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Williams MR, Telli AE, Telli N, Islam DT, Hashsham SA. Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens. Methods Mol Biol 2025; 2852:3-17. [PMID: 39235733 DOI: 10.1007/978-1-0716-4100-2_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] [Indexed: 09/06/2024]
Abstract
The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.
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Affiliation(s)
- Maggie R Williams
- School of Engineering & Technology, Institute for Great Lakes Research, Central Michigan University, Mt Pleasant, MI, USA
| | - Arife Ezgi Telli
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Nihat Telli
- Department of Food Technology, Vocational School of Technical Sciences, Konya Technical University, Konya, Turkey
| | - Dar Tafazul Islam
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
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2
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Mao Z, Lei H, Chen R, Ren S, Liu B, Gao Z. CRISPR/Cas13a analysis based on NASBA amplification for norovirus detection. Talanta 2024; 280:126725. [PMID: 39167939 DOI: 10.1016/j.talanta.2024.126725] [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: 02/20/2024] [Revised: 05/22/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Human norovirus (HuNoV) is a leading cause of foodborne diseases worldwide, making rapid and accurate detection crucial for prevention and control. In recent years, the CRISPR/Cas13a system, known for its single-base resolution in RNA recognition and unique collateral cleavage activity, is particularly suitable for sensitive and rapid RNA detection. However, isothermal amplification-based CRISPR/Cas13 assays often require an external transcription step, complicating the detection process. In our study, an efficient diagnostic technique based on the NASBA/Cas13a system was established to identify conserved regions at the ORF1-ORF2 junction of norovirus. The RNA amplification techniques [Nucleic Acid Sequence-Based Amplification (NASBA)] integrates reverse transcription and transcription steps, enabling sensitive, accurate, and rapid enrichment of low-abundance RNA. Furthermore, the CRISPR/Cas13a system provides secondary precise recognition of the amplified products, generating a fluorescence signal through its activated accessory collateral cleavage activity. We optimized the reaction kinetics parameters of Cas13a and achieved a detection limit as low as 51pM. The conditions for the cascade reaction involving CRISPR analysis and RNA amplification were optimized. Finally, we validated the reliability and accuracy of the NASBA/Cas13a method by detecting norovirus in shellfish, achieving results comparable to qRT-PCR in a shorter time and detecting viral loads as low as 10 copies/μL.
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Affiliation(s)
- Zefeng Mao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Huang Lei
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
| | - Baolin Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
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3
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Huang Z, Wei L, Zhou Y, Li Y, Chen Y. Guide DNA dephosphorylation-modulated Pyrococcus furiosus Argonaute fluorescence biosensor for the detection of alkaline phosphatase and aflatoxins B 1. Biosens Bioelectron 2024; 265:116692. [PMID: 39208510 DOI: 10.1016/j.bios.2024.116692] [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: 07/19/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Foodborne hazardous factors pose a significant risk to public health, emphasizing the need for the development of sensitive and user-friendly detection strategies to effectively manage and control these risks in the food supply chain. Pyrococcus furiosus argonaute (PfAgo)-based biosensing approaches have been extensively explored due to its built-in signal amplification. However, the property that PfAgo is a DNA-guided DNA endonuclease has enabled almost all the existing PfAgo-based reports to be used for the detection of nucleic acids. To lend PfAgo toolbox to extended non-nucleic acid detection, we systematically investigated the mechanism characteristic of PfAgo' preference for guide DNA (gDNA) and proposed a gDNA dephosphorylation-modulated PfAgo sensor for the detection of non-nucleic acid targets. Our results indicated that PfAgo exhibits preference for 5'-phosphorylated gDNA at a specific ratio of PfAgo to gDNA concentration. Leveraging this PfAgo' preference and the dephosphorylation activity of alkaline phosphatase (ALP), ALP could be detected as low as 2.7 U/L. Furthermore, the PfAgo was coupled with immunolabelled ALP to develop a PfAgo-based fluorescence immunosensor, which achieves aflatoxins B1 detection with a detection limit of 29.89 pg/mL and exhibits satisfactory recoveries in wheat and maize samples. The developed method broadens the application scope of PfAgo toolbox, and provides a simple, sensitive, and universal detection platform for a variety targets.
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Affiliation(s)
- Zhengzhang Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Luyu Wei
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanan Zhou
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yingjun Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, Liaoning, China; State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, 116034, Liaoning, China.
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4
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Xue G, Sui Z, Chen B, Xiao Z, Yao Y, Hua L, Xu J. Dimeric-molecular beacon based intramolecular strand displacement amplification enables robust analysis of miRNA. Talanta 2024; 280:126778. [PMID: 39191109 DOI: 10.1016/j.talanta.2024.126778] [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: 07/24/2024] [Revised: 08/15/2024] [Accepted: 08/24/2024] [Indexed: 08/29/2024]
Abstract
Given the critical role of miRNAs in regulating gene expression and their potential as biomarkers for various diseases, accurate and sensitive miRNA detection is essential for early diagnosis and monitoring of conditions such as cancer. In this study, we introduce a dimeric molecular beacon (Di-MB) based isothermal strand displacement amplification (ISDA) system (Di-MB-ISDA) for enhanced miRNA detection. The Di-MB system is composed of two monomeric MBs (Mono-MBs) connected by a double-stranded DNA linker with single-stranded sequences in the middle, facilitating binding with the flexible arms of the Mono-MBs. This design forms a compact, high-density structure, significantly improving biostability against nuclease degradation. In the absence of target miRNA, the Di-MB maintains its stable structure. When target miRNA is present, it binds to the stem-loop regions, causing the hairpin structure to unfold and expose the stem sequences. These sequences serve as templates for the built-in primers, triggering DNA replication through an intramolecular recognition mechanism. This spatial confinement effect accelerates the strand displacement reaction, allowing the target miRNA to initiate additional reaction cycles and amplify the detection signal. The Di-MB-ISDA system addresses key challenges such as poor biostability and limited sensitivity seen in traditional methods. By enhancing biostability and optimizing reaction conditions, this system demonstrates robust performance for miRNA detection with a detection limit of 100 pM. The findings highlight the potential of Di-MB-ISDA for sensitive and accurate miRNA analysis, paving the way for its application in biomedical study and disease diagnosis in complex biological samples.
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Affiliation(s)
- Guohui Xue
- Department of Clinical Laboratory, Jiujiang City Key Laboratory of Cell Therapy, Jiujiang NO.1 People's Hospital, Jiujiang, 332000, China.
| | - Zhuqi Sui
- College of Biological, Chemical Science and Engineering, Jiaxing University, Jiaxing, 314001, China
| | - Baoqiang Chen
- College of Biological, Chemical Science and Engineering, Jiaxing University, Jiaxing, 314001, China
| | - Zhubing Xiao
- School of Chemistry and Material Science, Huaibei Normal University, Huaibei, 235000, China.
| | - Yuanyuan Yao
- College of Biological, Chemical Science and Engineering, Jiaxing University, Jiaxing, 314001, China
| | - Lin Hua
- Department of Clinical Laboratory, Jiujiang City Key Laboratory of Cell Therapy, Jiujiang NO.1 People's Hospital, Jiujiang, 332000, China
| | - Jianguo Xu
- College of Biological, Chemical Science and Engineering, Jiaxing University, Jiaxing, 314001, China.
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5
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Deng R, Zhang X, Cao J, Liu X, Zhang Y, Wang F, Xia X. High-contrast imaging of cellular non-repetitive drug-resistant genes via in situ dead Cas12a-labeled PCR. Chem Commun (Camb) 2024; 60:10524-10527. [PMID: 39229640 DOI: 10.1039/d4cc03059a] [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: 09/05/2024]
Abstract
In situ imaging of genes of pathogenic bacteria can profile cellular heterogeneity, such as the emergence of drug resistance. Fluorescence in situ hybridization (FISH) serves as a classic approach to image mRNAs inside cells, but it remains challenging to elucidate genomic DNAs and relies on multiple fluorescently labeled probes. Herein, we present a dead Cas12a (dCas12a)-labeled polymerase chain reaction (CasPCR) assay for high-contrast imaging of cellular drug-resistant genes. We employed a syncretic dCas12a-green fluorescent protein (dCas12a-GFP) to tag the amplicons, thereby enabling high-contrast imaging and avoiding multiple fluorescently labeled probes. The CasPCR assay can quantify quinolone-resistant Salmonella enterica in mixed populations and identify them isolated from poultry farms.
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Affiliation(s)
- Ruijie Deng
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
| | - Xinlei Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, Liaoning 116600, China
| | - Xinmiao Liu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
| | - Yong Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
| | - Feng Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China.
| | - Xuhan Xia
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
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6
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Deng R, Shi Y, Zhang Y, Zhang X, Deng S, Xia X. Precise, Sensitive Detection of Viable Foodborne Pathogenic Bacteria with a 6-Order Dynamic Range via Digital Rolling Circle Amplification. ACS Sens 2024; 9:4127-4133. [PMID: 39028985 DOI: 10.1021/acssensors.4c01069] [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: 07/21/2024]
Abstract
The presence of viable pathogenic bacteria in food can lead to serious foodborne diseases, thus posing a risk to human health. Here, we develop a digital rolling circle amplification (dRCA) assay that enables the precise and sensitive quantification of viable foodborne pathogenic bacteria. Directly targeting pathogenic RNAs via a ligation-based padlock probe allows for precisely discriminating viable bacteria from dead one. The one-target-one-amplicon characteristic of dRCA enables high sensitivity and a broad quantitative detection range, conferring a detection limit of 10 CFU/mL and a dynamic range of 6 orders. dRCA can detect rare viable bacteria, even at a proportion as low as 0.1%, which is 50 times more sensitive than the live/dead staining method. The high sensitivity for detecting viable bacteria accommodates dRCA for assessing sterilization efficiency. Based on the assay, we found that, for pasteurization, slightly elevating the temperature to 68 °C can reduce the heating time to 10 min, which may minimize nutrient degradation caused by high-temperature exposure. The assay can serve as a precise tool for estimating the contamination by viable pathogenic bacteria and assessing sterilization, which facilitates food safety control.
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Affiliation(s)
- Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yachen Shi
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xinlei Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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7
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Xu Y, Zhang Q, Li Y, Pang X, Cheng N. A 3D-Printed Integrated Handheld Biosensor for the Detection of Vibrio parahaemolyticus. Foods 2024; 13:1775. [PMID: 38891003 PMCID: PMC11171811 DOI: 10.3390/foods13111775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is one of the important seafood-borne pathogens that cause a serious gastrointestinal disorder in humans. Recently, biosensors have attracted serious attention for precisely detecting and tracking risk factors in foods. However, a major consideration when fabricating biosensors is to match the low cost of portable devices to broaden its application. In this study, a 3D-printed integrated handheld biosensor (IHB) that combines RPA-CRISPR/Cas12a, a lateral flow strip (LFS), and a handheld device was developed for the ultrasensitive detection of V. parahaemolyticus. Using the preamplification of RPA on tlh gene of V. parahaemolyticus, a specific duplex DNA product was obtained to activate the trans-cleavage activity of CRISPR/Cas12a, which was then utilized to cleave the ssDNA probe. The ssDNA probe was then detected by the LFS, which was negatively correlated with the content of amplified RPA products of the tlh gene. The IHB showed high selectivity and excellent sensitivity for V. parahaemolyticus detection, and the limit of detection was 4.9 CFU/mL. The IHB also demonstrated great promise for the screening of V. parahaemolyticus in samples and had the potential to be applied to the rapid screening of other pathogen risks for seafood and marine environmental safety.
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Affiliation(s)
- Yuancong Xu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China;
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China;
| | - Qian Zhang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China;
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
| | - Yunyi Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
| | - Xiaoxu Pang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
| | - Nan Cheng
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China;
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Y.L.); (X.P.)
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8
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Liu Y, Jin L, Mao J, Deng R, Lin F, Cheng Y, Li M, Dai J. Signal amplified colorimetric nucleic acid detection based on autocatalytic hairpin assembly. RSC Adv 2024; 14:17152-17157. [PMID: 38808241 PMCID: PMC11130644 DOI: 10.1039/d4ra01982b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
Herein, a nucleic acid assay based on autocatalytic hairpin assembly (ACHA) was proposed. In this system, two split G-quadruplex sequences were integrated into H1 and H2, respectively. And a DNA strand with the same sequence to target DNA was integrated into the assistant hairpin H3. In the presence of target DNA, the hairpin structure of H1 was opened and catalytic hairpin assembly (CHA) was activated, and then a series of DNA assembly steps based on the toehold-mediated DNA strand displacement were triggered and the product H1-H2 with sticky ends on both sides was formed. On the one side of H1-H2, the split two G-quadruplex sequences were close enough to form the intact G-quadruplex for the signal readout. At the same time, two sticky ends on the other side of H1-H2 hybridized with H3 and a new sticky end with the sequence same to the target DNA was exposed, which can immediately trigger the autocatalytic hairpin assembly reaction, and then the reaction rate of CHA was effectively accelerated and the colorimetric signal was significantly amplified. This ACHA signal amplified strategy has been successfully applied for the rapid and colorimetric nucleic acid detection.
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Affiliation(s)
- Yunhua Liu
- School of Chemical Engineering, Guizhou Institute of Technology Guiyang 550000 China +86-13458610501
| | - Limin Jin
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences, Peking Union Medical College Tianjin 300192 China
| | - Jianfei Mao
- College of Chemistry, Sichuan University Chengdu 610064 China +86-18380216833
| | - Ru Deng
- College of Chemistry, Sichuan University Chengdu 610064 China +86-18380216833
| | - Fengyi Lin
- College of Chemistry, Sichuan University Chengdu 610064 China +86-18380216833
| | - Yuxin Cheng
- College of Chemistry, Sichuan University Chengdu 610064 China +86-18380216833
| | - Min Li
- College of Chemistry, Sichuan University Chengdu 610064 China +86-18380216833
| | - Jianyuan Dai
- College of Chemistry, Sichuan University Chengdu 610064 China +86-18380216833
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Lu Y, Wen J, Wang C, Wang M, Jiang F, Miao L, Xu M, Li Y, Chen X, Chen Y. Mesophilic Argonaute-Based Single Polystyrene Sphere Aptamer Fluorescence Platform for the Multiplexed and Ultrasensitive Detection of Non-Nucleic Acid Targets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308424. [PMID: 38081800 DOI: 10.1002/smll.202308424] [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: 09/22/2023] [Revised: 11/13/2023] [Indexed: 01/04/2024]
Abstract
The rapid, simultaneous, and accurate identification of multiple non-nucleic acid targets in clinical or food samples at room temperature is essential for public health. Argonautes (Agos) are guided, programmable, target-activated, next-generation nucleic acid endonucleases that could realize one-pot and multiplexed detection using a single enzyme, which cannot be achieved with CRISPR/Cas. However, currently reported thermophilic Ago-based multi-detection sensors are mainly employed in the detection of nucleic acids. Herein, this work proposes a Mesophilic Argonaute Report-based single millimeter Polystyrene Sphere (MARPS) multiplex detection platform for the simultaneous analysis of non-nucleic acid targets. The aptamer is utilized as the recognition element, and a single millimeter-sized polystyrene sphere (PSmm) with a large concentration of guide DNA on the surface served as the microreactor. These are combined with precise Clostridium butyricum Ago (CbAgo) cleavage and exonuclease I (Exo I) signal amplification to achieve the efficient and sensitive recognition of non-nucleic acid targets, such as mycotoxins (<60 pg mL-1) and pathogenic bacteria (<102 cfu mL-1). The novel MARPS platform is the first to use mesophilic Agos for the multiplex detection of non-nucleic acid targets, overcoming the limitations of CRISPR/Cas in this regard and representing a major advancement in non-nucleic acid target detection using a gene-editing-based system.
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Affiliation(s)
- Yingying Lu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junping Wen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chengming Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mengjiao Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Feng Jiang
- Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Hubei Provincial Institute for Food Supervision and Test, Wuhan, 430075, China
| | - Lin Miao
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Minggao Xu
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaohua Chen
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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10
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Xue P, Peng Y, Wang R, Wu Q, Chen Q, Yan C, Chen W, Xu J. Advances, challenges, and opportunities for food safety analysis in the isothermal nucleic acid amplification/CRISPR-Cas12a era. Crit Rev Food Sci Nutr 2024:1-16. [PMID: 38659323 DOI: 10.1080/10408398.2024.2343413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Global food safety stands out as a prominent public concern, affecting populations worldwide. The recurrent challenge of food safety incidents reveals the need for a robust inspection framework. In recent years, the integration of isothermal nucleic acid amplification with CRISPR-Cas12a techniques has emerged as a promising tool for molecular detection of food hazards, presenting next generation of biosensing for food safety detection. This paper provides a comprehensive review of the current state of research on the synergistic application of isothermal nucleic acid amplification and CRISPR-Cas12a technology in the field of food safety. This innovative combination not only enriches the analytical tools, but also improving assay performance such as sensitivity and specificity, addressing the limitations of traditional methods. The review summarized various detection methodologies by the integration of isothermal nucleic acid amplification and CRISPR-Cas12a technology for diverse food safety concerns, including pathogenic bacterium, viruses, mycotoxins, food adulteration, and genetically modified foods. Each section elucidates the specific strategies employed and highlights the advantages conferred. Furthermore, the paper discussed the challenges faced by this technology in the context of food safety, offering insightful discussions on potential solutions and future prospects.
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Affiliation(s)
- Pengpeng Xue
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, P. R. China
| | - Yubo Peng
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, P. R. China
| | - Renjing Wang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, P. R. China
| | - Qian Wu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, P. R. China
| | - Qi Chen
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, P. R. China
| | - Chao Yan
- School of Life Science, Anhui University, Hefei, P. R. China
| | - Wei Chen
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, P. R. China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, P. R. China
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, P. R. China
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11
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Zheng L, Jin M, Pan Y, Zheng Y, Lou Y. 3D-DNA walking nanomachine based on catalytic hairpin assembly and copper nanoclusters for sensitive detection of hepatitis C virus. Talanta 2024; 269:125478. [PMID: 38039675 DOI: 10.1016/j.talanta.2023.125478] [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: 08/18/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023]
Abstract
Rapid and accurate detection of the hepatitis C virus (HCV) is essential for early diagnosis and prevention of virus transmission. This study presents a novel approach that combines the three-dimensional (3D)-DNA walking nanomachine with catalytic hairpin assembly (CHA) and copper nanoclusters (CuNCs). By integrating CHA with the 3D DNA walking nanomachine, efficient target amplification on 3D surfaces was achieved, leading to improved reaction speed and detection performance. Terminal deoxynucleotidyl transferase (TdT) was utilized to generate T-rich DNA sequences. These sequences served as templates for the formation of CuNCs, which functioned as the readout signal. The optimized 3D-DNA walking nanomachine exhibited excellent sensitivity in detecting HCV, with a detection limit of 42.4 pM and a linear range of 100 pM to 2 nM. The biosensor demonstrated excellent selectivity and reproducibility, with a recovery rate ranging from 94% to 108% for the detection of real samples. This design holds great potential for sensitive, label-free, and reliable detection of HCV in clinical settings. Furthermore, the versatility of this approach allows for the customization of target sequences, thereby facilitating the detection of various nucleic acid targets. Therefore, this method has the potential to advance personalized medicine, disease management, and genetic analysis in the field of molecular diagnosis.
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Affiliation(s)
- Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Department of Endocrinology, Affiliated Yueqing Hospital, Wenzhou Medical University, Yueqing, 325600, China.
| | - Ming Jin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yajing Pan
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yan Zheng
- Department of Endocrinology, Affiliated Yueqing Hospital, Wenzhou Medical University, Yueqing, 325600, China.
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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12
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Trinh TND, Nam NN. Isothermal amplification-based microfluidic devices for detecting foodborne pathogens: a review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1150-1157. [PMID: 38323529 DOI: 10.1039/d3ay02039h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The gold standard for nucleic acid amplification-based diagnosis is the polymerase chain reaction (PCR). The PCR recognizes the targets such as foodborne pathogens by amplifying their specific genes. The integration of nucleic acid amplification-based assays on microfluidic platforms represents a highly promising solution for convenient, cheap, and effective control of foodborne pathogens. However, the application of the PCR is limited to on-site detection because the method requires sophisticated equipment for temperature control, which makes it complicated for microfluidic integration. Alternatively, isothermal amplification methods are promising tools for integrating microfluidic platforms for on-site detection of foodborne pathogens. This review summarized advances in isothermal amplification-based microfluidic devices for detecting foodborne pathogens. Different nucleic acid extraction approaches and the integration of these approaches in microfluidic platforms were first reviewed. Microfluidic platforms integrated with three common isothermal amplification methods including loop-mediated isothermal amplification, recombinase polymerase amplification, and recombinase-aided amplification were then described and discussed.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of Materials Science, School of Applied Chemistry, Tra Vinh University, Tra Vinh City 87000, Vietnam.
| | - Nguyen Nhat Nam
- Applied Biology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
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13
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Liu X, Yang H, Liu J, Liu K, Jin L, Zhang Y, Khan MR, Zhong K, Cao J, He Q, Xia X, Deng R. In Situ Cas12a-Based Allele-Specific PCR for Imaging Single-Nucleotide Variations in Foodborne Pathogenic Bacteria. Anal Chem 2024; 96:2032-2040. [PMID: 38277772 DOI: 10.1021/acs.analchem.3c04532] [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: 01/28/2024]
Abstract
In situ profiling of single-nucleotide variations (SNVs) can elucidate drug-resistant genotypes with single-cell resolution. The capacity to directly "see" genetic information is crucial for investigating the relationship between mutated genes and phenotypes. Fluorescence in situ hybridization serves as a canonical tool for genetic imaging; however, it cannot detect subtle sequence alteration including SNVs. Herein, we develop an in situ Cas12a-based amplification refractory mutation system-PCR (ARMS-PCR) method that allows the visualization of SNVs related to quinolone resistance inside cells. The capacity of discriminating SNVs is enhanced by incorporating optimized mismatched bases in the allele-specific primers, thus allowing to specifically amplify quinolone-resistant related genes. After in situ ARMS-PCR, we employed a modified Cas12a/CRISPR RNA to tag the amplicon, thereby enabling specific binding of fluorophore-labeled DNA probes. The method allows to precisely quantify quinolone-resistant Salmonella enterica in the bacterial mixture. Utilizing this method, we investigated the survival competition capacity of quinolone-resistant and quinolone-sensitive bacteria toward antimicrobial peptides and indicated the enrichment of quinolone-resistant bacteria under colistin sulfate stress. The in situ Cas12a-based ARMS-PCR method holds the potential for profiling cellular phenotypes and gene regulation with single-nucleotide resolution at the single-cell level.
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Affiliation(s)
- Xinmiao Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Hao Yang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jun Liu
- Chengdu Customs Technology Center, Chengdu 610041, China
| | - Kerui Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Lulu Jin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kai Zhong
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, Liaoning 116600, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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14
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Ndraha N, Lin HY, Wang CY, Hsiao HI, Lin HJ. Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 7:100183. [PMID: 37767229 PMCID: PMC10520789 DOI: 10.1016/j.fochms.2023.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/22/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
This article presents a review of recent advancements in the utilization of NAA-based techniques for detecting foodborne pathogens in food products, focusing on studies conducted within the past five years. This review revealed that recent research efforts have primarily aimed at enhancing sensitivity and specificity by improving sample pre-treatment/preparation, DNA isolation, and readout methods. Isothermal-based amplification methods, such as LAMP, RPA, RAA, and RCA, have emerged as promising approaches, providing rapid results within one h and often demonstrating comparable or superior sensitivity to conventional or qPCR methods. However, the attention paid to specific pathogens varies, with Salmonella spp., Listeria spp., E. coli, and V. parahaemolyticus receiving more focus than norovirus and other similar pathogens. NAA-based methods have the potential to significantly contribute to food safety and public health protection. However, further advancements are necessary to fully realize their benefits.
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Affiliation(s)
- Nodali Ndraha
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Hung-Yun Lin
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Chen-Yow Wang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Hsin-I Hsiao
- Department of Food Science, National Taiwan Ocean University, Keelung, 202301 Taiwan
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
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15
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Chen Z, Liu Z, Liu J, Xiao X. Research progress in the detection of common foodborne hazardous substances based on functional nucleic acids biosensors. Biotechnol Bioeng 2023; 120:3501-3517. [PMID: 37723667 DOI: 10.1002/bit.28555] [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: 06/14/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
With the further improvement of food safety requirements, the development of fast, highly sensitive, and portable methods for the determination of foodborne hazardous substances has become a new trend in the food industry. In recent years, biosensors and platforms based on functional nucleic acids, along with a range of signal amplification devices and methods, have been established to enable rapid and sensitive determination of specific substances in samples, opening up a new avenue of analysis and detection. In this paper, functional nucleic acid types including aptamers, deoxyribozymes, and G-quadruplexes which are commonly used in the detection of food source pollutants are introduced. Signal amplification elements include quantum dots, noble metal nanoparticles, magnetic nanoparticles, DNA walkers, and DNA logic gates. Signal amplification technologies including nucleic acid isothermal amplification, hybridization chain reaction, catalytic hairpin assembly, biological barcodes, and microfluidic system are combined with functional nucleic acids sensors and applied to the detection of many foodborne hazardous substances, such as foodborne pathogens, mycotoxins, residual antibiotics, residual pesticides, industrial pollutants, heavy metals, and allergens. Finally, the potential opportunities and broad prospects of functional nucleic acids biosensors in the field of food analysis are discussed.
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Affiliation(s)
- Zijie Chen
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, the People's Republic of China
| | - Zhen Liu
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, the People's Republic of China
| | - Jingjing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, Hunan, the People's Republic of China
| | - Xilin Xiao
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, the People's Republic of China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, the People's Republic of China
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16
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Yang R, Liu X, Hu J, Xu H, Song J, Zhou H, Li M, Huang Y, Zhang L, Fan Q. Robust nontarget DNA-triggered catalytic hairpin assembly amplification strategy for the improved sensing of microRNA in complex biological matrices. Analyst 2023; 148:5856-5863. [PMID: 37885382 DOI: 10.1039/d3an01411h] [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: 10/28/2023]
Abstract
A simple but robust fluorescence strategy based on a nontarget DNA-triggered catalytic hairpin assembly (CHA) was constructed to probe microRNA-21 (miR-21). A short ssDNA rather than degradable target miRNA was employed as an initiator. Two molecular beacons needed to assist the CHA process were simplified to avoid unfavorable nonspecific interactions. In the presence of the target, the initiator was released from a partially duplex and triggered the cyclic CHA reaction, resulting in a significantly amplified optical readout. A wide linear range from 0.1 pM to 1000 pM for the sensing of miR-21 in buffer was achieved with a low detection limit of 0.76 pM. Fortunately, this strategy demonstrated an obviously improved performance for miR-21 detection in diluted serum. The fluorescence signals were enhanced remarkably and the sensitivity was further improved to 0.12 pM in 10% serum. The stability for miR-21 quantification and the capability for the analysis of single nucleotide polymorphisms (SNPs) were also improved greatly. More importantly, the biosensor could be applied to image miR-21 in different living tumor cells with high resolution, illustrating its promising potential for the assay of miRNAs in various complex situations for early-stage disease diagnosis and biological studies in cells.
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Affiliation(s)
- Ruining Yang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Xingfen Liu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Junbo Hu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Hui Xu
- Huzhou Key Laboratory of Green Energy Materials and Battery Cascade Utilization, School of Intelligent Manufacturing, Huzhou College, Huzhou 313000, China
| | - Jixiang Song
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Huiyu Zhou
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Meixing Li
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yanqin Huang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lei Zhang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Quli Fan
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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17
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Sun X, Shan Y, Jian M, Wang Z. A Multichannel Fluorescence Isothermal Amplification Device with Integrated Internet of Medical Things for Rapid Sensing of Pathogens through Deep Learning. Anal Chem 2023; 95:15146-15152. [PMID: 37733965 DOI: 10.1021/acs.analchem.3c02973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
The landscape of diagnostic assessments has experienced a paradigm shift driven by the advent of isothermal amplification techniques on point-of-care testing (POCT). The development of compact, portable isothermal amplification devices further emphasizes their transformative influence on diagnostic approaches. However, in prioritizing portability, these devices may exhibit limitations in functionality, rendering them less effective in addressing urgent public health emergencies during sudden pathogen outbreaks. In this paper, an efficient isothermal fluorescence amplification device has been fabricated for the rapid detection of pathogens during public health crises. The device features multichannel capability for simultaneous detection of various targets, integrates with the Internet of Medical Things (IoMT) for remote control and data uploading, and includes a deep learning-based batch processing system for rapid (9.4 ms) and accurate discrimination of pathogen type with excellent accuracy. The device has been successfully employed to simultaneously detect Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus (MRSA) with limits of detection (LODs) of 18 CFU/mL (SA) and 20 CFU/mL (MRSA) within 35 min by multiplex RPA assay and CRISPR/Cas12a-mediated nucleic acid detection assay.
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Affiliation(s)
- Xudong Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yongjie Shan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Minghong Jian
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
- National Analytical Research Center of Electrochemistry and Spectroscopy, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
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18
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Liu Z, Liu C, He L, Liu J, Li L, Yang S, Tan Y, Liu X, Xiao X. A Cascade Signal Amplification Strategy for the Ultrasensitive Fluorescence Detection of Cu 2+ via λ-Exonuclease-Assisted Target Recycling with Mismatched Catalytic Hairpin Assembly. BIOSENSORS 2023; 13:918. [PMID: 37887111 PMCID: PMC10605925 DOI: 10.3390/bios13100918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
Herein, an ultrasensitive DNAzyme-based fluorescence biosensor for detecting Cu2+ was designed using the cascade signal amplification strategy, coupling λ-exonuclease-assisted target recycling and mismatched catalytic hairpin assembly (MCHA). In the designed detection system, the target, Cu2+, can activate the Cu2+-dependent DNAzyme to cause a cleavage reaction, releasing ssDNA (tDNA). Then, tDNA binds to hairpin DNA (H0) with an overhanging 5'-phosphorylated terminus to form dsDNA with a blunt 5'-phosphorylated terminus, which activates the dsDNA to be digested by λ-Exo and releases tDNA along with another ssDNA (iDNA). Subsequently, the iDNA initiates MCHA, which can restore the fluorescence of carboxyfluorescein (FAM) previously quenched by tetramethylrhodamine (TAMRA), resulting in a strong fluorescent signal. Furthermore, MCHA efficiently improves the signal-to-noise ratio of the detection system. More importantly, tDNA recycling can be achieved with the λ-Exo digestion reaction to release more iDNA, efficiently amplifying the fluorescent signal and further improving the sensitivity to Cu2+ with a detection limit of 60 fM. The practical application of the developed biosensor was also demonstrated by detecting Cu2+ in real samples, proving it to be an excellent analytical strategy for the ultrasensitive quantification of heavy metal ions in environmental water sources.
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Affiliation(s)
- Zhen Liu
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
| | - Chen Liu
- Hunan Province Key Laboratory for Typical Environmental Pollution and Health Hazards, School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China;
| | - Liqiong He
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
| | - Jinquan Liu
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
| | - Le Li
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
| | - Shengyuan Yang
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
| | - Yan Tan
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
| | - Xing Liu
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
| | - Xilin Xiao
- Hunan Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; (Z.L.); (L.H.); (L.L.); (S.Y.); (Y.T.); (X.L.)
- State Key Laboratory of Chemo & Biosensing and Chemometrics, Hunan University, Changsha 410082, China
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19
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Li X, Zhang H, Zhang Y, Zhao Y, Nguyen LV, Zhou X, Warren-Smith SC. Label-free DNA quantification using isothermal amplification on an exposed core optical fiber microfluidic platform. Analyst 2023; 148:4897-4904. [PMID: 37655735 DOI: 10.1039/d3an01047c] [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: 09/02/2023]
Abstract
Isothermal amplification technology has triggered a surge in research due to its compatibility with small and portable equipment, simplicity, and high efficiency, especially in light of the COVID-19 pandemic where reliable widescale testing is critical to outbreak management. In this paper, a label-free isothermal deoxyribonucleic acid (DNA) amplification method based on refractive index (RI) quantification is proposed and demonstrated for the first time by combining optical fiber sensing, microfluidics, and isothermal amplification. A highly RI-sensitive Mach-Zehnder (MZ) interference is formed by splicing a short length of an exposed-core fiber between two lengths of a single-mode fiber while the microfluidic liquid channel on the exposed side of the ECF is filled with target DNA and the amplification solution. Real-time quantitative measurement of the target DNA is then realized by monitoring the change in RI of the solution during the isothermal DNA amplification process. The experimental results show that the platform successfully realizes real-time label-free monitoring of isothermal amplification of 0.16 aM DNA samples. This method is a breakthrough for applications in the fields of DNA detection and quantification where simple operation, rapid detection, portability, small size, high selectivity, and high sensitivity are required.
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Affiliation(s)
- Xuegang Li
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - He Zhang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
| | - Yanan Zhang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - Yong Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - Linh Viet Nguyen
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Institute for Photonics and Advanced Sensing (IPAS) and School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Xue Zhou
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.
| | - Stephen C Warren-Smith
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Institute for Photonics and Advanced Sensing (IPAS) and School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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20
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Wang Y, Xia X, Wu M, Sun Q, Zhang W, Qiu Y, Deng R, Luo A. Species-Level Monitoring of Key Bacteria in Fermentation Processes Using Single-Nucleotide Resolved Nucleic Acid Assays Based on CRISPR/Cas12. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13147-13155. [PMID: 37624706 DOI: 10.1021/acs.jafc.3c04775] [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: 08/27/2023]
Abstract
Microorganisms can determine the flavor and quality of fermented food, such as Baijiu, which is produced via Daqu fermentation. Therefore, monitoring key microorganisms during fermentation is important for ensuring high-quality fermented food. Here, we report a single-nucleotide resolved nucleic acid assay based on the CRISPR/Cas12 system, enabling the quantification of Bacillus amyloliquefaciens, a key microorganism in Daqu fermentation at the species level. The assay employs an amplification-refractory mutation system derived from PCR to analyze minor genetic differences between different Bacillus species. The utilization of CRISPR/Cas12 further guaranties the specificity of identifying the PCR amplicon and enables the quantification of Bacillus amyloliquefaciens via end-measurement fluorescence. Compared to conventional qPCR, the assay allows for species-level detection of bacteria, thus enabling the precise detection of the Bacillus strain that yields high-level 2,3,5,6-tetramethylpyrazine. The assay promises the precise monitoring of bacterial growth and contribution to flavor during Daqu fermentation, thus facilitating fermented food quality control.
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Affiliation(s)
- Ying Wang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Minghua Wu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Qiyao Sun
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Wei Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yong Qiu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Aimin Luo
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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21
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Xue G, Cheng Y, Xu H, Xue C. Target-Induced Stepwise Disintegration of Starlike Branched and Multiplex Embedded Systems for Amplified Detection of Serum MicroRNA. Anal Chem 2023; 95:13140-13148. [PMID: 37602702 DOI: 10.1021/acs.analchem.3c01863] [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: 08/22/2023]
Abstract
DNA nanotechnology has shown great promise for biosensing and molecular recognition. However, the practical application of conventional DNA biosensors is constrained by inadequate target stimuli, intricate design schemes, multicomponent systems, and susceptibility to nuclease degradation. To overcome these limitations, we present a class of starlike branched and multiplex embedded system (SBES) with an integrated functional design and cascade exponential amplification for serum microRNA (miRNA) detection. The DNA arms can be integrated into an all-in-one system by surrounding a branch point, with each arm endowed with specific functionalities by embedding different DNA fragments. These fragments include a segment complementary to the target miRNA for the recognition element, palindromic tails for self-primed polymerization, and a region with the same sequences as the target serving as the target analogue. Upon exposure to a target miRNA, the DNA arms unwind in a stepwise manner through palindrome-mediated dimerization and polymerization. This enables target recycling for subsequent reactions while releasing the target analogue to generate a secondary response in a feedback manner. A comparative analysis illustrates that the signal-to-noise ratio (SNR) of a full SBES with a feedback strategy is approximately 250% higher than the system without a feedback design. We demonstrate that the four-arm 4pSBES has the benefits of multifunctional integration, enhanced sensitivity, and low false-positive signals, which makes this approach ideally suited for clinical diagnosis. Moreover, an upgraded SBES with additional DNA arms (e.g., 6pSBES) can be constructed to allow multifunctional extension, offering unprecedented opportunities to build versatile DNA nanostructures for biosensing.
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Affiliation(s)
- Guohui Xue
- Department of Clinical Laboratory, Jiujiang No.1 People's Hospital, Jiujiang, Jiangxi 332000, P. R. China
| | - Yinghao Cheng
- Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P. R. China
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Chang Xue
- Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P. R. China
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22
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Zhang Z, Guan L, Yao J, Li L, Liu C, Guo Y, Xie G. RART-LAMP: One-Step Extraction-Free Method for Genotyping within 40 min. Anal Chem 2023; 95:12487-12496. [PMID: 37534990 DOI: 10.1021/acs.analchem.3c02232] [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: 08/04/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a commonly used alternative to PCR for point-of-care detection of nucleic acids due to its rapidity, sensitivity, specificity, and simpler instrumentation. While dual-labeled TaqMan probes are widely used in PCR for single-nucleotide polymorphism (SNP) genotyping, real-time LAMP primarily relies on turbidimetry or intercalator fluorescence measurements, which can be non-specific and generate false-positive results. In this study, we propose a closed-tube, dual-labeled RNA-modified probes and RNase H II-assisted real-time LAMP (RART-LAMP) method for SNP genotyping. Our findings indicate that (1) fluorescence signals were predominantly derived from probe hydrolysis rather than hybridization, (2) temperature-controlled hybridization between the probe and template ensured the specificity of SNP analysis, and (3) RNase H II hydrolysis between the target containing SNP sites and probes did not exhibit sequence specificity. Our RART-LAMP approach demonstrated excellent performance in genotyping C677T clinical samples, including gDNA extracted from blood, saliva, and swabs. More importantly, saliva and swab samples could be directly analyzed without any pretreatment, indicating promising prospects for nucleic acid analysis at the point of care in resource-limited settings.
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Affiliation(s)
- Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Luhao Guan
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Medicine, Luzhou Traditional Chinese Medicine Hospital, Luzhou 646000, China
| | - Juan Yao
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Lijia Li
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Chunfang Liu
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Yongcan Guo
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
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23
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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24
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Wang X, Wang H, Zhang H, Yang T, Zhao B, Yan J. Investigation of the Impact of Hydrogen Bonding Degree in Long Single-Stranded DNA (ssDNA) Generated with Dual Rolling Circle Amplification (RCA) on the Preparation and Performance of DNA Hydrogels. BIOSENSORS 2023; 13:755. [PMID: 37504153 PMCID: PMC10377478 DOI: 10.3390/bios13070755] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023]
Abstract
DNA hydrogels have gained significant attention in recent years as one of the most promising functional polymer materials. To broaden their applications, it is critical to develop efficient methods for the preparation of bulk-scale DNA hydrogels with adjustable mechanical properties. Herein, we introduce a straightforward and efficient molecular design approach to producing physically pure DNA hydrogel and controlling its mechanical properties by adjusting the degree of hydrogen bonding in ultralong single-stranded DNA (ssDNA) precursors, which were generated using a dual rolling circle amplification (RCA)-based strategy. The effect of hydrogen bonding degree on the performance of DNA hydrogels was thoroughly investigated by analyzing the preparation process, morphology, rheology, microstructure, and entrapment efficiency of the hydrogels for Au nanoparticles (AuNPs)-BSA. Our results demonstrate that DNA hydrogels can be formed at 25 °C with simple vortex mixing in less than 10 s. The experimental results also indicate that a higher degree of hydrogen bonding in the precursor DNA resulted in stronger internal interaction forces, a more complex internal network of the hydrogel, a denser hydrogel, improved mechanical properties, and enhanced entrapment efficiency. This study intuitively demonstrates the effect of hydrogen bonding on the preparation and properties of DNA hydrogels. The method and results presented in this study are of great significance for improving the synthesis efficiency and economy of DNA hydrogels, enhancing and adjusting the overall quality and performance of the hydrogel, and expanding the application field of DNA hydrogels.
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Affiliation(s)
- Xinyu Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Huiyuan Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Hongmin Zhang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Tianxi Yang
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Bin Zhao
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Juan Yan
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
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25
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Ong KJ, Tejeda-Saldana Y, Duffy B, Holmes D, Kukk K, Shatkin JA. Cultured Meat Safety Research Priorities: Regulatory and Governmental Perspectives. Foods 2023; 12:2645. [PMID: 37509737 PMCID: PMC10379195 DOI: 10.3390/foods12142645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/23/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
As with every new technology, safety demonstration is a critical component of bringing products to market and gaining public acceptance for cultured meat and seafood. This manuscript develops research priorities from the findings of a series of interviews and workshops with governmental scientists and regulators from food safety agencies in fifteen jurisdictions globally. The interviews and workshops aimed to identify the key safety questions and priority areas of research. Participants raised questions about which aspects of cultured meat and seafood production are novel, and the implications of the paucity of public information on the topic. Novel parameters and targets may require the development of new analytical methods or adaptation and validation of existing ones, including for a diversity of product types and processes. Participants emphasized that data sharing of these efforts would be valuable, similar to those already developed and used in the food and pharmaceutical fields. Contributions to such databases from the private and public sectors would speed general understanding as well as efforts to make evaluations more efficient. In turn, these resources, combined with transparent risk assessment, will be critical elements of building consumer trust in cultured meat and seafood products.
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Affiliation(s)
| | | | | | - Dwayne Holmes
- Stichting New Harvest Netherlands, 1052 Amsterdam, The Netherlands
| | - Kora Kukk
- Vireo Advisors, LLC, Boston, MA 02130, USA
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26
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Liao X, Deng R, Warriner K, Ding T. Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers. Compr Rev Food Sci Food Saf 2023; 22:3212-3253. [PMID: 37222539 DOI: 10.1111/1541-4337.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/22/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
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Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- School of Mechanical and Energy Engineering, NingboTech University, Ningbo, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, China
| | - Keith Warriner
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
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27
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Jiang H, Lv X, Li A, Peng Z, Deng Y, Li X. A dual-labeled fluorescence quenching lateral flow assay based on one-pot enzyme-free isothermal cascade amplification for the rapid and sensitive detection of pathogens. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023. [PMID: 37203352 DOI: 10.1039/d3ay00526g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rapid detection of nucleic acids is integral for clinical diagnostics, especially if a major public-health emergency occurs. However, such detection cannot be carried out efficiently in remote areas limited by medical resources. Herein, a dual-labeled fluorescence resonance energy transfer (FRET) lateral flow assay (LFA) based on one-pot enzyme-free cascade amplification was developed for rapid, convenient, and sensitive detection of open reading frame (ORF)1ab of severe acute respiratory syndrome-coronavirus-2. The catalyzed hairpin assembly (CHA) reaction of two well-designed hairpin probes was initiated by a target sequence and generated a hybridization chain reaction (HCR) initiator. Then, HCR probes modified with biotin were initiated to produce long DNA nanowires. After two-level amplification, the cascade-amplified product was detected by dual-labeled lateral flow strips. Gold nanoparticles (AuNPs)-streptavidin combined with the product and then ran along a nitrocellulose membrane under the action of capillary force. After binding with fluorescent microsphere-labeled-specific probes on the T line, a positive signal (red color) could be observed. Meanwhile, AuNPs could quench the fluorescence of the T line, and an inverse relationship between fluorescence intensity and the concentration of the CHA-HCR-amplified product was formed. The proposed strategy achieved a satisfactory limit of detection of 2.46 pM for colorimetric detection and 174 fM for fluorescent detection, respectively. Benefitting from the features of being one-pot, enzyme-free, low background, high sensitivity, and selectivity, this strategy shows great potential in bioanalysis and clinical diagnostics upon further development.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Anyi Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Zhao Peng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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28
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Shi G, Yan C, Chen J. Fluorescent aptasensor for the ultrasensitive detection of antibiotic residue in food samples based on dumbbell DNA-mediated signal amplification. Biosens Bioelectron 2023; 228:115188. [PMID: 36871423 DOI: 10.1016/j.bios.2023.115188] [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: 11/04/2022] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/05/2023]
Abstract
Sensitive and reliable detection of antibiotics is of great significance for environmental and food safety due to its high risk in trace concentrations. Herein, we developed a fluorescence sensing system for chloramphenicol (CAP) detection based on dumbbell DNA-mediated signal amplification. Two hairpin dimers (2H1 and 2H2) were employed as the building blocks to construct the sensing scaffolds. The CAP-aptamer binding in another hairpin H0 can liberate the trigger DNA, which then activates the cyclic assembly reaction between 2H1 and 2H2. The separation of FAM and BHQ in the formed product of cascaded DNA ladder yields a high fluorescence signal for CAP monitoring. Compared with the monomer hairpin assembly between H1 and H2, the dimer hairpin assembly between 2H1 and 2H2 exhibits enhanced signal amplification efficiency and reduced reaction time. The developed CAP sensor showed a wide linear range from 10 fM to 10 nM with a detection limit of 2 fM. Importantly, this sensing platform has been successfully applied to the determination of CAP in fish, milk, and water samples with satisfactory recovery and accuracy. With the advantages of high sensitivity, mix-and-read pattern, and robustness, our proposed CAP sensor can be used as a simple and routine tool for the detection of trace amounts of antibiotic residues.
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Affiliation(s)
- Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
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29
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Trinh KTL, Do HDK, Lee NY. Recent Advances in Molecular and Immunological Diagnostic Platform for Virus Detection: A Review. BIOSENSORS 2023; 13:490. [PMID: 37185566 PMCID: PMC10137144 DOI: 10.3390/bios13040490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing coronavirus disease (COVID-19) outbreak and a rising demand for the development of accurate, timely, and cost-effective diagnostic tests for SARS-CoV-2 as well as other viral infections in general. Currently, traditional virus screening methods such as plate culturing and real-time PCR are considered the gold standard with accurate and sensitive results. However, these methods still require sophisticated equipment, trained personnel, and a long analysis time. Alternatively, with the integration of microfluidic and biosensor technologies, microfluidic-based biosensors offer the ability to perform sample preparation and simultaneous detection of many analyses in one platform. High sensitivity, accuracy, portability, low cost, high throughput, and real-time detection can be achieved using a single platform. This review presents recent advances in microfluidic-based biosensors from many works to demonstrate the advantages of merging the two technologies for sensing viruses. Different platforms for virus detection are classified into two main sections: immunoassays and molecular assays. Moreover, available commercial sensing tests are analyzed.
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Affiliation(s)
- Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 70000, Vietnam
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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30
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The innovative and accurate detection of heavy metals in foods: A critical review on electrochemical sensors. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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31
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Wang H, Wang X, Lai K, Yan J. Stimulus-Responsive DNA Hydrogel Biosensors for Food Safety Detection. BIOSENSORS 2023; 13:320. [PMID: 36979532 PMCID: PMC10046603 DOI: 10.3390/bios13030320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Food safety has always been a major global challenge to human health and the effective detection of harmful substances in food can reduce the risk to human health. However, the food industry has been plagued by a lack of effective and sensitive safety monitoring methods due to the tension between the cost and effectiveness of monitoring. DNA-based hydrogels combine the advantages of biocompatibility, programmability, the molecular recognition of DNA molecules, and the hydrophilicity of hydrogels, making them a hotspot in the research field of new nanomaterials. The stimulus response property greatly broadens the function and application range of DNA hydrogel. In recent years, DNA hydrogels based on stimulus-responsive mechanisms have been widely applied in the field of biosensing for the detection of a variety of target substances, including various food contaminants. In this review, we describe the recent advances in the preparation of stimuli-responsive DNA hydrogels, highlighting the progress of its application in food safety detection. Finally, we also discuss the challenges and future application of stimulus-responsive DNA hydrogels.
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32
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He F, Wang H, Du P, Li T, Wang W, Tan T, Liu Y, Ma Y, Wang Y, El-Aty A. Personal Glucose Meters Coupled with Signal Amplification Technologies for Quantitative Detection of Non-Glucose Targets: Recent Progress and Challenges in Food Safety Hazards Analysis. J Pharm Anal 2023; 13:223-238. [PMID: 37102109 PMCID: PMC10123950 DOI: 10.1016/j.jpha.2023.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Ensuring food safety is paramount worldwide. Developing effective detection methods to ensure food safety can be challenging owing to trace hazards, long detection time, and resource-poor sites, in addition to the matrix effects of food. Personal glucose meter (PGM), a classic point-of-care testing device, possesses unique application advantages, demonstrating promise in food safety. Currently, many studies have used PGM-based biosensors and signal amplification technologies to achieve sensitive and specific detection of food hazards. Signal amplification technologies have the potential to greatly improve the analytical performance and integration of PGMs with biosensors, which is crucial for solving the challenges associated with the use of PGMs for food safety analysis. This review introduces the basic detection principle of a PGM-based sensing strategy, which consists of three key factors: target recognition, signal transduction, and signal output. Representative studies of existing PGM-based sensing strategies combined with various signal amplification technologies (nanomaterial-loaded multienzyme labeling, nucleic acid reaction, DNAzyme catalysis, responsive nanomaterial encapsulation, and others) in the field of food safety detection are reviewed. Future perspectives and potential opportunities and challenges associated with PGMs in the field of food safety are discussed. Despite the need for complex sample preparation and the lack of standardization in the field, using PGMs in combination with signal amplification technology shows promise as a rapid and cost-effective method for food safety hazard analysis.
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33
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Zhou J, Gui Y, Lv X, He J, Xie F, Li J, Cai J. Nanomaterial-Based Fluorescent Biosensor for Food Safety Analysis. BIOSENSORS 2022; 12:1072. [PMID: 36551039 PMCID: PMC9775463 DOI: 10.3390/bios12121072] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Food safety issues have become a major threat to public health and have garnered considerable attention. Rapid and effective detection methods are crucial for ensuring food safety. Recently, nanostructured fluorescent materials have shown considerable potential for monitoring the quality and safety of food because of their fascinating optical characteristics at the nanoscale. In this review, we first introduce biomaterials and nanomaterials for food safety analysis. Subsequently, we perform a comprehensive analysis of food safety using fluorescent biosensors based on nanomaterials, including mycotoxins, heavy metals, antibiotics, pesticide residues, foodborne pathogens, and illegal additives. Finally, we provide new insights and discuss future approaches for the development of food safety detection, with the aim of improving fluorescence detection methods for the practical application of nanomaterials to ensure food safety and protect human health.
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Affiliation(s)
- Jiaojiao Zhou
- National R&D Center for Se-Rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yue Gui
- National R&D Center for Se-Rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xuqin Lv
- National R&D Center for Se-Rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jiangling He
- National R&D Center for Se-Rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Fang Xie
- National R&D Center for Se-Rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jinjie Li
- Institute of System and Engineering, Beijing 100010, China
| | - Jie Cai
- National R&D Center for Se-Rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
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34
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Xia J, Liu Z, Gao S, Wang Q, Xu J, Wu H. Intermolecular and Intramolecular Priming Co-directed Synergistic Multi-strand Displacement Amplification Empowers Ultrasensitive Determination of microRNAs. Anal Chem 2022; 94:16132-16141. [DOI: 10.1021/acs.analchem.2c03466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Juan Xia
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Chemistry and Materials Engineering, Fuyang Normal University, Anhui Fuyang 236037, P. R. China
| | - Zhaoqiang Liu
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Shulin Gao
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Qi Wang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Anhui, Hefei 230601, P. R. China
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Hai Wu
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Chemistry and Materials Engineering, Fuyang Normal University, Anhui Fuyang 236037, P. R. China
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35
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Sun Y, Xu YX, Wang N, Wang F, Hui CC, Cheng YW, Cui MJ, Huang QY, Xu JG, Kong XM. Time-resolved strand displacement amplification enables G-quadruplex-amplified detection of type 2 diabetes mellitus-related circulating microRNA-146a. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Xiao B, Zhao R, Wang N, Zhang J, Sun X, Chen A. Recent advances in centrifugal microfluidic chip-based loop-mediated isothermal amplification. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Liu J, Wu D, Chen J, Jia S, Chen J, Wu Y, Li G. CRISPR-Cas systems mediated biosensing and applications in food safety detection. Crit Rev Food Sci Nutr 2022; 64:2960-2985. [PMID: 36218189 DOI: 10.1080/10408398.2022.2128300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food safety, closely related to economic development of food industry and public health, has become a global concern and gained increasing attention worldwide. Effective detection technology is of great importance to guarantee food safety. Although several classical detection methods have been developed, they have some limitations in portability, selectivity, and sensitivity. The emerging CRISPR-Cas systems, uniquely integrating target recognition specificity, signal transduction, and efficient signal amplification abilities, possess superior specificity and sensitivity, showing huge potential to address aforementioned challenges and develop next-generation techniques for food safety detection. In this review, we focus on recent progress of CRISPR-Cas mediated biosensing and their applications in food safety monitoring. The properties and principles of commonly used CRISPR-Cas systems are highlighted. Notably, the frequently coupled nucleic acid amplification strategies to enhance their selectivity and sensitivity, especially isothermal amplification methods, as well as various signal output modes are also systematically summarized. Meanwhile, the application of CRISPR-Cas systems-based biosensors in food safety detection including foodborne virus, foodborne bacteria, food fraud, genetically modified organisms (GMOs), toxins, heavy metal ions, antibiotic residues, and pesticide residues is comprehensively described. Furthermore, the current challenges and future prospects in this field are tentatively discussed.
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Affiliation(s)
- Jianghua Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Jiahui Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Shijie Jia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jian Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
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Yang H, Yang S, Xia X, Deng R, Gao H, Dong Y. Sensitive Detection of a Single-Nucleotide Polymorphism in Foodborne Pathogens Using CRISPR/Cas12a-Signaling ARMS-PCR. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8451-8457. [PMID: 35767832 DOI: 10.1021/acs.jafc.2c03304] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Salmonella infection, particularly that caused by drug-resistant strain, has become a worldwide public health issue. Herein, we presented a CRISPR/Cas12a-signaling ARMS-PCR assay, termed cARMS, capable of sensitively detecting drug-resistant Salmonella enterica (S. enterica) involving single-nucleotide polymorphism (SNP). Owing to the dual-recognition processes, i.e., allele-specific primed polymerization and CRISPR/Cas12 binding, the cARMS assay yielded a high sensitivity for detecting SNP down to ∼0.5%. We used the cARMS assay to investigate the adaptation of SNP-involved drug-resistant S. enterica to salt stress. It was found that the mutants exhibited stronger adaptation to salt stress, indicating the potential risk of using high salt content as a sterilization strategy. The results verified the feasibility of the cARMS assay in controlling SNP-involved bacteria-associated biosafety.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Sen Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yi Dong
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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