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Kumarajith TM, Powell SM, Breadmore MC. Isotachophoretic quantification of total viable bacteria on meat and surfaces. Anal Chim Acta 2024; 1296:342253. [PMID: 38401922 DOI: 10.1016/j.aca.2024.342253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/18/2023] [Accepted: 01/13/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND The quantification of microbes, particularly live bacteria, is of utmost importance in assessing the quality of meat products. In the context of meat processing facilities, prompt identification and removal of contaminated carcasses or surfaces is crucial to ensuring the continuous production of safe meat for human consumption. The plate count method and other traditional detection methods are not only labour-intensive but also time-consuming taking 24-48 h. RESULTS In this report, we present a novel isotachophoretic quantification method utilizing two nucleic acid stains, SYTO9 and propionic iodide, for the detection of total viable bacteria. The study employed E. coli M23 bacteria as a model organism, with an analysis time of only 30 min. The method demonstrated a limit of detection (LOD) of 184 CFU mL-1 and 14 cells mL-1 for total viable count and total cell count, respectively. Furthermore, this new approach is capable of detecting the microbial quality standard limits for food contacting surfaces (10 CFU cm-2) and meat (1.99 × 104 CFU cm-2) by swabbing an area of 10 × 10 cm2. SIGNIFICANCE In contrast to the culture-based methods usually employed in food processing facilities, this isotachophoretic technique enables easy and rapid detection (<30 min) of microorganisms, facilitating crucial decision-making essential for maintaining product quality and safety.
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Affiliation(s)
- Thisara M Kumarajith
- Australia Centre for Research on Separation Science, Chemistry, School of Natural Sciences, Tasmania, Australia; Tasmanian Institute of Agriculture, Tasmania, Australia
| | | | - Michael C Breadmore
- Australia Centre for Research on Separation Science, Chemistry, School of Natural Sciences, Tasmania, Australia.
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2
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Bu Y, Ni S, Yobas L. Accelerated Electrophoretic Focusing and Purification of DNA Based on Synchronous Coefficient of Drag Alteration. Anal Chem 2023; 95:16453-16458. [PMID: 37916921 DOI: 10.1021/acs.analchem.3c03632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Synchronous coefficient of drag alteration refers to a multidimensional transport mechanism where a net drift of molecules is achieved under a zero-time-average alternating motive force by perturbing their drag coefficient synchronously with the applied force. An electrophoretic form of the method is often applied to focus and purify nucleic acids in a gel under rotating electric fields. However, this method requires lengthy operation due to the use of limited field strengths. Here, using DNA as target molecules, we demonstrate that the operation time can be reduced from hours to minutes by replacing polymer gel with a microfabricated artificial sieve. We also describe an electrophoretic protocol that facilitates the collection of purified DNA from the sieve, which is shown to yield amplifiable DNA from crude samples including the lysates of cultured cells and whole blood. The sieve can be further equipped with nucleic acid amplification and detection functions for a point-of-care diagnostic application.
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Affiliation(s)
- Yang Bu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR 999077, P.R.China
| | - Sheng Ni
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR 999077, P.R.China
| | - Levent Yobas
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR 999077, P.R.China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR 999077, P.R.China
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3
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Li S, Han B, Zhou D, Gu Y, Li B, Ma J, Fu R, Qi X, Liu P. One-Stop Extraction and In Situ RT-qPCR for Ultrasensitive Detection of Highly Diluted SARS-CoV-2 in Large-Volume Samples from Aquatic Environments. Anal Chem 2023; 95:2339-2347. [PMID: 36644822 DOI: 10.1021/acs.analchem.2c04224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Surveillance of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in aquatic environments attracted attention due to its considerable impacts on human health and ecology, especially in countries with poor sanitation standards. Based on a strategy of one-stop extraction and in situ amplification, we developed an ultrasensitive method that uses a polyacrylamide derivative-modified filter disc (PAD-FD), in which highly diluted RNA can be efficiently concentrated onto the filter disc and directly used for amplification. A newly designed spin column with a cup-like filter base facilitated the non-contact transfer of the affinity filter disc from the column to a PCR tube. The limit of detection of the PAD-FD coupled with RT-qPCR is 10 copies/mL. Using 32 suspected SARS-CoV-2 samples, we demonstrated that the detection rate of our method (62.5%, 20/32) was triple the rate of the commercial kit (18.8%, 6/32). Using a PAD-FD, 56.3% (18/32) and 40.6% (13/32) of the 10-fold-dilution samples with river and tap water, respectively, were detected. Even when diluted 100-fold, 28.1% (9/32) and 37.5% (12/32) were still detected in river and tap water, respectively. We believe that the PAD-FD method offers an accurate testing tool for monitoring viral RNA in aquatic environments, contributing to the forewarning of the SARS-CoV-2 outbreak and the breaking of the transmission chain.
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Affiliation(s)
- Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bingqian Han
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Donggen Zhou
- Ningbo International Travel Healthcare Center (Ningbo Port Hospital), Ningbo, Zhejiang 315012, China
| | - Yin Gu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, China
| | - Bao Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jianxin Ma
- Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing 100021, China
| | - Rongxin Fu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiao Qi
- Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing 100021, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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Abstract
INTRODUCTION The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis. AREAS COVERED This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications. EXPERT OPINION RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.
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Affiliation(s)
- Gihoon Choi
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Taylor J Moehling
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J Meagher
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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5
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Bender AT, Sullivan BP, Zhang JY, Juergens DC, Lillis L, Boyle DS, Posner JD. HIV detection from human serum with paper-based isotachophoretic RNA extraction and reverse transcription recombinase polymerase amplification. Analyst 2021; 146:2851-2861. [PMID: 33949378 PMCID: PMC9151496 DOI: 10.1039/d0an02483j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The number of people living with HIV continues to increase with the current total near 38 million, of which about 26 million are receiving antiretroviral therapy (ART). These treatment regimens are highly effective when properly managed, requiring routine viral load monitoring to assess successful viral suppression. Efforts to expand access by decentralizing HIV nucleic acid testing in low- and middle-income countries (LMICs) has been hampered by the cost and complexity of current tests. Sample preparation of blood samples has traditionally relied on cumbersome RNA extraction methods, and it continues to be a key bottleneck for developing low-cost POC nucleic acid tests. We present a microfluidic paper-based analytical device (μPAD) for extracting RNA and detecting HIV in serum, leveraging low-cost materials, simple buffers, and an electric field. We detect HIV virions and MS2 bacteriophage internal control in human serum using a novel lysis and RNase inactivation method, paper-based isotachophoresis (ITP) for RNA extraction, and duplexed reverse transcription recombinase polymerase amplification (RT-RPA) for nucleic acid amplification. We design a specialized ITP system to extract and concentrate RNA, while excluding harsh reagents used for lysis and RNase inactivation. We found the ITP μPAD can extract and purify 5000 HIV RNA copies per mL of serum. We then demonstrate detection of HIV virions and MS2 bacteriophage in human serum within 45-minutes.
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Affiliation(s)
- Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Jane Y Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - David C Juergens
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | | | | | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, USA. and Department of Chemical Engineering, University of Washington, Seattle, USA and Family Medicine, School of Medicine, University of Washington, Seattle, USA
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6
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Du X, Cheng X, Li W, Ge Z, Zhong C, Fan C, Gu H. Engineering Allosteric Ribozymes to Detect Thiamine Pyrophosphate in Whole Blood. Anal Chem 2021; 93:4277-4284. [PMID: 33635634 DOI: 10.1021/acs.analchem.0c05276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiamine deficiency contributes to several human diseases including Alzheimer's. As its biologically active form, thiamine pyrophosphate (TPP) has been considered as a potential biomarker for Alzheimer's disease (AD) based on several clinical reports that apparently lower blood TPP levels were found in patients with mild cognitive impairment to AD. However, highly sensitive and high-throughput detection of TPP in biological fluids remains an analytical challenge. Here, we report engineering RNA-based sensors to quantitatively measure TPP concentrations in whole blood samples with a detection limit down to a few nM. By fusing a TPP-specific aptamer with the hammerhead ribozyme for in vitro selection, we isolated an allosteric ribozyme with an EC50 value (68 nM) similar to the aptamer's KD value (50 nM) for TPP, which for the first time demonstrates the possibility to maintain the effector binding affinity of the aptamer in such engineered allosteric RNA constructs. Meanwhile, we developed a new blood sample preparation protocol to be compatible with RNA. By coupling the TPP-induced ribozyme cleavage event with isothermal amplification, we achieved fluorescence monitoring of whole blood TPP levels through the "mix-and-read" operation with high-throughput potential. We expect that the engineered TPP-sensing RNAs will facilitate clinical research on AD as well as other thiamine-related diseases.
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Affiliation(s)
- Xinyu Du
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Department of Neurology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaoqin Cheng
- Department of Neurology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Department of Neurology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunjiu Zhong
- Department of Neurology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Department of Neurology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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7
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Gharizadeh B, Yue J, Yu M, Liu Y, Zhou M, Lu D, Zhang J. Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management. IEEE Rev Biomed Eng 2021; 14:30-47. [PMID: 32356761 DOI: 10.1109/rbme.2020.2991444] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To counter COVID-19 spreading, an infrastructure to provide rapid and thorough molecular diagnostics and serology testing is the cornerstone of outbreak and pandemic management. We hereby review the clinical insights with regard to using molecular tests and immunoassays in the context of COVID-19 management life cycle: the preventive phase, the preparedness phase, the response phase and the recovery phase. The spatial and temporal distribution of viral RNA, antigens and antibodies during human infection is summarized to provide a biological foundation for accurate detection of the disease. We shared the lessons learned and the obstacles encountered during real world high-volume screening programs. Clinical needs are discussed to identify existing technology gaps in these tests. Leverage technologies, such as engineered polymerases, isothermal amplification, and direct amplification from complex matrices may improve the productivity of current infrastructure, while emerging technologies like CRISPR diagnostics, visual end point detection, and PCR free methods for nucleic acid sensing may lead to at-home tests. The lessons learned, and innovations spurred from the COVID-19 pandemic could upgrade our global public health infrastructure to better combat potential outbreaks in the future.
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8
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Sullivan BP, Bender AT, Ngyuen DN, Zhang JY, Posner JD. Nucleic acid sample preparation from whole blood in a paper microfluidic device using isotachophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1163:122494. [PMID: 33401049 DOI: 10.1016/j.jchromb.2020.122494] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023]
Abstract
Nucleic acid amplification tests (NAATs) are a crucial diagnostic and monitoring tool for infectious diseases. A key procedural step for NAATs is sample preparation: separating and purifying target nucleic acids from crude biological samples prior to nucleic acid amplification and detection. Traditionally, sample preparation has been performed with liquid- or solid-phase extraction, both of which require multiple trained user steps and significant laboratory equipment. The challenges associated with sample preparation have limited the dissemination of NAAT point-of-care diagnostics in low resource environments, including low- and middle-income countries. We report on a paper-based device for purification of nucleic acids from whole blood using isotachophoresis (ITP) for point-of-care NAATs. We show successful extraction and purification of target nucleic acids from large volumes (33 µL) of whole human blood samples with no moving parts and few user steps. Our device utilizes paper-based buffer reservoirs to fully contain the liquid ITP buffers and does not require complex filling procedures, instead relying on the natural wicking of integrated paper membranes. We perform on-device blood fractionation via filtration to remove leukocytes and erythrocytes from our sample, followed by integrated on-paper proteolytic digestion of endogenous plasma proteins to allow for successful isotachophoretic extraction. Paper-based isotachophoresis purifies and concentrates target nucleic acids that are added directly to recombinase polymerase amplification (RPA) reactions. We show consistent amplification of input copy concentrations of as low as 3 × 103 copies nucleic acid per mL input blood with extraction and purification taking only 30 min. By employing a paper architecture, we are able to incorporate these processes in a single, robust, low-cost design, enabling the direct processing of large volumes of blood, with the only intermediate user steps being the removal and addition of tape. Our device represents a step towards a simple, fully integrated sample preparation system for nucleic acid amplification tests at the point-of-care.
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Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Duy N Ngyuen
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jane Yuqian Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA; Department of Chemical Engineering, University of Washington, Seattle, WA, USA; Department of Family Medicine, University of Washington, Seattle, WA, USA.
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9
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Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2. Proc Natl Acad Sci U S A 2020; 117:29518-29525. [PMID: 33148808 PMCID: PMC7703567 DOI: 10.1073/pnas.2010254117] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Rapid, early-stage screening is crucial during pandemics for early identification of infected patients and control of disease spread. CRISPR biology offers new methods for rapid and accurate pathogen detection. Despite their versatility and specificity, existing CRISPR diagnostic methods suffer from the requirements of up-front nucleic acid extraction, large reagent volumes, and several manual steps—factors which prolong the process and impede use in low-resource settings. We here combine microfluidics, on-chip electric field control, and CRISPR to directly address limitations of current CRISPR diagnostic methods. We apply our method to the rapid detection of SARS-CoV-2 RNA in clinical samples. Our method takes about 35 min from raw sample to result, a significant improvement over existing nucleic acid-based diagnostic methods for COVID-19. The rapid spread of COVID-19 across the world has revealed major gaps in our ability to respond to new virulent pathogens. Rapid, accurate, and easily configurable molecular diagnostic tests are imperative to prevent global spread of new diseases. CRISPR-based diagnostic approaches are proving to be useful as field-deployable solutions. In one basic form of this assay, the CRISPR–Cas12 enzyme complexes with a synthetic guide RNA (gRNA). This complex becomes activated only when it specifically binds to target DNA and cleaves it. The activated complex thereafter nonspecifically cleaves single-stranded DNA reporter probes labeled with a fluorophore−quencher pair. We discovered that electric field gradients can be used to control and accelerate this CRISPR assay by cofocusing Cas12–gRNA, reporters, and target within a microfluidic chip. We achieve an appropriate electric field gradient using a selective ionic focusing technique known as isotachophoresis (ITP) implemented on a microfluidic chip. Unlike previous CRISPR diagnostic assays, we also use ITP for automated purification of target RNA from raw nasopharyngeal swab samples. We here combine this ITP purification with loop-mediated isothermal amplification and the ITP-enhanced CRISPR assay to achieve detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA (from raw sample to result) in about 35 min for both contrived and clinical nasopharyngeal swab samples. This electric field control enables an alternate modality for a suite of microfluidic CRISPR-based diagnostic assays.
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10
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Ouyang W, Han J. One‐Step Nucleic Acid Purification and Noise‐Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow‐Abundance Nucleic Acid Detection. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Wei Ouyang
- Department of Electrical Engineering and Computer Science and Research Laboratory of ElectronicsMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science and Research Laboratory of ElectronicsMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- Department of Biological EngineeringMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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11
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Ouyang W, Han J. One-Step Nucleic Acid Purification and Noise-Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow-Abundance Nucleic Acid Detection. Angew Chem Int Ed Engl 2020; 59:10981-10988. [PMID: 32246546 PMCID: PMC7560970 DOI: 10.1002/anie.201915788] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Indexed: 12/15/2022]
Abstract
Nucleic acid amplification tests (NAATs)integrated on a chip hold great promise for point-of-care diagnostics. Currently, nucleic acid (NA) purification remains time-consuming and labor-intensive, and it takes extensive efforts to optimize the amplification chemistry. Using selective electrokinetic concentration, we report one-step, liquid-phase NA purification that is simpler and faster than conventional solid-phase extraction. By further re-concentrating NAs and performing polymerase chain reaction (PCR) in a microfluidic chamber, our platform suppresses non-specific amplification caused by non-optimal PCR designs. We achieved the detection of 5 copies of M. tuberculosis genomic DNA (equaling 0.3 cell) in real biofluids using both optimized and non-optimal PCR designs, which is 10- and 1000-fold fewer than those of the standard bench-top method, respectively. By simplifying the workflow and shortening the development cycle of NAATs, our platform may find use in point-of-care diagnosis.
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Affiliation(s)
- Wei Ouyang
- Department of Electrical Engineering and Computer Science and Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science and Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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12
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Bender AT, Sullivan BP, Lillis L, Posner JD. Enzymatic and Chemical-Based Methods to Inactivate Endogenous Blood Ribonucleases for Nucleic Acid Diagnostics. J Mol Diagn 2020; 22:1030-1040. [PMID: 32450280 DOI: 10.1016/j.jmoldx.2020.04.211] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 01/28/2023] Open
Abstract
There are ongoing research efforts into simple and low-cost point-of-care nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. Herein, we investigate alternatives to standard guanidinium-based methods for RNase inactivation using an activity assay with an RNA substrate that fluoresces when cleaved. The effects of proteinase K, nonionic surfactants, SDS, dithiothreitol, and other additives on RNase activity in human serum are reported. Although proteinase K has been widely used in protocols for nuclease inactivation, it was found that high concentrations of proteinase K are unable to eliminate RNase activity in serum, unless used in concert with denaturing concentrations of SDS. It was observed that SDS must be combined with proteinase K, dithiothreitol, or both for irreversible and complete RNase inactivation in serum. This work provides an alternative chemistry for inactivating endogenous RNases for use in simple, low-cost point-of-care NATs for blood-borne pathogens.
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Affiliation(s)
- Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | | | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington; Department of Chemical Engineering, University of Washington, Seattle, Washington; Department of Family Medicine, University of Washington, Seattle, Washington.
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13
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Khnouf R, Han CM, Munro SA. Isolation of enriched small RNA from cell-lysate using on-chip isotachophoresis. Electrophoresis 2019; 40:3140-3147. [PMID: 31675123 DOI: 10.1002/elps.201900215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 11/08/2022]
Abstract
In spite of the growing interest in the roles and applications of small RNAs (sRNAs), sRNA isolation methods are inconsistent, tedious, and dependent on the starting number of cells. In this work, we employ ITP to isolate sRNAs from the cell-lysate of K562 (chronic myelogenous leukemia) cells in a polydimethylsiloxane (PDMS) mesofluidic device. Our method specifically purifies sRNA of <60 nucleotides from lysate of a wide range of cell number spanning from 100 to 1 000 000 cells. We measured the amount of sRNA using the Agilent Bioanalyzer and further verified the extraction efficiency by reverse transcription quantitative PCR. Our method was shown to be more efficient in sRNA extraction than commercial sRNA isolation kits, especially when using smaller numbers of starting cells. Our assay presents a simple and rapid sRNA extraction method with 20 min assay time and no intermediate transfer steps.
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Affiliation(s)
- Ruba Khnouf
- Department of Mechanical Engineering, Stanford University, Stanford, CA, United States.,Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid, Jordan
| | - Crystal M Han
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, United States.,Department of Mechanical Engineering, San Jose State University, San Jose, CA, United States
| | - Sarah A Munro
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, United States.,Minnesota Supercomputing Institute, University of Minnesota, MN, United States
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14
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Kooten XF, Petrini LFT, Kashyap A, Voith von Voithenberg L, Bercovici M, Kaigala GV. Spatially Resolved Genetic Analysis of Tissue Sections Enabled by Microscale Flow Confinement Retrieval and Isotachophoretic Purification. Angew Chem Int Ed Engl 2019; 58:15259-15262. [DOI: 10.1002/anie.201907150] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Xander F. Kooten
- IBM Research—Zurich Säumerstrasse 4 8803 Rüschlikon Switzerland
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology Technion City 3200003 Haifa Israel
| | | | - Aditya Kashyap
- IBM Research—Zurich Säumerstrasse 4 8803 Rüschlikon Switzerland
| | | | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology Technion City 3200003 Haifa Israel
- Department of Mechanical EngineeringThe University of Texas at Austin Austin TX 78712 USA
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15
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Kooten XF, Petrini LFT, Kashyap A, Voith von Voithenberg L, Bercovici M, Kaigala GV. Spatially Resolved Genetic Analysis of Tissue Sections Enabled by Microscale Flow Confinement Retrieval and Isotachophoretic Purification. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xander F. Kooten
- IBM Research—Zurich Säumerstrasse 4 8803 Rüschlikon Switzerland
- Faculty of Mechanical Engineering, Technion— Israel Institute of Technology Technion City 3200003 Haifa Israel
| | | | - Aditya Kashyap
- IBM Research—Zurich Säumerstrasse 4 8803 Rüschlikon Switzerland
| | | | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion— Israel Institute of Technology Technion City 3200003 Haifa Israel
- Department of Mechanical Engineering The University of Texas at Austin Austin TX 78712 USA
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16
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A supersensitive MSPQC bacterium sensor based on 16S rRNA and “DNA-RNA switch”. Biosens Bioelectron 2019; 138:111302. [DOI: 10.1016/j.bios.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022]
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17
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Zhao F, Lee EY, Shin Y. Improved Reversible Cross-Linking-Based Solid-Phase RNA Extraction for Pathogen Diagnostics. Anal Chem 2018; 90:1725-1733. [DOI: 10.1021/acs.analchem.7b03493] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fei Zhao
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center,
University of Ulsan College of Medicine, and Biomedical Engineering
Research Center, Asan Institute of Life Sciences, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
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18
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Eid C, Santiago JG. Assay for Listeria monocytogenes cells in whole blood using isotachophoresis and recombinase polymerase amplification. Analyst 2018; 142:48-54. [PMID: 27904893 DOI: 10.1039/c6an02119k] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We present a new approach which enables lysis, extraction, and detection of inactivated Listeria monocytogenes cells from blood using isotachophoresis (ITP) and recombinase polymerase amplification (RPA). We use an ITP-compatible alkaline and proteinase K approach for rapid and effective lysis. We then perform ITP purification to separate bacterial DNA from whole blood contaminants using a microfluidic device that processes 25 μL sample volume. Lysis, mixing, dispensing, and on-chip ITP purification are completed in a total of less than 50 min. We transfer extracted DNA directly into RPA master mix for isothermal incubation and detection, an additional 25 min. We first validate our assay in the detection of purified genomic DNA spiked into whole blood, and demonstrate a limit of detection of 16.7 fg μL-1 genomic DNA, the equivalent of 5 × 103 cells per mL. We then show detection of chemically-inactivated L. monocytogenes cells spiked into whole blood, and demonstrate a limit of detection of 2 × 104 cells per mL. Lastly, we show preliminary experimental data demonstrating the feasibility of the integration of ITP purification with RPA detection on a microfluidic chip. Our results suggest that ITP purification is compatible with RPA detection, and has potential to extend the applicability of RPA to whole blood.
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Affiliation(s)
- Charbel Eid
- Department of Mechanical Engineering, Stanford University, 440 Escondido Mall, Bldg 530, room 225, Stanford, CA 94305, USA.
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, 440 Escondido Mall, Bldg 530, room 225, Stanford, CA 94305, USA.
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19
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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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20
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Nacham O, Clark KD, Varona M, Anderson JL. Selective and Efficient RNA Analysis by Solid-Phase Microextraction. Anal Chem 2017; 89:10661-10666. [DOI: 10.1021/acs.analchem.7b02733] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Omprakash Nacham
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Kevin D. Clark
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L. Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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21
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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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22
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Microfluidics: innovative approaches for rapid diagnosis of antibiotic-resistant bacteria. Essays Biochem 2017; 61:91-101. [PMID: 28258233 DOI: 10.1042/ebc20160059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/17/2022]
Abstract
The emergence of antibiotic-resistant bacteria has become a major global health concern. Rapid and accurate diagnostic strategies to determine the antibiotic susceptibility profile prior to antibiotic prescription and treatment are critical to control drug resistance. The standard diagnostic procedures for the detection of antibiotic-resistant bacteria, which rely mostly on phenotypic characterization, are time consuming, insensitive and often require skilled personnel, making them unsuitable for point-of-care (POC) diagnosis. Various molecular techniques have therefore been implemented to help speed up the process and increase sensitivity. Over the past decade, microfluidic technology has gained great momentum in medical diagnosis as a series of fluid handling steps in a laboratory can be simplified and miniaturized on to a small platform, allowing marked reduction of sample amount, high portability and tremendous possibility for integration with other detection technologies. These advantages render the microfluidic system a great candidate to be developed into an easy-to-use sample-to-answer POC diagnosis suitable for application in remote clinical settings. This review provides an overview of the current development of microfluidic technologies for the nucleic acid based and phenotypic-based detections of antibiotic resistance.
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23
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Brennecke J, Kraut S, Zwadlo K, Gandi SK, Pritchard D, Templeton K, Bachmann T. High-yield extraction of Escherichia coli RNA from human whole blood. J Med Microbiol 2017; 66:301-311. [PMID: 28126043 DOI: 10.1099/jmm.0.000439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Studies of bacterial transcriptomics during bloodstream infections are limited to-date because unbiased extraction of bacterial mRNA from whole blood in sufficient quantity and quality has proved challenging. Problems include the high excess of human cells, the presence of PCR inhibitors and the short intrinsic half-life of bacterial mRNA. This study aims to provide a framework for the choice of the most suitable sample preparation method. METHODOLOGY Escherichia coli cells were spiked into human whole blood and the bacterial gene expression was stabilized with RNAprotect either immediately or after lysis of the red blood cells with Triton X-100, saponin, ammonium chloride or the commercial MolYsis buffer CM. RNA yield, purity and integrity were assessed by absorbance measurements at 260 and 280 nm, real-time PCR and capillary electrophoresis. RESULTS For low cell numbers, the best mRNA yields were obtained by adding the commercial RNAprotect reagent directly to the sample without prior lyses of the human blood cells. Using this protocol, significant amounts of human RNA were co-purified, however, this had a beneficial impact on the yields of bacterial mRNA. Among the tested lysis agents, Triton X-100 was the most effective and reduced the human RNA background by three to four orders of magnitude. CONCLUSION For most applications, lysis of the human blood cells is not required. However, co-purified human RNA may interfere with some downstream processes such as RNA sequencing. In this case, blood cell lysis with Triton X-100 is desirable.
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Affiliation(s)
- Johannes Brennecke
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK
| | - Simone Kraut
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK.,AG Aus- und Weiterbildung, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Klara Zwadlo
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK.,AG Aus- und Weiterbildung, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Senthil Kumar Gandi
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK
| | | | | | - Till Bachmann
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK
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24
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Affiliation(s)
- Charbel Eid
- Department
of Mechanical
Engineering, Stanford University, Stanford, California 94305, United States
| | - Juan G. Santiago
- Department
of Mechanical
Engineering, Stanford University, Stanford, California 94305, United States
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25
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Fu X, Mavrogiannis N, Ibo M, Crivellari F, Gagnon ZR. Microfluidic free-flow zone electrophoresis and isotachophoresis using carbon black nano-composite PDMS sidewall membranes. Electrophoresis 2016; 38:327-334. [DOI: 10.1002/elps.201600104] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaotong Fu
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
| | - Nicholas Mavrogiannis
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
| | - Markela Ibo
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
| | - Francesca Crivellari
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
| | - Zachary R. Gagnon
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
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26
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Exploring Gradients in Electrophoretic Separation and Preconcentration on Miniaturized Devices. SEPARATIONS 2016. [DOI: 10.3390/separations3020012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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27
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Abstract
Fast and reliable diagnoses are invaluable in clinical care. Samples (e.g., blood, urine, and saliva) are collected and analyzed for various biomarkers to quickly and sensitively assess disease progression, monitor response to treatment, and determine a patient's prognosis. Processing conventional samples entails many manual time-consuming steps. Consequently, clinical specimens must be processed by skilled technicians before antigens or nucleic acids are detected, and these are often present at dilute concentrations. Recently, several automated microchip technologies have been developed that potentially offer many advantages over traditional bench-top extraction methods. The smaller length scales and more refined transport mechanisms that characterize these microfluidic devices enable faster and more efficient biomarker enrichment and extraction. Additionally, they can be designed to perform multiple tests or experimental steps on one integrated, automated platform. This review explores the current research on microfluidic methods of sample preparation that are designed to aid diagnosis, and covers a broad spectrum of extraction techniques and designs for various types of samples and analytes.
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Affiliation(s)
- Francis Cui
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912;
| | - Minsoung Rhee
- Sandia National Laboratories, Livermore, California 94551-0969
| | - Anup Singh
- Sandia National Laboratories, Livermore, California 94551-0969
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912;
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28
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Counter-pressure-assisted ITP with electrokinetic injection under field-amplified conditions for bacterial analysis. Anal Bioanal Chem 2015; 407:6995-7002. [DOI: 10.1007/s00216-015-8838-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/24/2015] [Accepted: 06/09/2015] [Indexed: 11/26/2022]
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29
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Kuriyama K, Shintaku H, Santiago JG. Isotachophoresis for fractionation and recovery of cytoplasmic RNA and nucleus from single cells. Electrophoresis 2015; 36:1658-62. [PMID: 25820552 DOI: 10.1002/elps.201500040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/13/2015] [Accepted: 03/14/2015] [Indexed: 12/26/2022]
Abstract
There is a substantial need for simultaneous analyses of RNA and DNA from individual single cells. Such analysis provides unique evidence of cell-to-cell differences and the correlation between gene expression and genomic mutation in highly heterogeneous cell populations. We present a novel microfluidic system that leverages isotachophoresis to fractionate and isolate cytoplasmic RNA and genomic DNA (gDNA) from single cells. The system uniquely enables independent, sequence-specific analyses of these critical markers. Our system uses a microfluidic chip with a simple geometry and four end-channel electrodes, and completes the entire process in <5 min, including lysis, purification, fractionation, and delivery to DNA and RNA output reservoirs, each containing high quality and purity aliquots with no measurable cross-contamination of cytoplasmic RNA versus gDNA. We demonstrate our system with simultaneous, sequence-specific quantitation using off-chip RT-qPCR and qPCR for simultaneous cytoplasmic RNA and gDNA analyses, respectively.
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Affiliation(s)
- Kentaro Kuriyama
- Department of Mechanical Engineering, Stanford University, Escondido, Stanford, CA, USA
| | - Hirofumi Shintaku
- Department of Mechanical Engineering, Stanford University, Escondido, Stanford, CA, USA.,Department of Micro Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Escondido, Stanford, CA, USA
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30
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Borysiak MD, Kimura KW, Posner JD. NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification. LAB ON A CHIP 2015; 15:1697-707. [PMID: 25666345 DOI: 10.1039/c4lc01479k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications.
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Affiliation(s)
- Mark D Borysiak
- Chemical Engineering Department, University of Washington, Seattle, WA 98195, USA. E-mail:
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31
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Breadmore MC, Tubaon RM, Shallan AI, Phung SC, Abdul Keyon AS, Gstoettenmayr D, Prapatpong P, Alhusban AA, Ranjbar L, See HH, Dawod M, Quirino JP. Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2012-2014). Electrophoresis 2015; 36:36-61. [DOI: 10.1002/elps.201400420] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 09/25/2014] [Accepted: 09/25/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Michael C. Breadmore
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Ria Marni Tubaon
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Aliaa I. Shallan
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Sui Ching Phung
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Aemi S. Abdul Keyon
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
- Faculty of Science; Department of Chemistry, Universiti Teknologi Malaysia; Johor Malaysia
| | - Daniel Gstoettenmayr
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Pornpan Prapatpong
- Faculty of Pharmacy; Department of Pharmaceutical Chemistry, Mahidol University; Rajathevee Bangkok Thailand
| | - Ala A. Alhusban
- Faculty of Health Sciences, School of Pharmacy; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Leila Ranjbar
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
| | - Hong Heng See
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
- Ibnu Sina Institute for Fundamental Science Studies; Universiti Teknologi Malaysia; Johor Malaysia
| | - Mohamed Dawod
- Department of Chemistry; University of Michigan; Ann Arbor MI USA
- Faculty of Pharmacy; Department of Analytical Chemistry, Al-Azhar University; Cairo Egypt
| | - Joselito P. Quirino
- School of Physical Science; Australian Centre of Research on Separation Science, University of Tasmania; Hobart Tasmania Australia
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32
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Electrokinetics for sample preparation of biological molecules in biological samples using microfluidic systems. Bioanalysis 2014; 6:1961-74. [DOI: 10.4155/bio.14.140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sample preparation is the first part of every analytical method, but is often considered only after the optimization of the method. It is traditionally performed using a range of techniques requiring extensive manual handling, with solid-phase extraction, liquid–liquid extraction, protein precipitation and ultracentrfiguation, among others, being used depending on the targets and the application. In this article, we will focus on alternatives based on electrokinetics for applications including sample clean-up, concentration and derivatization of large biological molecules (DNA, peptides and proteins) of diagnostic importance, as well as small molecules as a tool for therapeutic drug monitoring. This article describes these approaches in terms of mechanisms, applicability and potential to be integrated into a lab-on-a-chip device for directly processing biological samples. Examples dealing with treated or clean samples have been excluded except where they show exceptionally high value.
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33
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Baratchi S, Khoshmanesh K, Sacristán C, Depoil D, Wlodkowic D, McIntyre P, Mitchell A. Immunology on chip: Promises and opportunities. Biotechnol Adv 2014; 32:333-46. [DOI: 10.1016/j.biotechadv.2013.11.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 11/04/2013] [Accepted: 11/17/2013] [Indexed: 01/09/2023]
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34
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Purification of nucleic acids using isotachophoresis. J Chromatogr A 2014; 1335:105-20. [DOI: 10.1016/j.chroma.2013.12.027] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/04/2013] [Accepted: 12/07/2013] [Indexed: 12/30/2022]
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35
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Shintaku H, Nishikii H, Marshall LA, Kotera H, Santiago JG. On-Chip Separation and Analysis of RNA and DNA from Single Cells. Anal Chem 2014; 86:1953-7. [DOI: 10.1021/ac4040218] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hirofumi Shintaku
- Department
of Micro Engineering, Kyoto University, Kyoto 606-8501, Japan
| | | | | | - Hidetoshi Kotera
- Department
of Micro Engineering, Kyoto University, Kyoto 606-8501, Japan
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36
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Marshall LA, Rogacs A, Meinhart CD, Santiago JG. An injection molded microchip for nucleic acid purification from 25 microliter samples using isotachophoresis. J Chromatogr A 2014; 1331:139-42. [PMID: 24485540 DOI: 10.1016/j.chroma.2014.01.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/07/2014] [Accepted: 01/10/2014] [Indexed: 11/24/2022]
Abstract
We present a novel microchip device for purification of nucleic acids from 25μL biological samples using isotachophoresis (ITP). The device design incorporates a custom capillary barrier structure to facilitate robust sample loading. The chip uses a 2mm channel width and 0.15mm depth to reduce processing time, mitigate Joule heating, and achieve high extraction efficiency. To reduce pH changes in the device due to electrolysis, we incorporated a buffering reservoir physically separated from the sample output reservoir. To reduce dispersion of the ITP-focused zone, we used optimized turn geometries. The chip was fabricated by injection molding PMMA and COC plastics through a commercial microfluidic foundry. The extraction efficiency of nucleic acids from the device was measured using fluorescent quantification, and an average recovery efficiency of 81% was achieved for nucleic acid masses between 250pg and 250ng. The devices were also used to purify DNA from whole blood, and the extracted DNA was amplified using qPCR to show the PCR compatibility of the purified sample.
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Affiliation(s)
- L A Marshall
- Department of Chemical Engineering, Stanford University, USA
| | - A Rogacs
- Department of Mechanical Engineering, Stanford University, USA
| | - C D Meinhart
- Department of Mechanical Engineering, UC Santa Barbara, USA
| | - J G Santiago
- Department of Mechanical Engineering, Stanford University, USA.
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37
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Smejkal P, Bottenus D, Breadmore MC, Guijt RM, Ivory CF, Foret F, Macka M. Microfluidic isotachophoresis: A review. Electrophoresis 2013; 34:1493-509. [DOI: 10.1002/elps.201300021] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Petr Smejkal
- ACROSS and School of Chemistry; University of Tasmania; Hobart; Australia
| | - Danny Bottenus
- Voiland School of Chemical Engineering and Bioengineering; Washington State University; Pullman; WA; USA
| | | | - Rosanne M. Guijt
- ACROSS and School of Pharmacy; University of Tasmania; Hobart; Australia
| | - Cornelius F. Ivory
- Voiland School of Chemical Engineering and Bioengineering; Washington State University; Pullman; WA; USA
| | - František Foret
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v.v.i., Brno; Czech Republic
| | - Mirek Macka
- ACROSS and School of Chemistry; University of Tasmania; Hobart; Australia
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Mikuš P, Veizerová L, Piešťanský J, Maráková K, Havránek E. On-line coupled capillary isotachophoresis-capillary zone electrophoresis in hydrodynamically closed separation system hyphenated with laser induced fluorescence detection. Electrophoresis 2013; 34:1223-31. [DOI: 10.1002/elps.201200556] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/05/2012] [Accepted: 12/05/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Peter Mikuš
- Department of Pharmaceutical Analysis and Nuclear Pharmacy; Faculty of Pharmacy, Comenius University; Odbojárov; Bratislava; Slovak Republic
| | - Lucia Veizerová
- Department of Pharmaceutical Analysis and Nuclear Pharmacy; Faculty of Pharmacy, Comenius University; Odbojárov; Bratislava; Slovak Republic
| | - Juraj Piešťanský
- Department of Pharmaceutical Analysis and Nuclear Pharmacy; Faculty of Pharmacy, Comenius University; Odbojárov; Bratislava; Slovak Republic
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy; Faculty of Pharmacy, Comenius University; Odbojárov; Bratislava; Slovak Republic
| | - Emil Havránek
- Department of Pharmaceutical Analysis and Nuclear Pharmacy; Faculty of Pharmacy, Comenius University; Odbojárov; Bratislava; Slovak Republic
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