1
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Lim J, Han W, Thang LTH, Lee YW, Shin JH. Customizable Nichrome Wire Heaters for Molecular Diagnostic Applications. BIOSENSORS 2024; 14:152. [PMID: 38534259 DOI: 10.3390/bios14030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Accurate sample heating is vital for nucleic acid extraction and amplification, requiring a sophisticated thermal cycling process in nucleic acid detection. Traditional molecular detection systems with heating capability are bulky, expensive, and primarily designed for lab settings. Consequently, their use is limited where lab systems are unavailable. This study introduces a technique for performing the heating process required in molecular diagnostics applicable for point-of-care testing (POCT), by presenting a method for crafting customized heaters using freely patterned nichrome (NiCr) wire. This technique, fabricating heaters by arranging protrusions on a carbon black-polydimethylsiloxane (PDMS) cast and patterning NiCr wire, utilizes cost-effective materials and is not constrained by shape, thereby enabling customized fabrication in both two-dimensional (2D) and three-dimensional (3D). To illustrate its versatility and practicality, a 2D heater with three temperature zones was developed for a portable device capable of automatic thermocycling for polymerase chain reaction (PCR) to detect Escherichia coli (E. coli) O157:H7 pathogen DNA. Furthermore, the detection of the same pathogen was demonstrated using a customized 3D heater surrounding a microtube for loop-mediated isothermal amplification (LAMP). Successful DNA amplification using the proposed heater suggests that the heating technique introduced in this study can be effectively applied to POCT.
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Affiliation(s)
- Juhee Lim
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Won Han
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Le Tran Huy Thang
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Yong Wook Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
- School of Electrical Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Joong Ho Shin
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
- Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence, Pukyong National University, Busan 48513, Republic of Korea
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2
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Bustin SA, Kirvell S, Nolan T, Shipley GL. FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols. Int J Mol Sci 2024; 25:2773. [PMID: 38474020 DOI: 10.3390/ijms25052773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
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3
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Song W, Zhang C, Lin H, Zhang T, Liu H, Huang X. Portable rotary PCR system for real-time detection of Pseudomonas aeruginosa in milk. LAB ON A CHIP 2023; 23:4592-4599. [PMID: 37772426 DOI: 10.1039/d3lc00401e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The rapid quantitative detection of Pseudomonas aeruginosa in milk is of great significance to food safety. Quantitative real-time polymerase chain reaction (qPCR) technology is a good choice to meet this requirement. A good qPCR system should show the advantages of being low cost, having low-power consumption, having potential for miniaturization and be portable. However, most of the time-domain-based qPCR systems reported to date do not meet these requirements. In this study, we propose a novel real-time rotary PCR reaction system (RRP) that meets all the abovementioned specifications, and contains four modules: a heating control module, a disposable PCR capillary tube, a mechanical control module, and a photoelectric detection module. The volume of our homemade-PCR capillary tube is only 3 μL. The total manufacturing cost is cheaper than $200, and the capillary tube is about 1.4 cents. The size parameter of the RRP is less than 300 mm × 150 mm × 150 mm, using low mobile power sources to operate. All the features mean that the RRP meets the advantages of low sample volumes, enhanced thermal conductivity and being portable. Through conducting the experimental quantitative detection of Pseudomonas aeruginosa in milk and theoretical simulations by COMSOL, we prove the feasibility of this rotary PCR real-time detection system, which has broad application prospects in the rapid detection of bacteria and food safety.
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Affiliation(s)
- Weidu Song
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Chuanhao Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Huichao Lin
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Taiyi Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Haixia Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Xiaowen Huang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
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4
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Wang K, Jiang Y, Guo Y, Geng M, Wu W. An Optimized Thermal Feedback Methodology for Accurate Temperature Control and High Amplification Efficiency during Fluorescent qPCR. Bioengineering (Basel) 2022; 9:bioengineering9060237. [PMID: 35735480 PMCID: PMC9220086 DOI: 10.3390/bioengineering9060237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/27/2022] Open
Abstract
Traditional qPCR instrument is combined with CMOS and a personal computer, and a photoelectric feedback automatic fluorescence detection system is designed to realize quantitative real-time PCR. The key to reaction efficiency lies in how to ensure that the temperature of the detection reagent completely matches the set temperature. However, for most traditional real-time fluorescent PCR systems, the temperature cycling is controlled by detecting the temperature of the heating well plate. It cannot directly measure the temperature in the reaction reagent PCR tube, which will cause the deviation in the actual temperature of the reagent to be as expected. Therefore, in this paper, we raise a method of directly detecting the temperature in the reaction tube of the reagent during the temperature cycling is adopted. According to the deviation from the expected value, the set temperature of the PCR instrument is adjusted to make the actual temperature of the reagent closer to the expected value. Through this method, we also realized the temperature calibration and optimization of the TEC circulation system we built. Experiments show that this low-cost, portable real-time quantitative PCR system can detect and analyze pathogens in situ.
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Affiliation(s)
- Kangning Wang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
| | - Yangyang Jiang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, Guangzhou 510006, China;
| | - Mingkun Geng
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China;
- Graduate School, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
- Correspondence:
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5
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Compressed Air-Driven Continuous-Flow Thermocycled Digital PCR for HBV Diagnosis in Clinical-Level Serum Sample Based on Single Hot Plate. Molecules 2020; 25:molecules25235646. [PMID: 33266146 PMCID: PMC7731400 DOI: 10.3390/molecules25235646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022] Open
Abstract
We report a novel compressed air-driven continuous-flow digital PCR (dPCR) system based on a 3D microfluidic chip and self-developed software system to realize real-time monitoring. The system can ensure the steady transmission of droplets in long tubing without an external power source and generate stable droplets of suitable size for dPCR by two needles and a narrowed Teflon tube. The stable thermal cycle required by dPCR can be achieved by using only one constant temperature heater. In addition, our system has realized the real-time detection of droplet fluorescence in each thermal cycle, which makes up for the drawbacks of the end-point detection method used in traditional continuous-flow dPCR. This continuous-flow digital PCR by the compressed air-driven method can meet the requirements of droplet thermal cycle and diagnosis in a clinical-level serum sample. Comparing the detection results of clinical samples (hepatitis B virus serum) with commercial instruments (CFX Connect; Bio Rad, Hercules, CA, USA), the linear correlation reached 0.9995. Because the system greatly simplified the traditional dPCR process, this system is stable and user-friendly.
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6
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Li B, Li Y, Jiang Y, Manz A, Wu W. A digital PCR system based on the thermal cycled chip with multi helix winding capillary. Sci Rep 2020; 10:17824. [PMID: 33082428 PMCID: PMC7576587 DOI: 10.1038/s41598-020-74711-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
This paper presents a digital PCR system based on a novel thermal cycled chip, which wraps microchannels on a trapezoidal structure made of polydimethylsiloxane (PDMS) in a multi-helix manner for the first time. It is found that compared to the single helix chip commonly used in previous reports, this kind of novel multi-helix chip can make the surface temperature in the renaturation zone more uniform, and even in the case of rapid fluid flow, it can improve the efficiency of the polymerase chain reaction. What’s more, the winding method of multi helix (such as double helix, six helix and eight helix) can obtain better temperature uniformity than the winding of odd helix (such as single helix and three helix). As a proof of concept, the temperature-optimized double-helical chip structure is applied to continuous-flow digital PCR and there is no need to add any surfactant to both the oil phase and reagent. In addition, we successfully analyzed the fluorescence signal of continuous-flow digital PCR by using CMOS camera. Finally, this method is applied for the absolute quantification of the clinical serum sample infected by HBV. The accuracy of the test results has been confirmed by commercial instruments.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanming Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Yangyang Jiang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Andreas Manz
- Systems Engineering Department, Saarland University, 66123, Saarbrücken, Germany.,Bio Sensor & Materials Group, KIST Europe, 66123, Saarbrücken, Germany
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.
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7
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Abstract
Reducing the risk of (cross-)contamination, improving the chain of custody, providing fast analysis times and options of direct analysis at crime scenes: these requirements within forensic DNA analysis can be met upon using microfluidic devices. To become generally applied in forensics, the most important requirements for microfluidic devices are: analysis time, method of DNA detection and biocompatibility of used materials. In this work an overview is provided about biosensing of DNA, by DNA profiling via standard short tandem repeat (STR) analysis or by next generation sequencing. The material of which a forensic microfluidic device is made is crucial: it should for example not inhibit DNA amplification and its thermal conductivity and optical transparency should be suitable for achieving fast analysis. The characteristics of three materials frequently used materials, i.e., glass, silicon and PDMS, are given, in addition to a promising alternative, viz. cyclic olefin copolymer (COC). New experimental findings are presented about the biocompatibility of COC and the use of COC chips for multiple displacement amplification and real-time monitoring of DNA amplification.
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8
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Progress in molecular detection with high-speed nucleic acids thermocyclers. J Pharm Biomed Anal 2020; 190:113489. [DOI: 10.1016/j.jpba.2020.113489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022]
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9
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Shi B, Li Y, Wu D, Wu W. A handheld continuous-flow real-time fluorescence qPCR system with a PVC microreactor. Analyst 2020; 145:2767-2773. [PMID: 32095799 DOI: 10.1039/c9an01894h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The polymerase chain reaction (PCR) has unique advantages of sensitivity, specificity and rapidity in pathogen detection, which makes it at the forefront of academia and application in molecular biology diagnosis. In this study, we proposed a hand-held real-time fluorescence qPCR system, which can be used for the quantitative analysis of nucleic acid molecules. For the first time, we use a PVC microreactor which improved the transmittance of the microreactor and made it easy to collect the fluorescence signal. In order to make it portable, the system adopted a passive syringe for sample injection and integrated temperature control and detection with a lithium battery for power supply. What's more, the fluorescence signal was captured by using a smartphone through an external automatic robotic arm. This real-time qPCR system can detect genomic DNA of the H7N9 avian influenza over four orders of magnitude of concentration from 107 to 104 copies per μL. In addition, it was verified that the fluorescence images obtained by this system were clearer than those obtained by a traditional system (using a PTFE spatial PCR microreactor) with two typical dyes and a probe tested-EvaGreen, SYBR Green and FAM.
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Affiliation(s)
- Bing Shi
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun, 130033, China. and University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Yuanming Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun, 130033, China.
| | - Di Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun, 130033, China. and University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun, 130033, China.
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10
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Tunable and precise miniature lithium heater for point-of-care applications. Proc Natl Acad Sci U S A 2020; 117:4632-4641. [PMID: 32071225 DOI: 10.1073/pnas.1916562117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Point-of-care diagnostic assays often involve multistep reactions, requiring a wide range of precise temperatures. Although precise heating is critical to performing these assays, it is challenging to provide it in an electricity-free format away from established infrastructure. Chemical heaters are electricity-free and use exothermic reactions. However, they are unsuitable for point-of-care multistep reactions because they sacrifice portability, have a narrow range of achievable temperatures, and long ramp-up times. Here we developed a miniature heater by modulating the lithium-water reaction kinetics using bubbles in a channel. Our heaters are up to 8,000 times smaller than current devices and can provide precise (within 5 °C) and tunable heating from 37 °C to 65 °C (∆TRT = 12 °C to 40 °C) with ramp-up times of a minute. We demonstrate field portablity and stability and show their use in an electricity-free multistep workflow that needs a range of temperatures. Ultimately, we envision providing better access to cutting edge biochemical techniques, including diagnostics, by making portable and electricity-free heating available at any location.
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11
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Sciuto EL, Petralia S, Calabrese G, Conoci S. An integrated biosensor platform for extraction and detection of nucleic acids. Biotechnol Bioeng 2020; 117:1554-1561. [PMID: 31997343 DOI: 10.1002/bit.27290] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 12/15/2022]
Abstract
The development of portable systems for analysis of nucleic acids (NAs) is crucial for the evolution of biosensing in the context of future healthcare technologies. The integration of NA extraction, purification, and detection modules, properly actuated by microfluidics technologies, is a key point for the development of portable diagnostic systems. In this paper, we describe an integrated biosensor platform based on a silicon-plastic hybrid lab-on-disk technology capable of managing NA extraction, purification, and detection processes in an integrated format. The sample preparation process is performed by solid-phase extraction technology using magnetic beads on a plastic disk, while detection is done through quantitative real-time polymerase chain reaction (qRT-PCR) on a miniaturized silicon device. The movement of sample and reagents is actuated by a centrifugal force induced by a disk actuator instrument. The assessment of the NA extraction and detection performance has been carried out by using hepatitis B virus (HBV) DNA genome as a biological target. The quantification of the qRT-PCR chip in the hybrid disk showed an improvement in sensitivity with respect to the qRT-PCR commercial platforms, which means an optimization of time and cost. Limit of detection and limit of quantification values of about 8 cps/reaction and 26 cps/reaction, respectively, were found by using analytical samples (synthetic clone), while the results with real samples (serum with spiked HBV genome) indicate that the system performs as well as the standard methods.
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Affiliation(s)
| | | | - Giovanna Calabrese
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, University of Messina, Messina, Italy
| | - Sabrina Conoci
- STMicroelectronics, Catania, Italy.,Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, University of Messina, Messina, Italy
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12
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Gorgannezhad L, Sreejith KR, Zhang J, Kijanka G, Christie M, Stratton H, Nguyen NT. Microfluidic Array Chip for Parallel Detection of Waterborne Bacteria. MICROMACHINES 2019; 10:E883. [PMID: 31888270 PMCID: PMC6952809 DOI: 10.3390/mi10120883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022]
Abstract
The polymerase chain reaction (PCR) is a robust technique used to make multiple copies of a segment of DNA. However, the available PCR platforms require elaborate and time-consuming operations or costly instruments, hindering their application. Herein, we introduce a sandwiched glass-polydimethylsiloxane (PDMS)-glass microchip containing an array of reactors for the real-time PCR-based detection of multiple waterborne bacteria. The PCR solution was loaded into the array of reactors in a single step utilising capillary filling, eliminating the need for pumps, valves, and liquid handling instruments. Issues of generating and trapping bubbles during the loading chip step were addressed by creating smooth internal reactor surfaces. Triton X-100 was used to enhance PCR compatibility in the chip by minimising the nonspecific adsorption of enzymes. A custom-made real-time PCR instrument was also fabricated to provide thermal cycling to the array chip. The microfluidic device was successfully demonstrated for microbial faecal source tracking (MST) in water.
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Affiliation(s)
- Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (L.G.); (K.R.S.); (J.Z.); (H.S.)
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia;
| | - Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (L.G.); (K.R.S.); (J.Z.); (H.S.)
| | - Jun Zhang
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (L.G.); (K.R.S.); (J.Z.); (H.S.)
| | - Gregor Kijanka
- Mater Research Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia;
| | - Melody Christie
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia;
| | - Helen Stratton
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (L.G.); (K.R.S.); (J.Z.); (H.S.)
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia;
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (L.G.); (K.R.S.); (J.Z.); (H.S.)
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13
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Gorgannezhad L, Stratton H, Nguyen NT. Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology. MICROMACHINES 2019; 10:E408. [PMID: 31248141 PMCID: PMC6630468 DOI: 10.3390/mi10060408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.
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Affiliation(s)
- Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Helen Stratton
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
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14
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Gregorini M, Mikutis G, Grass RN, Stark WJ. Small-Size Polymerase Chain Reaction Device with Improved Heat Transfer and Combined Feedforward/Feedback Control Strategy. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b01209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michele Gregorini
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland
| | - Gediminas Mikutis
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland
| | - Robert N. Grass
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland
| | - Wendelin J. Stark
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland
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15
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Shi B, He G, Wu W. A PCR microreactor machinery with passive micropump and battery-powered heater for thermo-cycled amplifications of clinical-level and multiplexed DNA targets. Mikrochim Acta 2018; 185:467. [DOI: 10.1007/s00604-018-3007-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/09/2018] [Indexed: 02/07/2023]
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16
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Ballard ZS, Brown C, Ozcan A. Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome. ACS NANO 2018; 12:3065-3082. [PMID: 29553706 DOI: 10.1021/acsnano.7b08660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The microbiome has been heralded as a gauge of and contributor to both human health and environmental conditions. Current challenges in probing, engineering, and harnessing the microbiome stem from its microscopic and nanoscopic nature, diversity and complexity of interactions among its members and hosts, as well as the spatiotemporal sampling and in situ measurement limitations induced by the restricted capabilities and norm of existing technologies, leaving some of the constituents of the microbiome unknown. To facilitate significant progress in the microbiome field, deeper understanding of the constituents' individual behavior, interactions with others, and biodiversity are needed. Also crucial is the generation of multimodal data from a variety of subjects and environments over time. Mobile imaging and sensing technologies, particularly through smartphone-based platforms, can potentially meet some of these needs in field-portable, cost-effective, and massively scalable manners by circumventing the need for bulky, expensive instrumentation. In this Perspective, we outline how mobile sensing and imaging technologies could lead the way to unprecedented insight into the microbiome, potentially shedding light on various microbiome-related mysteries of today, including the composition and function of human, animal, plant, and environmental microbiomes. Finally, we conclude with a look at the future, propose a computational microbiome engineering and optimization framework, and discuss its potential impact and applications.
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17
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Ganser P, Baum C, Chargin D, Sauer-Budge AF, Sharon A. A practical approach for the optimization of channel integrity in the sealing of shallow microfluidic devices made from cyclic olefin polymer. Biomed Microdevices 2018; 20:24. [PMID: 29478142 DOI: 10.1007/s10544-018-0265-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A reduced channel height in microfluidic Lab-on-a-Chip (LOC) devices enables a reduction in the required volume of sample and reagents. LOC devices are most often manufactured by microstructuring a planar substrate and subsequently sealing it with a cover film. However, shallow chip designs, made from polymers, are sensitive to channel deformation during the sealing of the microfluidic device. Inappropriate bonding conditions often result in the loss of the microfluidic functionality. A systematic and practical approach for the identification of suitable bonding process parameters is missing. In this article, a straightforward approach for the optimization of channel integrity in the sealing of shallow microfluidic devices made from Cyclic Olefin Polymer (COP) is presented. Two COP materials were tested: COP Zeonex 690R (Glass transition temperature Tg = 135 °C) both as a cover film and substrate material, and COP ZF14 (Tg = 135 °C) as a film material. A mechanical analysis using microstructured Zeonex 690R substrates was performed to generate a matrix of low-distortion bonding parameters, including temperature, pressure and time. The well-established method of solvent-assisted bonding was used to enhance the characteristically low bond strengths of the native COP material. In addition, plasma-assisted bonding was tested and compared. The optimization approach was validated by the manufacture of a microfluidic test device, the demonstration of its microfluidic functionality, and the quantitative evaluation of the achieved channel integrity.
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Affiliation(s)
- Philipp Ganser
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - Christoph Baum
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - David Chargin
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, MA, 02446, USA
| | - Alexis F Sauer-Budge
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, MA, 02446, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Exponent Inc., Natick, MA, 01760, USA.
| | - Andre Sharon
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, MA, 02446, USA.,Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
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Chen JJ, Li KT. Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System. MICROMACHINES 2018; 9:mi9020048. [PMID: 30393324 PMCID: PMC6187668 DOI: 10.3390/mi9020048] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/18/2018] [Accepted: 01/25/2018] [Indexed: 02/07/2023]
Abstract
In order to analyze the DNA amplification numerically with integration of the DNA kinetics, three-dimensional simulations, including flow and thermal fields, and one-dimensional polymerase chain reaction (PCR) kinetics are presented. The simulated results are compared with experimental data that have been applied to the operation of a continuous-flow PCR device. Microchannels fabricated by Micro Electro-Mechanical Systems (MEMS) technologies are shown. Comprehensive simulations of the flow and thermal fields and experiments measuring temperatures during thermal cycling are presented first. The resultant velocity and temperature profiles from the simulations are introduced to the mathematical models of PCR kinetics. Then kinetic equations are utilized to determine the evolution of the species concentrations inside the DNA mixture along the microchannel. The exponential growth of the double-stranded DNA concentration is investigated numerically with the various operational parameters during PCR. Next a 190-bp segment of Bartonella DNA is amplified to evaluate the PCR performance. The trends of the experimental results and numerical data regarding the DNA amplification are similar. The unique architecture built in this study can be applied to a low-cost portable PCR system in the future.
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Affiliation(s)
- Jyh Jian Chen
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan.
| | - Kun Tze Li
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan.
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19
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Fernández-Carballo BL, McBeth C, McGuiness I, Kalashnikov M, Baum C, Borrós S, Sharon A, Sauer-Budge AF. Continuous-flow, microfluidic, qRT-PCR system for RNA virus detection. Anal Bioanal Chem 2017; 410:33-43. [PMID: 29116351 DOI: 10.1007/s00216-017-0689-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/12/2017] [Accepted: 10/04/2017] [Indexed: 11/24/2022]
Abstract
One of the main challenges in the diagnosis of infectious diseases is the need for rapid and accurate detection of the causative pathogen in any setting. Rapid diagnosis is key to avoiding the spread of the disease, to allow proper clinical decisions to be made in terms of patient treatment, and to mitigate the rise of drug-resistant pathogens. In the last decade, significant interest has been devoted to the development of point-of-care reverse transcription polymerase chain reaction (PCR) platforms for the detection of RNA-based viral pathogens. We present the development of a microfluidic, real-time, fluorescence-based, continuous-flow reverse transcription PCR system. The system incorporates a disposable microfluidic chip designed to be produced industrially with cost-effective roll-to-roll embossing methods. The chip has a long microfluidic channel that directs the PCR solution through areas heated to different temperatures. The solution first travels through a reverse transcription zone where RNA is converted to complementary DNA, which is later amplified and detected in real time as it travels through the thermal cycling area. As a proof of concept, the system was tested for Ebola virus detection. Two different master mixes were tested, and the limit of detection of the system was determined, as was the maximum speed at which amplification occurred. Our results and the versatility of our system suggest its promise for the detection of other RNA-based viruses such as Zika virus or chikungunya virus, which constitute global health threats worldwide. Graphical abstract Photograph of the RT-PCR thermoplastic chip.
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Affiliation(s)
- B Leticia Fernández-Carballo
- Fraunhofer USA - Center for Manufacturing Innovation, 15 Saint Mary's Street, Brookline, MA, 02446, USA.,Grup d'Enginyeria de Materials (GEMAT), Institut Químic de Sarrià, Universitat Ramón Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Christine McBeth
- Fraunhofer USA - Center for Manufacturing Innovation, 15 Saint Mary's Street, Brookline, MA, 02446, USA
| | - Ian McGuiness
- Fraunhofer USA - Center for Manufacturing Innovation, 15 Saint Mary's Street, Brookline, MA, 02446, USA
| | - Maxim Kalashnikov
- Fraunhofer USA - Center for Manufacturing Innovation, 15 Saint Mary's Street, Brookline, MA, 02446, USA
| | - Christoph Baum
- Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany
| | - Salvador Borrós
- Grup d'Enginyeria de Materials (GEMAT), Institut Químic de Sarrià, Universitat Ramón Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Andre Sharon
- Fraunhofer USA - Center for Manufacturing Innovation, 15 Saint Mary's Street, Brookline, MA, 02446, USA.,Mechanical Engineering Department, Boston University, 110 Cummington Mall, Boston, MA, 02215, USA
| | - Alexis F Sauer-Budge
- Fraunhofer USA - Center for Manufacturing Innovation, 15 Saint Mary's Street, Brookline, MA, 02446, USA. .,Biomedical Engineering Department, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA.
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20
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Zhang L, Ding B, Chen Q, Feng Q, Lin L, Sun J. Point-of-care-testing of nucleic acids by microfluidics. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.013] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Nayak S, Blumenfeld NR, Laksanasopin T, Sia SK. Point-of-Care Diagnostics: Recent Developments in a Connected Age. Anal Chem 2017; 89:102-123. [PMID: 27958710 PMCID: PMC5793870 DOI: 10.1021/acs.analchem.6b04630] [Citation(s) in RCA: 281] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Samiksha Nayak
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nicole R. Blumenfeld
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Tassaneewan Laksanasopin
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
| | - Samuel K. Sia
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
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Petralia S, Sciuto EL, Di Pietro ML, Zimbone M, Grimaldi MG, Conoci S. An innovative chemical strategy for PCR-free genetic detection of pathogens by an integrated electrochemical biosensor. Analyst 2017; 142:2090-2093. [DOI: 10.1039/c7an00202e] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An innovative chemical strategy integrated in a miniaturized electrochemical device was developed for sensitive detection of a pathogen genome (HBV virus) without any amplification step.
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Affiliation(s)
- S. Petralia
- STMicroelectronics Stradale Primosole
- 50 - 95121 Catania
- Italy
| | - E. L. Sciuto
- Department of Physics and Astronomy University of Catania
- 95123 Catania
- Italy
| | | | - M. Zimbone
- Department of Physics and Astronomy University of Catania
- 95123 Catania
- Italy
| | - M. G. Grimaldi
- Department of Physics and Astronomy University of Catania
- 95123 Catania
- Italy
| | - S. Conoci
- STMicroelectronics Stradale Primosole
- 50 - 95121 Catania
- Italy
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