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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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2
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Politza AJ, Liu T, Guan W. Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need. LAB ON A CHIP 2023; 23:3882-3892. [PMID: 37551930 PMCID: PMC11218199 DOI: 10.1039/d3lc00545c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These processes are critical for ensuring the accuracy and sensitivity of downstream nucleic acid amplification and detection. However, current sample preparation methods are often laboratory-based, requiring specialized equipment, trained personnel, and several hours of processing time. As a result, sample preparation often limits the speed, portability, and cost-effectiveness of point-of-need nucleic acid testing. A universal, field-deployable sample preparation device is highly desirable for this critical need and unmet challenge. Here we reported a handheld, battery-powered, reconfigurable, and field-deployable nucleic acid sample preparation device. A programmable electromagnetic actuator was developed to drive a magnetic robot (ProMagBot) in X/Y 2D space, such that various magnetic bead-based sample preparations can be readily translated from the laboratory to point-of-need settings. The control of the electromagnetic actuator requires only a 3-phase unipolar voltage in X and Y directions, and therefore, the motion space is highly scalable. We validated the ProMagBot device with a model application by extracting HIV viral RNAs from plasma samples using two widely used magnetic bead kits: ChargeSwitch and MagMAX beads. In both cases, the ProMagBot could successfully extract viral RNAs from 50 μL plasma samples containing as low as 102 copies of viral RNAs in 20 minutes. Our results demonstrated the ability of ProMagBot to prepare samples from complex mediums at the point of need. We believe such a device would enable rapid and robust sample preparation in various settings, including resource-limited or remote environments, and accelerate the development of next-generation point-of-need nucleic acid testing.
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Affiliation(s)
- Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
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Rodriguez-Mateos P, Ngamsom B, Iles A, Pamme N. Microscale immiscible phase magnetic processing for bioanalytical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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4
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Zhang Z, Zhao S, Jiang L, Wu J, Zhao W, Guo X, Peng N, Hu F. A sample-to-answer DNA detection microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR. Analyst 2022; 147:4876-4887. [DOI: 10.1039/d2an00908k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR, paving the way for low-cost and rapid implementation of PCR diagnostics.
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Affiliation(s)
- Zengming Zhang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Shuhao Zhao
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Lei Jiang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Junjun Wu
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Wenhan Zhao
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Xiaoniu Guo
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Niancai Peng
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Fei Hu
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
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Can 3D Printing Bring Droplet Microfluidics to Every Lab?-A Systematic Review. MICROMACHINES 2021; 12:mi12030339. [PMID: 33810056 PMCID: PMC8004812 DOI: 10.3390/mi12030339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/14/2022]
Abstract
In recent years, additive manufacturing has steadily gained attention in both research and industry. Applications range from prototyping to small-scale production, with 3D printing offering reduced logistics overheads, better design flexibility and ease of use compared with traditional fabrication methods. In addition, printer and material costs have also decreased rapidly. These advantages make 3D printing attractive for application in microfluidic chip fabrication. However, 3D printing microfluidics is still a new area. Is the technology mature enough to print complex microchannel geometries, such as droplet microfluidics? Can 3D-printed droplet microfluidic chips be used in biological or chemical applications? Is 3D printing mature enough to be used in every research lab? These are the questions we will seek answers to in our systematic review. We will analyze (1) the key performance metrics of 3D-printed droplet microfluidics and (2) existing biological or chemical application areas. In addition, we evaluate (3) the potential of large-scale application of 3D printing microfluidics. Finally, (4) we discuss how 3D printing and digital design automation could trivialize microfluidic chip fabrication in the long term. Based on our analysis, we can conclude that today, 3D printers could already be used in every research lab. Printing droplet microfluidics is also a possibility, albeit with some challenges discussed in this review.
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Schneider L, Cui F, Tripathi A. Isolation of target DNA using synergistic magnetic bead transport and electrokinetic flow. BIOMICROFLUIDICS 2021; 15:024104. [PMID: 33763161 PMCID: PMC7972524 DOI: 10.1063/5.0045307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/07/2021] [Indexed: 05/13/2023]
Abstract
The advent and dissemination of next-generation sequencing (NGS) technologies such as Illumina's sequencing platforms has brought forth vast reductions in the cost, time, and technical difficulties associated with DNA and RNA sequencing. Despite this trend, the workflow required to generate nucleic acid libraries for sequencing remains time-consuming and laborious. The following research proposes a method for simplifying and streamlining this process by replacing the manual washing steps of the common magnetic bead-based cleanup with a novel microfluidic method by integrating magnetic separation and electrokinetic purification (MSEP). Requiring no pumps, pipette mixing, vortexing, or centrifugation, MSEP relies on selective adsorption of target DNA onto the magnetic beads with subsequent transport of beads through a microchannel undergoing an antiparallel electroosmotic flow. The synergetic flow conditions were optimized using a simple electrohydrodynamic flow model. This work demonstrates that MSEP is as effective in eliminating adapter-dimers from the post-ligation library mix as the manual method while also greatly reducing the hands-on time and amount of pipetting required. Although MSEP has been applied specifically toward NGS library preparation at this time, it has the potential to be adapted and employed for any bead-based separation scheme, namely, solid phase extraction, sequence-specific hybridization, and immunoprecipitation on a microscale.
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Affiliation(s)
- Lindsay Schneider
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, Rhode Island 02912, USA
| | - Francis Cui
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, Rhode Island 02912, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, Rhode Island 02912, USA
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Chen Y, Liu Y, Shi Y, Ping J, Wu J, Chen H. Magnetic particles for integrated nucleic acid purification, amplification and detection without pipetting. Trends Analyt Chem 2020; 127:115912. [PMID: 32382202 PMCID: PMC7202819 DOI: 10.1016/j.trac.2020.115912] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid amplification based detection plays an important role in food safety, environmental monitoring and clinical diagnosis. However, traditional nucleic acid detection process involves transferring liquid from one tube to another by pipetting. It requires trained persons, equipped labs and consumes lots of time. The ideal nucleic acid detection is integrated, closed, simplified and automated. Magnetic particles actuated by magnetic fields can efficiently adsorb nucleic acids and promote integrated nucleic acid assays without pipetting driven by pumps and centrifuges. We will comprehensively review magnetic particles assisted integrated system for nucleic acid detection and hope it can inspire further related study.
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Key Words
- ATP, adenosine triphosphate
- DLS, dynamic light scattering
- FMR, ferromagnetic resonance
- GTC, guanidinium thiocyanate
- ICP-AES, inductively coupled plasma atomic emission spectroscopy
- IFAST, immiscible filtration assisted by surface tension
- Immiscible interface
- Integrated detection
- LAMP, loop-mediated isothermal amplification
- Magnetic particles
- Nucleic acid
- PCR, polymerase chain reaction
- PEG, polyethylene glycol
- POCT, point-of-care testing
- RPA, recombinase polymerase amplification
- SQUID, superconducting quantum interference device magnetometer
- TEM, transmission electron microscopy
- XRD, X-Ray diffraction
- qPCR, quantitative PCR
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Affiliation(s)
- Yanju Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Liu
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Ya Shi
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China
| | - Huan Chen
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
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Yin J, Suo Y, Zou Z, Sun J, Zhang S, Wang B, Xu Y, Darland D, Zhao JX, Mu Y. Integrated microfluidic systems with sample preparation and nucleic acid amplification. LAB ON A CHIP 2019; 19:2769-2785. [PMID: 31365009 PMCID: PMC8876602 DOI: 10.1039/c9lc00389d] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Rapid, efficient and accurate nucleic acid molecule detection is important in the screening of diseases and pathogens, yet remains a limiting factor at point of care (POC) treatment. Microfluidic systems are characterized by fast, integrated, miniaturized features which provide an effective platform for qualitative and quantitative detection of nucleic acid molecules. The nucleic acid detection process mainly includes sample preparation and target molecule amplification. Given the advancements in theoretical research and technological innovations to date, nucleic acid extraction and amplification integrated with microfluidic systems has advanced rapidly. The primary goal of this review is to outline current approaches used for nucleic acid detection in the context of microfluidic systems. The secondary goal is to identify new approaches that will help shape future trends at the intersection of nucleic acid detection and microfluidics, particularly with regard to increasing disease and pathogen detection for improved diagnosis and treatment.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanjie Suo
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Jingjing Sun
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Shan Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Beng Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009 China and Institute of Translational Medicine, Zhejiang University, Hangzhou, 310029 China
| | - Yawei Xu
- College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, Jilin, 132000 China
| | - Diane Darland
- Department of Biology, University of North Dakota, USA.
| | | | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
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9
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Deraney RN, Troiano D, Joseph R, Sam SS, Caliendo AM, Tripathi A. Vortex- and Centrifugation-Free Extraction of HIV-1 RNA. Mol Diagn Ther 2019; 23:419-427. [PMID: 30911908 PMCID: PMC11289783 DOI: 10.1007/s40291-019-00394-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND OBJECTIVE HIV viral load measurements play a critical role in monitoring disease progression in those who are on antiretroviral treatment. In order to obtain an accurate measurement, rapid sample preparation techniques are required. There is an unmet need for HIV extraction instruments in resource-limited settings, where HIV prevalence is high. Therefore, the objective of our study was to develop a three-dimensional (3D) microfluidic system to extract HIV-1 RNA with minimal electricity and without complex laboratory instruments. METHODS A 3D microfluidic system was designed in which magnetic beads bound with nucleic acids move through immiscible oil-water interfaces to separate HIV-1 RNA from the sample. Polymerase chain reaction (PCR) amplification was used to quantify the total amount of HIV-1 RNA extracted as we optimized the system through chip design, bead type, carry-over volume, carrier RNA concentration, and elution buffer temperature. Additionally, the extraction efficiency of the 3D microfluidic system was evaluated by comparing with a Qiagen EZ1 Advanced XL instrument using 20 HIV-1-positive plasma samples. RESULTS Our method has near-perfect (100%) extraction efficiency in spiked serum samples with as little as 50 copies/mL starting sample. Furthermore, we report carry-over volumes of 0.31% ± 0.006% of total sample volume. Using the EZ1 Advanced XL as a gold standard, the average percentage HIV-1 RNA extracted using the microchip was observed to be 65.4% ± 24.6%. CONCLUSIONS From a clinical perspective, the success of our method opens up its possible use in diagnostic tests for HIV in the remote areas where access to vortexes and centrifuges is not available. Here we present a proof-of-concept device which, with further development, could be used for sample preparation at the point of care.
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Affiliation(s)
- Rachel N Deraney
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, RI, 02912, USA
| | - Derek Troiano
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, RI, 02912, USA
| | | | - Soya S Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, RI, USA
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, RI, 02912, USA.
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Hu F, Li J, Peng N, Li Z, Zhang Z, Zhao S, Duan M, Tian H, Li L, Zhang P. Rapid isolation of cfDNA from large-volume whole blood on a centrifugal microfluidic chip based on immiscible phase filtration. Analyst 2019; 144:4162-4174. [DOI: 10.1039/c9an00493a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The C-IFAST device enabled the rapid isolation of cfDNA, from 4 ml whole blood to 50 μl elution, within 15 min.
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Affiliation(s)
- Fei Hu
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Juan Li
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Niancai Peng
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Zheng Li
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Zengming Zhang
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Shuhao Zhao
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Mingyue Duan
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Hui Tian
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Lei Li
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Peng Zhang
- State Key Laboratory for Manufacturing Systems Engineering
- Xi'an Jiaotong University
- Xi'an
- P. R. China
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11
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Snider A, Nilsson M, Dupal M, Toloue M, Tripathi A. A Microfluidics Workflow for Sample Preparation for Next-Generation DNA Sequencing. SLAS Technol 2018; 24:196-208. [PMID: 30142015 DOI: 10.1177/2472630318796133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Next-generation sequencing technology requires amplified, short DNA fragments with known end sequences. Samples must undergo processing steps, including extraction and purification of genomic DNA (gDNA), fragmentation, end repair, adapter ligation, and amplification, to prepare a sequencing library. The process of sample preparation requires careful control of temperature and buffer conditions, as well as the stringent removal of contaminants. As a result, library preparation methods are often plagued by sample loss, long protocol times, numerous manual steps, and high cost. We attempt to understand and optimize each step of sample preparation on a microfluidic platform using magnetic bead motion through channels containing immiscible phases. Our platform integrates all steps associated with library preparation with no buffer exchanges and utilizes just 30-60 µL of reagents. Our chip shows a sixfold improvement in yield compared with an affinity spin column when capturing gDNA from samples of ~50 ± 4 MCF-7 cells. Finally, we show whole-genome shotgun sequencing results from 660 pg of human gDNA, in which >93 ± 1% of reads map to a reference genome at or above 99.9% confidence, matching a commercially available sample preparation kit optimized for low-cell-count samples.
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Affiliation(s)
- Adam Snider
- 1 Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | | | | | | | - Anubhav Tripathi
- 1 Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
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12
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Advances in point-of-care technologies for molecular diagnostics. Biosens Bioelectron 2017; 98:494-506. [DOI: 10.1016/j.bios.2017.07.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022]
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13
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Plevniak K, Campbell M. 3D printed microfluidic mixer for point-of-care diagnosis of anemia. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017; 2016:267-270. [PMID: 28268328 DOI: 10.1109/embc.2016.7590691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
3D printing has been an emerging fabrication tool in prototyping and manufacturing. We demonstrated a 3D microfluidic simulation guided computer design and 3D printer prototyping for quick turnaround development of microfluidic 3D mixers, which allows fast self-mixing of reagents with blood through capillary force. Combined with smartphone, the point-of-care diagnosis of anemia from finger-prick blood has been successfully implemented and showed consistent results with clinical measurements. Capable of 3D fabrication flexibility and smartphone compatibility, this work presents a novel diagnostic strategy for advancing personalized medicine and mobile healthcare.
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14
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Microfluidics: innovative approaches for rapid diagnosis of antibiotic-resistant bacteria. Essays Biochem 2017; 61:91-101. [PMID: 28258233 DOI: 10.1042/ebc20160059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/17/2022]
Abstract
The emergence of antibiotic-resistant bacteria has become a major global health concern. Rapid and accurate diagnostic strategies to determine the antibiotic susceptibility profile prior to antibiotic prescription and treatment are critical to control drug resistance. The standard diagnostic procedures for the detection of antibiotic-resistant bacteria, which rely mostly on phenotypic characterization, are time consuming, insensitive and often require skilled personnel, making them unsuitable for point-of-care (POC) diagnosis. Various molecular techniques have therefore been implemented to help speed up the process and increase sensitivity. Over the past decade, microfluidic technology has gained great momentum in medical diagnosis as a series of fluid handling steps in a laboratory can be simplified and miniaturized on to a small platform, allowing marked reduction of sample amount, high portability and tremendous possibility for integration with other detection technologies. These advantages render the microfluidic system a great candidate to be developed into an easy-to-use sample-to-answer POC diagnosis suitable for application in remote clinical settings. This review provides an overview of the current development of microfluidic technologies for the nucleic acid based and phenotypic-based detections of antibiotic resistance.
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15
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Troiano D, Deraney RN, Tripathi A. Effect of surfactants on carryover liquid volume in immiscible phase magnetic bead separation. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2016.10.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Plevniak K, Campbell M, Myers T, Hodges A, He M. 3D printed auto-mixing chip enables rapid smartphone diagnosis of anemia. BIOMICROFLUIDICS 2016; 10:054113. [PMID: 27733894 PMCID: PMC5055529 DOI: 10.1063/1.4964499] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/26/2016] [Indexed: 05/06/2023]
Abstract
Clinical diagnosis requiring central facilities and site visits can be burdensome for patients in resource-limited or rural areas. Therefore, development of a low-cost test that utilizes smartphone data collection and transmission would beneficially enable disease self-management and point-of-care (POC) diagnosis. In this paper, we introduce a low-cost iPOC3D diagnostic strategy which integrates 3D design and printing of microfluidic POC device with smartphone-based disease diagnosis in one process as a stand-alone system, offering strong adaptability for establishing diagnostic capacity in resource-limited areas and low-income countries. We employ smartphone output (AutoCAD 360 app) and readout (color-scale analytical app written in-house) functionalities for rapid 3D printing of microfluidic auto-mixers and colorimetric detection of blood hemoglobin levels. The auto-mixing of reagents with blood via capillary force has been demonstrated in 1 second without the requirement of external pumps. We employed this iPOC3D system for point-of-care diagnosis of anemia using a training set of patients (nanemia = 16 and nhealthy = 6), which showed consistent measurements of blood hemoglobin levels (a.u.c. = 0.97) and comparable diagnostic sensitivity and specificity, compared with standard clinical hematology analyzer. Capable of 3D fabrication flexibility and smartphone compatibility, this work presents a novel diagnostic strategy for advancing personalized medicine and mobile healthcare.
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Affiliation(s)
- Kimberly Plevniak
- Department of Biological and Agricultural Engineering, Kansas State University , Manhattan, Kansas 66506, USA
| | - Matthew Campbell
- Advanced Manufacturing Institute, Kansas State University , Manhattan, Kansas 66506, USA
| | - Timothy Myers
- Department of Science and Mathematics, MidAmerica Nazarene University , Olathe, Kansas 66062, USA
| | - Abby Hodges
- Department of Science and Mathematics, MidAmerica Nazarene University , Olathe, Kansas 66062, USA
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Hejazian M, Nguyen NT. Magnetofluidic concentration and separation of non-magnetic particles using two magnet arrays. BIOMICROFLUIDICS 2016; 10:044103. [PMID: 27478527 PMCID: PMC4947043 DOI: 10.1063/1.4955421] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/24/2016] [Indexed: 05/11/2023]
Abstract
The present paper reports the use of diluted ferrofluid and two arrays of permanent magnets for the size-selective concentration of non-magnetic particles. The micro magnetofluidic device consists of a straight channels sandwiched between two arrays of permanent magnets. The permanent magnets create multiple capture zones with minimum magnetic field strength along the channel. The complex interaction between magnetic forces and hydrodynamic force allows the device to operate in different regimes suitable for concentration of non-magnetic particles with small difference in size. Our experimental results show that non-magnetic particles with diameters of 3.1 μm and 4.8 μm can be discriminated and separated with this method. The results from this study could be used as a guide for the design of size-sensitive separation devices for particle and cell based on negative magnetophoresis.
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Affiliation(s)
- Majid Hejazian
- Queensland Micro and Nanotechnology Centre, Griffith University , Brisbane, Queensland 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre, Griffith University , Brisbane, Queensland 4111, Australia
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18
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Berry SM, Pezzi HM, LaVanway AJ, Guckenberger D, Anderson M, Beebe DJ. AirJump: Using Interfaces to Instantly Perform Simultaneous Extractions. ACS APPLIED MATERIALS & INTERFACES 2016; 8:15040-5. [PMID: 27249333 PMCID: PMC5058634 DOI: 10.1021/acsami.6b02555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Analyte isolation is an important process that spans a range of biomedical disciplines, including diagnostics, research, and forensics. While downstream analytical techniques have advanced in terms of both capability and throughput, analyte isolation technology has lagged behind, increasingly becoming the bottleneck in these processes. Thus, there exists a need for simple, fast, and easy to integrate analyte separation protocols to alleviate this bottleneck. Recently, a new class of technologies has emerged that leverages the movement of paramagnetic particle (PMP)-bound analytes through phase barriers to achieve a high efficiency separation in a single or a few steps. Specifically, the passage of a PMP/analyte aggregate through a phase interface (aqueous/air in this case) acts to efficiently "exclude" unbound (contaminant) material from PMP-bound analytes with higher efficiency than traditional washing-based solid-phase extraction (SPE) protocols (i.e., bind, wash several times, elute). Here, we describe for the first time a new type of "exclusion-based" sample preparation, which we term "AirJump". Upon realizing that much of the contaminant carryover stems from interactions with the sample vessel surface (e.g., pipetting residue, wetting), we aim to eliminate the influence of that factor. Thus, AirJump isolates PMP-bound analyte by "jumping" analyte directly out of a free liquid/air interface. Through careful characterization, we have demonstrated the validity of AirJump isolation through comparison to traditional washing-based isolations. Additionally, we have confirmed the suitability of AirJump in three important independent biological isolations, including protein immunoprecipitation, viral RNA isolation, and cell culture gene expression analysis. Taken together, these data sets demonstrate that AirJump performs efficiently, with high analyte yield, high purity, no cross contamination, rapid time-to-isolation, and excellent reproducibility.
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Zhang L, Deraney RN, Tripathi A. Adsorption and isolation of nucleic acids on cellulose magnetic beads using a three-dimensional printed microfluidic chip. BIOMICROFLUIDICS 2015; 9:064118. [PMID: 26734116 PMCID: PMC4693444 DOI: 10.1063/1.4938559] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 12/11/2015] [Indexed: 05/04/2023]
Abstract
While advances in genomics have enabled sensitive and highly parallel detection of nucleic acid targets, the isolation and extraction of the nucleic acids remain a critical bottleneck in the workflow. We present here a simple 3D printed microfluidic chip that allows for the vortex and centrifugation free extraction of nucleic acids. This novel microfluidic chip utilizes the presence of a water and oil interface to filter out the lysate contaminants. The pure nucleic acids, while bound on cellulose particles, are magnetically moved across the oil layer. We demonstrated efficient and rapid extraction of spiked Human Papillomavirus (HPV) 18 plasmids in specimen transport medium, in under 15 min. An overall extraction efficiency of 61% is observed across a range of HPV plasmid concentrations (5 × 10(1) to 5 × 10(6) copies/100 μl). The magnetic, interfacial, and viscous drag forces inside the microgeometries of the chip are modeled. We have also developed a kinetics model for the adsorption of nucleic acids on cellulose functionalized superparamagnetic beads. We also clarify here the role of carrier nucleic acids in the adsorption and isolation of nucleic acids. Based on the various mechanistic insights detailed here, customized microfluidic devices can be designed to meet the range of current and emerging point of care diagnostics needs.
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Affiliation(s)
- Lei Zhang
- Center for Biomedical Engineering, School of Engineering, Brown University , Providence, Rhode Island 02912, USA
| | - Rachel N Deraney
- Center for Biomedical Engineering, School of Engineering, Brown University , Providence, Rhode Island 02912, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University , Providence, Rhode Island 02912, USA
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