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Layne TR, Scott A, Cunha LL, Turiello R, Landers JP. Three-Dimensional-Printed Instrument for Isothermal Nucleic Acid Amplification with Real-Time Colorimetric Imaging. MICROMACHINES 2024; 15:271. [PMID: 38398999 PMCID: PMC10892149 DOI: 10.3390/mi15020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
Isothermal amplification methods have become popular in research due to the simplicity of the technology needed to run the reactions. Specifically, loop-mediated isothermal amplification (LAMP) has been widely used for various applications since first reported in 2000. LAMP reactions are commonly monitored with the use of colorimetry. Although color changes associated with positive amplification are apparent to the naked eye, this detection method is subjective due to inherent differences in visual perception from person to person. The objectivity of the colorimetric detection method may be improved by programmed image capture over time with simultaneous heating. As such, the development of a novel, one-step, automated, and integrated analysis system capable of performing these tasks in parallel is detailed herein. The device is adaptable to multiple colorimetric dyes, cost-effective, 3D-printed for single-temperature convective heating, and features an easy-to-use LabVIEW software program developed for automated image analysis. The device was optimized and subsequently validated using four messenger-RNA targets and mock forensic samples. The performance of our device was determined to be comparable to that of a conventional thermal cycler and smartphone image analysis, respectively. Moreover, the outlined system is capable of objective colorimetric analysis, with exceptional throughput of up to 96 samples at once.
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Affiliation(s)
- Tiffany R. Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Anchi Scott
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Larissa L. Cunha
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Rachelle Turiello
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - James P. Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22903, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
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2
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Du Z, Chen J, Yao W, Zhou H, Wang Z. The critical mixed transport process in remediation agent radial injection into contaminated aquifer plumes. JOURNAL OF CONTAMINANT HYDROLOGY 2024; 261:104301. [PMID: 38278021 DOI: 10.1016/j.jconhyd.2024.104301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/08/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
Accurately depicting the subsurface mixing of radially injected remediation agents with contaminated plumes remains paramount yet challenging for understanding and simulating reactive transport. To address this, the present research employed the mixing dynamics of a potassium permanganate plume injected into a pre-existing contaminated plume. Through combining colour deconvolution and thresholding, we effectively isolated local mixing values within the Gaussian annular narrow mixing zone from the noise of mixed double-plume images. Key findings revealed increasing injection rate promotes plume mixing while adding xanthan gum to increase fluid viscosity moderates interface mixing, reducing mixing zone width by 25.3% and 37.4% for 100 mg/L and 400 mg/L xanthan gum, respectively. Grain size is pivotal, with a 30% increase in mixing areas observed in coarse-grained sands over medium-grained sands. Balancing sufficient mixing and preventing contaminated plume growth is essential for effective remediation. Injection rates below 5 mL/min may suppress contaminated plume expansion, albeit at the possible cost of protracted remediation durations. For the attainment of optimal remediation, it's imperative to harmonize robust mixing processes with the mitigation of contaminated plume expansion - a balance that adding xanthan gum during the initial injection phase seems poised to achieve (xanthan gum optimized the average mixing index (AMI)). These findings provide valuable insights into groundwater plume mixing, supporting effective remediation strategies.
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Affiliation(s)
- Zhipeng Du
- Key Laboratory for Water and Sediment Sciences of Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jiajun Chen
- Key Laboratory for Water and Sediment Sciences of Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Wenqian Yao
- Key Laboratory for Water and Sediment Sciences of Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hongbo Zhou
- Key Laboratory for Water and Sediment Sciences of Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Zhenquan Wang
- Key Laboratory for Water and Sediment Sciences of Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, China
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Woolf MS, Dignan LM, Karas SM, Lewis HM, Kim SN, Geise GM, DeMers HL, Hau D, Gates-Hollingsworth MA, AuCoin DP, Landers JP. Digital image analysis for biothreat detection via rapid centrifugal microfluidic orthogonal flow immunocapture. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1870-1880. [PMID: 36975002 DOI: 10.1039/d3ay00073g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report clear proof-of-principle for centrifugally-driven, multiplexed, paper-based orthogonal flow sandwich-style immunocapture (cOFI) and colorimetric detection of Zaire Ebola virus-like particles. Capture antibodies are immobilized onto nanoporous nitrocellulose membranes that are then laminated into polymeric microfluidic discs to yield ready-to-use analytical devices. Fluid flow is controlled solely by rotational speed, obviating the need for complex pneumatic pumping systems, and providing more precise flow control than with the capillary-driven flow used in traditional lateral flow immunoassays (LFIs). Samples containing the antigen of interest and gold nanoparticle-labeled detection antibodies are pumped centrifugally through the embedded, prefunctionalized membrane where they are subsequently captured to generate a positive, colorimetric signal. When compared to the equivalent LFI counterparts, this cOFI approach generated immunochromatographic colorimetric responses that are objectively darker (saturation), more intense (grayscale), and less variable regarding total area of the color response. We also describe an image analysis approach that enables access to rich color data and area statistics without the need for a commercial 'strip reader' or custom-written image analysis algorithms. Instead, our analytical method exploits inexpensive equipment (e.g., smart phone, flatbed scanner, etc.) and freely available software (Fiji distribution of ImageJ) to permit characterization of immunochromatographic responses that includes multiple color metrics, offering insights beyond typical grayscale analysis. The findings reported here stand as clear proof-of-principle for the feasibility of disc-based, centrifugally driven orthogonal flow through a membrane with immunocapture (cOFI) and colorimetric readout of a sandwich-type immunoassay in less than 15 minutes. Once fully developed, this cOFI platform could render a faster, more accurate diagnosis, while processing multiple samples simul-taneously.
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Affiliation(s)
- M Shane Woolf
- Department of Chemistry, University of Virginia, USA
| | - Leah M Dignan
- Department of Chemistry, University of Virginia, USA
| | - Scott M Karas
- Department of Chemistry, University of Virginia, USA
| | | | - Sabrina N Kim
- Department of Chemistry, University of Virginia, USA
| | | | - Haley L DeMers
- Department of Microbiology and Immunology, University of Nevada, Reno, USA
| | - Derrick Hau
- Department of Microbiology and Immunology, University of Nevada, Reno, USA
| | | | - David P AuCoin
- Department of Microbiology and Immunology, University of Nevada, Reno, USA
| | - James P Landers
- Department of Chemistry, University of Virginia, USA
- Department of Mechanical Engineering, University of Virginia, USA
- Department of Pathology, University of Virginia, USA
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Li Y, Xue H, Fei Y, Yang Y, Huang D, Wang L, Xiong X, Xiong X. A rapid and closed-tube method based on the dual-color fluorescence loop-mediated isothermal amplification for visual detection of Atlantic salmon (Salmo salar). Food Chem 2023; 405:134975. [PMID: 36410220 DOI: 10.1016/j.foodchem.2022.134975] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/16/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) visual detection based on hydroxyl naphthol blue (HNB) and SYTO 9 is often confounded by the narrow color variation window and the requirement of empirical preset of cutoff intensity value. To improve the suitability for naked-eye inspection, the present work proposed a strategy based on the fluorescence property of SYTO 9 and HNB to enlarge the contrast and a novel dual-color fluorescence LAMP (dfLAMP) assay was developed for visual detection of Atlantic salmon. Specifically, HNB of 26.25 μM, blended with SYTO 9 of 0.75-1.5 μM, was added in the mixture before amplification, producing light green fluorescence for both positive and negative samples. After amplification, green or yellow-green fluorescence was observed for positive samples, while only orange-red fluorescence emitted for negative ones, enabling an easy and rapid distinguish. The optimized dfLAMP assay has proved its specificity and can detect as little as 1 fg Atlantic salmon DNA.
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Affiliation(s)
- Yi Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yanjing Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China.
| | - Danping Huang
- The State Light Industry Food Quality Supervision and Detection Station, Nanjing 210009, China
| | - Libin Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China.
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Shigemori H, Maejima K, Shibata H, Hiruta Y, Citterio D. Evaluation of cellophane as platform for colorimetric assays on microfluidic analytical devices. Mikrochim Acta 2023; 190:48. [PMID: 36622479 DOI: 10.1007/s00604-022-05622-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 01/10/2023]
Abstract
Due to their low cost, simplicity, and pump-free liquid transport properties, colorimetric assays on paper spots and microfluidic paper-based analytical devices (µPADs) are regarded as useful tools for point-of-care testing (POCT). However, for certain types of colorimetric assays, the "non-transparent" and "white" characters of paper can be a disadvantage. In this work, the possibilities of using cellophane as an alternative platform for colorimetric assays have been investigated. Cellophane is a low cost and easy-to-handle transparent film made of regenerated cellulose. Owing to its hydrophilic character, cellophane-based microfluidic channels fabricated through a print-cut-laminate approach enabled pump-free liquid transport into multiple detection areas, similar to µPADs. In addition, the water absorption characteristics of cellophane allowed the stable immobilization of water-soluble colorimetric indicators without any surface modification or additional reagents. The transparency of cellophane provides possibilities for simple background coloring of the substrates, increasing the dynamic signal range for hue-based colorimetric assays, as demonstrated for two model assays targeting H2O2 (46-fold increase) and creatinine (3.6-fold increase). Finally, a turbidity detection-based protein assay was realized on black background cellophane spots. The lowest limits of detection achieved with the cellophane-based devices were calculated as 7 µM for H2O2, 2.7 mg dL-1 for creatinine, and 3.5 mg dL-1 for protein (human serum albumin).
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Affiliation(s)
- Hiroki Shigemori
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan.,AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan.,Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-Ku, Kobe, Hyogo, 657-0011, Japan
| | - Kento Maejima
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Hiroyuki Shibata
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Hiruta
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Daniel Citterio
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, Kanagawa, 223-8522, Japan.
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Parween S, Asthana A, Nahar P. Fundamentals of Image-Based Assay (IBA) System for Affordable Point of Care Diagnostics. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Tan W, Zhang L, Jarujamrus P, C G Doery J, Shen W. Improvement Strategies on Colorimetric Performance and Practical Applications of Paper-based Analytical Devices. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tong L, Hutcheson JD. A surface-based calibration approach to enable dynamic and accurate quantification of colorimetric assay systems. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4290-4297. [PMID: 34473147 DOI: 10.1039/d1ay01130h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Colorimetry is widely used in assay systems for its low-cost, ease-of-use, rapidity, moderate storage requirements and intuitively visible effects. However, the application is limited due to its relatively low sensitivity. Conventional colorimetric calibration methods often use a fixed incubation time that can limit the detection range, system robustness and sensitivity. In this paper, we used color saturation to measure the accumulation of product (correlation coefficient R2 = 0.9872), and we created a novel "calibration mesh" method based on an expanded sigmoid function to enhance sensitivity. The novel calibration mesh method can be adapted for a wide variety of assay systems to improve robustness and detection range, and provide a dynamic and faster output.
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Affiliation(s)
- Lin Tong
- Department of Biomedical Engineering, Florida International University, 10555 W Flagler St, EC 2612, Miami, FL, 33174, USA.
| | - Joshua D Hutcheson
- Department of Biomedical Engineering, Florida International University, 10555 W Flagler St, EC 2612, Miami, FL, 33174, USA.
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Marshall JS, Sita ML, Landers JP. Microfluidic Device for the Identification of Biological Sex by Analysis of Latent Fingermark Deposits. MICROMACHINES 2021; 12:mi12040442. [PMID: 33921163 PMCID: PMC8071498 DOI: 10.3390/mi12040442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022]
Abstract
To date, most research regarding amino acid detection and quantification in fingermarks relies on spectrometric methods. Herein, the Sakaguchi colorimetric test was adapted to a rotationally-driven microfluidic platform and used to detect and quantify arginine in fingermarks deposited by male and female donors. A red color indicates the presence of arginine in a given sample following the reaction, and the intensity of this color is linearly proportional to the concentration. Objective detection and quantification of arginine were accomplished using image analysis software (freeware) based on this colorimetric result. The mean concentrations obtained in a blind study were 96.4 ± 5.1 µM for samples from female donors and 55.3 ± 5.3 µM for samples from males. These were not statistically different from the literature values of 94.8 µM ± 12.9 µM for females (p = 0.908) and 54.0 ± 12.6 µM for males (p = 0.914), respectively (± SEM in all cases). Conversely, the experimental means from males and female samples were statistically different from each other (p < 0.001). Objective differentiation between male and female fingermark deposits was achieved in a blind study with 93% accuracy. Additionally, the method was compatible both with samples lifted from common surfaces and with magnetically-powdered samples.
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Affiliation(s)
- Jamila S. Marshall
- Department of Chemistry, University of Virginia, Charlottesville, VA 22903, USA; (J.S.M.); (M.L.S.)
| | - Madelyn L. Sita
- Department of Chemistry, University of Virginia, Charlottesville, VA 22903, USA; (J.S.M.); (M.L.S.)
| | - James P. Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22903, USA; (J.S.M.); (M.L.S.)
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22903, USA
- Departments of Mechanical Engineering and Pathology, University of Virginia, Charlottesville, VA 22903, USA
- Correspondence:
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Digital postprocessing and image segmentation for objective analysis of colorimetric reactions. Nat Protoc 2020; 16:218-238. [PMID: 33299153 DOI: 10.1038/s41596-020-00413-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022]
Abstract
Recently, there has been an explosion of scientific literature describing the use of colorimetry for monitoring the progression or the endpoint result of colorimetric reactions. The availability of inexpensive imaging technology (e.g., scanners, Raspberry Pi, smartphones and other sub-$50 digital cameras) has lowered the barrier to accessing cost-efficient, objective detection methodologies. However, to exploit these imaging devices as low-cost colorimetric detectors, it is paramount that they interface with flexible software that is capable of image segmentation and probing a variety of color spaces (RGB, HSB, Y'UV, L*a*b*, etc.). Development of tailor-made software (e.g., smartphone applications) for advanced image analysis requires complex, custom-written processing algorithms, advanced computer programming knowledge and/or expertise in physics, mathematics, pattern recognition and computer vision and learning. Freeware programs, such as ImageJ, offer an alternative, affordable path to robust image analysis. Here we describe a protocol that uses the ImageJ program to process images of colorimetric experiments. In practice, this protocol consists of three distinct workflow options. This protocol is accessible to uninitiated users with little experience in image processing or color science and does not require fluorescence signals, expensive imaging equipment or custom-written algorithms. We anticipate that total analysis time per region of interest is ~6 min for new users and <3 min for experienced users, although initial color threshold determination might take longer.
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Scott AT, Layne TR, O’Connell KC, Tanner NA, Landers JP. Comparative Evaluation and Quantitative Analysis of Loop-Mediated Isothermal Amplification Indicators. Anal Chem 2020; 92:13343-13353. [DOI: 10.1021/acs.analchem.0c02666] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Anchi T. Scott
- Department of Chemistry, University of Virginia, McCormick Road,
P.O. Box 400319, Charlottesville, Virginia 22904, United States
| | - Tiffany R. Layne
- Department of Chemistry, University of Virginia, McCormick Road,
P.O. Box 400319, Charlottesville, Virginia 22904, United States
| | - Killian C. O’Connell
- Department of Chemistry, University of Virginia, McCormick Road,
P.O. Box 400319, Charlottesville, Virginia 22904, United States
| | - Nathan A. Tanner
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - James P. Landers
- Department of Chemistry, University of Virginia, McCormick Road,
P.O. Box 400319, Charlottesville, Virginia 22904, United States
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