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Seo SB, Lee J, Kim E, Lim J, Jang S, Son SU, Jeong Y, Kang T, Jung J, Lee KG, Lee SW, Kim K, Lim EK. On-site detection of methicillin-resistant Staphylococcus aureus (MRSA) utilizing G-quadruplex based isothermal exponential amplification reaction (GQ-EXPAR). Talanta 2024; 275:126073. [PMID: 38688085 DOI: 10.1016/j.talanta.2024.126073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/28/2024] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has a high incidence in infectious hospitals and communities, highlighting the need for early on-site detection due to its resistance to methicillin antibiotics. The present study introduces a highly sensitive detection system for mecA, a crucial methicillin marker, utilizing an RCA-based isothermal exponential amplification reaction. The G-quadruplex-based isothermal exponential amplification reaction (GQ-EXPAR) method designs probes to establish G-quadruplex secondary structures incorporating thioflavin T for fluorescence. The system, unlike conventional genetic detection methods, works with portable isothermal PCR devices (isoQuark), facilitating on-site detection. A detection limit of 0.1 fmol was demonstrated using synthetic DNA, and effective detection was proven using thermal lysis. The study also validated the detection of targets swabbed from surfaces within bacterial 3D nanostructures using the GQ-EXPAR method. After applying complementary sequences to the padlock probe for the target, the GQ-EXPAR method can be used on various targets. The developed method could facilitate rapid and accurate diagnostics within MRSA strains.
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Affiliation(s)
- Seung Beom Seo
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Cogno-Mechatronics Engineering, Pusan National University, Pusan, 46241, Republic of Korea
| | - Jina Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Eunjung Kim
- Department of Bioengineering and Nano-Bioengineering, Research Center for Bio Materials and Process, Incheon National University, Incheon, 22012, Republic of Korea; Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Jaewoo Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Medical Device Development Center, Osong Medical Innovation Foundation, 123, Osongsaengmyeong-ro, Chungcheongbuk-do, 28160, Republic of Korea
| | - Soojin Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Seong Uk Son
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Yeonwoo Jeong
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Taejeoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Kyoung G Lee
- Center for Nanobio Develpment, National NanoFab Center (NNFC), Daejeon, 34141, Republic of Korea
| | | | - Kyujung Kim
- Department of Cogno-Mechatronics Engineering, Pusan National University, Pusan, 46241, Republic of Korea.
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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2
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Zamuner FT, Ramos-López A, García-Negrón A, Purcell-Wiltz A, Cortés-Ortiz A, Cuevas AR, Gosala K, Winkler E, Sidransky D, Guerrero-Preston R. Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings. Biomed Rep 2024; 21:112. [PMID: 38912171 PMCID: PMC11190640 DOI: 10.3892/br.2024.1800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Late-stage cancers lack effective treatment, underscoring the need for early diagnosis to improve prognosis and decrease mortality rates. Molecular markers, such as DNA methylation, offer promise in early cancer detection. The present study compared commercial kits for analyzing DNA from cervical liquid cytology samples in cancer screening. Rapid bisulfite conversion kits using silica spin-columns and magnetic beads were assessed against standard DNA extraction and bisulfite conversion methods for profiling DNA methylation using quantitative methylation-specific PCR. β-actin amplification indicated the suitability of small sample volumes for methylation studies using either the pellet or supernatant (cell-free DNA) parts. Comparison of Bisulfite Conversion Kit-Whole Cell (Abcam), Methylamp Bisulfite Modification (Epigentek), EpiTect Fast LyseAll Bisulfite Kit (Qiagen GmbH) and EZ DNA Methylation-Direct Kit (Zymo Research Corp.) showed no significant differences in β-actin cycle threshold values. EZ-96 DNA Methylation-Lightning MagPrep (Zymo Research Corp.), a hybrid kit in a 96-well plate format, exhibited swift turnaround time and similar amplification efficiency. Automation with magnetic bead kits increased throughput without compromising amplification efficiency in open PCR systems. Cost analysis favored direct kits over the gold standard manual protocol. This comparison aids in selecting cost-effective DNA methylation diagnostic tests. The present study confirmed comparable kit performance in methylation-based analysis, highlighting the adequacy of cytology samples and the potential of bodily fluids as alternatives for liquid biopsy.
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Affiliation(s)
- Fernando T. Zamuner
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Ashley Ramos-López
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
| | | | - Ana Purcell-Wiltz
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00725, Puerto Rico
| | - Andrea Cortés-Ortiz
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00725, Puerto Rico
| | - Aniris Román Cuevas
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Biology, University of Puerto Rico, Río Piedras 00931, Puerto Rico
| | - Keerthana Gosala
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eli Winkler
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- New York University Langone Health, New York, NY 10016, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- LifeGene-Biomarks, FastForward Innovation Hub, Baltimore, MD 21205, USA
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3
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Kwon T, Leroux AC, Zang H, Pollard D, Zehe C, Akbari S. Cell-based shear stress sensor for bioprocessing. J Biotechnol 2024; 390:71-79. [PMID: 38685415 DOI: 10.1016/j.jbiotec.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/15/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Shear stress during bioreactor cultivation has significant impact on cell health, growth, and fate. Mammalian cells, such as T cells and stem cells, in next-generation cell therapies are especially more sensitive to shear stress present in their culture environment than bacteria. Therefore, a base knowledge about the shear stress imposed by the bioprocesses is needed to optimize the process parameters and enhance cell growth and yield. However, typical computational flow dynamics modeling or PCR-based assays have several limitations. Implementing and interpreting computational modeling often requires technical specialties and also relies on many simplifications in modeling. PCR-based assays evaluating changes in gene expression involve cumbersome sample preparation with the use of advanced lab equipment and technicians, hampering rapid and straightforward assessment of shear stress. Here, we developed a simple, cell-based shear stress sensor for measuring shear stress levels in different bioreactor types and operating conditions. We engineered a CHO-DG44 cell line to make its stress sensitive promoter EGR-1 control GFP expression. Subsequently, the stressed CHO cells were transferred into a 96 well plate, and their GFP levels (population mean fluorescence) were monitored using a cell analysis instrument (Incucyte®, Sartorius Stedim Biotech) over 24 hours. After conducting sensor characterization, which included chemical induced stress and fluid shear stress, and stability investigation, we tested the shear stress sensor in the Ambr® 250 bioreactor vessels (Sartorius Stedim Biotech) with different impeller and vessel designs. The results showed that the CHO cell-based shear stress sensors expressed higher GFP levels in response to higher shear stress magnitude or exposure time. These sensors are useful tools to assess shear stress imposed by bioreactor conditions and can facilitate the design of various bioreactor vessels with a low shear stress profile.
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Affiliation(s)
- Taehong Kwon
- Sartorius Stedim North America Inc., United States
| | | | - Han Zang
- Boston University, Boston, MA, USA
| | | | | | - Samin Akbari
- Sartorius Stedim North America Inc., United States.
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Jafar S, Jamil S, Yasin MS, Naseem A, Zahoor MY, Shehzad W, Imran M. Successful application of modified crude DNA extraction from muscle tissues for various types of PCR amplifications. Mol Biol Rep 2024; 51:490. [PMID: 38578476 DOI: 10.1007/s11033-024-09356-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND One of the most challenging aspects of nucleic acid amplification tests is the extraction of genomic DNA. However, achieving satisfactory quality and quantity of genomic DNA is not always easy, while the demand for rapid, low-cost and less laborious DNA isolation methods is ever-increasing. METHODS AND RESULTS We have developed a rapid (⁓2 min) crude DNA extraction method leading to direct-PCR that requires minimum reagents and laboratory equipment. It was developed by eliminating the time-consuming purification steps of DNA extraction, by processing the sample in optimized amounts of Taq KCl PCR buffer and DNARelease Additive/Proteinase K in only two minutes and carrying out amplification using conventional Taq DNA polymerase. The DNA preparation method was validated on muscle tissue samples from 12 different species as well as 48 cooked meat samples. Its compatibility was also successfully tested with different types of PCR amplification platforms extensively used for genetic analysis, such as simplex PCR, PCR-RFLP (Restriction Fragment Length Polymorphism), multiplex PCR, isothermal amplification, real-time PCR and DNA sequencing. CONCLUSIONS The developed protocol provides sufficient amount of crude DNA from muscle tissues of different species for PCR amplifications to identify species-of-origin via different techniques coupled with PCR. The simplicity and robustness of this protocol make nucleic acid amplification assays more accessible and affordable to researchers and authorities for both laboratory and point-of-care tests.
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Affiliation(s)
- Sana Jafar
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Salman Jamil
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Muhammad Sheraz Yasin
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Asif Naseem
- Institute of Molecular Biology and Biotechnology, The University of Lahore (Sargodha campus), 10-km Lahore road, Sargodha, Punjab, Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Wasim Shehzad
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Muhammad Imran
- Molecular Diagnostics Laboratory, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan.
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5
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Han DH, Lee G, Oh U, Choi Y, Park JK. Evaluation of Fluid Behaviors in a Pushbutton-Activated Microfluidic Device for User-Independent Flow Control. MICROMACHINES 2024; 15:465. [PMID: 38675276 PMCID: PMC11052212 DOI: 10.3390/mi15040465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Although numerous studies have been conducted to realize ideal point-of-care testing (POCT), the development of a user-friendly and user-independent power-free microfluidic platform is still a challenge. Among various methods, the finger-actuation method shows a promising technique that provides a user-friendly and equipment-free way of delivering fluid in a designated manner. However, the design criteria and elaborate evaluation of the fluid behavior of a pushbutton-activated microfluidic device (PAMD) remain a critical bottleneck to be widely adopted in various applications. In this study, we have evaluated the fluid behavior of the PAMD based on various parameters, such as pressing velocity and depth assisted by a press machine. We have further developed a user-friendly and portable pressing block that reduces user variation in fluid behavior based on the evaluation.
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Affiliation(s)
- Dong Hyun Han
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (D.H.H.); (G.L.); (U.O.); (Y.C.)
| | - Gihyun Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (D.H.H.); (G.L.); (U.O.); (Y.C.)
| | - Untaek Oh
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (D.H.H.); (G.L.); (U.O.); (Y.C.)
| | - Yejin Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (D.H.H.); (G.L.); (U.O.); (Y.C.)
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; (D.H.H.); (G.L.); (U.O.); (Y.C.)
- KI for Health Science and Technology, KAIST Institutes (KI), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KI for NanoCentury, KAIST Institutes (KI), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Supianto M, Yoo DK, Hwang H, Oh HB, Jhung SH, Lee HJ. Linker-Preserved Iron Metal-Organic Framework-Based Lateral Flow Assay for Sensitive Transglutaminase 2 Detection in Urine Through Machine Learning-Assisted Colorimetric Analysis. ACS Sens 2024; 9:1321-1330. [PMID: 38471126 DOI: 10.1021/acssensors.3c02250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
A groundbreaking demonstration of the utilization of the metal-organic framework MIL-101(Fe) as an exceptionally perceptive visual label in colorimetric lateral flow assays (LFA) is described. This pioneering approach enables the precise identification of transglutaminase 2 (TGM2), a recognized biomarker for chronic kidney disease (CKD), in urine specimens, which offers a remarkably sensitive naked-eye detection mechanism. The surface of MIL-101(Fe) was modified with oxalyl chloride, adipoyl chloride, and poly(acrylic) acid (PAA); these not only improved the labeling material stability in a complex matrix but also achieved a systematic control in the detection limit of the TGM2 concentration using our LFA platform. The advanced LFA with the MIL-101(Fe)-PAA label can detect TGM2 concentrations down to 0.012, 0.009, and 0.010 nM in Tris-HCl buffer, urine, and desalted urine, respectively, which are approximately 55-fold lower than those for a conventional AuNP-based LFAs. Aside from rapid TGM2 detection (i.e., within 20 min), the performance of the MIL-101(Fe)-PAA-based LFA on reproducibility [coefficients of variation (CV) < 2.9%] and recovery (95.9-103.2%) along with storage stability within 25 days of observation (CV < 6.0%) shows an acceptable parameter range for quantitative analysis. A sophisticated sensing method grounded in machine learning principles was also developed, specifically aimed at precisely deducing the TGM2 concentration by analyzing immunoreaction sites. More importantly, our developed LFA offers potential for clinical measurement of TGM2 concentration in normal human urine and CKD patients' samples.
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Affiliation(s)
- Mulya Supianto
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu-city 41566, Republic of Korea
| | - Dong Kyu Yoo
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu-city 41566, Republic of Korea
| | - Hagyeong Hwang
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Sung Hwa Jhung
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu-city 41566, Republic of Korea
| | - Hye Jin Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu-city 41566, Republic of Korea
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Lee S, Park JS, Woo H, Yoo YK, Lee D, Chung S, Yoon DS, Lee KB, Lee JH. Rapid deep learning-assisted predictive diagnostics for point-of-care testing. Nat Commun 2024; 15:1695. [PMID: 38402240 PMCID: PMC10894262 DOI: 10.1038/s41467-024-46069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/12/2024] [Indexed: 02/26/2024] Open
Abstract
Prominent techniques such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), and rapid kits are currently being explored to both enhance sensitivity and reduce assay time for diagnostic tests. Existing commercial molecular methods typically take several hours, while immunoassays can range from several hours to tens of minutes. Rapid diagnostics are crucial in Point-of-Care Testing (POCT). We propose an approach that integrates a time-series deep learning architecture and AI-based verification, for the enhanced result analysis of lateral flow assays. This approach is applicable to both infectious diseases and non-infectious biomarkers. In blind tests using clinical samples, our method achieved diagnostic times as short as 2 minutes, exceeding the accuracy of human analysis at 15 minutes. Furthermore, our technique significantly reduces assay time to just 1-2 minutes in the POCT setting. This advancement has the potential to greatly enhance POCT diagnostics, enabling both healthcare professionals and non-experts to make rapid, accurate decisions.
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Affiliation(s)
- Seungmin Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
| | - Jeong Soo Park
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Mechanical Engineering, Korea University, 145 Anam-ro, Seoungbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyowon Woo
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Yong Kyoung Yoo
- Department of Electronic Engineering, Catholic Kwandong University, 24, Beomil-ro 579 beon-gil, Gangneung-si, Gangwon-do, 25601, Republic of Korea
| | - Dongho Lee
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea
| | - Seok Chung
- School of Mechanical Engineering, Korea University, 145 Anam-ro, Seoungbuk-gu, Seoul, 02841, Republic of Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
- Astrion Inc, Seoul, 02841, Republic of Korea
| | - Ki-Baek Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea.
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea.
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Ahamed MA, Khalid MAU, Dong M, Politza AJ, Zhang Z, Kshirsagar A, Liu T, Guan W. Sensitive and specific CRISPR-Cas12a assisted nanopore with RPA for Monkeypox detection. Biosens Bioelectron 2024; 246:115866. [PMID: 38029710 PMCID: PMC10842690 DOI: 10.1016/j.bios.2023.115866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023]
Abstract
Monkeypox virus (MPXV) poses a global health emergency, necessitating rapid, simple, and accurate detection to manage its spread effectively. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technique has emerged as a promising next-generation molecular diagnostic approach. Here, we developed a highly sensitive and specific CRISPR-Cas12a assisted nanopore (SCAN) with isothermal recombinase polymerase amplification (RPA) for MPXV detection. The RPA-SCAN method offers a sensitivity unachievable with unamplified SCAN while also addressing the obstacles of PCR-SCAN for point-of-care applications. We demonstrated that size-counting of single molecules enables analysis of reaction-time dependent distribution of the cleaved reporter. Our MPXV-specific RPA assay achieved a limit of detection (LoD) of 19 copies in a 50 μL reaction system. By integrating 2 μL of RPA amplifications into a 20 μL CRISPR reaction, we attained an overall LoD of 16 copies/μL (26.56 aM) of MPXV at a 95% confidence level using the SCAN sensor. We also verified the specificity of RPA-SCAN in distinguishing MPXV from cowpox virus with 100% accuracy. These findings suggest that the isothermal RPA-SCAN device is well-suited for highly sensitive and specific Monkeypox detection. Given its electronic nature and miniaturization potential, the RPA-SCAN system paves the way for diagnosing a wide array of other infectious pathogens at the point of care.
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Affiliation(s)
- Md Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | | | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Zhikun Zhang
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Aneesh Kshirsagar
- Department of Electrical 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 Electrical Engineering, Pennsylvania State University, University Park, 16802, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA.
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Fan C, Xie L, Zhao F, Wang J, Lin X, Chen X. Novel fluorescence nano-orbital biosensor for highly sensitive microRNA detection. Anal Chim Acta 2024; 1288:342172. [PMID: 38220303 DOI: 10.1016/j.aca.2023.342172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/18/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND MicroRNAs play an important role in regulating cell function and gene expression. Early prevention and clinical diagnosis of diseases have high requirements for high-sensitivity detection of microRNAs. Due to the limitations of tedious operation and large sample size, miRNA with small molecular weight and low expression abundance cannot be accurately detected in traditional miRNA detection. To improve the sensitivity and accuracy of detection, we established a novel biosensor based on nucleic acid circuit of signal amplification, which converted miRNA recognition into a fluorescence signal for amplification. RESULTS We designed a biosensor based on an exponential amplification reaction with cascaded HCR and DNAzyme nucleic acid circuit (named E-NOF biosensor) by amplicon sub-fragments to trigger the construction of fluorescence nano-orbitals (NOF), which could be used to detect miRNA ultrasensitively. By modifying two fluorophores (Cy3 and Cy5) on the chain of constructing nano-orbitals, when the amplicon triggered the construction of nano-orbitals, fluorescence resonance energy transfer (FRET) occurred between Cy3 and Cy5, and then two fluorescence signals with different trends could be observed. Therefore, through the ratio of the two signals, we could quantitatively and quickly detect the miRNA from 1 fM to 100 nM, and the E-NOF biosensor detection limit was as low as 0.129 fM. Furthermore, the HCR nucleic acid circuit cascaded with DNAzyme could enrich the fluorophores on the nano-orbitals and significantly enhance the fluorescence signal by accelerating the reaction rate. SIGNIFICANCE According to our understanding, the E-NOF biosensor is the first strategy to cascade EXPAR with HCR and DNAzyme nucleic acid circuit for miRNA-1246 detection. Accurate results can be obtained in only 120 min. Compared with the traditional HCR system, the sensitivity of the new E-NOF biosensor is increased by 1 × 109 times. Furthermore, the biosensor can also detect biomarkers in human serum samples. It has great potential in miRNA detection and identification.
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Affiliation(s)
- Cong Fan
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China
| | - Longjie Xie
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China
| | - Feng Zhao
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Jingjing Wang
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China
| | - Xiandong Lin
- Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Xian Chen
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China.
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10
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Park DH, Haizan I, Ahn MJ, Choi MY, Kim MJ, Choi JH. One-Pot CRISPR-Cas12a-Based Viral DNA Detection via HRP-Enriched Extended ssDNA-Modified Au@Fe 3O 4 Nanoparticles. BIOSENSORS 2024; 14:26. [PMID: 38248403 PMCID: PMC10812942 DOI: 10.3390/bios14010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
In the context of virus outbreaks, the need for early and accurate diagnosis has become increasingly urgent. In addition to being crucial for effective disease control, timely and precise detection of viral infections is also necessary for the implementation of essential public health measures, especially during pandemics. Among these measures, point-of-care testing (POCT) stands out as a powerful approach with the potential to revolutionize the landscape of viral diagnosis. In this study, we developed a one-pot clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a-based viral DNA detection system tailored for POCT; this method utilizes multi-enzyme-modified Au@Fe3O4 nanoparticles. As an alternative to nucleic acid amplification, our method uses single-stranded DNA elongation to facilitate multi-enzyme modification; this guarantees heightened sensitivity and expedites the diagnostic process. We achieved a satisfactory limit of detection of 0.25 nM, demonstrating the remarkable sensitivity of the method without the need for sophisticated equipment. The incorporation of Au@Fe3O4 magnetic nanoparticles facilitates sample separation, further streamlining the workflow and reinforcing the simplicity of our method. This integrated approach offers a practical solution for sensitive viral DNA detection in POCT scenarios, advancing the field of rapid and accurate diagnostics.
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Affiliation(s)
- Dong Hyeok Park
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea; (D.H.P.); (M.Y.C.); (M.J.K.)
| | - Izzati Haizan
- Department of Bioprocess Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea;
| | - Min Ju Ahn
- Department of Biotechnology, Jeonbuk National University, 79 Gobongro, Iksan-si 54596, Jeollabuk-do, Republic of Korea;
| | - Min Yu Choi
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea; (D.H.P.); (M.Y.C.); (M.J.K.)
| | - Min Jung Kim
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea; (D.H.P.); (M.Y.C.); (M.J.K.)
| | - Jin-Ha Choi
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea; (D.H.P.); (M.Y.C.); (M.J.K.)
- Department of Bioprocess Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea;
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11
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Lee S, Bi L, Chen H, Lin D, Mei R, Wu Y, Chen L, Joo SW, Choo J. Recent advances in point-of-care testing of COVID-19. Chem Soc Rev 2023; 52:8500-8530. [PMID: 37999922 DOI: 10.1039/d3cs00709j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Advances in microfluidic device miniaturization and system integration contribute to the development of portable, handheld, and smartphone-compatible devices. These advancements in diagnostics have the potential to revolutionize the approach to detect and respond to future pandemics. Accordingly, herein, recent advances in point-of-care testing (POCT) of coronavirus disease 2019 (COVID-19) using various microdevices, including lateral flow assay strips, vertical flow assay strips, microfluidic channels, and paper-based microfluidic devices, are reviewed. However, visual determination of the diagnostic results using only microdevices leads to many false-negative results due to the limited detection sensitivities of these devices. Several POCT systems comprising microdevices integrated with portable optical readers have been developed to address this issue. Since the outbreak of COVID-19, effective POCT strategies for COVID-19 based on optical detection methods have been established. They can be categorized into fluorescence, surface-enhanced Raman scattering, surface plasmon resonance spectroscopy, and wearable sensing. We introduced next-generation pandemic sensing methods incorporating artificial intelligence that can be used to meet global health needs in the future. Additionally, we have discussed appropriate responses of various testing devices to emerging infectious diseases and prospective preventive measures for the post-pandemic era. We believe that this review will be helpful for preparing for future infectious disease outbreaks.
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Affiliation(s)
- Sungwoon Lee
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea.
| | - Liyan Bi
- School of Special Education and Rehabilitation, Binzhou Medical University, Yantai, 264003, China
| | - Hao Chen
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Dong Lin
- School of Pharmacy, Bianzhou Medical University, Yantai, 264003, China
| | - Rongchao Mei
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Yantai 264003, China
| | - Yixuan Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Yantai 264003, China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Yantai 264003, China
- School of Pharmacy, Bianzhou Medical University, Yantai, 264003, China
| | - Sang-Woo Joo
- Department of Information Communication, Materials, and Chemistry Convergence Technology, Soongsil University, Seoul 06978, South Korea
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea.
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12
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Calorenni P, Leonardi AA, Sciuto EL, Rizzo MG, Faro MJL, Fazio B, Irrera A, Conoci S. PCR-Free Innovative Strategies for SARS-CoV-2 Detection. Adv Healthc Mater 2023; 12:e2300512. [PMID: 37435997 DOI: 10.1002/adhm.202300512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 07/13/2023]
Abstract
The pandemic outbreak caused by SARS-CoV-2 coronavirus brought a crucial issue in public health causing up to now more than 600 million infected people and 6.5 million deaths. Conventional diagnostic methods are based on quantitative reverse transcription polymerase chain reaction (RT-qPCR assay) and immuno-detection (ELISA assay). However, despite these techniques have the advantages of being standardized and consolidated, they keep some main limitations in terms of accuracy (immunoassays), time/cost consumption of analysis, the need for qualified personnel, and lab constrain (molecular assays). There is crucial the need to develop new diagnostic approaches for accurate, fast and portable viral detection and quantification. Among these, PCR-free biosensors represent the most appealing solution since they can allow molecular detection without the complexity of the PCR. This will enable the possibility to be integrated in portable and low-cost systems for massive and decentralized screening of SARS-CoV-2 in a point-of-care (PoC) format, pointing to achieve a performant identification and control of infection. In this review, the most recent approaches for the SARS-CoV-2 PCR-free detection are reported, describing both the instrumental and methodological features, and highlighting their suitability for a PoC application.
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Affiliation(s)
- Paolo Calorenni
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Antonio A Leonardi
- Department of Physics and Astronomy, University of Catania, Via Santa Sofia 64, Catania, 95123, Italy
| | - Emanuele L Sciuto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Maria G Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Maria J Lo Faro
- Department of Physics and Astronomy, University of Catania, Via Santa Sofia 64, Catania, 95123, Italy
| | - Barbara Fazio
- URT Lab Sens Beyond Nano, CNR-DSFTM, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Alessia Irrera
- URT Lab Sens Beyond Nano, CNR-DSFTM, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Sabrina Conoci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
- URT Lab Sens Beyond Nano, CNR-DSFTM, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
- Department of Chemistry ''Giacomo Ciamician'', University of Bologna, Via Selmi 2, Bologna, 40126, Italy
- CNR-IMM, Institute for Microelectronics and Microsystems, Ottava Strada n.5, Catania, I-95121, Italy
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13
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Shin Y, Kwak T, Whang K, Jo Y, Hwang JH, Hwang I, An HJ, Lim Y, Choi I, Kim D, Lee LP, Kang T. Bubble-free diatoms polymerase chain reaction. Biosens Bioelectron 2023; 237:115489. [PMID: 37402347 DOI: 10.1016/j.bios.2023.115489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/16/2023] [Accepted: 06/18/2023] [Indexed: 07/06/2023]
Abstract
Polymerase chain reaction (PCR) in small fluidic systems not only improves speed and sensitivity of deoxyribonucleic acid (DNA) amplification but also achieves high-throughput quantitative analyses. However, air bubble trapping and growth during PCR has been considered as a critical problem since it causes the failure of DNA amplification. Here we report bubble-free diatom PCR by exploiting a hierarchically porous silica structure of single-celled algae. We show that femtoliters of PCR solution can be spontaneously loaded into the diatom interior without air bubble trapping due to the surface hydrophilicity and pore structure of the diatom. We discover that a large pressure gradient between air bubbles and nanopores rapidly removes residual air bubbles through the periodically arrayed nanopores during thermal cycling. We demonstrate the DNA amplification by diatom PCR without air bubble trapping and growth. Finally, we successfully detect DNA fragments of SARS-CoV-2 with as low as 10 copies/μl by devising a microfluidic device integrated with diatoms assembly. We believe that our work can be applied to many PCR applications for innovative molecular diagnostics and provides new opportunities for naturally abundant diatoms to create innovative biomaterials in real-world applications.
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Affiliation(s)
- Yonghee Shin
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 121-742, South Korea; Institute of Integrated Biotechnology, Sogang University, Seoul, 121-742, South Korea; Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Taejin Kwak
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Keumrai Whang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 121-742, South Korea
| | - Yuseung Jo
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 121-742, South Korea
| | - Jeong Ha Hwang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 121-742, South Korea
| | - Inhyeok Hwang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 121-742, South Korea
| | - Hyun Ji An
- Department of Life Science, University of Seoul, Seoul, 02504, South Korea
| | - Youngwook Lim
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Inhee Choi
- Department of Life Science, University of Seoul, Seoul, 02504, South Korea
| | - Dongchoul Kim
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea.
| | - Luke P Lee
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, USA; Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, 16419, South Korea.
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 121-742, South Korea; Institute of Integrated Biotechnology, Sogang University, Seoul, 121-742, South Korea.
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14
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Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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15
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Jiang K, Lee JH, Fung TS, Wu J, Liu C, Mi H, Rajapakse RPVJ, Balasuriya UBR, Peng YK, Go YY. Next-generation diagnostic test for dengue virus detection using an ultrafast plasmonic colorimetric RT-PCR strategy. Anal Chim Acta 2023; 1274:341565. [PMID: 37455070 DOI: 10.1016/j.aca.2023.341565] [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: 04/13/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023]
Abstract
The current global COVID-19 pandemic once again highlighted the urgent need for a simple, cost-effective, and sensitive diagnostic platform that can be rapidly developed for distribution and easy access in resource-limited areas. Here, we present a simple and low-cost plasmonic photothermal (PPT)-reverse transcription-colorimetric polymerase chain reaction (RTcPCR) for molecular diagnosis of dengue virus (DENV) infection. The assay can be completed within 54 min with an estimated detection limit of 1.6 copies/μL of viral nucleic acid. The analytical sensitivity and specificity of PPT-RTcPCR were comparable to that of the reference RT-qPCR assay. Moreover, the clinical performance of PPT-RTcPCR was evaluated and validated using 158 plasma samples collected from patients suspected of dengue infection. The results showed a diagnostic agreement of 97.5% compared to the reference RT-qPCR and demonstrated a clinical sensitivity and specificity of 97.0% and 100%, respectively. The simplicity and reliability of our PPT-RTcPCR strategy suggest it can provide a foundation for developing a field-deployable diagnostic assay for dengue and other infectious diseases.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, College of Science, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan, 31538, South Korea.
| | - To Sing Fung
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Congnuan Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - Hua Mi
- Department of Chemistry, College of Science, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - R P V Jayanthe Rajapakse
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Yung-Kang Peng
- Department of Chemistry, College of Science, City University of Hong Kong, Kowloon, 999077, Hong Kong, China.
| | - Yun Young Go
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong, China.
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16
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Luo F, Zhan L, Deng Y, Qiao K, Pan N, Weng Z, Lin C, Qiu B, Lin Z. Oxygen-induced dual-signal point-of-care testing aptasensor for aflatoxin B1 detection using platinum nanoparticle catalysis in visual fluorometry and gravimetry. Anal Chim Acta 2023; 1273:341544. [PMID: 37423670 DOI: 10.1016/j.aca.2023.341544] [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: 05/03/2023] [Revised: 06/16/2023] [Accepted: 06/18/2023] [Indexed: 07/11/2023]
Abstract
Point-of-care testing (POCT) has experienced rapid development owing to its advantages of rapid testing, low cost and strong operability, making it indispensable for analyte detection in outdoor or rural areas. In this study, we propose a novel method for the detection of aflatoxin B1 (AFB1) using a dual-signal readout approach within a unified system. This method employs dual channel modes, namely visual fluorescence and weight measurements, as the signal readouts. Specifically, a pressure-sensitive material is utilized as a visual fluorescent agent, its signal can be quenched in the presence of high oxygen pressure. Additionally, an electronic balance, commonly used for weight measurement, is adopted as another signal device, where the signal is generated through the catalytic decomposition of H2O2 by platinum nanoparticles. The experimental results demonstrate that the proposed device enables accurate AFB1 detection within the concentration range of 1.5-32 μg mL-1, with a detection limit of 0.47 μg mL-1. Moreover, this method has been successfully applied for practical AFB1 detection with satisfactory results. Notably, this study pioneers the use of a pressure-sensitive material as a visual signal in POCT. By addressing the limitations of single-signal readout approaches, our method fulfills requirements of intuitiveness, sensitivity, quantitative analysis and reusability.
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Affiliation(s)
- Fang Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China; MOE Key Laboratory of Analysis and Detection for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China.
| | - Linxiu Zhan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China; MOE Key Laboratory of Analysis and Detection for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Ye Deng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China; MOE Key Laboratory of Analysis and Detection for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Kun Qiao
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361013, China
| | - Nan Pan
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, 361013, China
| | - Zuquan Weng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Cuiying Lin
- MOE Key Laboratory of Analysis and Detection for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Bin Qiu
- MOE Key Laboratory of Analysis and Detection for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Zhenyu Lin
- MOE Key Laboratory of Analysis and Detection for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China.
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17
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Briciu-Burghina C, Power S, Delgado A, Regan F. Sensors for Coastal and Ocean Monitoring. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:451-469. [PMID: 37314875 DOI: 10.1146/annurev-anchem-091922-085746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In situ water monitoring sensors are critical to gain an understanding of ocean biochemistry and ecosystem health. They enable the collection of high-frequency data and capture ecosystem spatial and temporal changes, which in turn facilitate long-term global predictions. They are used as decision support tools in emergency situations and for risk mitigation, pollution source tracking, and regulatory monitoring. Advanced sensing platforms exist to support various monitoring needs together with state-of-the-art power and communication capabilities. To be fit-for-purpose, sensors must withstand the challenging marine environment and provide data at an acceptable cost. Significant technological advancements have catalyzed the development of new and improved sensors for coastal and oceanographic applications. Sensors are becoming smaller, smarter, more cost-effective, and increasingly specialized and diversified. This article, therefore, provides a review of the state-of-the art oceanographic and coastal sensors. Progress in sensor development is discussed in terms of performance and the key strategies used for achieving robustness, marine rating, cost reduction, and antifouling protection.
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Affiliation(s)
| | - Sean Power
- DCU Water Institute, School of Chemical Sciences, Dublin City University, Dublin, Ireland;
| | - Adrian Delgado
- DCU Water Institute, School of Chemical Sciences, Dublin City University, Dublin, Ireland;
| | - Fiona Regan
- DCU Water Institute, School of Chemical Sciences, Dublin City University, Dublin, Ireland;
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18
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Costantini F, Lovecchio N, Nandimandalam M, Manglli A, Faggioli F, Biasin M, Manetti C, Roversi PF, Nascetti A, de Cesare G, Caputo D. Biomolecular Monitoring Tool Based on Lab-on-Chip for Virus Detection. BIOSENSORS 2023; 13:bios13050544. [PMID: 37232905 DOI: 10.3390/bios13050544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Lab-on-Chip (LoC) devices for performing real-time PCR are advantageous compared to standard equipment since these systems allow to conduct in-field quick analysis. The development of LoCs, where the components for performing the nucleic acid amplification are all integrated, can be an issue. In this work, we present a LoC-PCR device where thermalization, temperature control and detection elements are all integrated on a single glass substrate named System-on-Glass (SoG) obtained using metal thin-film deposition. By using a microwell plate optically coupled with the SoG, real-time reverse transcriptase PCR of RNA extracted from both a plant and human virus has been carried out in the developed LoC-PCR device. The limit of detection and time of analysis for the detection of the two viruses by using the LoC-PCR were compared with those achieved by standard equipment. The results showed that the two systems can detect the same concentration of RNA; however, the LoC-PCR performs the analysis in half of the time compared to the standard thermocycler, with the advantage of the portability, leading to a point-of-care device for several diagnostic applications.
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Affiliation(s)
- Francesca Costantini
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Nicola Lovecchio
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome, 00184 Rome, Italy
| | - Manasa Nandimandalam
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Ariana Manglli
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Francesco Faggioli
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Cesare Manetti
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Augusto Nascetti
- School of Aerospace Engineering, Sapienza University of Rome, 00138 Rome, Italy
| | - Giampiero de Cesare
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Domenico Caputo
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
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19
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Bălan AM, Bodolea C, Trancă SD, Hagău N. Trends in Molecular Diagnosis of Nosocomial Pneumonia Classic PCR vs. Point-of-Care PCR: A Narrative Review. Healthcare (Basel) 2023; 11:healthcare11091345. [PMID: 37174887 PMCID: PMC10177880 DOI: 10.3390/healthcare11091345] [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: 03/24/2023] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Nosocomial pneumonia is one of the most frequent hospital-acquired infections. One of the types of nosocomial pneumonia is ventilator-associated pneumonia, which occurs in endotracheally intubated patients in intensive care units (ICU). Ventilator-associated pneumonia may be caused by multidrug-resistant pathogens, which increase the risk of complications due to the difficulty in treating them. Pneumonia is a respiratory disease that requires targeted antimicrobial treatment initiated as early as possible to have a good outcome. For the therapy to be as specific and started sooner, diagnostic methods have evolved rapidly, becoming quicker and simpler to perform. Polymerase chain reaction (PCR) is a rapid diagnostic technique with numerous advantages compared to classic plate culture-based techniques. Researchers continue to improve diagnostic methods; thus, the newest types of PCR can be performed at the bedside, in the ICU, so-called point of care testing-PCR (POC-PCR). The purpose of this review is to highlight the benefits and drawbacks of PCR-based techniques in managing nosocomial pneumonia.
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Affiliation(s)
- Andrei-Mihai Bălan
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Constantin Bodolea
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Sebastian Daniel Trancă
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Emergency Department, The Emergency County Hospital Cluj, 400347 Cluj-Napoca, Romania
| | - Natalia Hagău
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, "Regina Maria" Hospital, 400221 Cluj-Napoca, Romania
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Cui X, Ruan Q, Zhuo X, Xia X, Hu J, Fu R, Li Y, Wang J, Xu H. Photothermal Nanomaterials: A Powerful Light-to-Heat Converter. Chem Rev 2023. [PMID: 37133878 DOI: 10.1021/acs.chemrev.3c00159] [Citation(s) in RCA: 97] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
All forms of energy follow the law of conservation of energy, by which they can be neither created nor destroyed. Light-to-heat conversion as a traditional yet constantly evolving means of converting light into thermal energy has been of enduring appeal to researchers and the public. With the continuous development of advanced nanotechnologies, a variety of photothermal nanomaterials have been endowed with excellent light harvesting and photothermal conversion capabilities for exploring fascinating and prospective applications. Herein we review the latest progresses on photothermal nanomaterials, with a focus on their underlying mechanisms as powerful light-to-heat converters. We present an extensive catalogue of nanostructured photothermal materials, including metallic/semiconductor structures, carbon materials, organic polymers, and two-dimensional materials. The proper material selection and rational structural design for improving the photothermal performance are then discussed. We also provide a representative overview of the latest techniques for probing photothermally generated heat at the nanoscale. We finally review the recent significant developments of photothermal applications and give a brief outlook on the current challenges and future directions of photothermal nanomaterials.
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Affiliation(s)
- Ximin Cui
- State Key Laboratory of Radio Frequency Heterogeneous Integration, College of Electronics and Information Engineering, Shenzhen University, Shenzhen 518060, China
| | - Qifeng Ruan
- Ministry of Industry and Information Technology Key Lab of Micro-Nano Optoelectronic Information System & Guangdong Provincial Key Laboratory of Semiconductor Optoelectronic Materials and Intelligent Photonic Systems, Harbin Institute of Technology, Shenzhen 518055, China
| | - Xiaolu Zhuo
- Guangdong Provincial Key Lab of Optoelectronic Materials and Chips, School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Xinyue Xia
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Jingtian Hu
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Runfang Fu
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Yang Li
- State Key Laboratory of Radio Frequency Heterogeneous Integration, College of Electronics and Information Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jianfang Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Hongxing Xu
- School of Physics and Technology and School of Microelectronics, Wuhan University, Wuhan 430072, Hubei, China
- Henan Academy of Sciences, Zhengzhou 450046, Henan, China
- Wuhan Institute of Quantum Technology, Wuhan 430205, Hubei, China
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21
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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22
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Chang Y, Wang Y, Li W, Wei Z, Tang S, Chen R. Mechanisms, Techniques and Devices of Airborne Virus Detection: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085471. [PMID: 37107752 PMCID: PMC10138381 DOI: 10.3390/ijerph20085471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Airborne viruses, such as COVID-19, cause pandemics all over the world. Virus-containing particles produced by infected individuals are suspended in the air for extended periods, actually resulting in viral aerosols and the spread of infectious diseases. Aerosol collection and detection devices are essential for limiting the spread of airborne virus diseases. This review provides an overview of the primary mechanisms and enhancement techniques for collecting and detecting airborne viruses. Indoor virus detection strategies for scenarios with varying ventilations are also summarized based on the excellent performance of existing advanced comprehensive devices. This review provides guidance for the development of future aerosol detection devices and aids in the control of airborne transmission diseases, such as COVID-19, influenza and other airborne transmission viruses.
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Affiliation(s)
- Yuqing Chang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Yuqian Wang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Wen Li
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Shichuan Tang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Rui Chen
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
- Correspondence:
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23
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Rapid and ultrasensitive miRNA detection by combining endonuclease reactions in a rolling circle amplification (RCA)-based hairpin DNA fluorescent assay. Anal Bioanal Chem 2023; 415:1991-1999. [PMID: 36853410 DOI: 10.1007/s00216-023-04618-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
MicroRNA (miRNA) sensing strategies employing rolling circle amplification (RCA) coupled with the hairpin DNA (HD) probe-mediated FRET assay have shown promise, but achieving rapid, sensitive, and specific detection of target miRNA remains a challenge in clinical diagnostics. Herein, we incorporate PstI endonuclease cleavage (PEC) into a conventional RCA-based HD probe FRET assay to develop an effective and feasible method. Long single-stranded RCA products are synthesized from miRNA-21 loaded on a circular dumbbell DNA, and the resultant RCA products self-assemble to generate long HD structures with double-stranded stem regions that are specifically recognized and cleaved by PstI endonucleases when incubated with PstI enzymes. This releases large amounts of short single-stranded DNA fragments that hybridize and open to the complementary loop-stem regions of HD probes labeled with FAM at one end and BHQ-1 at the other, resulting in a reduction in FRET efficiency. This assay achieves a 39.7 aM detection limit for target miRNA-21, approximately 37-fold higher than that of the conventional assay (1.5 fM). Moreover, quantitative detection is possible in a wide range from 1 aM to 1 pM within 90 min with high sequence specificity. We demonstrate the assay with the detection of target miRNA-21 in total RNA extracted from MCF-7 cancer cells.
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24
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Krishnan SK, Nataraj N, Meyyappan M, Pal U. Graphene-Based Field-Effect Transistors in Biosensing and Neural Interfacing Applications: Recent Advances and Prospects. Anal Chem 2023; 95:2590-2622. [PMID: 36693046 DOI: 10.1021/acs.analchem.2c03399] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Siva Kumar Krishnan
- CONACYT-Instituto de Física, Benemérita Universidad Autónoma de Puebla, Apdo. Postal J-48, Puebla72570, Mexico
| | - Nandini Nataraj
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No.1, Section 3, Chung-Hsiao East Road, Taipei106, Taiwan
| | - M Meyyappan
- Centre for Nanotechnology, Indian Institute of Technology, Guwahati781039, Assam, India
| | - Umapada Pal
- Instituto de Física, Benemérita Universidad Autónoma de Puebla, Apdo. Postal J-48, Puebla72570, Mexico
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25
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Subodh, Ravina, Priyanka, Narang J, Mohan H. Biosensors for phytohormone Abscisic acid and its role in humans: A review. SENSORS INTERNATIONAL 2023. [DOI: 10.1016/j.sintl.2023.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
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26
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Pudasaini S, Thapa G, Marasini BP, Giri B. Smartphone-operated affordable PCR thermal cycler for the detection of antimicrobial resistant bacterial genes. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001120. [PMID: 36962978 PMCID: PMC10021165 DOI: 10.1371/journal.pgph.0001120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/27/2023] [Indexed: 03/03/2023]
Abstract
Antimicrobial resistance (AMR) is a global public health threat. Surveillance of AMR requires affordable, rapid, and user-friendly diagnostic methods. Our aim was to develop a low-cost thermocycler to perform polymerase chain reaction (PCR). We developed a smartphone-operated PCR thermal cycler using locally available recycled materials. The thermal cycler was used for the amplification for three bacterial genes-bla-TEM, bla-CTXM and 16s rRNA in human urine samples. The performance of custom-built thermal cycler was compared with commercial thermal cycler. The thermal cycler was portable (<1kg weight), required 12 V power supply, 25 μL of solution, and cost only USD50.0. Temperature and time conditions were instructed using a custom-built smartphone application. The ramping rate of was 0.23°C for heating and 0.43°C for cooling. The reported temperatures were within ± 0.5°C of set temperature. The human urine samples were highly resistance and multi-resistant. Nearly 46% (n = 54) E. coli isolates were positive in ESBL screening test. The custom-built thermocycler was able to accurately predict the presence of bla-TEM, bla-CTXM genes, and 16s rRNA (n = 6). We developed and demonstrated a portable, low-cost, easy-to-use, and smartphone-operated PCR thermal cycler. Since it is portable, it can be used in remote location and field settings, including places without stable power supply. The use of the thermal cycler system can be extended, beyond the detection of AMR genes, e.g., in clinical diagnosis, genetics, forensic analysis, and environmental protection.
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Affiliation(s)
- Sanam Pudasaini
- Center for Analytical Sciences, Kathmandu Institute of Applied Sciences, Kathmandu, Nepal
| | - Garima Thapa
- Center for Analytical Sciences, Kathmandu Institute of Applied Sciences, Kathmandu, Nepal
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Bishnu P Marasini
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Basant Giri
- Center for Analytical Sciences, Kathmandu Institute of Applied Sciences, Kathmandu, Nepal
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27
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Leonardi AA, Sciuto EL, Lo Faro MJ, Fazio B, Rizzo MG, Calabrese G, Francioso L, Picca R, Nastasi F, Mancuso G, Spinella C, Knoll W, Irrera A, Conoci S. SARS-CoV-2 and omicron variant detection with a high selectivity, sensitivity, and low-cost silicon bio-nanosensor. NANO SELECT 2022; 4:NANO202200188. [PMID: 36721465 PMCID: PMC9880655 DOI: 10.1002/nano.202200188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/25/2022] [Accepted: 11/13/2022] [Indexed: 12/30/2022] Open
Abstract
The recent SARS-CoV-2 pandemic has highlighted the urgent need for novel point-of-care devices to be promptly used for a rapid and reliable large screening analysis of several biomarkers like genetic sequences and antibodies. Currently, one of the main limitations of rapid tests is the high percentage of false negatives in the presence of variants and, in particular for the Omicron one. We demonstrate in this work the detection of SARS-CoV-2 and the Omicron variant with a cost-effective silicon nanosensor enabling high sensitivity, selectivity, and fast response. We have shown that a silicon (Si) nanowires (NW) platform detects both Sars-CoV-2 and its Omicron variant with a limit of detection (LoD) of four effective copies (cps), without any amplification of the genome, and with high selectivity. This ultrasensitive detection of 4 cps allows to obtain an extremely early diagnosis paving the way for efficient and widespread tracking. The sensor is made with industrially compatible techniques, which in perspective may allow easy and cost-effective industrialization.
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Affiliation(s)
- Antonio Alessio Leonardi
- Dipartimento di Fisica e Astronomia “Ettore Majorana”Università degli studi di CataniaCataniaItaly
- CNR‐IMM Catania UniversitàIstituto per la Microelettronica e MicrosistemiCataniaItaly
| | - Emanuele Luigi Sciuto
- Lab SENS Beyond NanoCNRMessinaItaly
- Dipartimento di Scienze ChimicheBiologiche, Farmaceutiche, ed AmbientaliUniversità degli studi di MessinaMessinaItaly
| | - Maria José Lo Faro
- Dipartimento di Fisica e Astronomia “Ettore Majorana”Università degli studi di CataniaCataniaItaly
- CNR‐IMM Catania UniversitàIstituto per la Microelettronica e MicrosistemiCataniaItaly
| | | | - Maria Giovanna Rizzo
- Dipartimento di Scienze ChimicheBiologiche, Farmaceutiche, ed AmbientaliUniversità degli studi di MessinaMessinaItaly
| | - Giovanna Calabrese
- Dipartimento di Scienze ChimicheBiologiche, Farmaceutiche, ed AmbientaliUniversità degli studi di MessinaMessinaItaly
| | - Luca Francioso
- CNR‐IMMIstituto per la Microelettronica e MicrosistemiVia MonteroniUniversity CampusLecceItaly
| | - Rosaria Picca
- Dipartimento di ChimicaUniversità degli studi di BariBariItaly
| | - Francesco Nastasi
- Dipartimento di Scienze ChimicheBiologiche, Farmaceutiche, ed AmbientaliUniversità degli studi di MessinaMessinaItaly
| | - Giuseppe Mancuso
- Dipartimento di Patologia Umana dell'adulto e dell'età evolutiva Gaetano BarresiUniversità degli studi MessinaGazzi (Me)Italy
| | - Corrado Spinella
- Lab SENS Beyond NanoCNRMessinaItaly
- CNR‐IMM Istituto per la Microelettronica e MicrosistemiZona IndustrialeCataniaItaly
| | - Wolfgang Knoll
- Department of Scientific Coordination and ManagementDanube Private UniversityKremsAustria
| | | | - Sabrina Conoci
- Lab SENS Beyond NanoCNRMessinaItaly
- Dipartimento di Scienze ChimicheBiologiche, Farmaceutiche, ed AmbientaliUniversità degli studi di MessinaMessinaItaly
- CNR‐IMM Istituto per la Microelettronica e MicrosistemiZona IndustrialeCataniaItaly
- Dipartimento di Chimica "G. Ciamician"Università degli studi di BolognaBolognaItaly
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28
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Bao M, Zhang S, Ten Pas C, Dollery SJ, Bushnell RV, Yuqing FNU, Liu R, Lu G, Tobin GJ, Du K. Computer vision enabled funnel adapted sensing tube (FAST) for power-free and pipette-free nucleic acid detection. LAB ON A CHIP 2022; 22:4849-4859. [PMID: 36111877 DOI: 10.1039/d2lc00586g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A simple, portable, and low-cost microfluidic system-funnel adapted sensing tube (FAST) is developed as an integrated, power-free, and pipette-free biosensor for viral nucleic acids. This FAST chip consists of four reaction chambers separated by carbon fiber rods, and the reagents in each chamber are transferred and mixed by manually removing the rods. Rather than using electrical heaters, only a hand warmer pouch is used for an isothermal recombinase polymerase amplification (RPA) and CRISPR-Cas12a reaction. The signal produced by the RPA-CRISPR reaction is observed by the naked eye using an inexpensive flashlight as a light source. The FAST chip is fabricated using water-soluble polyvinyl alcohol (PVA) as a sacrificial core, which is simple and environmentally friendly. Using a SARS-CoV-2 fragment as a target, a ∼10 fM (6 × 103 copies per μL) detection limit is achieved. To generalize standard optical readout for individuals without training, a linear kernel algorithm is created, showing an accuracy of ∼100% for identifying both positive and negative samples in FAST. This power-free, pipette-free, disposable, and simple device will be a promising tool for nucleic acid diagnostics in either clinics or low-resource settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Shuhuan Zhang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Chad Ten Pas
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | | | - Ruth V Bushnell
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - F N U Yuqing
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Rui Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Guoyu Lu
- Department of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - Gregory J Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
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29
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Joung Y, Kim K, Lee S, Chun BS, Lee S, Hwang J, Choi S, Kang T, Lee MK, Chen L, Choo J. Rapid and Accurate On-Site Immunodiagnostics of Highly Contagious Severe Acute Respiratory Syndrome Coronavirus 2 Using Portable Surface-Enhanced Raman Scattering-Lateral Flow Assay Reader. ACS Sens 2022; 7:3470-3480. [PMID: 36374202 DOI: 10.1021/acssensors.2c01808] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In early 2022, the number of people infected with the highly contagious mutant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), called Omicron, was increasing worldwide. Therefore, several countries approved the lateral flow assay (LFA) strip as a diagnostic method for confirming SARS-CoV-2 instead of reverse transcription-polymerase chain reaction (RT-PCR), which takes a long time to generate the results. However, owing to the limitation of detection sensitivity, commercial LFA strips have high false-negative diagnosis rates for patients with low virus concentrations. Therefore, in this study, we developed a portable surface-enhanced Raman scattering (SERS)-LFA reader based on localized surface plasmon effects to solve the sensitivity problem of the commercial LFA strip. We tested 54 clinical samples using this portable SERS-LFA reader, which generated 49 positive and 5 negative results. Out of the 49 positive results, SERS-LFA classified only 2 as false negative, while the commercial LFA classified 21 as false negative. This confirmed that the false-negative rate had significantly improved compared to that of commercial LFA strips. We believe that the proposed SERS-LFA system can be utilized as a point-of-care diagnostic system to quickly and accurately determine a virus infection that could spread significantly within a short period.
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Affiliation(s)
- Younju Joung
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Kihyun Kim
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Seungwoo Lee
- Nanoscope Systems Inc., Daejeon 34016, South Korea
| | | | - Sangyeop Lee
- Department of Innovative Diagnostics, SG Medical Inc., Seoul 05548, South Korea
| | - Joonki Hwang
- Department of Innovative Diagnostics, SG Medical Inc., Seoul 05548, South Korea
| | - Suji Choi
- Department of Innovative Diagnostics, SG Medical Inc., Seoul 05548, South Korea
| | - Taejoon Kang
- Bionanotechnology, Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea.,School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Mi-Kyung Lee
- Department of Laboratory Medicine, College of Medicine, Chung-Ang University, Seoul 06973, South Korea
| | - Lingxin Chen
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
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30
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Burnet M, Metcalf DG, Milo S, Gamerith C, Heinzle A, Sigl E, Eitel K, Haalboom M, Bowler PG. A Host-Directed Approach to the Detection of Infection in Hard-to-Heal Wounds. Diagnostics (Basel) 2022; 12:diagnostics12102408. [PMID: 36292097 PMCID: PMC9601189 DOI: 10.3390/diagnostics12102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 01/08/2023] Open
Abstract
Wound infection is traditionally defined primarily by visual clinical signs, and secondarily by microbiological analysis of wound samples. However, these approaches have serious limitations in determining wound infection status, particularly in early phases or complex, chronic, hard-to-heal wounds. Early or predictive patient-derived biomarkers of wound infection would enable more timely and appropriate intervention. The observation that immune activation is one of the earliest responses to pathogen activity suggests that immune markers may indicate wound infection earlier and more reliably than by investigating potential pathogens themselves. One of the earliest immune responses is that of the innate immune cells (neutrophils) that are recruited to sites of infection by signals associated with cell damage. During acute infection, the neutrophils produce oxygen radicals and enzymes that either directly or indirectly destroy invading pathogens. These granular enzymes vary with cell type but include elastase, myeloperoxidase, lysozyme, and cathepsin G. Various clinical studies have demonstrated that collectively, these enzymes, are sensitive and reliable markers of both early-onset phases and established infections. The detection of innate immune cell enzymes in hard-to-heal wounds at point of care offers a new, simple, and effective approach to determining wound infection status and may offer significant advantages over uncertainties associated with clinical judgement, and the questionable value of wound microbiology. Additionally, by facilitating the detection of early wound infection, prompt, local wound hygiene interventions will likely enhance infection resolution and wound healing, reduce the requirement for systemic antibiotic therapy, and support antimicrobial stewardship initiatives in wound care.
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Affiliation(s)
- Michael Burnet
- Synovo GmbH, Paul Ehrlich Straße 15, 72076 Tuebingen, Germany
- Correspondence:
| | - Daniel G. Metcalf
- ConvaTec Ltd., First Avenue, Deeside Industrial Park, Deeside CH5 2NU, UK
| | - Scarlet Milo
- ConvaTec Ltd., First Avenue, Deeside Industrial Park, Deeside CH5 2NU, UK
| | - Clemens Gamerith
- Austrian Centre of Industrial Biotechnology, Krennagsse 37, A-8010 Graz, Austria
| | - Andrea Heinzle
- Qualizyme Diagnostics GmbH & Co. KG, Neue Stiftingtalstrasse 2, A-8010 Graz, Austria
| | - Eva Sigl
- Qualizyme Diagnostics GmbH & Co. KG, Neue Stiftingtalstrasse 2, A-8010 Graz, Austria
| | - Kornelia Eitel
- Synovo GmbH, Paul Ehrlich Straße 15, 72076 Tuebingen, Germany
| | - Marieke Haalboom
- Medical School Twente, Medisch Spectrum Twente, 7512 KZ Enschede, The Netherlands
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31
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Krolicka A, Mæland Nilsen M, Klitgaard Hansen B, Wulf Jacobsen M, Provan F, Baussant T. Sea lice (Lepeophtherius salmonis) detection and quantification around aquaculture installations using environmental DNA. PLoS One 2022; 17:e0274736. [PMID: 36129924 PMCID: PMC9491551 DOI: 10.1371/journal.pone.0274736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
The naturally occurring ectoparasite salmon lice (Lepeophtherirus salmonis) poses a great challenge for the salmon farming industry, as well as for wild salmonids in the Northern hemisphere. To better control the infestation pressure and protect the production, there is a need to provide fish farmers with sensitive and efficient tools for rapid early detection and monitoring of the parasitic load. This can be achieved by targeting L. salmonis DNA in environmental samples. Here, we developed and tested a new L. salmonis specific DNA-based assay (qPCR assay) for detection and quantification from seawater samples using an analytical pipeline compatible with the Environmental Sample Processor (ESP) for autonomous water sample analysis of gene targets. Specificity of the L. salmonis qPCR assay was demonstrated through in-silico DNA analyses covering sequences of different L. salmonis isolates. Seawater was spiked with known numbers of nauplii and copepodite free-swimming (planktonic) stages of L. salmonis to investigate the relationship with the number of marker gene copies (MGC). Finally, field samples collected at different times of the year in the vicinity of a salmon production farm in Western Norway were analyzed for L. salmonis detection and quantification. The assay specificity was high and a high correlation between MGC and planktonic stages of L. salmonis was established in the laboratory conditions. In the field, L. salmonis DNA was consequently detected, but with MGC number below that expected for one copepodite or nauplii. We concluded that only L. salmonis tissue or eDNA residues were detected. This novel study opens for a fully automatized L. salmonis DNA quantification using ESP robotic to monitor the parasitic load, but challenges remain to exactly transfer information about eDNA quantities to decisions by the farmers and possible interventions.
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Affiliation(s)
| | | | | | - Magnus Wulf Jacobsen
- Danish Technical University, Section for Marine Living Resources, Silkeborg, Denmark
| | - Fiona Provan
- Norwegian Research Centre AS (NORCE), Stavanger, Norway
| | - Thierry Baussant
- Norwegian Research Centre AS (NORCE), Stavanger, Norway
- * E-mail:
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32
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González-López A, Cima-Cabal MD, Rioboó-Legaspi P, Costa-Rama E, García-Suárez MDM, Fernández-Abedul MT. Electrochemical Detection for Isothermal Loop-Mediated Amplification of Pneumolysin Gene of Streptococcus pneumoniae Based on the Oxidation of Phenol Red Indicator. Anal Chem 2022; 94:13061-13067. [PMID: 36106671 PMCID: PMC9523611 DOI: 10.1021/acs.analchem.2c02127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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A highly sensitive electrochemical methodology for end-point detection
of loop-mediated isothermal nucleic acid amplification reactions was
developed. It is based on the oxidation process of phenol red (PR),
commonly used as a visual indicator. The dependence of its redox process
on pH, which changes during amplification, allows performing quantitative
measurements. Thus, the change in the oxidation potential of PR during
the amplification is used, for the first time, as the analytical signal
that correlates with the number of initial DNA copies. As a proof-of-concept,
the amplification of the pneumolysin gene from Streptococcus
pneumoniae, one of the main pathogens causing community-acquired
pneumonia, is performed. Combination of isothermal amplification with
electrochemical detection, performed on small-size flexible electrodes,
allows easy decentralization. Adaptation to the detection of other
pathogens causing infectious diseases would be very useful in the
prevention of future epidemics.
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Affiliation(s)
- Andrea González-López
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - María Dolores Cima-Cabal
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Avda. de La Paz 137, Logroño 26006, Spain
| | - Pablo Rioboó-Legaspi
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - Estefanía Costa-Rama
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | | | - M. Teresa Fernández-Abedul
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
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33
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Liu YQ, Zhu W, Yuan Q, Hu JM, Zhang X, Shen AG. Photoreduced Ag+ surrounding single poly(4-cyanostyrene) nanoparticles for undifferentiated SERS sensing and killing of bacteria. Talanta 2022; 245:123450. [DOI: 10.1016/j.talanta.2022.123450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 11/26/2022]
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34
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Nikolaou P, Sciuto EL, Zanut A, Petralia S, Valenti G, Paolucci F, Prodi L, Conoci S. Ultrasensitive PCR-Free detection of whole virus genome by electrochemiluminescence. Biosens Bioelectron 2022; 209:114165. [DOI: 10.1016/j.bios.2022.114165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 12/21/2022]
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35
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Li Y, Li W, Xu W, Huang J, Sun Z, Liao T, Kovaleva EG, Xu C, Cheng J, Li H. Specific extraction of nucleic acids employing pillar[6]arene-functionalized nanochannel platforms. Chem Commun (Camb) 2022; 58:9278-9281. [PMID: 35904069 DOI: 10.1039/d2cc02693g] [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
The rapid extraction of high-purity nucleic acids from complex biological samples using conventional methods is complicated. Therefore, in this study, glycine-pillar[6]arene (Gly-P6)-functionalized tapered nanochannels were constructed using 32-mer single-stranded E. coli DNA (ssDNA) as a model sequence, which can selectively transport ssDNA by multiple noncovalent forces (transport flux of 2.65 nM cm-2 h-1) under the interference of amino acids and other substances. In view of these prospective results, the selective transport of nucleic acids with nanochannels could be applied in the design of nucleic acid enrichment and separation systems in the future.
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Affiliation(s)
- Yu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, China.,Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Wenjie Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Weiwei Xu
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jinmei Huang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Zhongyue Sun
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, P. R. China
| | - Tangbin Liao
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, P. R. China
| | - Elena G Kovaleva
- Department of Technology for Organic Synthesis, Ural Federal University, Mira Street, 28, 620002 Yekaterinburg, Russia
| | - Chuanlai Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, China
| | - Jing Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, China.,Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Haibing Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, China.,Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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36
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A Miniaturized Silicon Lab-on-Chip for Integrated PCR and Hybridization Microarray for High Multiplexing Nucleic Acids Analysis. BIOSENSORS 2022; 12:bios12080563. [PMID: 35892460 PMCID: PMC9332503 DOI: 10.3390/bios12080563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022]
Abstract
A silicon lab-on-chip, for the detection of nucleic acids through the integrated PCR and hybridization microarray, was developed. The silicon lab-on-chip manufactured through bio-MEMS technology is composed of two PCR microreactors (each volume 11.2 µL) and a microarray-hybridization microchamber (volume 30 µL), fluidically connected by buried bypass. It contains heaters and temperature sensors for the management and control of the temperature cycles during the PCR amplification and hybridization processes. A post-silicon process based on (i) plasmo-O2 cleaning/activation, (ii) vapor phase epoxy silanization, (iii) microarray fabrication and (iv) a protein-based passivation step was developed and fully characterized. The ssDNA microarray (4 rows × 10 columns) composed of 400 spots (spot size—70 ± 12 µm; spot-to-spot distance—130 ± 13 µm) was manufactured by piezo-dispense technology. A DNA microarray probe density in the range of 1310 to 2070 probe µm−2 was observed, together with a limit of detection of about 19 target µm−2. The performances of the silicon lab-on-chip were validated by the detection of the beta-globin gene directly from human blood. Remarkable sensitivity, multiplexing analysis and specificity were demonstrated for the detection of beta-globin and mycobacterium tuberculosis sequences.
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37
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Xie NG, Zhang K, Song P, Li R, Luo J, Zhang DY. High-Throughput Variant Detection Using a Color-Mixing Strategy. J Mol Diagn 2022; 24:878-892. [PMID: 35718091 PMCID: PMC9379672 DOI: 10.1016/j.jmoldx.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/04/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Many diseases are related to multiple genetic alterations along a single gene. Probing for highly multiple (>10) variants in a single quantitative PCR tube is not possible because of a limited number of fluorescence channels and one variant per channel, so many more tubes are needed. Herein, a novel color-mixing strategy that uses fluorescence combinations as digital color codes to probe multiple variants simultaneously was experimentally validated. The color-mixing strategy relies on a simple intratube assay that can probe for 15 variants as part of an intertube assay that can probe for an exponentially increased number of variants. This strategy is achieved by using multiplex double-stranded toehold probes modified with fluorophores and quenchers; the probes are designed to be quenched or luminous after binding to wild-type or variant templates. The color-mixing strategy was used to probe for 21 pathogenic variants in thalassemia and to distinguish between heterozygous and homozygous variants in six tubes, with a specificity of 99% and a sensitivity of 94%. To support tuberculosis diagnosis, the same strategy was applied to simultaneously probe in Mycobacterium tuberculosis for rifampicin-resistance mutations occurring within one 81-bp region and one 48-bp region in the rpoB gene, plus five isoniazid-resistance mutations in the inhA and katG genes.
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Affiliation(s)
- Nina Guanyi Xie
- Department of Bioengineering, Rice University, Houston, Texas
| | - Kerou Zhang
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, Texas
| | | | | | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas.
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38
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Nobusawa K, Han HW, Takei F, Chu TC, Hashida N, Yamashita I. Electrochemical Impedimetric Real-Time Polymerase Chain Reactions Using Anomalous Charge Transfer Enhancement. Anal Chem 2022; 94:7747-7751. [PMID: 35609246 DOI: 10.1021/acs.analchem.2c01659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed a new electrochemical impedimetric method for the real-time detection of polymerase chain reactions (PCR) based on our recent discovery that the DNA intercalator, [Ru(bpy)2DPPZ]2+, anomalously enhances charge transfer between redox mediators, K4[Fe(CN)6]/K3[Fe(CN)6], and a carbon electrode. Three mM [Fe(CN)6]3-/4- and 5 μM [Ru(bpy)2DPPZ]2+ were added to the PCR solution, and electrochemical impedance spectroscopy (EIS) measurements were performed at each elongation heat cycle. The charge transfer resistance (Rct) was initially low due to the presence of [Ru(bpy)2DPPZ]2+ in the solution. As PCR progressed, amplicon dsDNA was produced exponentially, and intercalated [Ru(bpy)2DPPZ]2+ ions, which could be detected as a steep Rct, increased at specific heat cycles depending on the amount of template DNA. The Rct increase per heat cycle, ΔRct, showed a peak at the same heat cycle as optical detection, proving that PCR can be accurately monitored in real time by impedance measurement. This simple method will enable a cost-effective and portable PCR device.
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Affiliation(s)
- Kazuyuki Nobusawa
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Huan-Wen Han
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumie Takei
- National Defense Medical College, 3-2 Namiki, Tokorozawa-shi, Saitama 359-8513, Japan
| | - Ting-Chieh Chu
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Noriyasu Hashida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, 2-2 E7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ichiro Yamashita
- Graduate School of Engineering, Osaka University 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
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39
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Yoon T, Shin J, Choi HJ, Park KS. Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. Biosens Bioelectron 2022; 208:114221. [PMID: 35421842 PMCID: PMC8968188 DOI: 10.1016/j.bios.2022.114221] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022]
Abstract
The negative global impact of the coronavirus disease pandemic has highlighted the crucial need for a rapid and convenient method of viral RNA detection. In this study, we report a novel method, termed as the split T7 promoter-based isothermal transcription amplification with light-up RNA aptamer (STAR), for one-pot detection of viral RNA. STAR uses a split T7 promoter that is applied to a three-way junction to mediate the selective transcription by the T7 RNA polymerase in the presence of target RNA. In addition, a light-up RNA aptamer is used for signal amplification. STAR can detect viral RNA in less than 30 min with high specificity and sensitivity. By testing of 60 nasopharyngeal SARS-CoV-2 samples, the STAR assay demonstrates an excellent sensitivity and specificity of 96.7% and 100%, respectively. Moreover, we provide experimental evidence of the broad applicability of this assay through the multiplex detection of SARS-CoV-2 variants (D614G mutation) and direct detection of bacterial 16S rRNA.
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Affiliation(s)
- Taehwi Yoon
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jiye Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyun-Jung Choi
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hospital, Gwangju, Republic of Korea.
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
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40
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Qin J, Wang W, Gao L, Yao SQ. Emerging biosensing and transducing techniques for potential applications in point-of-care diagnostics. Chem Sci 2022; 13:2857-2876. [PMID: 35382472 PMCID: PMC8905799 DOI: 10.1039/d1sc06269g] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022] Open
Abstract
With the deepening of our understanding in life science, molecular biology, nanotechnology, optics, electrochemistry and other areas, an increasing number of biosensor design strategies have emerged in recent years, capable of providing potential practical applications for point-of-care (POC) diagnosis in various human diseases. Compared to conventional biosensors, the latest POC biosensor research aims at improving sensor precision, cost-effectiveness and time-consumption, as well as the development of versatile detection strategies to achieve multiplexed analyte detection in a single device and enable rapid diagnosis and high-throughput screening. In this review, various intriguing strategies in the recognition and transduction of POC (from 2018 to 2021) are described in light of recent advances in CRISPR technology, electrochemical biosensing, and optical- or spectra-based biosensing. From the perspective of promoting emerging bioanalytical tools into practical POC detecting and diagnostic applications, we have summarized key advances made in this field in recent years and presented our own perspectives on future POC development and challenges.
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Affiliation(s)
- Junjie Qin
- Department of Chemistry, National University of Singapore 4 Science Drive 2 Singapore 117544
| | - Wei Wang
- Department of Chemistry, National University of Singapore 4 Science Drive 2 Singapore 117544 .,School of Pharmaceutical Sciences, Sun Yat-sen University Shenzhen 518107 P. R. China
| | - Liqian Gao
- School of Pharmaceutical Sciences, Sun Yat-sen University Shenzhen 518107 P. R. China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore 4 Science Drive 2 Singapore 117544
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41
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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42
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Kajal N, Singh V, Gupta R, Gautam S. Metal organic frameworks for electrochemical sensor applications: A review. ENVIRONMENTAL RESEARCH 2022; 204:112320. [PMID: 34740622 DOI: 10.1016/j.envres.2021.112320] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/01/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Metal-organic frameworks (MOFs) are broadly known as porous coordination polymers, synthesized by metal-based nodes and organic linkers. MOFs are used in various fields like catalysis, energy storage, sensors, drug delivery etc., due to their versatile properties (tailorable pore size, high surface area, and exposed active sites). This review presents a detailed discussion of MOFs as an electrochemical sensor and their enhancement in the selectivity and sensitivity of the sensor. These sensors are used for the detection of heavy metal ions like Cd2+, Pb2+, Hg2+, and Cu2+ from groundwater. Various types of organic pollutants are also detected from the water bodies using MOFs. Furthermore, electrochemical sensing of antibiotics, phenolic compounds, and pesticides has been explored. In addition to this, there is also a detailed discussion of metal nano-particles and metal-oxide based composites which can sense various compounds like glucose, amino acids, uric acid etc. The review will be helpful for young researchers, and an inspiration to future research as challenges and future opportunities of MOF-based electrochemical sensors are also reported.
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Affiliation(s)
- Navdeep Kajal
- Advanced Functional Materials Lab., Dr. S. S. Bhatnagar University Institute of Chemical Engineering & Technology, Panjab University, Chandigarh, 160 014, India
| | - Vishavjeet Singh
- Advanced Functional Materials Lab., Dr. S. S. Bhatnagar University Institute of Chemical Engineering & Technology, Panjab University, Chandigarh, 160 014, India
| | - Ritu Gupta
- Advanced Functional Materials Lab., Dr. S. S. Bhatnagar University Institute of Chemical Engineering & Technology, Panjab University, Chandigarh, 160 014, India
| | - Sanjeev Gautam
- Advanced Functional Materials Lab., Dr. S. S. Bhatnagar University Institute of Chemical Engineering & Technology, Panjab University, Chandigarh, 160 014, India.
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43
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Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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44
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Vinayaka AC, Golabi M, Than TLQ, Wolff A, Bang DD. Point-of-care diagnosis of invasive non-typhoidal Salmonella enterica in bloodstream infections using immunomagnetic capture and loop-mediated isothermal amplification. N Biotechnol 2022; 66:1-7. [PMID: 34428583 DOI: 10.1016/j.nbt.2021.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/18/2022]
Abstract
Invasive non-typhoidal salmonellosis is gaining worldwide attention as an emerging disease cluster among bloodstream infections. The disease has the highest burden among immunocompromised and malnourished children in resource-limited areas due to poor access to reliable and rapid diagnostics. Point-of-care (POC) diagnostics are promising for use in such low infrastructure laboratory settings. However, there still remains a major challenge for POC testing to deal with the complexity of blood matrices in rapid detection of an extremely low concentration of blood-borne pathogens. In this work, the challenges were addressed by combining magnetic bead based pathogen concentration and Loop Mediated Isothermal Amplification (LAMP) technology. Sensitivity and performance of the combined approach were determined and compared with a direct PCR method. A direct visual detection strategy, adapted using SYTO-24 DNA intercalating dye, resulted in a limit of detection (LoD) as low as 14 CFU/mL in blood samples with a total analysis time of less than 2 h, including sample preparation. This approach has the potential for wide application as a high-throughput POC testing method to analyze pathogens in clinical, food, feed and environmental samples.
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Affiliation(s)
- Aaydha C Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, DK-2800, Lyngby, Denmark.
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Thi Linh Quyen Than
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Anders Wolff
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Dang D Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
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45
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Kang J, Kang D, Yeom G, Park CJ. Molecular Diagnostic System Using Engineered Fusion Protein-Conjugated Magnetic Nanoparticles. Anal Chem 2021; 93:16804-16812. [PMID: 34886672 DOI: 10.1021/acs.analchem.1c03247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To effectively control the spread of new infectious diseases, there is a need for highly sensitive diagnostic methods to detect viral nucleic acids rapidly. This study outlines a universal and simple detection strategy that uses magnetic nanoparticles (MNPs) and a novel MagR-MazE fusion protein for molecular diagnostics to facilitate sensitive detection. This study has engineered a novel MNP conjugate that can be generated easily, without using many chemical reagents. The technique is a nucleic acid detection method, using MagR-MazE fusion protein-conjugated MNPs, where the results can be visualized with the naked eye, regardless of the oligonucleotide sequences of the target in the lateral flow assay. This method could sensitively detect polymerase chain reaction (PCR) products of 16S ribosomal RNA (rRNA) and the 2019-nCoV-N-positive control gene in 5 min. It shows a low limit of detection (LoD) of 0.013 ng/μL for dsDNA. It is simpler and more rapid, sensitive, and versatile than other techniques, making it suitable for point-of-care testing. The proposed detection system and MNP conjugation strategy using a fusion protein can be widely applied to various fields requiring rapid on-site diagnosis.
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Affiliation(s)
- Juyoung Kang
- SB BIOSCIENCE Co., Ltd., Daejeon34141, South Korea
| | - Donguk Kang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Gyuho Yeom
- SB BIOSCIENCE Co., Ltd., Daejeon34141, South Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
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Ilkhani H, Hedayat N, Farhad S. Novel approaches for rapid detection of COVID-19 during the pandemic: A review. Anal Biochem 2021; 634:114362. [PMID: 34478703 PMCID: PMC8406551 DOI: 10.1016/j.ab.2021.114362] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 02/03/2023]
Abstract
The rapid spread of the SARS-CoV-2 virus that caused the COVID-19 disease, has highlighted our urgent need for sensitive, fast and accurate diagnostic technologies. In fact, one of the main challenges for flatting COVID-19 spread charts is the ability to accurately and rapidly identify asymptomatic cases that result in spreading the virus to close contacts. SARS-CoV-2 virus mutation is also relatively rapid, which makes the detection of COVID-19 diseases still crucial even after the vaccination. Conventional techniques, which are commercially available have focused on clinical manifestation, along with molecular and serological detection tools that can identify the SARS-CoV-2 virus however, owing to various disadvantages including low specificity and sensitivity, a quick, low cost and easy approach is needed for diagnosis of COVID-19. Scientists are now showing extensive interest in an effective portable and simple detection method to diagnose COVID-19. There are several novel methods and approaches that are considered viable advanced systems that can meet the demands. This study reviews the new approaches and sensing technologies that work on COVID-19 diagnosis for easy and successful detection of SARS-CoV-2 virus.
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Affiliation(s)
- Hoda Ilkhani
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, 87144, United States,Corresponding author
| | - Nader Hedayat
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, United States
| | - Siamak Farhad
- Advanced Energy & Sensor Lab, Department of Mechanical Engineering, The University of Akron, Akron, OH, 44325, United States,Corresponding author
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Lee S, Song J, Kim S. A simple and innovative sample preparation method for on-site SARS-CoV-2 molecular diagnostics. Analyst 2021; 146:6917-6923. [PMID: 34643630 DOI: 10.1039/d1an01401c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nucleic acid amplification is a widely used diagnostic tool, although it requires a relatively time-consuming and complicated extraction step. To address this issue outside the laboratory, we investigated a sample preparation system and determined that a silica membrane and silica-coated beads are powerful tools for the extraction from raw samples: nucleic acids are kept in the silica membrane, retained during a single wash step, and released at the elution step. The eluent is appropriate for the quantitative real-time polymerase chain reaction (qPCR) and loop-mediated amplification (LAMP) assay in terms of purity and quantity. We also built an innovative equipment-free nucleic acid extraction squeeze system which requires less than 20 min. The sample with improved purity augments the specificity and sensitivity. This system is simple, user-friendly, low-cost, and equipment-free, thus making nucleic acid extraction more accessible and affordable for researchers and untrained users. Furthermore, when combined with the reverse-transcription quantitative real-time polymerase chain reaction method, the method will accelerate the detection of diseases. The same goes when combined with the LAMP assay, especially in developing countries.
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Affiliation(s)
- Songhyun Lee
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea.
| | - Junkyu Song
- Philmedi R&D Center, Philmedi Ltd, Seongnam, 13120, Republic of Korea
| | - Sanghyo Kim
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea.
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Nucleic Acids Analytical Methods for Viral Infection Diagnosis: State-of-the-Art and Future Perspectives. Biomolecules 2021; 11:biom11111585. [PMID: 34827583 PMCID: PMC8615992 DOI: 10.3390/biom11111585] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
The analysis of viral nucleic acids (NA), DNA or RNA, is a crucial issue in the diagnosis of infections and the treatment and prevention of related human diseases. Conventional nucleic acid tests (NATs) require multistep approaches starting from the purification of the pathogen genetic material in biological samples to the end of its detection, basically performed by the consolidated polymerase chain reaction (PCR), by the use of specialized instruments and dedicated laboratories. However, since the current NATs are too constraining and time and cost consuming, the research is evolving towards more integrated, decentralized, user-friendly, and low-cost methods. These will allow the implementation of massive diagnoses addressing the growing demand of fast and accurate viral analysis facing such global alerts as the pandemic of coronavirus disease of the recent period. Silicon-based technology and microfluidics, in this sense, brought an important step up, leading to the introduction of the genetic point-of-care (PoC) systems. This review goes through the evolution of the analytical methods for the viral NA diagnosis of infection diseases, highlighting both advantages and drawbacks of the innovative emerging technologies versus the conventional approaches.
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Lin PH, Li BR. Passively driven microfluidic device with simple operation in the development of nanolitre droplet assay in nucleic acid detection. Sci Rep 2021; 11:21019. [PMID: 34697372 PMCID: PMC8549005 DOI: 10.1038/s41598-021-00470-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/07/2021] [Indexed: 01/20/2023] Open
Abstract
Since nucleic acid amplification technology has become a vital tool for disease diagnosis, the development of precise applied nucleic acid detection technologies in point-of care testing (POCT) has become more significant. The microfluidic-based nucleic acid detection platform offers a great opportunity for on-site diagnosis efficiency, and the system is aimed at user-friendly access. Herein, we demonstrate a microfluidic system with simple operation that provides reliable nucleic acid results from 18 uniform droplets via LAMP detection. By using only micropipette regulation, users are able to control the nanoliter scale of the droplets in this valve-free and pump-free microfluidic (MF) chip. Based on the oil enclosure method and impermeable fabrication, we successfully preserved the reagent inside the microfluidic system, which significantly reduced the fluid loss and condensation. The relative standard deviation (RSD) of the fluorescence intensity between the droplets and during the heating process was < 5% and 2.0%, respectively. Additionally, for different nucleic acid detection methods, the MF-LAMP chip in this study showed good applicability to both genome detection and gene expression analysis.
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Affiliation(s)
- Pei-Heng Lin
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, 1001 Ta-Hseh Rd., Hsinchu, Taiwan
- Department of Electrical and Computer Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Bor-Ran Li
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, 1001 Ta-Hseh Rd., Hsinchu, Taiwan.
- Department of Electrical and Computer Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
- Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
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Khan S, Burciu B, Filipe CDM, Li Y, Dellinger K, Didar TF. DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective. ACS NANO 2021; 15:13943-13969. [PMID: 34524790 DOI: 10.1021/acsnano.1c04327] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.
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Affiliation(s)
- Shadman Khan
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Brenda Burciu
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, 2907 East Gate City Boulevard, Greensboro, North Carolina 27401, United States
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, 2907 East Gate City Boulevard, Greensboro, North Carolina 27401, United States
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- Department of Mechanical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
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