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Chang YW, Lin JP, Ling SJ, Chen YC, Liu HM, Lu YW. Pipette-operable microfluidic devices with hydrophobic valves in sequential dispensing with various liquid samples: multiplex disease assay by RT-LAMP. LAB ON A CHIP 2024; 24:3112-3124. [PMID: 38758131 DOI: 10.1039/d4lc00209a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Microfluidic dispensing technologies often require additional equipment, posing challenges for their integration into point-of-care testing (POCT) applications. In response to this challenge, we have developed a pipette-operable microfluidic device fabricated using 3D printing technology for precise liquid dispensing. This device features three reaction chambers and three distinct hydrophobic valves to control the flow direction of liquids. Through these valves, the pipette-operable microfluidic device can sequentially dispense and isolate the liquid into the three reaction chambers, allowing for the individual conduction of three distinct reactions. These hydrophobic valves, with optimized flow resistance and burst pressure, can sustain a volumetric flow rate of up to 25 μL s-1, making them compatible with a standard pipette, a syringe, or a dropper operation. Furthermore, the device is successfully used to operate with various liquids, including BSA, DMEM, FBS, plasma, and blood, representing that the device has the potential to be used for various applications. Additionally, distinct RT-LAMP primer sets have been incorporated for diagnosing SARS-CoV-2, influenza A, and influenza B within each chamber through lyophilization. This pipette-operable microfluidic device serves as a versatile tool for diagnosing these three diseases using a single loading process, with results readable by the naked eye or image assay within 30 minutes of incubation. Finally, the design concepts are extended to engineer a microfluidic device with 20 reaction chambers, offering significant potential for multi-disease diagnostics.
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Affiliation(s)
- Yen-Wei Chang
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan, R.O.C.
| | - Jhih-Pu Lin
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan, R.O.C
| | - Shiu-Jie Ling
- Department of Clinical Laboratory Science and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, R.O.C
| | - Yen-Chun Chen
- Department of Clinical Laboratory Science and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan, R.O.C
| | - Helene Minyi Liu
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan, R.O.C
| | - Yen-Wen Lu
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan, R.O.C.
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan, R.O.C
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2
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Sial MU, Farooq T, Khalaf LK, Rahman S, Asad M, Ahamad Paray B. Two-step method for rapid isolation of genomic DNA and validation of R81T insecticide resistance mutation in Myzus persicae. Saudi J Biol Sci 2023; 30:103791. [PMID: 37711971 PMCID: PMC10497781 DOI: 10.1016/j.sjbs.2023.103791] [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: 06/12/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023] Open
Abstract
Isolation and amplification of nucleic acid (DNA) is considered a vital and potent instrument in molecular biological research. However, its functioning outside of a laboratory setting is difficult because of complex procedures that demand expert personnel and expensive equipment in addition to the fulfillment of several additional requirements. DNA isolation from minute insects is sometimes difficult, making diagnostic and genotyping procedures problematic. Thus, the current work offers a high-throughput, cost-effective, straightforward, and faster approach for isolating DNA from the aphid Myzus persicae. Intriguingly, two-step DNA extraction process yielded a high yield of extremely pure genomic DNA and required only 10 s to complete. PCR investigation aiming at amplifying the non-synonymous R81T region on the loop D site of the nAChR gene of M. persicae was subsequently utilized to successfully validate the recovered DNA. Moreover, the proposed method was compared in terms of yield and purity with conventionally used DNA isolation methods including, phenol:chloroform, salt out, and commercially available kits. In conclusion, this newly developed method would enable researchers to quickly process many biological samples used to analyze genetic diversity, mutant screening, and large spectrum diagnosis both in laboratory and field conditions.
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Affiliation(s)
- Muhammad Umair Sial
- Department of Entomology, University of Agriculture, Faisalabad 38000, Pakistan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Tahir Farooq
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Luaay Kahtan Khalaf
- Department of Plant Protection, College of Agricultural Engineering Science, University of Baghdad, Baghdad, Iraq
| | - Saqib Rahman
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Bilal Ahamad Paray
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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3
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Liu W, Lee LP. Toward Rapid and Accurate Molecular Diagnostics at Home. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206525. [PMID: 36416278 DOI: 10.1002/adma.202206525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Indexed: 05/26/2023]
Abstract
The global outbreaks of infectious diseases have significantly driven an imperative demand for rapid and accurate molecular diagnostics. Nucleic acid amplification tests (NAATs) feature high sensitivity and high specificity; however, the labor-intensive sample preparation and nucleic acid amplification steps remain challenging in order to carry out rapid and precision molecular diagnostics at home. This review discusses the advances and challenges of automatic solutions of sample preparation integrated with on-chip nucleic acid amplification for effective and accurate molecular diagnostics at home. The sample preparation methods of whole blood, urine, saliva/nasal swab, and stool on chip are examined. Then, the repurposable integrated sample preparation on a chip using various biological samples is investigated. Finally, the on-chip NAATs that can be integrated with automated sample preparation are evaluated. The user-friendly approaches with combined sample preparation and NAATs can be the game changers for next-generation rapid and precision home diagnostics.
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Affiliation(s)
- Wenpeng Liu
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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4
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Myers FB, Moffatt B, El Khaja R, Chatterjee T, Marwaha G, McGee M, Mitra D. A robust, low-cost instrument for real-time colorimetric isothermal nucleic acid amplification. PLoS One 2022; 17:e0256789. [PMID: 36178899 PMCID: PMC9524685 DOI: 10.1371/journal.pone.0256789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/19/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic has highlighted the need for broader access to molecular diagnostics. Colorimetric isothermal nucleic acid amplification assays enable simplified instrumentation over more conventional PCR diagnostic assays and, as such, represent a promising approach for addressing this need. In particular, colorimetric LAMP (loop-mediated isothermal amplification) has received a great deal of interest recently. However, there do not currently exist robust instruments for performing these kinds of assays in high throughput with real-time readout of amplification signals. To address this need, we developed LARI, the LAMP Assay Reader Instrument. We have deployed over 50 LARIs for routine use in R&D and production environments, with over 12,000 assays run to date. In this paper, we present the design and construction of LARI along with thermal, optical, and assay performance characteristics. LARI can be produced for under $1500 and has broad applications in R&D, point-of-care diagnostics, and global health.
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Affiliation(s)
- Frank B. Myers
- Research & Development, Lucira Health, Inc., Emeryville, CA, United States of America
- * E-mail:
| | - Brian Moffatt
- Manufacturing Engineering, Lucira Health, Inc., Emeryville, CA, United States of America
| | - Ragheb El Khaja
- Research & Development, Lucira Health, Inc., Emeryville, CA, United States of America
| | - Titatsh Chatterjee
- Research & Development, Lucira Health, Inc., Emeryville, CA, United States of America
| | - Gurmeet Marwaha
- Quality Control, Lucira Health Inc., Emeryville, CA, United States of America
| | - Max McGee
- Research & Development, Lucira Health, Inc., Emeryville, CA, United States of America
| | - Debkishore Mitra
- Research & Development, Lucira Health, Inc., Emeryville, CA, United States of America
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Liu T, Choi G, Tang Z, Kshirsagar A, Politza AJ, Guan W. Fingerpick Blood-Based Nucleic Acid Testing on A USB Interfaced Device towards HIV self-testing. Biosens Bioelectron 2022; 209:114255. [PMID: 35429770 PMCID: PMC9110109 DOI: 10.1016/j.bios.2022.114255] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/25/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
HIV self-testing is an emerging innovative approach that allows individuals who want to know their HIV status to collect their own specimen, perform a test, and interpret the results privately. Existing HIV self-testing methods rely on rapid diagnostic tests (RDTs) to detect the presence of HIV-1/2 antibodies, which could miss a significant portion of asymptomatic carriers during the window period. In this work, we present a fully integrated nucleic acid testing (NAT) device towards streamlined HIV self-testing using 100 μL finger-prick whole blood. The device consists of a ready-to-use microfluidic reagent cartridge and an ultra-compact NAT-on-USB analyzer. The test requires simple steps from the user to drop the finger-prick blood sample into a collection tube with lysis buffer and load the lysate onto the microfluidic cartridge, and the testing result can be easily read out by a custom-built graphical user interface (GUI). The microfluidic cartridge and the analyzer automatically handle the complexity of sample preparation, purification, and real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP). With a turnaround time of ∼60 min, we achieved a limit of detection (LoD) of 214 viral RNA copies/mL of whole blood at a 95% confidence level. Due to its ease of use and high sensitivity, we anticipate the HIV NAT-on-USB device would be particularly useful for the high-risk populations seeking private self-testing at the early stages of exposure.
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Niu M, Han Y, Dong X, Yang L, Li F, Zhang Y, Hu Q, Xia X, Li H, Sun Y. Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a. Front Bioeng Biotechnol 2022; 10:831332. [PMID: 35497364 PMCID: PMC9039052 DOI: 10.3389/fbioe.2022.831332] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
As SARS-CoV-2 variants continue to evolve, identifying variants with adaptive diagnostic tool is critical to containing the ongoing COVID-19 pandemic. Herein, we establish a highly sensitive and portable on-site detection method for the HV69-70del which exist in SARS-CoV-2 Alpha and Omicron variants using a PCR-based CRISPR/Cas13a detection system (PCR-CRISPR). The specific crRNA (CRISPR RNA) targeting the HV69-70del is screened using the fluorescence-based CRISPR assay, and the sensitivity and specificity of this method are evaluated using diluted nucleic acids of SARS-CoV-2 variants and other pathogens. The results show that the PCR-CRISPR detection method can detect 1 copies/μL SARS-CoV-2 HV69-70del mutant RNA and identify 0.1% of mutant RNA in mixed samples, which is more sensitive than the RT-qPCR based commercial SARS-CoV-2 variants detection kits and sanger sequencing. And it has no cross reactivity with ten other pathogens nucleic acids. Additionally, by combined with our previously developed ERASE (Easy-Readout and Sensitive Enhanced) lateral flow strip suitable for CRISPR detection, we provide a novel diagnosis tool to identify SARS-CoV-2 variants in primary and resource-limited medical institutions without professional and expensive fluorescent detector.
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Affiliation(s)
- Mengwei Niu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yao Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xue Dong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lan Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fan Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Youcui Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qiang Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yansong Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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7
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Chen H, Lin S, Wang Y, Fu S, Ma Y, Xia Q, Lin Y. Paper-based detection of Epstein-Barr virus using asymmetric polymerase chain reaction and gold silicon particles. Anal Chim Acta 2022; 1197:339514. [DOI: 10.1016/j.aca.2022.339514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/27/2022]
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8
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Choi G, Guan W. An Ultracompact Real-Time Fluorescence Loop-Mediated Isothermal Amplification (LAMP) Analyzer. Methods Mol Biol 2022; 2393:257-278. [PMID: 34837184 PMCID: PMC9191622 DOI: 10.1007/978-1-0716-1803-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Low-cost access to the highly sensitive and specific detection of the pathogen in the field is a crucial attribute for the next generation point-of-care (POC) platforms. In this work, we developed a real-time fluorescence nucleic acid testing device with automated and scalable sample preparation capability for field malaria diagnosis. The palm-sized battery-powered analyzer equipped with a disposable microfluidic reagent compact disc described in the companion Chap. 16 which facilitates four isothermal nucleic acid tests in parallel from raw blood samples to answer. The platform has a user-friendly interface such as touchscreen LCD and smartphone data connectivity for on-site and remote healthcare delivery, respectively. The chapter mainly focuses on describing integration procedures of the real-time fluorescence LAMP analyzer and the validation of its subsystems. The device cost is significantly reduced compared to the commercial benchtop real-time machine and other existing POC platforms. As a platform technology, self-sustainable, portable, low-cost, and easy-to-use analyzer design should create a new paradigm of molecular diagnosis toward a variety of infectious diseases at the point of need.
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Affiliation(s)
- Gihoon Choi
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, USA.
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA.
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9
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Liu W, Yue F, Lee LP. Integrated Point-of-Care Molecular Diagnostic Devices for Infectious Diseases. Acc Chem Res 2021; 54:4107-4119. [PMID: 34699183 DOI: 10.1021/acs.accounts.1c00385] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The global outbreaks of deadly infectious diseases caused by pathogenic microorganisms have threatened public health worldwide and significantly motivated scientists to satisfy an urgent need for a rapid and accurate detection of pathogens. Traditionally, the culture-based technique is considered as the gold standard for pathogen detection, yet it has a long turnaround time due to the overnight culturing and pathogen isolation. Alternatively, nucleic acid amplification tests provide a relatively shorter turnaround time to identify whether pathogens exist in individuals with high sensitivity and high specificity. In most cases, nucleic acid amplification tests undergo three steps: sample preparation, nucleic acid amplification, and signal transduction. Despite the explosive advancement in nucleic acid amplification and signal transduction technologies, the complex and labor-intensive sample preparation steps remain a bottleneck to create a transformative integrated point-of-care (POC) molecular diagnostic device. Researchers have attempted to simplify and integrate the sample preparations for nucleic acid-based molecular diagnostic devices with innovative progress in integration strategies, engineered materials, reagent storages, and fluid actuation. Therefore, understanding the know-how and obtaining truthful knowledge of existing integrated POC molecular diagnostic devices comprising sample preparations, nucleic acid amplification, and signal transduction can generate innovative solutions to achieve personalized precision medicine and improve global health.In this Account, we discuss the challenges of automated sample preparation solutions integrated with nucleic acid amplification and signal transduction for rapid and precise home diagnostics. Blood, nasal swab, saliva, urine, and stool are emphasized as the most commonly used clinical samples for integrated POC molecular diagnostics of infectious diseases. Even though these five types of samples possess relatively correlated biomarkers due to the human body's circulatory system, each shows unique properties and exclusive advantages for molecular diagnostics in specific situations, which are included in this Account. We examine different integrated POC devices for sample preparation, which includes pathogen isolation and enrichment from the crude sample and nucleic acid purification from isolated pathogens. We present the promising on-chip integration approaches for nucleic acid amplification. We also investigate the on-chip integration methods for reagent storage, which is crucial to simplify the manual operation for end-users. Finally, we present several integrated POC molecular diagnostic devices for infectious diseases. The integrated sample preparation and nucleic acid amplification approach reviewed here can potentially impact the next generation of POC molecular home diagnostic chips, which will significantly impact public health, emergency medicine, and global biosecurity.
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Affiliation(s)
- Wenpeng Liu
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Fei Yue
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Luke P Lee
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley 94720, California, United States
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
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10
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Sharma A, Tok AIY, Alagappan P, Liedberg B. Point of care testing of sports biomarkers: Potential applications, recent advances and future outlook. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116327] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Advances in Continuous Microfluidics-Based Technologies for the Study of HIV Infection. Viruses 2020; 12:v12090982. [PMID: 32899657 PMCID: PMC7552050 DOI: 10.3390/v12090982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 12/31/2022] Open
Abstract
HIV-1 is the causative agent of acquired immunodeficiency syndrome (AIDS). It affects millions of people worldwide and the pandemic persists despite the implementation of highly active antiretroviral therapy. A wide spectrum of techniques has been implemented in order to diagnose and monitor AIDS progression over the years. Besides the conventional approaches, microfluidics has provided useful methods for monitoring HIV-1 infection. In this review, we introduce continuous microfluidics as well as the fabrication and handling of microfluidic chips. We provide a review of the different applications of continuous microfluidics in AIDS diagnosis and progression and in the basic study of the HIV-1 life cycle.
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12
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Maia Chagas A, Molloy JC, Prieto-Godino LL, Baden T. Leveraging open hardware to alleviate the burden of COVID-19 on global health systems. PLoS Biol 2020; 18:e3000730. [PMID: 32330124 PMCID: PMC7182255 DOI: 10.1371/journal.pbio.3000730] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment. Shortcomings are evident across the board, from staffing, facilities for rapid and reliable testing to availability of hospital beds and key medical-grade equipment. The scale and breadth of the problem calls for an equally substantive response not only from frontline workers such as medical staff and scientists, but from skilled members of the public who have the time, facilities and knowledge to meaningfully contribute to a consolidated global response. Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics.
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Affiliation(s)
- Andre Maia Chagas
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- TReND in Africa, Brighton, United Kingdom
- Gathering for Open Science Hardware
| | - Jennifer C. Molloy
- Gathering for Open Science Hardware
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Lucia L. Prieto-Godino
- TReND in Africa, Brighton, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- FENS-KAVLI Network of Excellence
| | - Tom Baden
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- TReND in Africa, Brighton, United Kingdom
- FENS-KAVLI Network of Excellence
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
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13
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Zhong R, Liu S, Zhang G, Wang M, Sun Y. iso-μmGene: an isothermal amplification-based portable microfluidic system for simple, reliable and flexibly multiplexed genetic identification and quantification. Analyst 2020; 145:4627-4636. [DOI: 10.1039/d0an00560f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a portable microfluidic LAMP system (iso-μmGene) with features of multi-well chips for convenient filling and reliable sealing, flexible detection throughput, and stand-alone and well-performing point of care device for genetic testing.
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Affiliation(s)
- Runtao Zhong
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Shilin Liu
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Guohao Zhang
- Beijing Baicare Biotechnology Co
- Ltd
- Beijing 102206
- China
| | - Mengyu Wang
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Yeqing Sun
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
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14
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Mason MG, Blackall PJ, Botella JR, Templeton JM. An easy-to-perform, culture-free Campylobacter point-of-management assay for processing plant applications. J Appl Microbiol 2019; 128:620-629. [PMID: 31705613 PMCID: PMC7027919 DOI: 10.1111/jam.14509] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/22/2019] [Accepted: 11/07/2019] [Indexed: 12/16/2022]
Abstract
Aims Current culture‐based methods for detection and determination of Campylobacter levels on processed chickens takes at least 2 days. Here we sought to develop a new complete, low‐cost and rapid (approximately 2·5 h) detection system requiring minimal operator input. Methods and Results We observed a strong correlation between culture‐based cell counts and our ability to detect either Campylobacter jejuni or Campylobacter coli by loop‐mediated isothermal amplification from the same samples. This knowledge was used to develop a rapid and simple five‐step assay to quantify Campylobacter, which was subsequently assessed for its specificity, reproducibility and accuracy in quantifying Campylobacter levels from processed chickens. The assay was found to be highly specific for C. jejuni and C. coli and was capable of distinguishing between samples that are either within or exceeding the industry set target of 6000 Campylobacter colony forming units (CFU) per carcass (equivalent to 12 CFU per ml of chicken rinse) with >90% accuracy relative to culture‐based methods. Conclusions Our method can reliably quantify Campylobacter counts of processed chickens with an accuracy comparable to culture‐based assays but provides results within hours as opposed to days. Significance and Impact of the Study The research presented here will help improve food safety by providing fast Campylobacter detection that will enable the implementation of real‐time risk management strategies in poultry processing plants to rapidly test processed chickens and identify effective intervention strategies. This technology is a powerful tool that can be easily adapted for other organisms and thus could be highly beneficial for a broad range of industries.
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Affiliation(s)
- M G Mason
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Qld, Australia
| | - P J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Qld, Australia
| | - J R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Qld, Australia
| | - J M Templeton
- Animal Science, Department of Agriculture and Fisheries, EcoSciences Precinct, Dutton Park, Qld, Australia
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15
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Chen Z, Huang J, Zhang F, Zhou Y, Huang H. Detection of shrimp hemocyte iridescent virus by recombinase polymerase amplification assay. Mol Cell Probes 2019; 49:101475. [PMID: 31655105 DOI: 10.1016/j.mcp.2019.101475] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Shrimp hemocyte iridescent virus (SHIV), which was first identified in white leg shrimp (Litopenaeus vannamei) in China in 2014, can cause extensive shrimp mortality and major economic losses in the shrimp farming industry in China. In this study, a novel real-time isothermal recombinase polymerase amplification (RPA) assay was developed using a TwistAmp exo kit for SHIV detection. First, five primers and a probe were designed for the major capsid protein gene (GenBank: KY681039.1) according to the TwistDx manual; next, the optimal primers were selected by a comparison experiment. The primers and probe were specific for SHIV and did not react with shrimp white spot syndrome virus (WSSV), shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV), shrimp enterocytozoon hepatopenaei (EHP), and macrobrachium rosenbergii nodavirus (MrNV) samples, as well as pathogens of acute hepatopancreatic necrosis disease (AHPND). The RPA assay reached a detection limit of 11 copies per reaction according to probit regression analysis. In addition, RPA assay detected the positive plasmid samples at concentration of 1000 copies/μL within 16.04 ± 0.72 min at a single low operation temperature (39 °C). The results proved that the proposed RPA method was an accurate, sensitive, affordable, and rapid detection tool that can be suitably applied for the diagnosis of SHIV in field conditions and in resource-poor settings.
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Affiliation(s)
- Zhengwei Chen
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China; Center of Engineering Training, Zhejiang University of Science and Technology, Hangzhou, P.R. China.
| | - Jun Huang
- College of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Fang Zhang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China.
| | - Yang Zhou
- College of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Huijie Huang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China.
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16
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Kong M, Li Z, Wu J, Hu J, Sheng Y, Wu D, Lin Y, Li M, Wang X, Wang S. A wearable microfluidic device for rapid detection of HIV-1 DNA using recombinase polymerase amplification. Talanta 2019; 205:120155. [PMID: 31450450 DOI: 10.1016/j.talanta.2019.120155] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/07/2019] [Accepted: 07/13/2019] [Indexed: 12/26/2022]
Abstract
Although isothermal nucleic acid amplification is advantageous in pathogen detection in resource-limited settings, an electricity-dependent heating module is often required. Here, we developed a wearable microfluidic device combined with recombinase polymerase amplification (RPA) for simple and rapid amplification of HIV-1 DNA using human body heat. The human body temperature at the human wrist varied from 33 to 34 °C in the ambient environment, which is sufficient to perform RPA reactions. With the aid of a cellphone-based fluorescence detection system, this device detected HIV-1 DNA quantitatively ranging from 102 to 105 copies/mL with a log linearity of 0.98 in 24 min. These results demonstrate that this wearable point-of-care (POC) nucleic acid testing method is advantageous over traditional PCR and other isothermal nucleic acid amplification methods in terms of time, portability and independence on electricity. This wearable microfluidic device in conjunction with a cellphone-based fluorescence detection system can be potentially used for the detection of HIV-1 and adapted for POC detection of a broad range of infectious pathogens in resource-limited settings.
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Affiliation(s)
- Mengqi Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, 310003, China; Institute for Translational Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310029, China
| | - Zihan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, 310003, China; Institute for Translational Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310029, China
| | - Jianguo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, 310003, China; Institute for Translational Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310029, China
| | - Jie Hu
- Biomedical Institute for Global Health Research and Technology (BIGHEART), National University of Singapore (NUS), 117599, Singapore
| | - Yefeng Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, 310003, China; Institute for Translational Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310029, China
| | - Di Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, 310003, China; Institute for Translational Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310029, China
| | - Yong Lin
- College of Science, Ningbo University of Technology, Ningbo, China
| | - Ming Li
- State Key Laboratory of CAD &CG, Zhejiang University, Hangzhou, China
| | - Xiaozhi Wang
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, Zhejiang Province, 310029, China
| | - ShuQi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, 310003, China; Institute for Translational Medicine, Zhejiang University, Hangzhou, Zhejiang Province, 310029, China.
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17
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Pardy T, Sink H, Koel A, Rang T. Development of a Low-Cost, Wireless Smart Thermostat for Isothermal DNA Amplification in Lab-On-A-Chip Devices. MICROMACHINES 2019; 10:E437. [PMID: 31262090 PMCID: PMC6680506 DOI: 10.3390/mi10070437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 01/16/2023]
Abstract
Nucleic acid amplification tests (NAAT) are widely used for the detection of living organisms, recently applied in Lab-on-a-Chip (LoC) devices to make portable DNA analysis platforms. While portable LoC-NAAT can provide definitive test results on the spot, it requires specialized temperature control equipment. This work focuses on delivering a generalized low-cost, wireless smart thermostat for isothermal NAAT protocols in 2 cm × 3 cm LoC cartridges. We report on the design, prototyping, and evaluation results of our smart thermostat. The thermostat was evaluated by experimental and simulated thermal analysis using 3D printed LoC cartridges, in order to verify its applicability to various isothermal NAAT protocols. Furthermore, it was tested at the boundaries of its operating ambient temperature range as well as its battery life was evaluated. The prototype thermostat was proven functional in 20-30 °C ambient range, capable of maintaining the required reaction temperature of 12 isothermal NAAT protocols with 0.7 °C steady-state error in the worst case.
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Affiliation(s)
- Tamas Pardy
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia.
| | - Henri Sink
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia
| | - Ants Koel
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia
| | - Toomas Rang
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia
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18
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LampPort: a handheld digital microfluidic device for loop-mediated isothermal amplification (LAMP). Biomed Microdevices 2019; 21:9. [DOI: 10.1007/s10544-018-0354-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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19
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Moody L, Mantha S, Chen H, Pan YX. Computational methods to identify bimodal gene expression and facilitate personalized treatment in cancer patients. J Biomed Inform 2019; 100S:100001. [PMID: 34384574 DOI: 10.1016/j.yjbinx.2018.100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 11/03/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
Abstract
Standard methods for detecting cancer-associated genes rely on comparison of sample means between cancer patients and healthy controls. While such methods have successfully identified several oncogenes and tumor suppressor genes, they neglect to account for heterogeneity within the cancer population. Genetic mutations, translocations, and amplifications are often inconsistent across tumors, and instead they often affect smaller subsets of patients. This concept gives rise to the idea of bimodally expressed genes, or genes that display two modes of expression within one population. Analysis of bimodal gene expression has been explored via a variety of techniques including test statistics and clustering. In this review, we summarize the methodologies used to quantify bimodal gene expression and address the utility of these genes in patient stratification and specialized therapeutics in breast and lung cancer. Finally we discuss the limitations and future directions for bimodal genes in the era of high-throughput sequencing and personalized medicine.
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Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| | - Suparna Mantha
- Carle Physician Group, Carle Cancer Center, Carle Foundation Hospital, Urbana, IL 61802, United States.
| | - Hong Chen
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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20
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Chiriacò MS, Bianco M, Nigro A, Primiceri E, Ferrara F, Romano A, Quattrini A, Furlan R, Arima V, Maruccio G. Lab-on-Chip for Exosomes and Microvesicles Detection and Characterization. SENSORS (BASEL, SWITZERLAND) 2018; 18:E3175. [PMID: 30241303 PMCID: PMC6210978 DOI: 10.3390/s18103175] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/05/2018] [Accepted: 09/16/2018] [Indexed: 12/11/2022]
Abstract
Interest in extracellular vesicles and in particular microvesicles and exosomes, which are constitutively produced by cells, is on the rise for their huge potential as biomarkers in a high number of disorders and pathologies as they are considered as carriers of information among cells, as well as being responsible for the spreading of diseases. Current methods of analysis of microvesicles and exosomes do not fulfill the requirements for their in-depth investigation and the complete exploitation of their diagnostic and prognostic value. Lab-on-chip methods have the potential and capabilities to bridge this gap and the technology is mature enough to provide all the necessary steps for a completely automated analysis of extracellular vesicles in body fluids. In this paper we provide an overview of the biological role of extracellular vesicles, standard biochemical methods of analysis and their limits, and a survey of lab-on-chip methods that are able to meet the needs of a deeper exploitation of these biological entities to drive their use in common clinical practice.
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Affiliation(s)
| | - Monica Bianco
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy.
| | - Annamaria Nigro
- Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy.
| | | | - Francesco Ferrara
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy.
- STMicroelectronics, Via Monteroni, I-73100 Lecce, Italy.
| | - Alessandro Romano
- Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Angelo Quattrini
- Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Roberto Furlan
- Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Valentina Arima
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy.
| | - Giuseppe Maruccio
- CNR NANOTEC Institute of Nanotechnology, via Monteroni, 73100 Lecce, Italy.
- Department of Mathematics and Physics, University of Salento, via Monteroni, 73100 Lecce, Italy.
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21
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Yu T, Wei Q. Plasmonic molecular assays: Recent advances and applications for mobile health. NANO RESEARCH 2018; 11:5439-5473. [PMID: 32218913 PMCID: PMC7091255 DOI: 10.1007/s12274-018-2094-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 05/15/2023]
Abstract
Plasmonics-based biosensing assays have been extensively employed for biomedical applications. Significant advancements in use of plasmonic assays for the construction of point-of-care (POC) diagnostic methods have been made to provide effective and urgent health care of patients, especially in resourcelimited settings. This rapidly progressive research area, centered on the unique surface plasmon resonance (SPR) properties of metallic nanostructures with exceptional absorption and scattering abilities, has greatly facilitated the development of cost-effective, sensitive, and rapid strategies for disease diagnostics and improving patient healthcare in both developed and developing worlds. This review highlights the recent advances and applications of plasmonic technologies for highly sensitive protein and nucleic acid biomarker detection. In particular, we focus on the implementation and penetration of various plasmonic technologies in conventional molecular diagnostic assays, and discuss how such modification has resulted in simpler, faster, and more sensitive alternatives that are suited for point-of-use. Finally, integration of plasmonic molecular assays with various portable POC platforms for mobile health applications are highlighted.
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Affiliation(s)
- Tao Yu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Campus Box 7905, Raleigh, NC 27695 USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Campus Box 7905, Raleigh, NC 27695 USA
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22
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Satoh T, Kouroki S, Ogawa K, Tanaka Y, Matsumura K, Iwase S. Development of mRNA-based body fluid identification using reverse transcription loop-mediated isothermal amplification. Anal Bioanal Chem 2018; 410:4371-4378. [PMID: 29696299 DOI: 10.1007/s00216-018-1088-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 11/24/2022]
Abstract
Identifying body fluids from forensic samples can provide valuable evidence for criminal investigations. Messenger RNA (mRNA)-based body fluid identification was recently developed, and highly sensitive parallel identification using reverse transcription polymerase chain reaction (RT-PCR) has been described. In this study, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a simple, rapid assay for identifying three common forensic body fluids, namely blood, semen, and saliva, and evaluated its specificity and sensitivity. Hemoglobin beta (HBB), transglutaminase 4 (TGM4), and statherin (STATH) were selected as marker genes for blood, semen, and saliva, respectively. RT-LAMP could be performed in a single step including both reverse transcription and DNA amplification under an isothermal condition within 60 min, and detection could be conveniently performed via visual fluorescence. Marker-specific amplification was performed in each assay, and no cross-reaction was observed among five representative forensically relevant body fluids. The detection limits of the assays were 0.3 nL, 30 nL, and 0.3 μL for blood, semen, and saliva, respectively, and their sensitivities were comparable with those of RT-PCR. Furthermore, RT-LAMP assays were applicable to forensic casework samples. It is considered that RT-LAMP is useful for body fluid identification.
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Affiliation(s)
- Tetsuya Satoh
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan.
| | - Seiya Kouroki
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Keita Ogawa
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Yorika Tanaka
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Kazutoshi Matsumura
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Susumu Iwase
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
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23
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Mauk MG, Song J, Liu C, Bau HH. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests. BIOSENSORS 2018; 8:E17. [PMID: 29495424 PMCID: PMC5872065 DOI: 10.3390/bios8010017] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 01/10/2023]
Abstract
Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges ('chips') that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.
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Affiliation(s)
- Michael G Mauk
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Jinzhao Song
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Changchun Liu
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Haim H Bau
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
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24
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Zou Y, Mason MG, Wang Y, Wee E, Turni C, Blackall PJ, Trau M, Botella JR. Nucleic acid purification from plants, animals and microbes in under 30 seconds. PLoS Biol 2017; 15:e2003916. [PMID: 29161268 PMCID: PMC5697807 DOI: 10.1371/journal.pbio.2003916] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022] Open
Abstract
Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries.
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Affiliation(s)
- Yiping Zou
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
| | - Michael Glenn Mason
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
| | - Yuling Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Eugene Wee
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, Australia
| | - Patrick J. Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Jose Ramon Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
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25
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de Oliveira KG, Borba JC, Bailão AM, de Almeida Soares CM, Carrilho E, Duarte GRM. Loop-mediated isothermal amplification in disposable polyester-toner microdevices. Anal Biochem 2017; 534:70-77. [DOI: 10.1016/j.ab.2017.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 10/19/2022]
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26
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McArdle H, Jimenez-Mateos EM, Raoof R, Carthy E, Boyle D, ElNaggar H, Delanty N, Hamer H, Dogan M, Huchtemann T, Kӧrtvelyessy P, Rosenow F, Forster RJ, Henshall DC, Spain E. "TORNADO" - Theranostic One-Step RNA Detector; microfluidic disc for the direct detection of microRNA-134 in plasma and cerebrospinal fluid. Sci Rep 2017; 7:1750. [PMID: 28496112 PMCID: PMC5431952 DOI: 10.1038/s41598-017-01947-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/05/2017] [Indexed: 11/25/2022] Open
Abstract
Diagnosis of seizure disorders such as epilepsy currently relies on clinical examination and electroencephalogram recordings and is associated with substantial mis-diagnosis. The miRNA, miR-134 (MIR134 in humans), has been found to be elevated in brain tissue after experimental status epilepticus and in human epilepsy cells and their detection in biofluids may serve as unique biomarkers. miRNAs from unprocessed human plasma and human cerebrospinal fluid samples were used in a novel electrochemical detection based on electrocatalytic platinum nanoparticles inside a centrifugal microfluidic device where the sandwich assay is formed using an event triggered release system, suitable for the rapid point-of-care detection of low abundance biomarkers of disease. The device has the advantage of controlling the rotation speed of the centrifugal device to pump nanoliter volumes of fluid at a set time and manipulate the transfer of liquids within the device. The centrifugal platform improves reaction rates and yields by proposing efficient mixing strategies to overcome diffusion-limited processes and improve mass transport rates, resulting in reduced hybridization times with a limit of detection of 1 pM target concentration. Plasma and cerebrospinal fluid samples (unprocessed) from patients with epilepsy or who experienced status epilepticus were tested and the catalytic response obtained was in range of the calibration plot. This study demonstrates a rapid and simple detection for epilepsy biomarkers in biofluid.
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Affiliation(s)
- Hazel McArdle
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Eva M Jimenez-Mateos
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Rana Raoof
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Eadaoin Carthy
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - David Boyle
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Hany ElNaggar
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Neurological Services, Beaumont Hospital, Dublin 9, Ireland
| | - Norman Delanty
- Neurological Services, Beaumont Hospital, Dublin 9, Ireland
| | - Hajo Hamer
- University Hospital Erlangen, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Muejgdan Dogan
- University Hospital Erlangen, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Tessa Huchtemann
- Department of Neurology, University hospital Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany
| | - Peter Kӧrtvelyessy
- Department of Neurology, University hospital Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany
| | - Felix Rosenow
- Epilepsy Center Hessen, Department of Neurology, Baldingerstr, 35043, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, Goethe-University, Schleusenweg 2-16, Haus 95, 60528, Frankfurt a.M., Germany
| | - Robert J Forster
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Elaine Spain
- School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland.
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27
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An integrated versatile lab-on-a-chip platform for the isolation and nucleic acid-based detection of pathogens. Future Sci OA 2017; 3:FSO177. [PMID: 28670469 PMCID: PMC5481810 DOI: 10.4155/fsoa-2016-0088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/18/2017] [Indexed: 11/29/2022] Open
Abstract
Aim: Processing of the samples in molecular diagnostics is complex and labor-intensive. An integrated and automated platform for sample preparation and nucleic acid-based detection can significantly relieve this burden for the users. Results: We present a prototype of a versatile and integrated platform for the detection of pathogens in various liquid media. We describe a proof-of-concept for the integrated isolation of bacteria, cell lysis with optional DNA extraction, DNA amplification and detection in two different reactions, loop-mediated isothermal amplification and PCR, on a single microfluidic platform. Conclusion: The platform enables the transition from large sample volume to microfluidic format. The design and open interface enable its versatile application for various nucleic acid-based assays, from simple to complex setups. DNA-based detection of the pathogens in liquid samples demands many complex steps, various pieces of equipment, and experienced personnel. We developed and demonstrated a platform that can perform these steps automatically on a single instrument. This can enable molecular diagnostics in the places and situations where it was not possible before.
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28
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Nanayakkara IA, Cao W, White IM. Simplifying Nucleic Acid Amplification from Whole Blood with Direct Polymerase Chain Reaction on Chitosan Microparticles. Anal Chem 2017; 89:3773-3779. [DOI: 10.1021/acs.analchem.7b00274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Imaly A. Nanayakkara
- Fischell
Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Weidong Cao
- Canon U.S. Life Sciences, Inc., Rockville, Maryland 20850, United States
| | - Ian M. White
- Fischell
Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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29
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Yeh EC, Fu CC, Hu L, Thakur R, Feng J, Lee LP. Self-powered integrated microfluidic point-of-care low-cost enabling (SIMPLE) chip. SCIENCE ADVANCES 2017; 3:e1501645. [PMID: 28345028 PMCID: PMC5362183 DOI: 10.1126/sciadv.1501645] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/09/2017] [Indexed: 05/07/2023]
Abstract
Portable, low-cost, and quantitative nucleic acid detection is desirable for point-of-care diagnostics; however, current polymerase chain reaction testing often requires time-consuming multiple steps and costly equipment. We report an integrated microfluidic diagnostic device capable of on-site quantitative nucleic acid detection directly from the blood without separate sample preparation steps. First, we prepatterned the amplification initiator [magnesium acetate (MgOAc)] on the chip to enable digital nucleic acid amplification. Second, a simplified sample preparation step is demonstrated, where the plasma is separated autonomously into 224 microwells (100 nl per well) without any hemolysis. Furthermore, self-powered microfluidic pumping without any external pumps, controllers, or power sources is accomplished by an integrated vacuum battery on the chip. This simple chip allows rapid quantitative digital nucleic acid detection directly from human blood samples (10 to 105 copies of methicillin-resistant Staphylococcus aureus DNA per microliter, ~30 min, via isothermal recombinase polymerase amplification). These autonomous, portable, lab-on-chip technologies provide promising foundations for future low-cost molecular diagnostic assays.
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Affiliation(s)
- Erh-Chia Yeh
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chi-Cheng Fu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lucy Hu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rohan Thakur
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeffrey Feng
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Luke P. Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA
- Corresponding author.
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30
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Ying N, Ju C, Li Z, Liu W, Wan J. Visual detection of nucleic acids based on lateral flow biosensor and hybridization chain reaction amplification. Talanta 2017; 164:432-438. [DOI: 10.1016/j.talanta.2016.10.098] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/27/2016] [Accepted: 10/29/2016] [Indexed: 12/21/2022]
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31
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Nicolini AM, McCracken KE, Yoon JY. Future developments in biosensors for field-ready Zika virus diagnostics. J Biol Eng 2017; 11:7. [PMID: 28127399 PMCID: PMC5260080 DOI: 10.1186/s13036-016-0046-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/27/2016] [Indexed: 12/11/2022] Open
Abstract
Since early reports of the recent Zika virus outbreak in May 2015, much has been learned and discussed regarding Zika virus infection and transmission. However, many opportunities still remain for translating these findings into field-ready sensors and diagnostics. In this brief review, we discuss current diagnostic methods, consider the prospects of translating other flavivirus biosensors directly to Zika virus sensing, and look toward the future developments needed for high-sensitivity and high-specificity biosensors to come.
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Affiliation(s)
- Ariana M. Nicolini
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721 USA
| | - Katherine E. McCracken
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
| | - Jeong-Yeol Yoon
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721 USA
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
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32
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Ahmad F, Stedtfeld RD, Waseem H, Williams MR, Cupples AM, Tiedje JM, Hashsham SA. Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min. J Microbiol Methods 2016; 132:27-33. [PMID: 27856278 DOI: 10.1016/j.mimet.2016.11.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/12/2016] [Accepted: 11/12/2016] [Indexed: 01/20/2023]
Abstract
We are reporting a most probable number approach integrated to loop mediated isothermal technique (MPN-LAMP) focusing on Gram-negative Escherichia coli and Gram-positive Enterococcus faecalis bacterial cells without nucleic acids extraction. LAMP assays for uidA from E. coli and gelE from E. faecalis were successfully performed directly on cells up to single digit concentration using a commercial real time PCR instrument. Threshold time values of LAMP assays of bacterial cells, heat treated bacterial cells (95°C for 5min), and their purified genomic DNA templates were similar, implying that amplification could be achieved directly from bacterial cells at 63°C. Viability of bacterial cells was confirmed by using propidium monoazide in a LAMP assay with E. faecalis. To check its functionality on a microfluidic platform, MPN-LAMP assays targeting <10CFU of bacteria were also translated onto polymeric microchips and monitored by a low-cost fluorescence imaging system. The overall system provided signal-to-noise (SNR) ratios up to 800, analytical sensitivity of <10CFU, and time to positivity of about 20min. MPN-LAMP assays were performed for cell concentrations in the range of 105CFU to <10CFU. MPN values from LAMP assays confirmed that the amplifications were from <10CFU. The method described here, applicable directly on cells at 63°C, eliminates the requirement of complex nucleic acids extraction steps, facilitating the development of sensitive, rapid, low-cost, and field-deployable systems. This rapid MPN-LAMP approach has the potential to replace conventional MPN method for waterborne pathogens.
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Affiliation(s)
- Farhan Ahmad
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Hassan Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - James M Tiedje
- The Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA; The Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
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33
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Choi G, Song D, Shrestha S, Miao J, Cui L, Guan W. A field-deployable mobile molecular diagnostic system for malaria at the point of need. LAB ON A CHIP 2016; 16:4341-4349. [PMID: 27722377 PMCID: PMC5089926 DOI: 10.1039/c6lc01078d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In response to the urgent need of a field-deployable and highly sensitive malaria diagnosis, we developed a standalone, "sample-in-answer-out" molecular diagnostic system (AnyMDx) to enable quantitative molecular analysis of blood-borne malaria in low resource areas. The system consists of a durable battery-powered analyzer and a disposable microfluidic compact disc loaded with reagents ready for use. A low power thermal module and a novel fluorescence-sensing module are integrated into the analyzer for real-time monitoring of loop-mediated isothermal nucleic acid amplification (LAMP) of target parasite DNA. With 10 μL of raw blood sample, the AnyMDx system automates the nucleic acid sample preparation and subsequent LAMP and real-time detection. Under laboratory conditions with whole-blood samples spiked with cultured Plasmodium falciparum, we achieved a detection limit of ∼0.6 parasite per μL, much lower than those for the conventional microscopy and rapid diagnostic tests (∼50-100 parasites per μL). The turnaround time from sample to answer is less than 40 minutes. The AnyMDx is user-friendly requiring minimal technological training. The analyzer and the disposable reagent compact discs are cost-effective, making AnyMDx a potential tool for malaria molecular diagnosis under field settings for malaria elimination.
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Affiliation(s)
- Gihoon Choi
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA.
| | - Daniel Song
- Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Sony Shrestha
- Department of Entomology, Pennsylvania State University, University Park, 16802, USA
| | - Jun Miao
- Department of Entomology, Pennsylvania State University, University Park, 16802, USA
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, 16802, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA. and Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA
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34
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Dong YS, Xiong XH, Lu XW, Wu ZQ, Chen H. Antibacterial surfaces based on poly(cationic liquid) brushes: switchability between killing and releasing via anion counterion switching. J Mater Chem B 2016; 4:6111-6116. [PMID: 32263499 DOI: 10.1039/c6tb01464j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The development of a smart antibacterial surface that can both kill attached live bacteria and release dead bacteria is reported. The surface consists of counterion-responsive poly(cationic liquid) brushes of poly(1-(2-methacryloyloxyhexyl)-3-methylimidazolium bromide) (PIL(Br)), the properties of which can be switched repeatedly between bacterial killing and bacterial release. Upon counter-anion exchange of PIL(Br) chains using lithium bis(trifluoromethanesulfonyl) amide (LiTf2N) to yield PIL(Tf2N), the wettability of the surface changes from hydrophilic (water contact angle ∼52°) to hydrophobic (∼97°). The PIL(Br) chains adopt an extended conformation with bactericidal properties. Counter-anion switching to PIL(Tf2N) gives a collapsed chain conformation allowing the release of killed bacteria. The switchable killing and releasing actions of the surface were maintained over three cycles. Thus it is concluded that PIL(Br) layers provide a viable approach for the fabrication of "smart" antibacterial surfaces.
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Affiliation(s)
- Yi-Shi Dong
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou 215123, P. R. China.
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Lifson MA, Ozen MO, Inci F, Wang S, Inan H, Baday M, Henrich TJ, Demirci U. Advances in biosensing strategies for HIV-1 detection, diagnosis, and therapeutic monitoring. Adv Drug Deliv Rev 2016; 103:90-104. [PMID: 27262924 PMCID: PMC4943868 DOI: 10.1016/j.addr.2016.05.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 01/01/2023]
Abstract
HIV-1 is a major global epidemic that requires sophisticated clinical management. There have been remarkable efforts to develop new strategies for detecting and treating HIV-1, as it has been challenging to translate them into resource-limited settings. Significant research efforts have been recently devoted to developing point-of-care (POC) diagnostics that can monitor HIV-1 viral load with high sensitivity by leveraging micro- and nano-scale technologies. These POC devices can be applied to monitoring of antiretroviral therapy, during mother-to-child transmission, and identification of latent HIV-1 reservoirs. In this review, we discuss current challenges in HIV-1 diagnosis and therapy in resource-limited settings and present emerging technologies that aim to address these challenges using innovative solutions.
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Affiliation(s)
- Mark A Lifson
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Radiology Department, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mehmet Ozgun Ozen
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Radiology Department, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Fatih Inci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Radiology Department, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - ShuQi Wang
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Radiology Department, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China; Institute for Translational Medicine, Zhejiang University, Hangzhou, China
| | - Hakan Inan
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Radiology Department, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA; Medicine Faculty, Zirve University, Gaziantep, Turkey
| | - Murat Baday
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Radiology Department, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Utkan Demirci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Radiology Department, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
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36
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Choi S. Powering point-of-care diagnostic devices. Biotechnol Adv 2016; 34:321-30. [DOI: 10.1016/j.biotechadv.2015.11.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022]
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37
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Huckle D. The impact of new trends in POCTs for companion diagnostics, non-invasive testing and molecular diagnostics. Expert Rev Mol Diagn 2016; 15:815-27. [PMID: 25990929 DOI: 10.1586/14737159.2015.1033405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Point-of-care diagnostics have been slowly developing over several decades and have taken on a new importance in current healthcare delivery for both diagnostics and development of new drugs. Molecular diagnostics have become a key driver of technology change and opened up new areas in companion diagnostics for use alongside pharmaceuticals and in new clinical approaches such as non-invasive testing. Future areas involving smartphone and other information technology advances, together with new developments in molecular biology, microfluidics and surface chemistry are adding to advances in the market. The focus for point-of-care tests with molecular diagnostic technologies is focused on advancing effective applications.
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Affiliation(s)
- David Huckle
- Adams Business Associates, 2 Buckingham Place, Bellfield Road, High Wycombe HP13 5HW, UK
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38
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39
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Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification. MICROARRAYS 2015; 4:474-89. [PMID: 27600235 PMCID: PMC4996405 DOI: 10.3390/microarrays4040474] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 10/02/2015] [Accepted: 10/10/2015] [Indexed: 02/06/2023]
Abstract
Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.
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40
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Craw P, Mackay RE, Naveenathayalan A, Hudson C, Branavan M, Sadiq ST, Balachandran W. A Simple, Low-Cost Platform for Real-Time Isothermal Nucleic Acid Amplification. SENSORS 2015; 15:23418-30. [PMID: 26389913 PMCID: PMC4610544 DOI: 10.3390/s150923418] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 11/17/2022]
Abstract
Advances in microfluidics and the introduction of isothermal nucleic acid amplification assays have resulted in a range of solutions for nucleic acid amplification tests suited for point of care and field use. However, miniaturisation of instrumentation for such assays has not seen such rapid advances and fluorescence based assays still depend on complex, bulky and expensive optics such as fluorescence microscopes, photomultiplier tubes and sensitive lens assemblies. In this work we demonstrate a robust, low cost platform for isothermal nucleic acid amplification on a microfluidic device. Using easily obtainable materials and commercial off-the-shelf components, we show real time fluorescence detection using a low cost photodiode and operational amplifier without need for lenses. Temperature regulation on the device is achieved using a heater fabricated with standard printed circuit board fabrication methods. These facile construction methods allow fabrications at a cost compatible with widespread deployment to resource poor settings.
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Affiliation(s)
- Pascal Craw
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK.
- Oceans and Atmosphere flagship, Commonwealth Science and Industrial Research Organisation (CSIRO), Hobart, Tasmania 7001, Australia.
| | - Ruth E Mackay
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK.
| | - Angel Naveenathayalan
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK.
| | - Chris Hudson
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK.
| | - Manoharanehru Branavan
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK.
| | - S Tariq Sadiq
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, UK.
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK.
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41
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Damhorst GL, Duarte-Guevara C, Chen W, Ghonge T, Cunningham BT, Bashir R. Smartphone-Imaged HIV-1 Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) on a Chip from Whole Blood. ENGINEERING (BEIJING, CHINA) 2015; 1:324-335. [PMID: 26705482 PMCID: PMC4687746 DOI: 10.15302/j-eng-2015072] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Viral load measurements are an essential tool for the long-term clinical care of hum an immunodeficiency virus (HIV)-positive individuals. The gold standards in viral load instrumentation, however, are still too limited by their size, cost, and sophisticated operation for these measurements to be ubiquitous in remote settings with poor healthcare infrastructure, including parts of the world that are disproportionately affected by HIV infection. The challenge of developing a point-of-care platform capable of making viral load more accessible has been frequently approached but no solution has yet emerged that meets the practical requirements of low cost, portability, and ease-of-use. In this paper, we perform reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on minimally processed HIV-spiked whole blood samples with a microfluidic and silicon microchip platform, and perform fluorescence measurements with a consumer smartphone. Our integrated assay shows amplification from as few as three viruses in a ~ 60 nL RT-LAMP droplet, corresponding to a whole blood concentration of 670 viruses per µL of whole blood. The technology contains greater power in a digital RT-LAMP approach that could be scaled up for the determination of viral load from a finger prick of blood in the clinical care of HIV-positive individuals. We demonstrate that all aspects of this viral load approach, from a drop of blood to imaging the RT-LAMP reaction, are compatible with lab-on-a-chip components and mobile instrumentation.
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Affiliation(s)
- Gregory L. Damhorst
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Carlos Duarte-Guevara
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weili Chen
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tanmay Ghonge
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian T. Cunningham
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rashid Bashir
- Department of Bioengineering, The University of Illinois at
Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, The University of
Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, The
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence author.
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42
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Choi JR, Tang R, Wang S, Wan Abas WAB, Pingguan-Murphy B, Xu F. Paper-based sample-to-answer molecular diagnostic platform for point-of-care diagnostics. Biosens Bioelectron 2015; 74:427-39. [PMID: 26164488 DOI: 10.1016/j.bios.2015.06.065] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/15/2015] [Accepted: 06/27/2015] [Indexed: 01/04/2023]
Abstract
Nucleic acid testing (NAT), as a molecular diagnostic technique, including nucleic acid extraction, amplification and detection, plays a fundamental role in medical diagnosis for timely medical treatment. However, current NAT technologies require relatively high-end instrumentation, skilled personnel, and are time-consuming. These drawbacks mean conventional NAT becomes impractical in many resource-limited disease-endemic settings, leading to an urgent need to develop a fast and portable NAT diagnostic tool. Paper-based devices are typically robust, cost-effective and user-friendly, holding a great potential for NAT at the point of care. In view of the escalating demand for the low cost diagnostic devices, we highlight the beneficial use of paper as a platform for NAT, the current state of its development, and the existing challenges preventing its widespread use. We suggest a strategy involving integrating all three steps of NAT into one single paper-based sample-to-answer diagnostic device for rapid medical diagnostics in the near future.
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Affiliation(s)
- Jane Ru Choi
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Ruihua Tang
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, PR China; Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, PR China
| | - ShuQi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China; Institute for Translational Medicine, Zhejiang University, Hangzhou, PR China
| | - Wan Abu Bakar Wan Abas
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| | - Belinda Pingguan-Murphy
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China.
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43
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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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Mauk MG, Liu C, Sadik M, Bau HH. Microfluidic devices for nucleic acid (NA) isolation, isothermal NA amplification, and real-time detection. Methods Mol Biol 2015; 1256:15-40. [PMID: 25626529 PMCID: PMC6540113 DOI: 10.1007/978-1-4939-2172-0_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Molecular (nucleic acid)-based diagnostics tests have many advantages over immunoassays, particularly with regard to sensitivity and specificity. Most on-site diagnostic tests, however, are immunoassay-based because conventional nucleic acid-based tests (NATs) require extensive sample processing, trained operators, and specialized equipment. To make NATs more convenient, especially for point-of-care diagnostics and on-site testing, a simple plastic microfluidic cassette ("chip") has been developed for nucleic acid-based testing of blood, other clinical specimens, food, water, and environmental samples. The chip combines nucleic acid isolation by solid-phase extraction; isothermal enzymatic amplification such as LAMP (Loop-mediated AMPlification), NASBA (Nucleic Acid Sequence Based Amplification), and RPA (Recombinase Polymerase Amplification); and real-time optical detection of DNA or RNA analytes. The microfluidic cassette incorporates an embedded nucleic acid binding membrane in the amplification reaction chamber. Target nucleic acids extracted from a lysate are captured on the membrane and amplified at a constant incubation temperature. The amplification product, labeled with a fluorophore reporter, is excited with a LED light source and monitored in situ in real time with a photodiode or a CCD detector (such as available in a smartphone). For blood analysis, a companion filtration device that separates plasma from whole blood to provide cell-free samples for virus and bacterial lysis and nucleic acid testing in the microfluidic chip has also been developed. For HIV virus detection in blood, the microfluidic NAT chip achieves a sensitivity and specificity that are nearly comparable to conventional benchtop protocols using spin columns and thermal cyclers.
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Affiliation(s)
- Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 220 South 33rd Street, 107 towne building, Philadelphia, PA, 19104-6315, USA
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Microfluidic platform towards point-of-care diagnostics in infectious diseases. J Chromatogr A 2014; 1377:13-26. [PMID: 25544727 DOI: 10.1016/j.chroma.2014.12.041] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 01/09/2023]
Abstract
Rapid and timely diagnosis of infectious diseases is a critical determinant of clinical outcomes and general public health. For the detection of various pathogens, microfluidics-based platforms offer many advantages, including speed, cost, portability, high throughput, and automation. This review provides an overview of the recent advances in microfluidic technologies for point-of-care (POC) diagnostics for infectious diseases. The key aspects of such technologies for the development of a fully integrated POC platform are introduced, including sample preparation, on-chip nucleic acid analysis and immunoassay, and system integration/automation. The current challenges to practical implementation of this technology are discussed together with future perspectives.
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Mani V, Wang S, Inci F, De Libero G, Singhal A, Demirci U. Emerging technologies for monitoring drug-resistant tuberculosis at the point-of-care. Adv Drug Deliv Rev 2014; 78:105-17. [PMID: 24882226 DOI: 10.1016/j.addr.2014.05.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 04/29/2014] [Accepted: 05/25/2014] [Indexed: 01/18/2023]
Abstract
Infectious diseases are the leading cause of death worldwide. Among them, tuberculosis (TB) remains a major threat to public health, exacerbated by the emergence of multiple drug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (Mtb). MDR-Mtb strains are resistant to first-line anti-TB drugs such as isoniazid and rifampicin; whereas XDR-Mtb strains are resistant to additional drugs including at least to any fluoroquinolone and one of the second-line anti-TB injectable drugs such as kanamycin, capreomycin, or amikacin. Clinically, these strains have significantly impacted the management of TB in high-incidence developing countries, where systemic surveillance of TB drug resistance is lacking. For effective management of TB on-site, early detection of drug resistance is critical to initiate treatment, to reduce mortality, and to thwart drug-resistant TB transmission. In this review, we discuss the diagnostic challenges to detect drug-resistant TB at the point-of-care (POC). Moreover, we present the latest advances in nano/microscale technologies that can potentially detect TB drug resistance to improve on-site patient care.
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Crannell ZA, Rohrman B, Richards-Kortum R. Equipment-free incubation of recombinase polymerase amplification reactions using body heat. PLoS One 2014; 9:e112146. [PMID: 25372030 PMCID: PMC4221156 DOI: 10.1371/journal.pone.0112146] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/13/2014] [Indexed: 11/28/2022] Open
Abstract
The development of isothermal amplification platforms for nucleic acid detection has the potential to increase access to molecular diagnostics in low resource settings; however, simple, low-cost methods for heating samples are required to perform reactions. In this study, we demonstrated that human body heat may be harnessed to incubate recombinase polymerase amplification (RPA) reactions for isothermal amplification of HIV-1 DNA. After measuring the temperature of mock reactions at 4 body locations, the axilla was chosen as the ideal site for comfortable, convenient incubation. Using commonly available materials, 3 methods for securing RPA reactions to the body were characterized. Finally, RPA reactions were incubated using body heat while control RPA reactions were incubated in a heat block. At room temperature, all reactions with 10 copies of HIV-1 DNA and 90% of reactions with 100 copies of HIV-1 DNA tested positive when incubated with body heat. In a cold room with an ambient temperature of 10 degrees Celsius, all reactions containing 10 copies or 100 copies of HIV-1 DNA tested positive when incubated with body heat. These results suggest that human body heat may provide an extremely low-cost solution for incubating RPA reactions in low resource settings.
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Affiliation(s)
| | - Brittany Rohrman
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
- * E-mail:
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de Koning TJ, Jongbloed JDH, Sikkema-Raddatz B, Sinke RJ. Targeted next-generation sequencing panels for monogenetic disorders in clinical diagnostics: the opportunities and challenges. Expert Rev Mol Diagn 2014; 15:61-70. [PMID: 25367078 DOI: 10.1586/14737159.2015.976555] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) will soon be used for clinically heterogeneous, inherited disorders and the increasing number of disease-causing genes reported. Diagnostic laboratories therefore need to decide which NGS methods they are going to invest in and how to implement them. We discuss here the challenges and opportunities of using targeted resequencing (TRS) panels for diagnosing monogenetic disorders. Of the different NGS approaches available, TRS panels offer the opportunity to sequence and analyze a limited set of predetermined target genes. At present, TRS panels offer better base-pair coverage, running times, costs and dataset handling than other NGS applications such as whole genome sequencing and whole exome sequencing. However, working with TRS panels also poses new challenges in variant interpretation, data handling and bioinformatic analyses. To optimize the analyses, TRS panel testing should be performed by bioinformaticians, clinicians and laboratory staff in close collaboration.
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Affiliation(s)
- Tom J de Koning
- University of Groningen, University Medical Center Groningen, Department of Genetics, CB 50, PO Box 30.001, 9700 RB Groningen, The Netherlands
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Gulley ML, Morgan DR. Molecular oncology testing in resource-limited settings. J Mol Diagn 2014; 16:601-11. [PMID: 25242061 PMCID: PMC4210462 DOI: 10.1016/j.jmoldx.2014.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 12/14/2022] Open
Abstract
Cancer prevalence and mortality are high in developing nations, where resources for cancer control are inadequate. Nearly one-quarter of cancers in resource-limited nations are infection related, and molecular assays can capitalize on this relationship by detecting pertinent pathogen genomes and human gene variants to identify those at highest risk for progression to cancer, to classify lesions, to predict effective therapy, and to monitor tumor burden over time. Prime examples are human papillomavirus in cervical neoplasia, Helicobacter pylori and Epstein-Barr virus in gastric adenocarcinoma and lymphoma, and hepatitis B or C virus in hepatocellular cancer. Research is underway to engineer devices that overcome social, economic, and technical barriers limiting effective laboratory support. Additional challenges include an educated workforce, infrastructure for quality metrics and record keeping, and funds to sustain molecular test services. The combination of well-designed interfaces, novel and robust electrochemical technology, and telemedicine tools will promote adoption by frontline providers. Fast turnaround is crucial for surmounting loss to follow-up, although increased use of cell phones, even in rural areas, enhances options for patient education and engagement. Links to a broadband network facilitate consultation and centralized storage of medical data. Molecular technology shows promise to address gaps in health care through rapid, user-friendly, and cost-effective devices reflecting clinical priorities in resource-poor areas.
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Affiliation(s)
- Margaret L Gulley
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.
| | - Douglas R Morgan
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University, Nashville, Tennessee
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Cai D, Xiao M, Xu P, Xu YC, Du W. An integrated microfluidic device utilizing dielectrophoresis and multiplex array PCR for point-of-care detection of pathogens. LAB ON A CHIP 2014; 14:3917-3924. [PMID: 25082458 DOI: 10.1039/c4lc00669k] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The early identification of causative pathogens in clinical specimens that require no cultivation is essential for directing evidence-based antimicrobial treatments in resource limited settings. Here, we describe an integrated microfluidic device for the rapid identification of pathogens in complex physiological matrices such as blood. The device was designed and fabricated using SlipChip technologies, which integrated four channels processing independent samples and identifying up to twenty different pathogens. Briefly, diluted whole human blood samples were directly injected into the device for analysis. The pathogens were extracted from the blood by dielectrophoresis, retained in an array of grooves, and identified by multiplex array PCR in nanoliter volumes with end-point fluorescence detection. The universality of the dielectrophoretic separation of pathogens from physiological fluids was evaluated with a panel of clinical isolates covering predominant bacterial and fungal species. Using this system, we simultaneously identified Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli O157:H7 within 3 h. In addition to the prompt diagnosis of bloodstream infections, this method may also be utilized for differentiating microorganisms in contaminated water and environmental samples.
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Affiliation(s)
- Dongyang Cai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China.
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