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Ma Z, Ma M, Cao X, Jiang Y, Gao D. Droplet digital molecular beacon-LAMP assay via pico-injection for ultrasensitive detection of pathogens. Mikrochim Acta 2024; 191:430. [PMID: 38949666 DOI: 10.1007/s00604-024-06509-8] [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: 03/19/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
A pico-injection-aided digital droplet detection platform is presented that integrates loop-mediated isothermal amplification (LAMP) with molecular beacons (MBs) for the ultrasensitive and quantitative identification of pathogens, leveraging the sequence-specific detection capabilities of MBs. The microfluidic device contained three distinct functional units including droplet generation, pico-injection, and droplet counting. Utilizing a pico-injector, MBs are introduced into each droplet to specifically identify LAMP amplification products, thereby overcoming issues related to temperature incompatibility. Our methodology has been validated through the quantitative detection of Escherichia coli, achieving a detection limit as low as 9 copies/μL in a model plasmid containing the malB gene and 3 CFU/μL in a spiked milk sample. The total analysis time was less than 1.5 h. The sensitivity and robustness of this platform further demonstrated the potential for rapid pathogen detection and diagnosis, particularly when integrated with cutting-edge microfluidic technologies.
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Affiliation(s)
- Zhiyuan Ma
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Mengshao Ma
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Xiaobao Cao
- Guangzhou Laboratory, Guangdong Province, 510320, China.
| | - Yuyang Jiang
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Department of HIV/AIDS Prevention and Control, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518000, China
| | - Dan Gao
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.
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2
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Chen F, Wang J, Ma J, Song L, Yan H, Wang F, Yang Z, Li F. Novel DNA Biosensing Platform for Detecting HIV Integrase for Highly Sensitive and Quantitative HIV Detection, Diagnosis, and Therapeutic Monitoring. ACS OMEGA 2024; 9:25042-25053. [PMID: 38882085 PMCID: PMC11170629 DOI: 10.1021/acsomega.4c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/11/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024]
Abstract
Straightforward, sensitive, and specific human immunodeficiency virus (HIV) assays are urgently needed. The creation of a point-of-care (POC) device for decentralized diagnostics has the potential to significantly reduce the time to treatment, especially for infectious diseases. Notably, however, many POC solutions proposed to date fall short of meeting the ASSURED guidelines, which are crucial for effective deployment in the field. Herein, we developed a DNA biosensor platform for the specific and quantitative detection of HIV. The platform contains a rolling circle amplification (RCA)-based DNA biosensor and a portable fluorescence detector, in which HIV-encoded integrase (IN) enzyme activity is used as a biomarker to achieve HIV-specific detection. The cleavage and integration reaction of IN on the sensor surface and RCA are combined in this detection platform to perform detection signal cascade amplification, ultimately achieving a detection limit of 0.125 CFU/μL of HIV particles. Moreover, the DNA sensor system exhibited high sensitivity and accuracy for detecting HIV in clinical samples, suggesting that it has potential for application in clinical settings to detect retroviruses other than HIV. In addition, quantitative detection based on this biosensing platform was significantly correlated with the CD4+ lymphocytes count, which can provide guidance for antiretroviral therapy and which affects long-term death risk assessment in HIV patients. Therefore, this DNA biosensing platform based on IN activity is expected to be useful for rapid HIV testing, diagnosis, and treatment monitoring, enabling the development of new POC diagnostic tests and will thus be highly valuable for developing HIV prevention strategies and effective treatments.
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Affiliation(s)
- Fuming Chen
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
- GuangDong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
| | - Jing Wang
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
- GuangDong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
| | - Jie Ma
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
- GuangDong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
| | - Li Song
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
- GuangDong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
| | - Haojie Yan
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
- GuangDong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
| | - Feng Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen Institute of Dermatology, Shenzhen 518020, China
| | - Zhengrong Yang
- Shenzhen Pingshan Center for Disease Control and Prevention, Shenzhen 518118, China
| | - Furong Li
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
- GuangDong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen 518020, China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen 518055, China
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3
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Lee J, Lee T, Lee HN, Kim H, Kang YK, Ryu S, Chung HJ. Simple and Multiplexed Detection of Nucleic Acid Targets Based on Fluorescent Ring Patterns and Deep Learning Analysis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:54335-54345. [PMID: 37970793 DOI: 10.1021/acsami.3c14112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Simple diagnostic tests for nucleic acid targets can provide great advantages for applications such as rapid pathogen detection. Here, we developed a membrane assay for multiplexed detection of nucleic acid targets based on the visualization of two-dimensional fluorescent ring patterns. A droplet of the assay solution is applied to a cellulose nitrate membrane, and upon radial chromatographic flow and evaporation of the solvent, fluorescent patterns appear under UV irradiation. The target nucleic acid is isothermally amplified and is immediately hybridized with fluorescent oligonucleotide probes in a one-pot reaction. We established the fluorescent ring assay integrated with isothermal amplification (iFluor-RFA = isothermal fluorescent ring-based radial flow assay), and feasibility was tested using nucleic acid targets of the receptor binding domain (RBD) and RNA-dependent RNA polymerase (RdRp) genes of SARS-CoV-2. We demonstrate that the iFluor-RFA method is capable of specific and sensitive detection in the subpicomole range, as well as multiplexed detection even in complex solutions. Furthermore, we applied deep learning analysis of the fluorescence images, showing that patterns could be classified as positive or negative and that quantitative amounts of the target could be predicted. The current technique, which is a membrane pattern-based nucleic acid assay combined with deep learning analysis, provides a novel approach in diagnostic platform development that can be versatilely applied for the rapid detection of infectious pathogens.
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Affiliation(s)
- Juhee Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Taegu Lee
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ha Neul Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyoungsoo Kim
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yoo Kyung Kang
- College of Pharmacy, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Seunghwa Ryu
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Jung Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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Zhou J, Wang TY, Lan Z, Yang HJ, Ye XJ, Min R, Wang ZH, Huang Q, Cao J, Gao YE, Wang WL, Sun XL, Zhang Y. Strategy of functional nucleic acids-mediated isothermal amplification for detection of foodborne microbial contaminants: A review. Food Res Int 2023; 173:113286. [PMID: 37803599 DOI: 10.1016/j.foodres.2023.113286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/08/2023]
Abstract
Foodborne microbial contamination (FMC) is the leading cause of food poisoning and foodborne illness. The foodborne microbial detection methods based on isothermal amplification have high sensitivity and short detection time, and functional nucleic acids (FNAs) could extend the detectable object of isothermal amplification to mycotoxins. Therefore, the strategy of FNAs-mediated isothermal amplification has been emergingly applied in biosensors for foodborne microbial contaminants detection, making biosensors more sensitive with lower cost and less dependent on nanomaterials for signal output. Here, the mechanism of six isothermal amplification technologies and their application in detecting FMC is firstly introduced. Then the strategy of FNAs-mediated isothermal amplification is systematically discussed from perspectives of FNAs' versatility including recognition elements (Aptamer, DNAzyme), programming tools (DNA tweezer, DNA walker and CRISPR-Cas) and signal units (G-quadruplex, FNAs-based nanomaterials). Finally, challenges and prospects are presented in terms of addressing the issue of nonspecific amplification reaction, developing better FNAs-based sensing elements and eliminating food matrix effects.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Teng-Yu Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhi Lan
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Han-Jie Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xing-Jian Ye
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Rui Min
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhao-Hui Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qing Huang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Cao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yu-E Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wen-Long Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Lan Sun
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yi Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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Abbas N, Song S, Chang MS, Chun MS. Point-of-Care Diagnostic Devices for Detection of Escherichia coli O157:H7 Using Microfluidic Systems: A Focused Review. BIOSENSORS 2023; 13:741. [PMID: 37504139 PMCID: PMC10377133 DOI: 10.3390/bios13070741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023]
Abstract
Bacterial infections represent a serious and global threat in modern medicine; thus, it is very important to rapidly detect pathogenic bacteria, such as Escherichia coli (E. coli) O157:H7. Once treatments are delayed after the commencement of symptoms, the patient's health quickly deteriorates. Hence, real-time detection and monitoring of infectious agents are highly critical in early diagnosis for correct treatment and safeguarding public health. To detect these pathogenic bacteria, many approaches have been applied by the biosensors community, for example, widely-used polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), culture-based method, and adenosine triphosphate (ATP) bioluminescence. However, these approaches have drawbacks, such as time-consumption, expensive equipment, and being labor-intensive, making it critical to develop ultra-sensitive and highly selective detection. The microfluidic platform based on surface plasmon resonance (SPR), electrochemical sensing, and rolling circle amplification (RCA) offers proper alternatives capable of supplementing the technological gap for pathogen detection. Note that the microfluidic biochip allows to develop rapid, sensitive, portable, and point-of-care (POC) diagnostic tools. This review focuses on recent studies regarding accurate and rapid detection of E. coli O157:H7, with an emphasis on POC methods and devices that complement microfluidic systems. We also examine the efficient whole-body detection by employing antimicrobial peptides (AMPs), which has attracted growing attention in many applications.
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Affiliation(s)
- Naseem Abbas
- Department of Mechanical Engineering, Sejong University, Gwangjin-gu, Seoul 05006, Republic of Korea
| | - Sehyeon Song
- Laboratory of Stem Cell & Neurobiology, Department of Oral Anatomy & Dental Research Institute, Seoul National University School of Dentistry, Jongno-gu, Seoul 03080, Republic of Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Natural Sciences, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Mi-Sook Chang
- Laboratory of Stem Cell & Neurobiology, Department of Oral Anatomy & Dental Research Institute, Seoul National University School of Dentistry, Jongno-gu, Seoul 03080, Republic of Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Natural Sciences, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Myung-Suk Chun
- Sensor System Research Center, Advanced Materials Research Division, Korea Institute of Science and Technology (KIST), Seongbuk-gu, Seoul 02792, Republic of Korea
- Biomedical Engineering Division, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
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Atay E, Altan A. Nanomaterial interfaces designed with different biorecognition elements for biosensing of key foodborne pathogens. Compr Rev Food Sci Food Saf 2023; 22:3151-3184. [PMID: 37222549 DOI: 10.1111/1541-4337.13179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023]
Abstract
Foodborne diseases caused by pathogen bacteria are a serious problem toward the safety of human life in a worldwide. Conventional methods for pathogen bacteria detection have several handicaps, including trained personnel requirement, low sensitivity, laborious enrichment steps, low selectivity, and long-term experiments. There is a need for precise and rapid identification and detection of foodborne pathogens. Biosensors are a remarkable alternative for the detection of foodborne bacteria compared to conventional methods. In recent years, there are different strategies for the designing of specific and sensitive biosensors. Researchers activated to develop enhanced biosensors with different transducer and recognition elements. Thus, the aim of this study was to provide a topical and detailed review on aptamer, nanofiber, and metal organic framework-based biosensors for the detection of food pathogens. First, the conventional methods, type of biosensors, common transducer, and recognition element were systematically explained. Then, novel signal amplification materials and nanomaterials were introduced. Last, current shortcomings were emphasized, and future alternatives were discussed.
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Affiliation(s)
- Elif Atay
- Department of Food Engineering, Mersin University, Mersin, Turkey
| | - Aylin Altan
- Department of Food Engineering, Mersin University, Mersin, Turkey
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Yu H, Zhu J, Shen G, Deng Y, Geng X, Wang L. Improving aptamer performance: key factors and strategies. Mikrochim Acta 2023; 190:255. [PMID: 37300603 DOI: 10.1007/s00604-023-05836-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.
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Affiliation(s)
- Hong Yu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Jiangxiong Zhu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Guoqing Shen
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yun Deng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xueqing Geng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Lumei Wang
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China.
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China.
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Mitrogiannopoulou AM, Tselepi V, Ellinas K. Polymeric and Paper-Based Lab-on-a-Chip Devices in Food Safety: A Review. MICROMACHINES 2023; 14:986. [PMID: 37241610 PMCID: PMC10223399 DOI: 10.3390/mi14050986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023]
Abstract
Food quality and safety are important to protect consumers from foodborne illnesses. Currently, laboratory scale analysis, which takes several days to complete, is the main way to ensure the absence of pathogenic microorganisms in a wide range of food products. However, new methods such as PCR, ELISA, or even accelerated plate culture tests have been proposed for the rapid detection of pathogens. Lab-on-chip (LOC) devices and microfluidics are miniaturized devices that can enable faster, easier, and at the point of interest analysis. Nowadays, methods such as PCR are often coupled with microfluidics, providing new LOC devices that can replace or complement the standard methods by offering highly sensitive, fast, and on-site analysis. This review's objective is to present an overview of recent advances in LOCs used for the identification of the most prevalent foodborne and waterborne pathogens that put consumer health at risk. In particular, the paper is organized as follows: first, we discuss the main fabrication methods of microfluidics as well as the most popular materials used, and then we present recent literature examples for LOCs used for the detection of pathogenic bacteria found in water and other food samples. In the final section, we summarize our findings and also provide our point of view on the challenges and opportunities in the field.
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Affiliation(s)
| | | | - Kosmas Ellinas
- Department of Food Science and Nutrition, School of the Environment, University of the Aegean, Ierou Lochou & Makrygianni St, GR 81400 Myrina, Greece
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Zhou J, Wang Y, Zhou C, Zheng L, Fu L. A ratiometric fluorescent aptasensor based on EXPAR to detect shellfish tropomyosin in food system. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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A novel ADA-coated UCNPs@NB sensing platform combined with nucleic acid amplification for rapid detection of Escherichia coli. Anal Chim Acta 2023; 1239:340751. [PMID: 36628739 DOI: 10.1016/j.aca.2022.340751] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022]
Abstract
In this study, we reported a novel sensing platform based on fluorescence quenching composed of alendronic acid (ADA) coated upconversion nanoparticles (UCNPs) and Nile Blue (NB) combined with polymerase chain reaction (PCR) for rapid, sensitive, and specific detection of Escherichia coli (E. coli). As a fluorescence acceptor, NB has a broad absorption band and can quench upconversion fluorescence intensity at 544 nm and 658 nm based on IFE. PCR is a double-stranded DNA (dsDNA) amplification technique with high specificity. The NB-dsDNA complex can be formed by intercalation of NB between base pairs and groove of dsDNA, leading to upconversion fluorescence recovery. The ADA-coated UCNPs@NB sensing platform achieved to detect E. coli in 1.5 h, with a lower limit of detection (33 CFU mL-1). In addition, the sensitivity of the ADA@UCNPs-NB fluorescence sensor under different PCR cycle numbers was discussed. The results showed that the proposed sensor could effectively shorten the assay time (1.0 h) while maintaining excellent sensitivity. This study demonstrated a rapid and sensitive analytical method for detecting E. coli in chicken, providing a reference for constructing PCR fluorescence sensors.
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Liu J, Xie G, Lv S, Xiong Q, Xu H. Recent applications of rolling circle amplification in biosensors and DNA nanotechnology. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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12
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Gao D, Ma Z, Jiang Y. Recent advances in microfluidic devices for foodborne pathogens detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Chen W, Zhang J, Li D, Wang Y. Application of Isothermal Signal Amplification Technique in the Etiological Diagnosis of Gonorrhea and Drug Resistance Gene Detection. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5989889. [PMID: 35813416 PMCID: PMC9270114 DOI: 10.1155/2022/5989889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 11/18/2022]
Abstract
Background: Isothermal signal amplification technique is developed based on the rolling ring amplification mechanism of cyclic DNA molecules in nature. This technique plays an extremely beneficial role in gonorrhea pathogen identification and drug resistance gene detection. Aims: This study analyzes the isothermal signal amplification techniques in the etiological diagnosis of gonorrhea and drug resistance gene detection. Materials and Methods: Urethral, cervical secretion, or prostatic fluid samples from 322 cases of gonorrhea collected from January 2018 to December 2021 at the STD clinic of our hospital dermatology department were selected for direct smear examination and gonococcal culture examination; DNA was extracted from urethral, cervical secretion, or prostatic fluid samples and then used for pathogen identification by SAT assay and rolling loop nucleic acid amplification technique, smear examination and pathogen culture examination methods, SAT assay, and isothermal signal amplification technique for comparative sensitivity and specificity analysis. Results: The highest rate of gonorrhea positivity was for the urine rolling loop nucleic acid amplification technique, followed by the swab rolling loop nucleic acid amplification technique, and the lowest rate of gonorrhea positivity was for the urine SAT test. The difference in the positivity rate between the two urine testing methods was statistically significant (P < 0.05). The highest sensitivity of the urine rolling loop nucleic acid amplification technique method for the detection of gonorrhea pathogens and the lowest sensitivity of the urine SAT method were statistically significant (P < 0.01). The differences in sensitivity and specificity between the swab rolling loop nucleic acid amplification technique and the swab SAT method were not statistically significant (P > 0.05). ROC curves were plotted based on sensitivity and specificity, with swab SAT assay (AUC = 0.998) > rolling loop nucleic acid amplification technique (AUC = 0.981). Comparing the negative rates of urine and swab rolling loop nucleic acid amplification technique and urine SAT assay, the differences were not statistically significant (P > 0.05). Conclusion: The isothermal signal amplification technique improves the shortcomings of gonorrhea pathogen identification means and drug resistance gene detection methods, with good detection sensitivity and specificity, simple operation, low price, and easy promotion, which has obvious advantages in clinical applications and epidemiological studies.
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Affiliation(s)
- Wei Chen
- Wuhan Fourth Hospital, Oncology Department, China
| | | | - Dongsheng Li
- Wuhan No.1 Hospital, Department of Dermatology, China
| | - Yue Wang
- Wuhan No.1 Hospital, Department of Dermatology, China
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Xu R, Cheng Y, Li X, Zhang Z, Zhu M, Qi X, Chen L, Han L. Aptamer-based signal amplification strategies coupled with microchips for high-sensitivity bioanalytical applications: A review. Anal Chim Acta 2022; 1209:339893. [DOI: 10.1016/j.aca.2022.339893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023]
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Lu H, Zhu J, Zhang T, Zhang X, Chen X, Zhao W, Yao Y, Zhao W, Sui G. A rapid multiplex nucleic acid detection system of airborne fungi by an integrated DNA release device and microfluidic chip. Talanta 2022; 246:123467. [PMID: 35489097 DOI: 10.1016/j.talanta.2022.123467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
Abstract
Occupational health problems, such as asthma, in specific work environments arise from the presence of airborne fungi. Rapid detection of pathogenic airborne fungi is therefore important to reduce or avoid any adverse effects on staff health. Herein, we established a new integrated rapid Lyticase-Motor-Chemical reagent nucleic acid releasing (LMC) method for the release of fungal DNA. Aspergillus fumigatus, Aspergillus flavus, and Cryptococcus neoformans were chosen to evaluate the LMC method. The results of Loop-Mediated Isothermal Amplification (LAMP) analyses showed that this method could release the nucleic acid of 4 × 104 fungal spores, equaling to 400 copies per microliter. This rapid multiplex nucleic acid detection system of airborne fungi included an integrated DNA release device and a portable microfluidic chip. The integrated DNA release device combined mechanical lysing and biochemical reagent treatment to automate DNA release. The microfluidic chip was capable of multiplex nucleic acid detection. The detection limit of this system was 4 × 104 spores per test, meeting the requirement of early warnings. The whole analysis from the sample input to readout could be completed within 90 min, including 30 min for fungal DNA release and 45 min for LAMP analysis. The integrated DNA release device and microfluidic chip were portable, showing tremendous potential in point-of-care tests of airborne fungi.
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Affiliation(s)
- Huijun Lu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China
| | - Jinhui Zhu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China
| | - Tong Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China
| | - Xinlian Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China; School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Xi Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China
| | - Wei Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China
| | - YuHan Yao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China
| | - Wang Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China.
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, PR China; Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, 200032, PR China.
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16
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Multivalent Aptamer Approach: Designs, Strategies, and Applications. MICROMACHINES 2022; 13:mi13030436. [PMID: 35334728 PMCID: PMC8956053 DOI: 10.3390/mi13030436] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/26/2022] [Accepted: 03/10/2022] [Indexed: 12/04/2022]
Abstract
Aptamers are short and single-stranded DNA or RNA molecules with highly programmable structures that give them the ability to interact specifically with a large variety of targets, including proteins, cells, and small molecules. Multivalent aptamers refer to molecular constructs that combine two or more identical or different types of aptamers. Multivalency increases the avidity of aptamers, a particularly advantageous feature that allows for significantly increased binding affinities in comparison with aptamer monomers. Another advantage of multivalency is increased aptamer stabilities that confer improved performances under physiological conditions for various applications in clinical settings. The current study aims to review the most recent developments in multivalent aptamer research. The review will first discuss structures of multivalent aptamers. This is followed by detailed discussions on design strategies of multivalent aptamer approaches. Finally, recent developments of the multivalent aptamer approach in biosensing and biomedical applications are highlighted.
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17
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Li N, Zhang W, Lin J, Xing G, Li H, Lin JM. A Specific Mass-Tag Approach for Detection of Foodborne Pathogens Using MALDI-TOF Mass Spectrometry. Anal Chem 2022; 94:3963-3969. [PMID: 35195984 DOI: 10.1021/acs.analchem.1c05069] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pathogen infections present a considerable threat to global health owing to the high morbidity and mortality, and usually multiple pathogens coexist in food and the environment. Consequently, it is in urgent need to develop some multiplexed and sensitive approaches for pathogen detection. Here, we presented a novel strategy using mass tag-mediated surface engineering for simultaneous detection of multiple bacteria by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Following aptamer binding, primer amplification, and DNA hybridization, bacteria were specifically labeled by their corresponding mass tags, which could be released and ionized after laser irradiation. This strategy converted the detection of bacteria to the analysis of mass tags, allowing simultaneous detection of multiple bacteria and avoiding the dependence of microbial mass spectra databases. In addition, this approach applied two rolling circle amplification (RCA) reactions to improve both the capture efficiency and detection sensitivity of the target bacteria. The specificity and the real sample detection were evaluated, and the results demonstrated a potential application of this approach in milk safety monitoring.
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Affiliation(s)
- Nan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Weifei Zhang
- Division of Chemistry and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Jing Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaowa Xing
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Haifang Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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Mi F, Hu C, Wang Y, Wang L, Peng F, Geng P, Guan M. Recent advancements in microfluidic chip biosensor detection of foodborne pathogenic bacteria: a review. Anal Bioanal Chem 2022; 414:2883-2902. [PMID: 35064302 PMCID: PMC8782221 DOI: 10.1007/s00216-021-03872-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 12/19/2022]
Abstract
Foodborne diseases caused by pathogenic bacteria pose a serious threat to human health. Early and rapid detection of foodborne pathogens is an urgent task for preventing disease outbreaks. Microfluidic devices are simple, automatic, and portable miniaturized systems. Compared with traditional techniques, microfluidic devices have attracted much attention because of their high efficiency and convenience in the concentration and detection of foodborne pathogens. This article firstly reviews the bio-recognition elements integrated on microfluidic chips in recent years and the progress of microfluidic chip development for pathogen pretreatment. Furthermore, the research progress of microfluidic technology based on optical and electrochemical sensors for the detection of foodborne pathogenic bacteria is summarized and discussed. Finally, the future prospects for the application and challenges of microfluidic chips based on biosensors are presented.
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Affiliation(s)
- Fang Mi
- College of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, 830017, China
- Department of Cuisine and Tourism, Xinjiang Bingtuan Xingxin Vocational and Technical College, Urumqi, 830074, China
| | - Cunming Hu
- College of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, 830017, China
| | - Ying Wang
- College of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, 830017, China
| | - Li Wang
- Department of Cuisine and Tourism, Xinjiang Bingtuan Xingxin Vocational and Technical College, Urumqi, 830074, China
| | - Fei Peng
- College of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, 830017, China
| | - PengFei Geng
- College of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, 830017, China
| | - Ming Guan
- College of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi, 830017, China.
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19
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [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
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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20
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Garafutdinov RR, Sakhabutdinova AR, Gilvanov AR, Chemeris AV. Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:1172-1189. [PMID: 34931113 PMCID: PMC8675116 DOI: 10.1134/s1068162021060078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/23/2022]
Abstract
Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.
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Affiliation(s)
- R. R. Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Gilvanov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. V. Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
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21
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Yang L, Yi W, Sun F, Xu M, Zeng Z, Bi X, Dong J, Xie Y, Li M. Application of Lab-on-Chip for Detection of Microbial Nucleic Acid in Food and Environment. Front Microbiol 2021; 12:765375. [PMID: 34803990 PMCID: PMC8600318 DOI: 10.3389/fmicb.2021.765375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022] Open
Abstract
Various diseases caused by food-borne or environmental pathogenic microorganisms have been a persistent threat to public health and global economies. It is necessary to regularly detect microorganisms in food and environment to prevent infection of pathogenic microorganisms. However, most traditional detection methods are expensive, time-consuming, and unfeasible in practice in the absence of sophisticated instruments and trained operators. Point-of-care testing (POCT) can be used to detect microorganisms rapidly on site and greatly improve the efficiency of microbial detection. Lab-on-chip (LOC) is an emerging POCT technology with great potential by integrating most of the experimental steps carried out in the laboratory into a single monolithic device. This review will primarily focus on principles and techniques of LOC for detection of microbial nucleic acid in food and environment, including sample preparation, nucleic acid amplification and sample detection.
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Affiliation(s)
- Liu Yang
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Wei Yi
- Department of Gynecology and Obstetrics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fangfang Sun
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mengjiao Xu
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhan Zeng
- Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Xiaoyue Bi
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jianping Dong
- Department of Infectious Diseases, Haidian Hospital, Beijing Haidian Section of Peking University Third Hospital, Beijing, China
| | - Yao Xie
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Minghui Li
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
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22
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Nesakumar N, Lakshmanakumar M, Srinivasan S, Jayalatha JBB A, Balaguru Rayappan JB. Principles and Recent Advances in Biosensors for Pathogens Detection. ChemistrySelect 2021. [DOI: 10.1002/slct.202101062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Noel Nesakumar
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Chemical and Biotechnology SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Muthaiyan Lakshmanakumar
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Soorya Srinivasan
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Arockia Jayalatha JBB
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - John Bosco Balaguru Rayappan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
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24
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Abnous K, Danesh NM, Ramezani M, Alibolandi M, Nameghi MA, Zavvar TS, Taghdisi SM. A novel colorimetric aptasensor for ultrasensitive detection of aflatoxin M 1 based on the combination of CRISPR-Cas12a, rolling circle amplification and catalytic activity of gold nanoparticles. Anal Chim Acta 2021; 1165:338549. [PMID: 33975697 DOI: 10.1016/j.aca.2021.338549] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022]
Abstract
Colorimetric approaches have received noticeable attention among sensing methods in view of simplicity and watching the color change of sample by the naked eyes. However, developing colorimetric sensing methods which show high sensitivity is still problematic. Herein, based on CRISPR-Cas12a, rolling circle amplification (RCA) and catalytic activity of gold nanoparticles (AuNPs), a colorimetric aptasensor was introduced for highly sensitive detection of aflatoxin M1 (AFM1). In the presence of AFM1, the CRISPR-Cas12a is inactivated and large single-stranded DNA (ssDNA) structures are formed on the surface of AuNPs following the addition of T4 DNA ligase and phi29 DNA polymerase. So, the sample color remains yellow after addition of 4-nitrophenol. However, no huge DNA structure is observed on the surface of AuNPs in the absence of target because of activation of CRISPR-Cas12a and digestion of primer. So, the color of sample switches to colorless. The results indicated that the biosensor had high selectivity toward AFM1 and the approach achieved a detection limit as low as 0.05 ng/L. In addition, it could sensitively identify AFM1 in the spiked milk samples. Overall, this approach is highly sensitive and does not require sophisticated equipment. Therefore, it maintains promising potential for other mycotoxins detection in real samples by simply replacing the applied sequences.
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Affiliation(s)
- Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Noor Mohammad Danesh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Research Institute of Sciences and New Technology, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Morteza Alinezhad Nameghi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Taraneh Sadat Zavvar
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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25
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Ng HY, Lee WC, Kung CT, Li LC, Lee CT, Fu LM. Recent Advances in Microfluidic Devices for Contamination Detection and Quality Inspection of Milk. MICROMACHINES 2021; 12:558. [PMID: 34068982 PMCID: PMC8156775 DOI: 10.3390/mi12050558] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 02/08/2023]
Abstract
Milk is a necessity for human life. However, it is susceptible to contamination and adulteration. Microfluidic analysis devices have attracted significant attention for the high-throughput quality inspection and contaminant analysis of milk samples in recent years. This review describes the major proposals presented in the literature for the pretreatment, contaminant detection, and quality inspection of milk samples using microfluidic lab-on-a-chip and lab-on-paper platforms in the past five years. The review focuses on the sample separation, sample extraction, and sample preconcentration/amplification steps of the pretreatment process and the determination of aflatoxins, antibiotics, drugs, melamine, and foodborne pathogens in the detection process. Recent proposals for the general quality inspection of milk samples, including the viscosity and presence of adulteration, are also discussed. The review concludes with a brief perspective on the challenges facing the future development of microfluidic devices for the analysis of milk samples in the coming years.
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Affiliation(s)
- Hwee-Yeong Ng
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung 833, Taiwan; (H.-Y.N.); (W.-C.L.); (L.-C.L.); (C.-T.L.)
| | - Wen-Chin Lee
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung 833, Taiwan; (H.-Y.N.); (W.-C.L.); (L.-C.L.); (C.-T.L.)
| | - Chia-Te Kung
- Department of Emergency Medicine, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung 833, Taiwan;
| | - Lung-Chih Li
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung 833, Taiwan; (H.-Y.N.); (W.-C.L.); (L.-C.L.); (C.-T.L.)
| | - Chien-Te Lee
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung 833, Taiwan; (H.-Y.N.); (W.-C.L.); (L.-C.L.); (C.-T.L.)
| | - Lung-Ming Fu
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
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26
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Saad M, Faucher SP. Aptamers and Aptamer-Coupled Biosensors to Detect Water-Borne Pathogens. Front Microbiol 2021; 12:643797. [PMID: 33679681 PMCID: PMC7933031 DOI: 10.3389/fmicb.2021.643797] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Aptamers can serve as efficient bioreceptors for the development of biosensing detection platforms. Aptamers are short DNA or RNA oligonucleotides that fold into specific structures, which enable them to selectively bind to target analytes. The method used to identify aptamers is Systematic Evolution of Ligands through Exponential Enrichment (SELEX). Target properties can have an impact on aptamer efficiencies. Therefore, characteristics of water-borne microbial targets must be carefully considered during SELEX for optimal aptamer development. Several aptamers have been described for key water-borne pathogens. Here, we provide an exhaustive overview of these aptamers and discuss important microbial aspects to consider when developing such aptamers.
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Affiliation(s)
- Mariam Saad
- Department of Natural Resources, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
| | - Sebastien P. Faucher
- Department of Natural Resources, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
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In situ rolling circle amplification surface modifications to improve E. coli O157:H7 capturing performances for rapid and sensitive microfluidic detection applications. Anal Chim Acta 2021; 1150:338229. [PMID: 33583552 DOI: 10.1016/j.aca.2021.338229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/01/2021] [Accepted: 01/14/2021] [Indexed: 11/24/2022]
Abstract
We investigated the application of rolling circle amplification (RCA) to modify microfluidic channels for potential sensitive detection applications. To this end, a novel in situ capturing RCA (cRCA) strategy was used to modify the inner surfaces of microfluidic channels with cRCA products that featured repeating tandem capturing aptamers specific for E. coli O157:H7 cells. We showed that the in situ cRCA reaction modified microfluidic channels demonstrated significantly enhanced capturing efficiency in a wide range of flow rates when compared with the unit-aptamer approach. We demonstrated for the first time that microfluidic surfaces modified with the in situ cRCA products showed peak capturing performances both in terms of target capturing efficiency and specificity, and this was likely due to unexpected base-pairing that resulted in altered secondary structures of the capturing aptamers. Our data suggest that the in situ cRCA surface modification is a promising strategy to improve capturing performances in microfluidic devices in sensitive detection applications that also require high throughput. However, cRCA reaction conditions, particularly reaction time and concentrations of initial circular template, must be carefully investigated before the potentials of the in situ cRCA surface modification approach can be fully realized.
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Ziółkowski R, Jarczewska M, Górski Ł, Malinowska E. From Small Molecules Toward Whole Cells Detection: Application of Electrochemical Aptasensors in Modern Medical Diagnostics. SENSORS (BASEL, SWITZERLAND) 2021; 21:724. [PMID: 33494499 PMCID: PMC7866209 DOI: 10.3390/s21030724] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023]
Abstract
This paper focuses on the current state of art as well as on future trends in electrochemical aptasensors application in medical diagnostics. The origin of aptamers is presented along with the description of the process known as SELEX. This is followed by the description of the broad spectrum of aptamer-based sensors for the electrochemical detection of various diagnostically relevant analytes, including metal cations, abused drugs, neurotransmitters, cancer, cardiac and coagulation biomarkers, circulating tumor cells, and viruses. We described also possible future perspectives of aptasensors development. This concerns (i) the approaches to lowering the detection limit and improvement of the electrochemical aptasensors selectivity by application of the hybrid aptamer-antibody receptor layers and/or nanomaterials; and (ii) electrochemical aptasensors integration with more advanced microfluidic devices as user-friendly medical instruments for medical diagnostic of the future.
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Affiliation(s)
- Robert Ziółkowski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
| | - Marta Jarczewska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
| | - Łukasz Górski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
| | - Elżbieta Malinowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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