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Hasan J, Bok S. Plasmonic Fluorescence Sensors in Diagnosis of Infectious Diseases. BIOSENSORS 2024; 14:130. [PMID: 38534237 DOI: 10.3390/bios14030130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
The increasing demand for rapid, cost-effective, and reliable diagnostic tools in personalized and point-of-care medicine is driving scientists to enhance existing technology platforms and develop new methods for detecting and measuring clinically significant biomarkers. Humanity is confronted with growing risks from emerging and recurring infectious diseases, including the influenza virus, dengue virus (DENV), human immunodeficiency virus (HIV), Ebola virus, tuberculosis, cholera, and, most notably, SARS coronavirus-2 (SARS-CoV-2; COVID-19), among others. Timely diagnosis of infections and effective disease control have always been of paramount importance. Plasmonic-based biosensing holds the potential to address the threat posed by infectious diseases by enabling prompt disease monitoring. In recent years, numerous plasmonic platforms have risen to the challenge of offering on-site strategies to complement traditional diagnostic methods like polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). Disease detection can be accomplished through the utilization of diverse plasmonic phenomena, such as propagating surface plasmon resonance (SPR), localized SPR (LSPR), surface-enhanced Raman scattering (SERS), surface-enhanced fluorescence (SEF), surface-enhanced infrared absorption spectroscopy, and plasmonic fluorescence sensors. This review focuses on diagnostic methods employing plasmonic fluorescence sensors, highlighting their pivotal role in swift disease detection with remarkable sensitivity. It underscores the necessity for continued research to expand the scope and capabilities of plasmonic fluorescence sensors in the field of diagnostics.
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Affiliation(s)
- Juiena Hasan
- Department of Electrical and Computer Engineering, Ritchie School of Engineering and Computer Science, University of Denver, Denver, CO 80208, USA
| | - Sangho Bok
- Department of Electrical and Computer Engineering, Ritchie School of Engineering and Computer Science, University of Denver, Denver, CO 80208, USA
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Ultrafast PCR Detection of COVID-19 by Using a Microfluidic Chip-Based System. Bioengineering (Basel) 2022; 9:bioengineering9100548. [PMID: 36290516 PMCID: PMC9598518 DOI: 10.3390/bioengineering9100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
With the evolution of the pandemic caused by the Coronavirus disease of 2019 (COVID-19), reverse transcriptase-polymerase chain reactions (RT-PCR) have invariably been a golden standard in clinical diagnosis. Nevertheless, the traditional polymerase chain reaction (PCR) is not feasible for field application due to its drawbacks, such as time-consuming and laboratory-based dependence. To overcome these challenges, a microchip-based ultrafast PCR system called SWM-02 was proposed to make PCR assay in a rapid, portable, and low-cost strategy. This novel platform can perform 6-sample detection per run using multiple fluorescent channels and complete an ultrafast COVID-19 RT-PCR test within 40 min. Here, we evaluated the performance of the microdevice using the gradient-diluted COVID-19 reference samples and commercial PCR kit and determined its limit-of-detection (LoD) as 500 copies/mL, whose variation coefficients for the nucleocapsid (N) gene and open reading frame 1 ab region (ORF1ab) gene are 1.427% and 0.7872%, respectively. The system also revealed an excellent linear correlation between cycle threshold (Ct) values and dilution factors (R2 > 0.99). Additionally, we successfully detected the target RNAs and internal gene in the clinical samples by fast PCR, which shows strong consistency with conventional PCR protocol. Hence, with compact dimension, user-friendly design, and fast processing time, SWM-02 has the capability of offering timely and sensitive on-site molecular diagnosis for prevention and control of pathogen transmission.
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Kim JM, Jung S, Jeon EJ, Kim BK, No JY, Kim MJ, Kim H, Song CS, Kim SK. Highly Selective Multiplex Quantitative Polymerase Chain Reaction with a Nanomaterial Composite Hydrogel for Precise Diagnosis of Viral Infection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:30295-30305. [PMID: 34165969 DOI: 10.1021/acsami.1c03434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As viruses have been threatening global public health, fast diagnosis has been critical to effective disease management and control. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is now widely used as the gold standard for detecting viruses. Although a multiplex assay is essential for identifying virus types and subtypes, the poor multiplicity of RT-qPCR makes it laborious and time-consuming. In this paper, we describe the development of a multiplex RT-qPCR platform with hydrogel microparticles acting as independent reactors in a single reaction. To build target-specific particles, target-specific primers and probes are integrated into the particles in the form of noncovalent composites with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs). The thermal release characteristics of DNA, primer, and probe from the composites of primer-BNNT and probe-CNT allow primer and probe to be stored in particles during particle production and to be delivered into the reaction. In addition, BNNT did not absorb but preserved the fluorescent signal, while CNT protected the fluorophore of the probe from the free radicals present during particle production. Bicompartmental primer-incorporated network (bcPIN) particles were designed to harness the distinctive properties of two nanomaterials. The bcPIN particles showed a high RT-qPCR efficiency of over 90% and effective suppression of non-specific reactions. 16-plex RT-qPCR has been achieved simply by recruiting differently coded bcPIN particles for each target. As a proof of concept, multiplex one-step RT-qPCR was successfully demonstrated with a simple reaction protocol.
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Affiliation(s)
- Jung Min Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Eui Ju Jeon
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bong Kyun Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Jin Yong No
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Myung Jong Kim
- Functional Composite Materials Research Center, KIST, Jeonbuk 55324, Republic of Korea
| | - Heesuk Kim
- Photo-Electronic Hybrids Research Center, KIST, Seoul 02792, Republic of Korea
- Division of Energy and Environmental Technology, KIST School, UST, Daejeon 34113, Republic of Korea
| | - Chang Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
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Kang J, Yeom G, Jang H, Park CJ, Kim MG. Highly sensitive and universal detection strategy based on a colorimetric assay using target-specific heterogeneous sandwich DNA aptamer. Anal Chim Acta 2020; 1123:73-80. [PMID: 32507242 DOI: 10.1016/j.aca.2020.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 12/20/2022]
Abstract
A simple, universal, and sensitive colorimetric biosensor for detecting of various biomarkers was devised using a target-specific DNA aptamer, as the recognition element, and engineered with streptavidin-fusion replication protein A 70 kDa (RPA70A) linked to biotin-horseradish peroxidase, as the colorimetric element. To improve sensitivity and stability compared to other colorimetric sensing platforms, we developed a novel detection strategy by integrating a newly selected heterogeneous sandwich DNA aptamer and protein engineering in this study. The proposed method is based on a change in color from colorless to blue due to the interaction of the aptamer with RPA70A in the presence of the target; this color change could be observed by the naked eye or measured with a UV-vis spectrometer. We confirmed its high sensitivity and specificity for two model targets using their aptamers under optimal experimental conditions. In addition, the feasibility of the assay was investigated in clinical samples containing NPs of influenza A or B virus. These results suggest that our detection system developed herein can be universally applied to the diagnosis of various diseases owing to its stability, sensitivity, and specificity.
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Affiliation(s)
- Juyoung Kang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Gyuho Yeom
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Hyungjun Jang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea.
| | - Min-Gon Kim
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea.
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Zhu C, Hu A, Cui J, Yang K, Zhu X, Liu Y, Deng G, Zhu L. A Lab-on-a-Chip Device Integrated DNA Extraction and Solid Phase PCR Array for the Genotyping of High-Risk HPV in Clinical Samples. MICROMACHINES 2019; 10:mi10080537. [PMID: 31443221 PMCID: PMC6722547 DOI: 10.3390/mi10080537] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 02/01/2023]
Abstract
Point-of-care (POC) molecular diagnostics play a crucial role in the prevention and treatment of infectious diseases. It is necessary to develop portable, easy-to-use, inexpensive and rapid molecular diagnostic tools. In this study, we proposed a lab-on-a-chip device that integrated DNA extraction, solid-phase PCR and genotyping detection. The ingenious design of the pneumatic microvalves enabled the fluid mixing and reagent storage to be organically combined, significantly reducing the size of the chip. The solid oligonucleotide array incorporated into the chip allowed the spatial separation of the primers and minimized undesirable interactions in multiplex amplification. As a proof-of-concept for POC molecular diagnostics on the device, five genotypes of high-risk human papillomavirus (HPV) (HPV16/HPV18/HPV31/HPV33/HPV58) were examined. Positive quality control samples and HPV patient cervical swab specimens were analyzed on the integrated microdevice. The platform was capable of detection approximately 50 copies of HPV virus per reaction during a single step, including DNA extraction, solid-phase PCR and genotype detection, in 1 h from samples being added to the chip. This simple and inexpensive microdevice provided great utility for the screening and monitoring of HPV genotypes. The sample-to-result platform will pave the way for wider application of POC molecular testing in the fields of clinical diagnostics, food safety, and environmental monitoring.
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Affiliation(s)
- Cancan Zhu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China
- Science Island Branch, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei 230000, China
| | - Anzhong Hu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China
| | - Junsheng Cui
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China
| | - Ke Yang
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China
| | - Xinchao Zhu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China
- Science Island Branch, University of Science and Technology of China, No. 96, JinZhai Road Baohe District, Hefei 230000, China
| | - Yong Liu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China
| | - Guoqing Deng
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China
| | - Ling Zhu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 2221 Changjiang Road, Hefei 230000, China.
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Franco-Duarte R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF. Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present. Microorganisms 2019; 7:E130. [PMID: 31086084 PMCID: PMC6560418 DOI: 10.3390/microorganisms7050130] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal.
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Snehal Kadam
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Karishma S Kaushik
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran.
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Katarzyna Dybka-Stępień
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Martyna Leszczewicz
- Laboratory of Industrial Biotechnology, Bionanopark Ltd, Dubois 114/116, 93-465 Lodz, Poland.
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | | | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal.
| | - Célia F Rodrigues
- LEPABE⁻Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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Kant K, Ngo T. Solid Phase PCR on 3D Microstructure ArrayChip for Pathogen Detection Application. Bio Protoc 2019; 9:e3323. [DOI: 10.21769/bioprotoc.3323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 11/02/2022] Open
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Koo KM, Dey S, Trau M. A Sample-to-Targeted Gene Analysis Biochip for Nanofluidic Manipulation of Solid-Phase Circulating Tumor Nucleic Acid Amplification in Liquid Biopsies. ACS Sens 2018; 3:2597-2603. [PMID: 30461262 DOI: 10.1021/acssensors.8b01011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The use of circulating tumor nucleic acids (ctNA) in patient liquid biopsies for targeted genetic analysis is rapidly increasing in clinical oncology. Still, the call for an integrated methodology, which is both rapid and sensitive for analyzing trace ctNA amount in liquid biopsies, has unfortunately not been fully realized. Herein, we performed complex liquid biopsy sample-to-targeted genetic analysis on a biochip with a 50 copies-detection limit within 30 min. Our biochip uniquely integrated the following: (1) electrical lysis and release of cellular targets with minimal processing; (2) nanofluidic manipulation to accelerate molecular kinetics of solid-phase isothermal amplification; and (3) single-step capture and amplification of multiple NA targets prior to nanozyme-mediated electrochemical detection. Using prostate cancer liquid biopsies, we successfully demonstrated multifunctionality for cancer risk prediction; correlation of serum and urine analyses; and cancer relapse monitoring.
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Affiliation(s)
- Kevin M. Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shuvashis Dey
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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Xu X, Luo Y, Song X, Ying J, Ye J, Lu Y, Cai J, Ma J, Wang X, Yu W, Wang Y, Jin D. Evaluation of an UltraFast LabChip V280 assay for detection of toxigenic Clostridium difficile. Diagn Microbiol Infect Dis 2018; 92:279-283. [PMID: 30029809 DOI: 10.1016/j.diagmicrobio.2018.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/21/2018] [Accepted: 06/23/2018] [Indexed: 01/03/2023]
Abstract
In this study, we compared the performance of an UltraFast LabChip (UL) V280 system for Clostridium difficile detection in stool with that of Xpert C. difficile/Epi and VIDAS CDAB. Among 176 stool specimens, UL V280 detected toxigenic C. difficile in 22 (22/176, 12.5%) with a sensitivity, specificity, positive predictive value, negative predictive value (NPV) of 100.0%, 99.4%, 99.5% and 100.0%, respectively, which were higher than 95.2%, 97.4%, 83.3%, and 99.3% of Xpert C. difficile/Epi (P > 0.05). Notably, the sensitivity and NPV of ULV280 were significantly higher than those of VIDAS CDAB 52.4% (P < 0.001, odds ratio [OR] = 20.0, 95% confidence interval [CI] = 2.26-176.81) and 93.8% (P = 0.002, OR = 10.27, 95% CI = 1.30-81.17). UL V280 turnaround time (35 min) and cost (6.24 Dollars [$]) per specimen were less than those for Xpert C. difficile/Epi (47 min, 59.26 $) and VIDAS CDAB (65 min, 11.70 $). UL V280 possessed an analytical sensitivity limit of 2500 CFU/ml, 95% [CI] = (Ct: 30.76-34.90), and no cross-reactions with other pathogens were found. The study demonstrates that UL V280 based on a microfluidic chip is a rapid, accurate, easy, and cost-effective diagnostic test for toxigenic C. difficile in stool.
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Affiliation(s)
- Xingxing Xu
- Department of Laboratory Medicine, Zhejiang Chinese Medical University affiliated Hangzhou First Hospital, Hangzhou, Zhejiang, 310006, China; Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China
| | - Yun Luo
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China
| | - Xiaojun Song
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China
| | - Jianfei Ying
- Department of Laboratory Medicine, Ningbo Yinzhou People's Hospital, Ningbo, Zhejiang, 315040, China
| | - Julian Ye
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China
| | - Yong Lu
- Department of Laboratory Medicine, Ningbo Yinzhou People's Hospital, Ningbo, Zhejiang, 315040, China
| | - Jian Cai
- Department of Disease Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China
| | - Jian Ma
- Department of Respiratory Medicine, Ningbo Yinzhou People's Hospital, Ningbo, Zhejiang, 315040, China
| | - Xianjun Wang
- Department of Laboratory Medicine, Zhejiang Chinese Medical University affiliated Hangzhou First Hospital, Hangzhou, Zhejiang, 310006, China
| | - Wanjun Yu
- Department of Respiratory Medicine, Ningbo Yinzhou People's Hospital, Ningbo, Zhejiang, 315040, China
| | - Yiping Wang
- Department of Laboratory Medicine, Ningbo Yinzhou People's Hospital, Ningbo, Zhejiang, 315040, China
| | - Dazhi Jin
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China.
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Zhang D, Bi H, Liu B, Qiao L. Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods. Anal Chem 2018; 90:5512-5520. [PMID: 29595252 DOI: 10.1021/acs.analchem.8b00399] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microfluidics based biochemical analysis shows distinctive advantages for fast detection of pathogenic microorganisms. This Feature summarizes the progress in the past decade on microfluidic methods for purification and detection of pathogenic bacteria and viruses as well as their applications in food safety control, environmental monitoring, and clinical diagnosis.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai , China 200433
| | - Hongyan Bi
- College of Food Science and Engineering , Shanghai Ocean University , Shanghai , China 201306
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai , China 200433
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai , China 200433
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Chim W, Sedighi A, Brown CL, Pantophlet R, Li PC. Effect of buffer composition on PNA–RNA hybridization studied in the microfluidic microarray chip. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Herein, we report that peptide nucleic acid sequences (PNAs) have been used as the probe species for detection of RNA and that a microfluidic microarray (MMA) chip is used as the platform for detection of hybridizations between immobilized PNA probes and RNA targets. The RNA targets used are derived from influenza A sequences. This paper discusses the optimization of two probe technologies used for RNA detection and investigates how the composition of the probe buffer and the content of the hybridization solution can influence the overall results. Our data show that the PNA probe is a better choice than the DNA probe when there is low salt in the probe buffer composition. Furthermore, we show that the absence of salt (NaCl) in the hybridization buffer does not hinder the detection of RNA sequences. The results provide evidence that PNA probes are superior to DNA probes in term of sensitivity and adaptability, as PNA immobilization and PNA–RNA hybridization are less affected by salt content in the reaction buffers unlike DNA probes.
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Affiliation(s)
- Wilson Chim
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Abootaleb Sedighi
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Christopher L. Brown
- School of Natural Sciences and Queensland Micro- and Nanotechnology Centre, Griffith University, Brisbane, Queensland, Australia
| | - Ralph Pantophlet
- Faculty of Health Sciences and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Paul C.H. Li
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Zhuang B. Introduction. DEVELOPMENT OF A FULLY INTEGRATED “SAMPLE-IN-ANSWER-OUT” SYSTEM FOR AUTOMATIC GENETIC ANALYSIS 2018:1-30. [DOI: 10.1007/978-981-10-4753-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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14
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Coarsey CT, Esiobu N, Narayanan R, Pavlovic M, Shafiee H, Asghar W. Strategies in Ebola virus disease (EVD) diagnostics at the point of care. Crit Rev Microbiol 2017; 43:779-798. [PMID: 28440096 PMCID: PMC5653233 DOI: 10.1080/1040841x.2017.1313814] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/21/2016] [Accepted: 03/25/2017] [Indexed: 12/13/2022]
Abstract
Ebola virus disease (EVD) is a devastating, highly infectious illness with a high mortality rate. The disease is endemic to regions of Central and West Africa, where there is limited laboratory infrastructure and trained staff. The recent 2014 West African EVD outbreak has been unprecedented in case numbers and fatalities, and has proven that such regional outbreaks can become a potential threat to global public health, as it became the source for the subsequent transmission events in Spain and the USA. The urgent need for rapid and affordable means of detecting Ebola is crucial to control the spread of EVD and prevent devastating fatalities. Current diagnostic techniques include molecular diagnostics and other serological and antigen detection assays; which can be time-consuming, laboratory-based, often require trained personnel and specialized equipment. In this review, we discuss the various Ebola detection techniques currently in use, and highlight the potential future directions pertinent to the development and adoption of novel point-of-care diagnostic tools. Finally, a case is made for the need to develop novel microfluidic technologies and versatile rapid detection platforms for early detection of EVD.
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Affiliation(s)
- Chad T. Coarsey
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Nwadiuto Esiobu
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Ramswamy Narayanan
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Mirjana Pavlovic
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Waseem Asghar
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
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15
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Basha IHK, Ho ETW, Yousuff CM, Hamid NHB. Towards Multiplex Molecular Diagnosis-A Review of Microfluidic Genomics Technologies. MICROMACHINES 2017; 8:E266. [PMID: 30400456 PMCID: PMC6190060 DOI: 10.3390/mi8090266] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/30/2017] [Accepted: 07/16/2017] [Indexed: 12/21/2022]
Abstract
Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.
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Affiliation(s)
- Ismail Hussain Kamal Basha
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Eric Tatt Wei Ho
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Caffiyar Mohamed Yousuff
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Nor Hisham Bin Hamid
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
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Hung TQ, Chin WH, Sun Y, Wolff A, Bang DD. A novel lab-on-chip platform with integrated solid phase PCR and Supercritical Angle Fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection. Biosens Bioelectron 2017; 90:217-223. [DOI: 10.1016/j.bios.2016.11.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 11/29/2022]
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17
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Solid-phase PCR for rapid multiplex detection of Salmonella spp. at the subspecies level, with amplification efficiency comparable to conventional PCR. Anal Bioanal Chem 2017; 409:2715-2726. [PMID: 28190106 DOI: 10.1007/s00216-017-0216-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/10/2017] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
Abstract
Solid-phase PCR (SP-PCR) has attracted considerable interest in different research fields since it allows parallel DNA amplification on the surface of a solid substrate. However, the applications of SP-PCR have been hampered by the low efficiency of the solid-phase amplification. In order to increase the yield of the solid-phase amplification, we studied various parameters including the length, the density, as well as the annealing position of the solid support primer. A dramatic increase in the signal-to-noise (S/N) ratio was observed when increasing the length of solid support primers from 45 to 80 bp. The density of the primer on the surface was found to be important for the S/N ratio of the SP-PCR, and the optimal S/N was obtained with a density of 1.49 × 1011 molecules/mm2. In addition, the use of solid support primers with a short overhang at the 5' end would help improve the S/N ratio of the SP-PCR. With optimized conditions, SP-PCR can achieve amplification efficiency comparable to conventional PCR, with a limit of detection of 1.5 copies/μl (37.5 copies/reaction). These improvements will pave the way for wider applications of SP-PCR in various fields such as clinical diagnosis, high-throughput DNA sequencing, and single-nucleotide polymorphism analysis. Graphical abstract Schematic representation of solid-phase PCR.
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DNA Microarray Detection of 18 Important Human Blood Protozoan Species. PLoS Negl Trop Dis 2016; 10:e0005160. [PMID: 27911895 PMCID: PMC5135439 DOI: 10.1371/journal.pntd.0005160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/03/2016] [Indexed: 01/22/2023] Open
Abstract
Background Accurate detection of blood protozoa from clinical samples is important for diagnosis, treatment and control of related diseases. In this preliminary study, a novel DNA microarray system was assessed for the detection of Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia in humans, animals, and vectors, in comparison with microscopy and PCR data. Developing a rapid, simple, and convenient detection method for protozoan detection is an urgent need. Methodology/Principal Findings The microarray assay simultaneously identified 18 species of common blood protozoa based on the differences in respective target genes. A total of 20 specific primer pairs and 107 microarray probes were selected according to conserved regions which were designed to identify 18 species in 5 blood protozoan genera. The positive detection rate of the microarray assay was 91.78% (402/438). Sensitivity and specificity for blood protozoan detection ranged from 82.4% (95%CI: 65.9% ~ 98.8%) to 100.0% and 95.1% (95%CI: 93.2% ~ 97.0%) to 100.0%, respectively. Positive predictive value (PPV) and negative predictive value (NPV) ranged from 20.0% (95%CI: 2.5% ~ 37.5%) to 100.0% and 96.8% (95%CI: 95.0% ~ 98.6%) to 100.0%, respectively. Youden index varied from 0.82 to 0.98. The detection limit of the DNA microarrays ranged from 200 to 500 copies/reaction, similar to PCR findings. The concordance rate between microarray data and DNA sequencing results was 100%. Conclusions/Significance Overall, the newly developed microarray platform provides a convenient, highly accurate, and reliable clinical assay for the determination of blood protozoan species. More than 1 billion people are infected with blood protozoan diseases worldwide. The most common blood protozoa in humans, animals, and vectors include Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia. Due to similar morphology among different blood protozoan species, misdiagnosis always occurs. Most molecular techniques are only carried out in laboratories, with a small number of samples detected simultaneously. Meanwhile, common detection methods may not be convenient for field investigation of large amounts of samples. In order to better manage blood protozoan infection, proper tools are required for the monitoring of these pathogens. Here, a comprehensive and sensitive DNA microarray was developed and tested, which allowed the parallel detection of 18 blood protozoan species.
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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Liu J, Zhao J, Petrochenko P, Zheng J, Hewlett I. Sensitive detection of influenza viruses with Europium nanoparticles on an epoxy silica sol-gel functionalized polycarbonate-polydimethylsiloxane hybrid microchip. Biosens Bioelectron 2016; 86:150-155. [PMID: 27362253 DOI: 10.1016/j.bios.2016.06.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/23/2016] [Accepted: 06/14/2016] [Indexed: 12/01/2022]
Abstract
In an effort to develop new tools for diagnosing influenza in resource-limited settings, we fabricated a polycarbonate (PC)-polydimethylsiloxane (PDMS) hybrid microchip using a simple epoxy silica sol-gel coating/bonding method and employed it in sensitive detection of influenza virus with Europium nanoparticles (EuNPs). The incorporation of sol-gel material in device fabrication provided functionalized channel surfaces ready for covalent immobilization of primary antibodies and a strong bonding between PDMS substrates and PC supports without increasing background fluorescence. In microchip EuNP immunoassay (µENIA) of inactivated influenza viruses, replacing native PDMS microchips with hybrid microchips allowed the achievement of a 6-fold increase in signal-to-background ratio, a 12-fold and a 6-fold decreases in limit-of-detection (LOD) in influenza A and B tests respectively. Using influenza A samples with known titers, the LOD of influenza µENIA on hybrid microchips was determined to be ~10(4) TCID50 titer/mL and 10(3)-10(4) EID50 titer/mL. A comparison test indicated that the sensitivity of influenza µENIA enhanced using the hybrid microchips even surpassed that of a commercial laboratory influenza ELISA test. In addition to the sensitivity improvement, assay variation was clearly reduced when hybrid microchips instead of native PDMS microchips were used in the µENIA tests. Finally, infectious reference viruses and nasopharyngeal swab patient specimens were successfully tested using μENIA on hybrid microchip platforms, demonstrating the potential of this unique microchip nanoparticle assay in clinical diagnosis of influenza. Meanwhile, the tests showed the necessity of using nucleic acid confirmatory tests to clarify ambiguous test results obtained from prototype or developed point-of-care testing devices for influenza diagnosis.
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Affiliation(s)
- Jikun Liu
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States.
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States
| | - Peter Petrochenko
- Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, United States
| | - Jiwen Zheng
- Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD 20993, United States
| | - Indira Hewlett
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States.
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HE QD, HUANG DP, HUANG G, CHEN ZG. Advance in Research of Microfluidic Polymerase Chain Reaction Chip. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60921-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Damin F, Galbiati S, Ferrari M, Chiari M. DNA microarray-based solid-phase PCR on copoly (DMA-NAS-MAPS) silicon coated slides: An example of relevant clinical application. Biosens Bioelectron 2015; 78:367-373. [PMID: 26655175 DOI: 10.1016/j.bios.2015.11.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
In a previous study we developed a highly sensitive DNA microarray for the detection of common KRAS oncogenic mutations, which has been proven to be highly specific in assigning the correct genotype without any enrichment strategy even in the presence of minority mutated alleles. However, in this approach, the need of a spotter for the deposition of the purified PCR products on the substrates and the purification step of the conventional PCR are serious drawbacks. To overcome these limitations we have introduced the solid-phase polymerase chain reaction (SP-PCR) to form the array of PCR products starting from the oligonucleotide primers. This work was possible thanks to the great thermal stability of the copoly (DMA-NAS-MAPS) coating which withstands PCR thermal cycling temperatures. As an example of the application of this platform we performed the analysis of six common mutations in the codon 12 of KRAS gene (G12A, G12C, G12D, G12R, G12S, and G12V). In conclusion solid-phase PCR, combined with dual-color hybridization, allows mutation analysis in a shorter time span and is more suitable for automation.
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Affiliation(s)
- Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy.
| | - Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Italy; Università Vita-Salute San Raffaele, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy
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Jung JH, Park BH, Oh SJ, Choi G, Seo TS. Integration of reverse transcriptase loop-mediated isothermal amplification with an immunochromatographic strip on a centrifugal microdevice for influenza A virus identification. LAB ON A CHIP 2015; 15:718-25. [PMID: 25426967 DOI: 10.1039/c4lc01033g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A novel centrifugal microdevice which could perform reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and immunochromatographic strip (ICS) based amplicon detection was demonstrated for simple and cost-effective influenza A virus identification. The proposed centrifugal microdevice consists of the sample and running buffer loading reservoirs, the RT-LAMP chamber, and the ICS for detecting gene expression. The entire process could be completed sequentially and automatically by simply controlling the rotation speed and by optimizing the microfluidic design. Monoplex and multiplex RT-LAMP reactions targeting H1 and/or M gene were executed at 66 °C for 40 min, and the resultant amplicons were successfully analysed on the ICS within 15 min. Influenza A H1N1 virus was subtyped by detecting H1 and M gene on the ICS even with 10 copies of viral RNAs. Highly specific and multiplex viral typing of the integrated RT-LAMP-ICS microdevice was also demonstrated. The combination of the rapid isothermal amplification with the simple colorimetric detection on a strip in a single centrifugal microdevice will provide an advanced genetic analysis platform in the field of on-site pathogen diagnostics.
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Affiliation(s)
- J H Jung
- Department of Chemical and Biomolecular Engineering (BK21 Plus program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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24
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Jung JH, Park BH, Oh SJ, Choi G, Seo TS. Integrated centrifugal reverse transcriptase loop-mediated isothermal amplification microdevice for influenza A virus detection. Biosens Bioelectron 2014; 68:218-224. [PMID: 25569879 PMCID: PMC7111304 DOI: 10.1016/j.bios.2014.12.043] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/12/2014] [Accepted: 12/20/2014] [Indexed: 11/29/2022]
Abstract
An integrated reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) microdevice which consists of microbead-assisted RNA purification and RT-LAMP with real-time monitoring by a miniaturized optical detector was demonstrated. The integrated RT-LAMP microdevice includes four reservoirs for a viral RNA sample (purified influenza A viral RNA or lysates), a washing solution (70% ethanol), an elution solution (RNase-free water), and an RT-LAMP cocktail, and two chambers (a waste chamber and an RT-LAMP reaction chamber). The separate reservoirs for a washing solution, an elution solution, and an RT-LAMP cocktail were designed with capillary valves for stable storage. Three influenza A virus strains (A/H1N1, A/H3N2, and A/H5N1) were used for RNA templates, and RT-LAMP primer sets were designed to detect hemagglutinin (HA) and conserved M gene. Sequential sample flow to the microbeads for RNA purification was achieved by centrifugal force with optimization of capillary valves and a siphon channel. Furthermore, the purified RNA solution was successfully isolated from the waste solution by changing the rotational direction, and combined with the RT-LAMP cocktail in the RT-LAMP reaction chamber for target gene amplification. Total process from the sample injection to the result was completed in 47 min. Influenza A H1N1 virus was confirmed on the integrated RT-LAMP microdevice even with 10 copies of viral RNAs, which revealed 10-fold higher sensitivity than that of a conventional RT-PCR. Subtyping and specificity test of influenza A H1N1 viral lysates were also performed and clinical samples were successfully genotyped to confirm influenza A virus on our proposed integrated microdevice. An integrated microdevice cosistng of RNA purification and RT-LAMP with real-time monitoring was demonstrated. Sequential sample transportation and purified RNA separation were automatically controlled by centrifugal force and optimized microchannels. Influenza viruses were isothermally amplified and the products were identified by using a miniaturized fluorescence detector. Limit of detection for influenza A H1N1 was 10 copies. Clinical samples were successfully analyzed on the microdevice.
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Affiliation(s)
- Jae Hwan Jung
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Byung Hyun Park
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Seung Jun Oh
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Goro Choi
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 PLUS Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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Jung JH, Oh SJ, Kim YT, Kim SY, Kim WJ, Jung J, Seo TS. Combination of multiplex reverse-transcription loop-mediated isothermal amplification with an immunochromatographic strip for subtyping influenza A virus. Anal Chim Acta 2014; 853:541-547. [PMID: 25467501 PMCID: PMC7094724 DOI: 10.1016/j.aca.2014.10.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/30/2014] [Accepted: 10/13/2014] [Indexed: 11/15/2022]
Abstract
Multiplex RT-LAMP for HA and M genes was developed for subtyping influenza A virus. Multiplex RT-LAMP amplicons were simply analyzed by the colorimetric ICS detection. Multiplex RT-LAMP (40 min) and ICS detection (15 min) could be complete in 55 min. Detection sensitivity for the multiplex RT-LAMP and ICS was 10 copies of viral RNA. Our methodology provides simple, rapid genetic analysis platform for viral detection.
Considering the fatal human victims and economic loss by the annual epidemic influenza virus, the development of a rapid and convenient genetic analysis methodology is demanding for timely on-site pathogen detection. In this study, we utilized reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for multiplex target gene amplification, and the resultant amplicons were analyzed on the immunochromatographic strip (ICS) for subtyping influenza A virus. Through the optimized primer design, reaction temperature and time, and concentration of enzymes (Bst DNA polymerase and AMV reverse transcriptase) and dNTP, the HA (H1, H3, and H5 gene) and conserved M gene were amplified. The ICS contains two test lines in addition to a control line in order to detect the presence of the HA and M gene, thereby informing us of influenza virus A type as well as its subtype (H1N1, H3N2, and H5N1). The combination of the multiplex RT-LAMP with the ICS could be complete in 40 min and the pathotyping and subtyping of influenza A virus were performed even with 10 copies of viral RNA templates. Moreover, the subtyping of clinical samples, which were obtained from patients infected by influenza A virus was successfully confirmed using the multiplex RT-LAMP and ICS techniques, showing great feasibility of our methodology for real sample analysis with high speed, simplicity and sensitivity.
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Affiliation(s)
- Jae Hwan Jung
- Department of Chemical and Biomolecular Engineering (BK21+ Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Seung Jun Oh
- Department of Chemical and Biomolecular Engineering (BK21+ Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Yong Tae Kim
- Department of Chemical and Biomolecular Engineering (BK21+ Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - So Yeon Kim
- Medisensor GH, Inc., 155-1 Nongso-ri, Juchon-myeon, Gimhae-si, Gyeongsangnam-do 621-841, Republic of Korea.
| | - Won-Jung Kim
- Medisensor GH, Inc., 155-1 Nongso-ri, Juchon-myeon, Gimhae-si, Gyeongsangnam-do 621-841, Republic of Korea.
| | - Jaean Jung
- Medisensor GH, Inc., 155-1 Nongso-ri, Juchon-myeon, Gimhae-si, Gyeongsangnam-do 621-841, Republic of Korea.
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21+ Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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Bos LDJ, de Jong MD, Sterk PJ, Schultz MJ. How integration of global omics-data could help preparing for pandemics - a scent of influenza. Front Genet 2014; 5:80. [PMID: 24795745 PMCID: PMC4000993 DOI: 10.3389/fgene.2014.00080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/25/2014] [Indexed: 01/14/2023] Open
Abstract
Pandemics caused by novel emerging or re-emerging infectious diseases could lead to high mortality and morbidity world-wide when left uncontrolled. In this perspective, we evaluate the possibility of integration of global omics-data in order to timely prepare for pandemics. Such an approach requires two major innovations. First, data that is obtained should be shared with the global community instantly. The strength of rapid integration of simple signals is exemplified by Google's(TM) Flu Trend, which could predict the incidence of influenza-like illness based on online search engine queries. Second, omics technologies need to be fast and high-throughput. We postulate that analysis of the exhaled breath would be a simple, rapid and non-invasive alternative. Breath contains hundreds of volatile organic compounds that are altered by infection and inflammation. The molecular fingerprint of breath (breathprint) can be obtained using an electronic nose, which relies on sensor technology. These breathprints can be stored in an online database (a "breathcloud") and coupled to clinical data. Comparison of the breathprint of a suspected subject to the breathcloud allows for a rapid decision on the presence or absence of a pathogen.
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Affiliation(s)
- Lieuwe D J Bos
- Department of Intensive Care Medicine, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands ; Department of Respiratory Medicine, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands ; Laboratory of Experimental Intensive Care and Anesthesiology, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| | - Marcus J Schultz
- Department of Intensive Care Medicine, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands ; Laboratory of Experimental Intensive Care and Anesthesiology, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
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27
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Khodakov DA, Ellis AV. Recent developments in nucleic acid identification using solid-phase enzymatic assays. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1167-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ritzi-Lehnert M. Development of chip-compatible sample preparation for diagnosis of infectious diseases. Expert Rev Mol Diagn 2014; 12:189-206. [DOI: 10.1586/erm.11.98] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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29
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Integration of sample pretreatment, μPCR, and detection for a total genetic analysis microsystem. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1128-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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30
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Microdroplet sandwich real-time rt-PCR for detection of pandemic and seasonal influenza subtypes. PLoS One 2013; 8:e73497. [PMID: 24066051 PMCID: PMC3774678 DOI: 10.1371/journal.pone.0073497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/23/2013] [Indexed: 12/16/2022] Open
Abstract
As demonstrated by the recent 2012/2013 flu epidemic, the continual emergence of new viral strains highlights the need for accurate medical diagnostics in multiple community settings. If rapid, robust, and sensitive diagnostics for influenza subtyping were available, it would help identify epidemics, facilitate appropriate antiviral usage, decrease inappropriate antibiotic usage, and eliminate the extra cost of unnecessary laboratory testing and treatment. Here, we describe a droplet sandwich platform that can detect influenza subtypes using real-time reverse-transcription polymerase chain reaction (rtRT-PCR). Using clinical samples collected during the 2010/11 season, we effectively differentiate between H1N1p (swine pandemic), H1N1s (seasonal), and H3N2 with an overall assay sensitivity was 96%, with 100% specificity for each subtype. Additionally, we demonstrate the ability to detect viral loads as low as 104 copies/mL, which is two orders of magnitude lower than viral loads in typical infected patients. This platform performs diagnostics in a miniaturized format without sacrificing any sensitivity, and can thus be easily developed into devices which are ideal for small clinics and pharmacies.
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Integrated RNA extraction and RT-PCR for semi-quantitative gene expression studies on a microfluidic device. J Transl Med 2013; 93:961-6. [PMID: 23711823 DOI: 10.1038/labinvest.2013.76] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/08/2022] Open
Abstract
This paper describes the development of a microfluidic methodology, using RNA extraction and reverse transcription PCR, for investigating expression levels of cytochrome P450 genes. Cytochrome P450 enzymes are involved in the metabolism of xenobiotics, including many commonly prescribed drugs, therefore information on their expression is useful in both pharmaceutical and clinical settings. RNA extraction, from rat liver tissue or primary rat hepatocytes, was performed using a silica-based solid-phase extraction technique. Following elution of the purified RNA, amplification of target sequences for the housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the cytochrome P450 gene CYP1A2, was carried out using a one-step reverse transcription PCR. Once the microfluidic methodology had been optimized, analysis of control and 3-methylcholanthrene-induced primary rat hepatocytes were used to evaluate the system. As expected, GAPDH was consistently expressed, whereas CYP1A2 levels were found to be raised in the drug-treated samples. The proposed system offers an initial platform for development of both rapid throughput analyzers for pharmaceutical drug screening and point-of-care diagnostic tests to aid provision of drug regimens, which can be tailor-made to the individual patient.
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Saadin K, White IM. Breast cancer stem cell enrichment and isolation by mammosphere culture and its potential diagnostic applications. Expert Rev Mol Diagn 2013; 13:49-60. [PMID: 23256703 DOI: 10.1586/erm.12.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Emerging knowledge about cancer stem cells (CSCs) is raising attention about the need to provide a more precise and complete diagnosis including the molecular profile of a patient's CSCs. As opposed to simply treating the bulk of the tumor, a more complete diagnosis can lead to treatment regimens designed to eradicate CSCs from a patient. In this review the authors detail the application of the mammosphere assay in the study of breast CSCs. The authors then describe the potential transition of the mammosphere assay from the research laboratory to the clinic by leveraging microsystems technology, which enables the integration of multiple functions into a single automated device. To conclude the review, the authors project that future clinical devices will be capable of isolating circulating metastatic cells from patient blood, enriching the dangerous CSCs, and providing a molecular profile of the CSCs, thus arming physicians with the information to select a treatment program that combats CSCs.
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Affiliation(s)
- Katayoon Saadin
- Chemical Physics Program, University of Maryland, College Park, MD 20742, USA
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Zhang Y, Qiao L, Ren Y, Wang X, Gao M, Tang Y, Jeff Xi J, Fu TM, Jiang X. Two dimensional barcode-inspired automatic analysis for arrayed microfluidic immunoassays. BIOMICROFLUIDICS 2013; 7:34110. [PMID: 24404030 PMCID: PMC3695989 DOI: 10.1063/1.4811278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/03/2013] [Indexed: 05/09/2023]
Abstract
The usability of many high-throughput lab-on-a-chip devices in point-of-care applications is currently limited by the manual data acquisition and analysis process, which are labor intensive and time consuming. Based on our original design in the biochemical reactions, we proposed here a universal approach to perform automatic, fast, and robust analysis for high-throughput array-based microfluidic immunoassays. Inspired by two-dimensional (2D) barcodes, we incorporated asymmetric function patterns into a microfluidic array. These function patterns provide quantitative information on the characteristic dimensions of the microfluidic array, as well as mark its orientation and origin of coordinates. We used a computer program to perform automatic analysis for a high-throughput antigen/antibody interaction experiment in 10 s, which was more than 500 times faster than conventional manual processing. Our method is broadly applicable to many other microchannel-based immunoassays.
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Affiliation(s)
- Yi Zhang
- College of Engineering and School of Physics, Peking University, Beijing 100871, China ; National Center for Nanoscience and Technology, Beijing 100190, China
| | - Lingbo Qiao
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China ; Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, China
| | - Yunke Ren
- College of Engineering and School of Physics, Peking University, Beijing 100871, China
| | - Xuwei Wang
- State Key Laboratory for Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080, China
| | - Ming Gao
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Yunfang Tang
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jianzhong Jeff Xi
- College of Engineering and School of Physics, Peking University, Beijing 100871, China
| | - Tzung-May Fu
- College of Engineering and School of Physics, Peking University, Beijing 100871, China
| | - Xingyu Jiang
- National Center for Nanoscience and Technology, Beijing 100190, China
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Shin Y, Perera AP, Kim KW, Park MK. Real-time, label-free isothermal solid-phase amplification/detection (ISAD) device for rapid detection of genetic alteration in cancers. LAB ON A CHIP 2013; 13:2106-14. [PMID: 23609609 DOI: 10.1039/c3lc50129a] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Here, we first present an isothermal solid-phase amplification/detection (ISAD) technique for the detection of single-point mutations that can be performed without labelling in real-time by utilizing both silicon microring-based solid-phase amplification and isothermal recombinase polymerase amplification (RPA). The ISAD technique was performed on a silicon microring device with a plastic chamber containing 10 μL of the reaction mixture, and characterized with an assay for the detection of the HRAS (Harvey RAS) gene single-point mutation. For the solid-phase amplification, the primer of the gene was directly attached to the surface of the device via an amine modification reaction. The amplified DNA was detected, without a label, by measuring the optical wavelength shift of the silicon microring resonator during the reaction. We demonstrated that the sensitivity of the ISAD technique was 100-times higher than that of RPA and conventional PCR methods. Moreover, this technique can be used to distinguish a single-point mutation of the HRAS gene via target amplification. This novel DNA amplification/detection technique will be useful for the detection of sequence alterations such as mutations and single-nucleotide polymorphisms as DNA biomarkers in human diseases.
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Affiliation(s)
- Yong Shin
- Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, Singapore 117685
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35
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Sun Y, Høgberg J, Christine T, Florian L, Monsalve LG, Rodriguez S, Cao C, Wolff A, Ruano-Lopez JM, Bang DD. Pre-storage of gelified reagents in a lab-on-a-foil system for rapid nucleic acid analysis. LAB ON A CHIP 2013; 13:1509-14. [PMID: 23377124 DOI: 10.1039/c2lc41386h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Reagent pre-storage in a microfluidic chip can enhance operator convenience, simplify the system design, reduce the cost of storage and shipment, and avoid the risk of cross-contamination. Although dry reagents have long been used in lateral flow immunoassays, they have rarely been used for nucleic acid-based point-of-care (POC) assays due to the lack of reliable techniques to dehydrate and store fragile molecules involved in the reaction. In this study, we describe a simple and efficient method for prolonged on-chip storage of PCR reagents. The method is based on gelification of all reagents required for PCR as a ready-to-use product. The approach was successfully implemented in a lab-on-a-foil system, and the gelification process was automated for mass production. Integration of reagents on-chip by gelification greatly facilitated the development of easy-to-use lab-on-a-chip (LOC) devices for fast and cost-effective POC analysis.
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Affiliation(s)
- Yi Sun
- DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark
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Song HO, Kim JH, Ryu HS, Lee DH, Kim SJ, Kim DJ, Suh IB, Choi DY, In KH, Kim SW, Park H. Polymeric LabChip real-time PCR as a point-of-care-potential diagnostic tool for rapid detection of influenza A/H1N1 virus in human clinical specimens. PLoS One 2012; 7:e53325. [PMID: 23285281 PMCID: PMC3532060 DOI: 10.1371/journal.pone.0053325] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 11/30/2012] [Indexed: 12/23/2022] Open
Abstract
It is clinically important to be able to detect influenza A/H1N1 virus using a fast, portable, and accurate system that has high specificity and sensitivity. To achieve this goal, it is necessary to develop a highly specific primer set that recognizes only influenza A viral genes and a rapid real-time PCR system that can detect even a single copy of the viral gene. In this study, we developed and validated a novel fluidic chip-type real-time PCR (LabChip real-time PCR) system that is sensitive and specific for the detection of influenza A/H1N1, including the pandemic influenza strain A/H1N1 of 2009. This LabChip real-time PCR system has several remarkable features: (1) It allows rapid quantitative analysis, requiring only 15 min to perform 30 cycles of real-time PCR. (2) It is portable, with a weight of only 5.5 kg. (3) The reaction cost is low, since it uses disposable plastic chips. (4) Its high efficiency is equivalent to that of commercially available tube-type real-time PCR systems. The developed disposable LabChip is an economic, heat-transferable, light-transparent, and easy-to-fabricate polymeric chip compared to conventional silicon- or glass-based labchip. In addition, our LabChip has large surface-to-volume ratios in micro channels that are required for overcoming time consumed for temperature control during real-time PCR. The efficiency of the LabChip real-time PCR system was confirmed using novel primer sets specifically targeted to the hemagglutinin (HA) gene of influenza A/H1N1 and clinical specimens. Eighty-five human clinical swab samples were tested using the LabChip real-time PCR. The results demonstrated 100% sensitivity and specificity, showing 72 positive and 13 negative cases. These results were identical to those from a tube-type real-time PCR system. This indicates that the novel LabChip real-time PCR may be an ultra-fast, quantitative, point-of-care-potential diagnostic tool for influenza A/H1N1 with a high sensitivity and specificity.
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Affiliation(s)
- Hyun-Ok Song
- Zoonosis Research Center, Department of Infection Biology, Wonkwang University School of Medicine, Iksan, Jeonbuk, Republic of Korea
| | - Je-Hyoung Kim
- Zoonosis Research Center, Department of Infection Biology, Wonkwang University School of Medicine, Iksan, Jeonbuk, Republic of Korea
| | - Ho-Sun Ryu
- NanoBioSys Inc., Geumcheon-gu, Seoul, Republic of Korea
| | - Dong-Hoon Lee
- NanoBioSys Inc., Geumcheon-gu, Seoul, Republic of Korea
| | - Sun-Jin Kim
- NanoBioSys Inc., Geumcheon-gu, Seoul, Republic of Korea
| | | | - In Bum Suh
- Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Kangwon-do, Republic of Korea
| | - Du Young Choi
- Department of Pediatrics, Wonkwang University School of Medicine, Iksan, Jeonbuk, Republic of Korea
| | - Kwang-Ho In
- Department of Medicine, Korea University School of Medicine, Seoul, Republic of Korea
| | - Sung-Woo Kim
- NanoBioSys Inc., Geumcheon-gu, Seoul, Republic of Korea
- * E-mail: (SK); (HP)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, Wonkwang University School of Medicine, Iksan, Jeonbuk, Republic of Korea
- * E-mail: (SK); (HP)
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Gold Nanoparticles-Coated SU-8 for Sensitive Fluorescence-Based Detections of DNA. Diagnostics (Basel) 2012; 2:72-82. [PMID: 26859400 PMCID: PMC4665555 DOI: 10.3390/diagnostics2040072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 10/24/2012] [Accepted: 11/26/2012] [Indexed: 11/21/2022] Open
Abstract
SU-8 epoxy-based negative photoresist has been extensively employed as a structural material for fabrication of numerous biological microelectro-mechanical systems (Bio-MEMS) or lab-on-a-chip (LOC) devices. However, SU-8 has a high autofluorescence level that limits sensitivity of microdevices that use fluorescence as the predominant detection workhorse. Here, we show that deposition of a thin gold nanoparticles layer onto the SU-8 surface significantly reduces the autofluorescence of the coated SU-8 surface by as much as 81% compared to bare SU-8. Furthermore, DNA probes can easily be immobilized on the Au surface with high thermal stability. These improvements enabled sensitive DNA detection by simple DNA hybridization down to 1 nM (a two orders of magnitude improvement) or by solid-phase PCR with sub-picomolar sensitivity. The approach is simple and easy to perform, making it suitable for various Bio-MEMs and LOC devices that use SU-8 as a structural material.
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Lim G, Kim J, Kim JH. Optimization of the masking molecule for active-site-protected immobilization of Taq DNA polymerase and its application. Anal Biochem 2012; 432:139-41. [PMID: 23036837 DOI: 10.1016/j.ab.2012.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 11/17/2022]
Abstract
The method of oriented and activity-preserved immobilization of biologically active proteins based on concepts of active-site masking and kinetic control was further developed in this study. Minimal requirements for the masking DNA molecule were found to be a 5'overhang of 5-7 nucleotides and a double-stranded region of 11-13 bp to retain approximately 70% of the enzyme activity. The amplification range of protected immobilized (PIM) Taq DNA polymerase was over 1.2 kb. These data suggest that PIM Taq DNA polymerase can be used for various commercial applications.
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Affiliation(s)
- Gumjung Lim
- Department of Chemistry, Kyung Hee University, Seoul 130-701, Republic of Korea
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Hoffmann J, Trotter M, von Stetten F, Zengerle R, Roth G. Solid-phase PCR in a picowell array for immobilizing and arraying 100,000 PCR products to a microscope slide. LAB ON A CHIP 2012; 12:3049-3054. [PMID: 22820686 DOI: 10.1039/c2lc40534b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present a method for performing highly parallel PCR reactions in a picowell array (PWA) simultaneously immobilizing generated PCR products in a covalent and spatially-resolved manner onto a microscope slide via solid-phase PCR (SP-PCR). This so called PWA-SP-PCR was performed in picowell arrays featuring 100,000 wells cm(-2) of 19 pL reaction volumes with a surface-to-volume ratio of 0.2 μm(-1). Positive signals were obtained in 97.2% of the 110,000 wells in an area of 110 mm(2). Immobilized DNA was either indirectly detected using streptavidin-Cy5 or directly by molecular hybridisation of Cy3- and/or Cy5-labelled probes. Amplification and immobilization was demonstrated for template DNA ranging from 100 bp up to 1513 bp lengths. Even single DNA molecules were successfully amplified and immobilized demonstrating digital solid-phase PCR. Compared to widely established emulsion based PCR (emPCR) approaches, leading to PCR products immobilized onto bead surfaces in a highly parallel manner, the novel technique results in direct spatial registration of immobilized PCR products in a microarray format. This enables the subsequent use for massively parallel analysis similar to standard microarrays.
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Affiliation(s)
- Jochen Hoffmann
- Laboratory for MEMS Applications, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, Freiburg, 79110, Germany
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40
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Schulze H, Barl T, Vase H, Baier S, Thomas P, Giraud G, Crain J, Bachmann TT. Enzymatic on-chip enhancement for high resolution genotyping DNA microarrays. Anal Chem 2012; 84:5080-4. [PMID: 22548504 DOI: 10.1021/ac3007945] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antibiotic resistance among pathogenic microorganisms is emerging as a major human healthcare concern. While there are a variety of resistance mechanisms, many can be related to single nucleotide polymorphisms and for which DNA microarrays have been widely deployed in bacterial genotyping. However, genotyping by means of allele-specific hybridization can suffer from the drawback that oligonucleotide probes with different nucleotide composition have varying thermodynamic parameters. This results in unpredictable hybridization behavior of mismatch probes. Consequently, the degree of discrimination between perfect match and mismatch probes is insufficient in some cases. We report here an on-chip enzymatic procedure to improve this discrimination in which false-positive hybrids are selectively digested. We find that the application of CEL1 Surveyor nuclease, a mismatch-specific endonuclease, significantly enhances the discrimination fidelity, as demonstrated here on a microarray for the identification of variants of carbapenem resistant Klebsiella pneumoniae carbapenemases and monitored by end point detection of fluorescence intensity. Further fundamental investigations applying total internal reflection fluorescence detection for kinetic real-time measurements confirmed the enzymatic enhancement for SNP discrimination.
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Affiliation(s)
- Holger Schulze
- Division of Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK
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41
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Hoffmann J, Hin S, Stetten FV, Zengerle R, Roth G. Universal protocol for grafting PCR primers onto various lab-on-a-chip substrates for solid-phase PCR. RSC Adv 2012. [DOI: 10.1039/c2ra01250b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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42
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Pabbaraju K, Wong S, Drews SJ. Rethinking approaches to improve the utilization of nucleic acid amplification tests for detection and characterization of influenza A in diagnostic and reference laboratories. Future Microbiol 2011; 6:1443-60. [PMID: 22122441 DOI: 10.2217/fmb.11.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Influenza A virus (IFVA) is a significant cause of respiratory infections worldwide and was also responsible for a recent pandemic in 2009. Laboratory identification of IFVA can guide antiviral therapy, assist in cohorting of patients and prevent antibiotic use. Characterization of the virus can track the emergence of novel strains, identify resistance and determine how circulating strains match with vaccine components. The gold standard for detection and characterization of IFVA is nucleic acid amplification technology (e.g., reverse transcriptase PCR [RT-PCR]), which must contend with a constantly evolving viral genome. Although molecular technology has been available for over two decades, there is still an operational gap between assay design and utilization of these tests for the diagnosis and characterization of IFVA. This review will discuss issues surrounding the implementation and use of RT-PCR for the identification and characterization of IFVA, and speculate on why RT-PCR has not been used more widely in clinical laboratories or moved closer to the patient. Newer, less widely used technologies that may change our laboratory practices will be identified and the authors will close with an attempt to identify some future applications of RT-PCR-based technologies for the detection and characterization of IFVA.
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Affiliation(s)
- Kanti Pabbaraju
- Provincial Laboratory for Public Health, Microbiology, 3030 Hospital Drive NW, Calgary, Alberta T2N 4W4, Canada
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Sun Y, Perch-Nielsen I, Dufva M, Sabourin D, Bang DD, Høgberg J, Wolff A. Direct immobilization of DNA probes on non-modified plastics by UV irradiation and integration in microfluidic devices for rapid bioassay. Anal Bioanal Chem 2011; 402:741-8. [PMID: 22028019 PMCID: PMC3249165 DOI: 10.1007/s00216-011-5459-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 11/24/2022]
Abstract
DNA microarrays have become one of the most powerful tools in the field of genomics and medical diagnosis. Recently, there has been increased interest in combining microfluidics with microarrays since this approach offers advantages in terms of portability, reduced analysis time, low consumption of reagents, and increased system integration. Polymers are widely used for microfluidic systems, but fabrication of microarrays on such materials often requires complicated chemical surface modifications, which hinders the integration of microarrays into microfluidic systems. In this paper, we demonstrate that simple UV irradiation can be used to directly immobilize poly(T)poly(C)-tagged DNA oligonucleotide probes on many different types of plastics without any surface modification. On average, five- and fourfold improvement in immobilization and hybridization efficiency have been achieved compared to surface-modified slides with aminated DNA probes. Moreover, the TC tag only costs 30% of the commonly used amino group modifications. Using this microarray fabrication technique, a portable cyclic olefin copolymer biochip containing eight individually addressable microfluidic channels was developed and used for rapid and parallel identification of Avian Influenza Virus by DNA hybridization. The one-step, cost-effective DNA-linking method on non-modified polymers significantly simplifies microarray fabrication procedures and permits great flexibility to plastic material selection, thus making it convenient to integrate microarrays into plastic microfluidic systems.
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Affiliation(s)
- Yi Sun
- DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, Kgs. Lyngby, Denmark
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Konry T, Bale SS, Bhushan A, Shen K, Seker E, Polyak B, Yarmush M. Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection. Mikrochim Acta 2011; 176:251-269. [PMID: 25378716 DOI: 10.1007/s00604-011-0705-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is a growing need for diagnostic technologies that provide laboratories with solutions that improve quality, enhance laboratory system productivity, and provide accurate detection of a broad range of infectious diseases and cancers. Recent advances in micro- and nanoscience and engineering, in particular in the areas of particles and microfluidic technologies, have advanced the "lab-on-a-chip" concept towards the development of a new generation of point-of-care diagnostic devices that could significantly enhance test sensitivity and speed. In this review, we will discuss many of the recent advances in microfluidics and particle technologies with an eye towards merging these two technologies for application in medical diagnostics. Although the potential diagnostic applications are virtually unlimited, the most important applications are foreseen in the areas of biomarker research, cancer diagnosis, and detection of infectious microorganisms.
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Affiliation(s)
- Tania Konry
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Shyam Sundhar Bale
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Abhinav Bhushan
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Keyue Shen
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Erkin Seker
- Department of Electrical and Computer Engineering, University of California, Davis, 3177 Kemper Hall, Davis, CA 95616, USA
| | - Boris Polyak
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Martin Yarmush
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
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45
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Walczak R. Fluorescence detection by miniaturized instrumentation based on non-cooled CCD minicamera and dedicated for lab-on-a-chip applications. BIOCHIP JOURNAL 2011. [DOI: 10.1007/s13206-011-5312-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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