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Liu CW, Tsutsui H. Sample-to-answer sensing technologies for nucleic acid preparation and detection in the field. SLAS Technol 2023; 28:302-323. [PMID: 37302751 DOI: 10.1016/j.slast.2023.06.002] [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: 03/23/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Efficient sample preparation and accurate disease diagnosis under field conditions are of great importance for the early intervention of diseases in humans, animals, and plants. However, in-field preparation of high-quality nucleic acids from various specimens for downstream analyses, such as amplification and sequencing, is challenging. Thus, developing and adapting sample lysis and nucleic acid extraction protocols suitable for portable formats have drawn significant attention. Similarly, various nucleic acid amplification techniques and detection methods have also been explored. Combining these functions in an integrated platform has resulted in emergent sample-to-answer sensing systems that allow effective disease detection and analyses outside a laboratory. Such devices have a vast potential to improve healthcare in resource-limited settings, low-cost and distributed surveillance of diseases in food and agriculture industries, environmental monitoring, and defense against biological warfare and terrorism. This paper reviews recent advances in portable sample preparation technologies and facile detection methods that have been / or could be adopted into novel sample-to-answer devices. In addition, recent developments and challenges of commercial kits and devices targeting on-site diagnosis of various plant diseases are discussed.
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Affiliation(s)
- Chia-Wei Liu
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA
| | - Hideaki Tsutsui
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA; Department of Bioengineering, University of California, Riverside, CA 92521, USA.
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2
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Yeap CSY, Chaibun T, Lee SY, Zhao B, Jan Y, La-O-Vorakiat C, Surareungchai W, Song S, Lertanantawong B. Ultrasensitive pathogen detection with a rolling circle amplification-empowered multiplex electrochemical DNA sensor. Chem Commun (Camb) 2021; 57:12155-12158. [PMID: 34726213 DOI: 10.1039/d1cc05181d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a highly sensitive and selective multiplex assay by empowering an electrochemical DNA sensor with isothermal rolling circle amplification. The assay could simultaneously detect and discriminate three common entero-pathogens in a single reaction, with femtomolar sensitivity. It is useful for field- or resource-limited settings.
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Affiliation(s)
- Cheryl S Y Yeap
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand. .,Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 1402/2, 461 17 Liberec, Czech Republic.,Pilot Plant and Development Training Institute, Nanoscience and Nanotechnology Research Cluster, King Mongkut's University of Technology Thonburi (KMUTT), Bang Khun Thian Campus, Bangkok 10150, Thailand
| | - Thanyarat Chaibun
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand. .,Pilot Plant and Development Training Institute, Nanoscience and Nanotechnology Research Cluster, King Mongkut's University of Technology Thonburi (KMUTT), Bang Khun Thian Campus, Bangkok 10150, Thailand
| | - Su Yin Lee
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio) and Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Kedah, 08100, Malaysia
| | - Bin Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yuan Jan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Chan La-O-Vorakiat
- Pilot Plant and Development Training Institute, Nanoscience and Nanotechnology Research Cluster, King Mongkut's University of Technology Thonburi (KMUTT), Bang Khun Thian Campus, Bangkok 10150, Thailand
| | - Werasak Surareungchai
- Pilot Plant and Development Training Institute, Nanoscience and Nanotechnology Research Cluster, King Mongkut's University of Technology Thonburi (KMUTT), Bang Khun Thian Campus, Bangkok 10150, Thailand.,School of Bioresources & Technology, King Mongkut's University of Technology Thonburi, Thailand
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Benchaporn Lertanantawong
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand. .,Pilot Plant and Development Training Institute, Nanoscience and Nanotechnology Research Cluster, King Mongkut's University of Technology Thonburi (KMUTT), Bang Khun Thian Campus, Bangkok 10150, Thailand
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Nichols ZE, Geddes CD. Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review. Molecules 2021; 26:5666. [PMID: 34577137 PMCID: PMC8470389 DOI: 10.3390/molecules26185666] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Sample preparation is an essential step for nearly every type of biochemical analysis in use today. Among the most important of these analyses is the diagnosis of diseases, since their treatment may rely greatly on time and, in the case of infectious diseases, containing their spread within a population to prevent outbreaks. To address this, many different methods have been developed for use in the wide variety of settings for which they are needed. In this work, we have reviewed the literature and report on a broad range of methods that have been developed in recent years and their applications to point-of-care (POC), high-throughput screening, and low-resource and traditional clinical settings for diagnosis, including some of those that were developed in response to the coronavirus disease 2019 (COVID-19) pandemic. In addition to covering alternative approaches and improvements to traditional sample preparation techniques such as extractions and separations, techniques that have been developed with focuses on integration with smart devices, laboratory automation, and biosensors are also discussed.
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Affiliation(s)
- Zach E. Nichols
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
| | - Chris D. Geddes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
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Gartshore A, Kidd M, Joshi LT. Applications of Microwave Energy in Medicine. BIOSENSORS 2021; 11:96. [PMID: 33810335 PMCID: PMC8065940 DOI: 10.3390/bios11040096] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Microwaves are a highly utilized electromagnetic wave, used across a range of industries including food processing, communications, in the development of novel medical treatments and biosensor diagnostics. Microwaves have known thermal interactions and theorized non-thermal interactions with living matter; however, there is significant debate as to the mechanisms of action behind these interactions and the potential benefits and limitations of their use. This review summarizes the current knowledge surrounding the implementation of microwave technologies within the medical industry.
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Affiliation(s)
| | - Matt Kidd
- Emblation Microwave Ltd., Alloa, Scotland FK10 2HU, UK;
| | - Lovleen Tina Joshi
- School of Biomedical Science, University of Plymouth, Plymouth PL4 8AA, UK;
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Santaus TM, Greenberg K, Suri P, Geddes CD. Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It. PLoS One 2019; 14:e0225475. [PMID: 31790434 PMCID: PMC6886747 DOI: 10.1371/journal.pone.0225475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/05/2019] [Indexed: 01/11/2023] Open
Abstract
Rapid sample preparation is one of the leading bottlenecks to low-cost and efficient sample component detection. To overcome this setback, a technology known as Lyse-It has been developed to rapidly (less than 60 seconds) lyse Gram-positive and-negative bacteria alike, while simultaneously fragmenting DNA/RNA and proteins into tunable sizes. This technology has been used with a variety of organisms, but the underlying mechanism behind how the technology actually works to fragment DNA/RNA and proteins has hitherto been studied. It is generally understood how temperature affects cellular lysing, but for DNA/RNA and protein degradation, the temperature and amount of energy introduced by microwave irradiation of the sample, cannot explain the degradation of the biomolecules to the extent that was being observed. Thus, an investigation into the microwave generation of reactive oxygen species, in particular singlet oxygen, hydroxyl radicals, and superoxide anion radicals, was undertaken. Herein, we probe one aspect, the generation of reactive oxygen species (ROS), which is thought to contribute to a non-thermal mechanism behind biomolecule fragmentation with the Lyse-It technology. By utilizing off/on (Photoinduced electron transfer) PET fluorescent-based probes highly specific for reactive oxygen species, it was found that as oxygen concentration in the sample and/or microwave irradiation power increases, more reactive oxygen species are generated and ultimately, more oxidation and biomolecule fragmentation occurs within the microwave cavity.
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Affiliation(s)
- Tonya M. Santaus
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Ken Greenberg
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Prabhdeep Suri
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Chris D. Geddes
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
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Santaus TM, Zhang F, Li S, Stine OC, Geddes CD. Effects of Lyse-It on endonuclease fragmentation, function and activity. PLoS One 2019; 14:e0223008. [PMID: 31568482 PMCID: PMC6768537 DOI: 10.1371/journal.pone.0223008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Nucleases are enzymes that can degrade genomic DNA and RNA that decrease the accuracy of quantitative measures of those nucleic acids. Here, we study conventional heating, standard microwave irradiation, and Lyse-It, a microwave-based lysing technology, for the potential to fragment and inactivate DNA and RNA endonucleases. Lyse-It employs the use of highly focused microwave irradiation to the sample ultimately fragmenting and inactivating RNase A, RNase B, and DNase I. Nuclease size and fragmentation were determined visually and quantitatively by SDS polyacrylamide gel electrophoresis and the mini-gel Agilent 2100 Bioanalyzer system, with a weighted size calculated to depict the wide range of nuclease fragmentation. Enzyme activity assays were conducted, and the rates were calculated to determine the effect of various lysing conditions on each of the nucleases. The results shown in this paper clearly demonstrate that Lyse-It is a rapid and highly efficient way to degrade and inactivate nucleases so that nucleic acids can be retained for down-stream detection.
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Affiliation(s)
- Tonya M. Santaus
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Fan Zhang
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Shan Li
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - O. Colin Stine
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Chris D. Geddes
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
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Santaus TM, Li S, Saha L, Chen WH, Bhagat S, Stine OC, Geddes CD. A comparison of Lyse-It to other cellular sample preparation, bacterial lysing, and DNA fragmentation technologies. PLoS One 2019; 14:e0220102. [PMID: 31335892 PMCID: PMC6650070 DOI: 10.1371/journal.pone.0220102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/08/2019] [Indexed: 02/05/2023] Open
Abstract
The ability for safe and rapid pathogenic sample transportation and subsequent detection is an increasing challenge throughout the world. Herein, we describe and use bead-beating, vortex, sonication, 903 protein saver cards, and Lyse-It methods, aiming to inactivate Gram-positive and -negative bacteria with subsequent genome DNA (quantitative Polymerase Chain Reaction) qPCR detection. The basic concepts behind the four chosen technologies is their versatility, cost, and ease of use in developed and underdeveloped countries. The four methods target the testing of bacterial resilience, cellular extraction from general and complex media and subsequent DNA extraction for qPCR detection and amplification. These results demonstrate that conventional high temperature heating, 903 protein saver cards, and Lyse-It are all viable options for inactivating bacterial growth for safe shipping. Additionally, Lyse-It was found to be particularly useful as this technology can inactivate bacteria, extract cells from 903 protein saver cards, lyse bacterial cells, and additionally keep genomic DNA viable for qPCR detection.
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Affiliation(s)
- Tonya M. Santaus
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - Shan Li
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Lahari Saha
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - Wilbur H. Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Siya Bhagat
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - O. Colin Stine
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Chris D. Geddes
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, MD, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, MD, United States of America
- * E-mail:
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