive/negative determination of target sequences, including integrated experimental controls, in approximately 30 min. Our approach utilizes loop-mediated isothermal amplification (LAMP) reagents predeposited into distinct lanes of the microfluidic chip, which when exposed to target nucleic acid sequences from the test sample, generates fluorescent products that when excited by appropriately selected light emitting diodes (LEDs), are visualized and automatically analyzed by a software application running on the smartphone microprocessor. The system achieves detection limits comparable to those obtained by laboratory-based methods and instruments. Assay information is combined with the information from the cartridge and the patient to populate a cloud-based database for epidemiological reporting of test results.
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Affiliation(s)
- Weili Chen
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Hojeong Yu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Akid Ornob
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ryan Brisbin
- Center for Urban Waters & The School of Interdisciplinary Arts and Sciences, University of Washington Tacoma , Tacoma, Washington 98402, United States
| | - Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Vinay Vemuri
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Piotr Strzebonski
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Guangzhe Cui
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Karen J Allen
- School of Information Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Smit A Desai
- School of Information Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Weiran Lin
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - David M Nash
- Private veterinary practice , Lexington, Kentucky 40509, United States
| | - David L Hirschberg
- Center for Urban Waters & The School of Interdisciplinary Arts and Sciences, University of Washington Tacoma , Tacoma, Washington 98402, United States.,Readiness Acceleration and Innovation Network , Tacoma, Washington 98402, United States
| | - Ian Brooks
- School of Information Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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30
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Droplet-based non-faradaic impedance sensors for assessment of susceptibility of Escherichia coli to ampicillin in 60 min. Biomed Microdevices 2017; 19:27. [DOI: 10.1007/s10544-017-0165-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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31
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Kaushik A, Tiwari S, Jayant RD, Vashist A, Nikkhah-Moshaie R, El-Hage N, Nair M. Electrochemical Biosensors for Early Stage Zika Diagnostics. Trends Biotechnol 2017; 35:308-317. [PMID: 28277248 PMCID: PMC5366270 DOI: 10.1016/j.tibtech.2016.10.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 02/06/2023]
Abstract
Health agencies have declared the recent Zika virus (ZIKV) infection an epidemic and a public health emergency of global concern due to its association with microcephaly and serious neurological disorders. The unavailability of effective drugs, vaccines, and diagnostic tools increases the demand for efficient analytical devices to detect ZIKV infection. However, high costs, longer diagnostic times, and stringent expertise requirements limit the utility of reverse transcriptase-PCR methods for rapid diagnostics. Therefore, developing portable, sensitive, selective, and cost-effective sensing systems to detect ZIKV at picomolar concentrations in biofluids would be a breakthrough in diagnostics and therapeutics. This paper highlights the advancements in developing smart sensing strategies to monitor ZIKV progression, with rapid point-of-care diagnostics as the ultimate aim.
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Affiliation(s)
- Ajeet Kaushik
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
| | - Sneham Tiwari
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rahul D Jayant
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Arti Vashist
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Roozbeh Nikkhah-Moshaie
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Nazira El-Hage
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Madhavan Nair
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
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32
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Lin S, Kang TS, Lu L, Wang W, Ma DL, Leung CH. A G-quadruplex-selective luminescent probe with an anchor tail for the switch-on detection of thymine DNA glycosylase activity. Biosens Bioelectron 2016; 86:849-857. [DOI: 10.1016/j.bios.2016.07.082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/23/2016] [Accepted: 07/23/2016] [Indexed: 11/25/2022]
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Martin A, Grant KB, Stressmann F, Ghigo JM, Marchal D, Limoges B. Ultimate Single-Copy DNA Detection Using Real-Time Electrochemical LAMP. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00125] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alexandra Martin
- Laboratoire
d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Kathryn B. Grant
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Franziska Stressmann
- Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, 25-28 rue du Dr. Roux, F-75015 Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, 25-28 rue du Dr. Roux, F-75015 Paris, France
| | - Damien Marchal
- Laboratoire
d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Benoît Limoges
- Laboratoire
d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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34
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Lin YJ, Wu YC, Mani V, Huang ST, Huang CH, Hu YC, Peter Shan HC. Designing anthraquinone–pyrrole redox intercalating probes for electrochemical gene detection. Biosens Bioelectron 2016; 79:294-9. [DOI: 10.1016/j.bios.2015.12.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/30/2015] [Accepted: 12/15/2015] [Indexed: 10/22/2022]
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35
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Comparison of isothermal helicase-dependent amplification and PCR for the detection of Mycobacterium tuberculosis by an electrochemical genomagnetic assay. Anal Bioanal Chem 2016; 408:8603-8610. [DOI: 10.1007/s00216-016-9514-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 01/09/2023]
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Safavieh M, Kanakasabapathy MK, Tarlan F, Ahmed MU, Zourob M, Asghar W, Shafiee H. Emerging Loop-Mediated Isothermal Amplification-Based Microchip and Microdevice Technologies for Nucleic Acid Detection. ACS Biomater Sci Eng 2016; 2:278-294. [PMID: 28503658 PMCID: PMC5425166 DOI: 10.1021/acsbiomaterials.5b00449] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective pathogen detection is of paramount importance in infectious disease diagnosis and treatment monitoring. Currently available diagnostic assays based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) are time-consuming, complex, and relatively expensive, thus limiting their utility in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been used extensively in the development of rapid and sensitive diagnostic assays for pathogen detection and nucleic acid analysis and hold great promise for revolutionizing point-of-care molecular diagnostics. Here, we review novel LAMP-based lab-on-a-chip (LOC) diagnostic assays developed for pathogen detection over the past several years. We review various LOC platforms based on their design strategies for pathogen detection and discuss LAMP-based platforms still in development and already in the commercial pipeline. This review is intended as a guide to the use of LAMP techniques in LOC platforms for molecular diagnostics and genomic amplifications.
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Affiliation(s)
- Mohammadali Safavieh
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Manoj K. Kanakasabapathy
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Farhang Tarlan
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Minhaz U. Ahmed
- Biosensors and Biotechnology Laboratory, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, Negara Brunei Darussalam
| | - Mohammed Zourob
- Department of Chemistry, College of Science, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Waseem Asghar
- Department of Computer Engineering & Electrical Engineering and Computer Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | - Hadi Shafiee
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
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37
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Martin A, Bouffier L, Grant KB, Limoges B, Marchal D. Real-time electrochemical LAMP: a rational comparative study of different DNA intercalating and non-intercalating redox probes. Analyst 2016; 141:4196-203. [DOI: 10.1039/c6an00867d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The main objective of this study is provide guidelines in the search for ideal redox-active reporters in real-time electrochemical LAMP.
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Affiliation(s)
- Alexandra Martin
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - Laurent Bouffier
- Institut des Sciences Moléculaires
- UMR 5255 CNRS
- Université Bordeaux
- 33400 Talence
- France
| | | | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - Damien Marchal
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
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38
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Besant JD, Sargent EH, Kelley SO. Rapid electrochemical phenotypic profiling of antibiotic-resistant bacteria. LAB ON A CHIP 2015; 15:2799-807. [PMID: 26008802 DOI: 10.1039/c5lc00375j] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Rapid phenotyping of bacteria to identify drug-resistant strains is an important capability for the treatment and management of infectious disease. At present, the rapid determination of antibiotic susceptibility is hindered by the requirement that, in existing devices, bacteria must be pre-cultured for 2-3 days to reach detectable levels. Here we report a novel electrochemical approach that achieves rapid readout of the antibiotic susceptibility profile of a bacterial infection within one hour. The electrochemical reduction of a redox-active molecule is monitored that reports on levels of metabolically-active bacteria. Bacteria are captured in miniaturized wells, incubated with antimicrobials and monitored for resistance. This electrochemical phenotyping approach is effective with clinically-relevant levels of bacteria, and provides results comparable to culture-based analysis. Results, however, are delivered on a much faster timescale, with resistance profiles available after a one hour incubation period.
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Affiliation(s)
- Justin D Besant
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
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39
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Li F, Yu Z, Xu Y, Ma H, Zhang G, Song Y, Yan H, He X. Using the synergism strategy for highly sensitive and specific electrochemical sensing of Streptococcus pneumoniae Lyt-1 gene sequence. Anal Chim Acta 2015; 886:175-81. [DOI: 10.1016/j.aca.2015.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
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40
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Karsten SL, Tarhan MC, Kudo LC, Collard D, Fujita H. Point-of-care (POC) devices by means of advanced MEMS. Talanta 2015; 145:55-9. [PMID: 26459443 DOI: 10.1016/j.talanta.2015.04.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/12/2015] [Indexed: 12/21/2022]
Abstract
Microelectromechanical systems (MEMS) have become an invaluable technology to advance the development of point-of-care (POC) devices for diagnostics and sample analyses. MEMS can transform sophisticated methods into compact and cost-effective microdevices that offer numerous advantages at many levels. Such devices include microchannels, microsensors, etc., that have been applied to various miniaturized POC products. Here we discuss some of the recent advances made in the use of MEMS devices for POC applications.
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Affiliation(s)
- Stanislav L Karsten
- NeuroInDx, Inc., E. 28th Street, Signal Hill, CA 90755, USA; Center for International Research on MicroMechatronics, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
| | - Mehmet C Tarhan
- Center for International Research on MicroMechatronics, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; LIMMS/CNRS-IIS (UMI 2820), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Lili C Kudo
- NeuroInDx, Inc., E. 28th Street, Signal Hill, CA 90755, USA
| | - Dominique Collard
- Center for International Research on MicroMechatronics, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; LIMMS/CNRS-IIS (UMI 2820), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hiroyuki Fujita
- Center for International Research on MicroMechatronics, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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41
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Besant JD, Das J, Burgess IB, Liu W, Sargent EH, Kelley SO. Ultrasensitive visual read-out of nucleic acids using electrocatalytic fluid displacement. Nat Commun 2015; 6:6978. [PMID: 25901450 PMCID: PMC4421844 DOI: 10.1038/ncomms7978] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/17/2015] [Indexed: 12/12/2022] Open
Abstract
Diagnosis of disease outside of sophisticated laboratories urgently requires low-cost, user-friendly devices. Disposable, instrument-free testing devices are used for home and physician office testing, but are limited in applicability to a small class of highly abundant analytes. Direct, unambiguous visual read-out is an ideal way to deliver a result on a disposable device; however, existing strategies that deliver appropriate sensitivity produce only subtle colour changes. Here we report a new approach, which we term electrocatalytic fluid displacement, where a molecular binding event is transduced into an electrochemical current, which drives the electrodeposition of a metal catalyst. The catalyst promotes bubble formation that displaces a fluid to reveal a high contrast change. We couple the read-out system to a nanostructured microelectrode and demonstrate direct visual detection of 100 fM DNA in 10 min. This represents the lowest limit of detection of nucleic acids reported using high contrast visual read-out.
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Affiliation(s)
- Justin D Besant
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada M5S 3G9
| | - Jagotamoy Das
- Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada M5S 3M2
| | - Ian B Burgess
- Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada M5S 3M2
| | - Wenhan Liu
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada M5S 3G9
| | - Edward H Sargent
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Canada M5S 3G4
| | - Shana O Kelley
- 1] Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada M5S 3G9 [2] Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada M5S 3M2 [3] Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Canada M5S 1A8
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42
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Hsieh K, Ferguson BS, Eisenstein M, Plaxco KW, Soh HT. Integrated electrochemical microsystems for genetic detection of pathogens at the point of care. Acc Chem Res 2015; 48:911-20. [PMID: 25785632 DOI: 10.1021/ar500456w] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The capacity to achieve rapid, sensitive, specific, quantitative, and multiplexed genetic detection of pathogens via a robust, portable, point-of-care platform could transform many diagnostic applications. And while contemporary technologies have yet to effectively achieve this goal, the advent of microfluidics provides a potentially viable approach to this end by enabling the integration of sophisticated multistep biochemical assays (e.g., sample preparation, genetic amplification, and quantitative detection) in a monolithic, portable device from relatively small biological samples. Integrated electrochemical sensors offer a particularly promising solution to genetic detection because they do not require optical instrumentation and are readily compatible with both integrated circuit and microfluidic technologies. Nevertheless, the development of generalizable microfluidic electrochemical platforms that integrate sample preparation and amplification as well as quantitative and multiplexed detection remains a challenging and unsolved technical problem. Recognizing this unmet need, we have developed a series of microfluidic electrochemical DNA sensors that have progressively evolved to encompass each of these critical functionalities. For DNA detection, our platforms employ label-free, single-step, and sequence-specific electrochemical DNA (E-DNA) sensors, in which an electrode-bound, redox-reporter-modified DNA "probe" generates a current change after undergoing a hybridization-induced conformational change. After successfully integrating E-DNA sensors into a microfluidic chip format, we subsequently incorporated on-chip genetic amplification techniques including polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) to enable genetic detection at clinically relevant target concentrations. To maximize the potential point-of-care utility of our platforms, we have further integrated sample preparation via immunomagnetic separation, which allowed the detection of influenza virus directly from throat swabs and developed strategies for the multiplexed detection of related bacterial strains from the blood of septic mice. Finally, we developed an alternative electrochemical detection platform based on real-time LAMP, which not is only capable of detecting across a broad dynamic range of target concentrations, but also greatly simplifies quantitative measurement of nucleic acids. These efforts represent considerable progress toward the development of a true sample-in-answer-out platform for genetic detection of pathogens at the point of care. Given the many advantages of these systems, and the growing interest and innovative contributions from researchers in this field, we are optimistic that iterations of these systems will arrive in clinical settings in the foreseeable future.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, ‡Institute
for Collaborative Biotechnologies, §Interdepartmental Program in Biomolecular
Science and Engineering, ∥Department of Chemistry and Biochemistry, and ⊥Materials
Department, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - B. Scott Ferguson
- Department of Mechanical Engineering, ‡Institute
for Collaborative Biotechnologies, §Interdepartmental Program in Biomolecular
Science and Engineering, ∥Department of Chemistry and Biochemistry, and ⊥Materials
Department, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael Eisenstein
- Department of Mechanical Engineering, ‡Institute
for Collaborative Biotechnologies, §Interdepartmental Program in Biomolecular
Science and Engineering, ∥Department of Chemistry and Biochemistry, and ⊥Materials
Department, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin W. Plaxco
- Department of Mechanical Engineering, ‡Institute
for Collaborative Biotechnologies, §Interdepartmental Program in Biomolecular
Science and Engineering, ∥Department of Chemistry and Biochemistry, and ⊥Materials
Department, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - H. Tom Soh
- Department of Mechanical Engineering, ‡Institute
for Collaborative Biotechnologies, §Interdepartmental Program in Biomolecular
Science and Engineering, ∥Department of Chemistry and Biochemistry, and ⊥Materials
Department, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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43
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Goda T, Tabata M, Miyahara Y. Electrical and electrochemical monitoring of nucleic Acid amplification. Front Bioeng Biotechnol 2015; 3:29. [PMID: 25798440 PMCID: PMC4350426 DOI: 10.3389/fbioe.2015.00029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
Nucleic acid amplification is a gold standard technique for analyzing a tiny amount of nucleotides in molecular biology, clinical diagnostics, food safety, and environmental testing. Electrical and electrochemical monitoring of the amplification process draws attention over conventional optical methods because of the amenability toward point-of-care applications as there is a growing demand for nucleic acid sensing in situations outside the laboratory. A number of electrical and electrochemical techniques coupled with various amplification methods including isothermal amplification have been reported in the last 10 years. In this review, we highlight recent developments in the electrical and electrochemical monitoring of nucleic acid amplification.
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Affiliation(s)
- Tatsuro Goda
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Miyuki Tabata
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
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44
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White SP, Dorfman KD, Frisbie CD. Label-free DNA sensing platform with low-voltage electrolyte-gated transistors. Anal Chem 2015; 87:1861-6. [PMID: 25569583 DOI: 10.1021/ac503914x] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a method to measure DNA hybridization potentiometrically in a manner conducive to portable or hand-held biosensors. An electrolyte-gated transistor (EGT) based on poly(3-hexylthiophene) (P3HT) and an ion-gel serves as a transducer for surface hybridization of DNA. The key aspect of the design is the use of a floating-gate electrode functionalized with ssDNA whose potential is determined by both capacitive coupling with a primary, addressable gate electrode and the presence of adsorbed molecules. When DNA is hybridized at the floating gate, it offsets the primary gate voltage felt by the P3HT semiconductor; the offset is directly measurable and quantitatively related to the number density of dsDNA molecules. The presented sensing strategy can be readily adapted to other biomolecules of interest and integrated into a microfluidic system for field applications of biosensors.
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Affiliation(s)
- Scott P White
- Department of Chemical Engineering and Materials Science, University of Minnesota , Minneapolis, Minnesota 55455, United States
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45
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Song HY, Wong TI, Sadovoy A, Wu L, Bai P, Deng J, Guo S, Wang Y, Knoll W, Zhou X. Imprinted gold 2D nanoarray for highly sensitive and convenient PSA detection via plasmon excited quantum dots. LAB ON A CHIP 2015; 15:253-63. [PMID: 25360665 DOI: 10.1039/c4lc00978a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We designed and fabricated two new nanostructured biosensing chips, with which the sensitive detection of prostate specific antigen (PSA) as low as 100 pg ml(-1) can be achieved, by measuring the plasmon enhanced fluorescence through a conventional dark field microscope. The gold nanostructure arrays, one with gold nanopillars of 140 nm, the other with gold nanoholes of 140 nm, were fabricated via nanoimprinting onto glass substrate, as localized surface plasmon resonance (LSPR) generators to enhance the fluorescent emission of fluorophore, e.g. quantum dot (QD). A sandwich bioassay of capture anti-PSA antibody (cAb)/PSA/detection anti-PSA (dAb) labeled by QD-655 was established on the nanostructures, and the perfect LSPR excitation distance (10-15 nm) between the nanostructure and QD-655 was simulated and controlled by a cleft cAb fragment and streptavidin modified QD. QD was chosen in this study due to its photo stability, broad Stokes shift, and long lifetime. As far as we know, this is the first time that QD is applied for PSA detection on the uniform nanostructured sensing chips based on the LSPR enhanced fluorescence. Due to the miniaturized nanoarray sensing chip (1.8 mm × 1.8 mm), the convenience and specificity for the detection of PSA via the sandwich assay, and the high optical detection sensitivity, the platform has great potential for the development of a portable point-of-care (POC) system for outpatient diagnosis and treatment monitoring.
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Affiliation(s)
- Hong Yan Song
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602.
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46
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Gulley ML, Morgan DR. Molecular oncology testing in resource-limited settings. J Mol Diagn 2014; 16:601-11. [PMID: 25242061 PMCID: PMC4210462 DOI: 10.1016/j.jmoldx.2014.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 12/14/2022] Open
Abstract
Cancer prevalence and mortality are high in developing nations, where resources for cancer control are inadequate. Nearly one-quarter of cancers in resource-limited nations are infection related, and molecular assays can capitalize on this relationship by detecting pertinent pathogen genomes and human gene variants to identify those at highest risk for progression to cancer, to classify lesions, to predict effective therapy, and to monitor tumor burden over time. Prime examples are human papillomavirus in cervical neoplasia, Helicobacter pylori and Epstein-Barr virus in gastric adenocarcinoma and lymphoma, and hepatitis B or C virus in hepatocellular cancer. Research is underway to engineer devices that overcome social, economic, and technical barriers limiting effective laboratory support. Additional challenges include an educated workforce, infrastructure for quality metrics and record keeping, and funds to sustain molecular test services. The combination of well-designed interfaces, novel and robust electrochemical technology, and telemedicine tools will promote adoption by frontline providers. Fast turnaround is crucial for surmounting loss to follow-up, although increased use of cell phones, even in rural areas, enhances options for patient education and engagement. Links to a broadband network facilitate consultation and centralized storage of medical data. Molecular technology shows promise to address gaps in health care through rapid, user-friendly, and cost-effective devices reflecting clinical priorities in resource-poor areas.
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Affiliation(s)
- Margaret L Gulley
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.
| | - Douglas R Morgan
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University, Nashville, Tennessee
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47
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Adley CC. Past, Present and Future of Sensors in Food Production. Foods 2014; 3:491-510. [PMID: 28234333 PMCID: PMC5302250 DOI: 10.3390/foods3030491] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 12/16/2022] Open
Abstract
Microbial contamination management is a crucial task in the food industry. Undesirable microbial spoilage in a modern food processing plant poses a risk to consumers' health, causing severe economic losses to the manufacturers and retailers, contributing to wastage of food and a concern to the world's food supply. The main goal of the quality management is to reduce the time interval between the filling and the detection of a microorganism before release, from several days, to minutes or, at most, hours. This would allow the food company to stop the production, limiting the damage to just a part of the entire batch, with considerable savings in terms of product value, thereby avoiding the utilization of raw materials, packaging and strongly reducing food waste. Sensor systems offer major advantages over current systems as they are versatile and affordable but need to be integrated in the existing processing systems as a process analytical control (PAT) tool. The desire for good selectivity, low cost, portable and usable at working sites, sufficiently rapid to be used at-line or on-line, and no sample preparation devices are required. The application of biosensors in the food industry still has to compete with the standard analytical techniques in terms of cost, performance and reliability.
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Affiliation(s)
- Catherine C Adley
- Microbiology Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.
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