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Schoepp NG, Liaw EJ, Winnett A, Savela ES, Garner OB, Ismagilov RF. Differential DNA accessibility to polymerase enables 30-minute phenotypic β-lactam antibiotic susceptibility testing of carbapenem-resistant Enterobacteriaceae. PLoS Biol 2020; 18:e3000652. [PMID: 32191697 PMCID: PMC7081982 DOI: 10.1371/journal.pbio.3000652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/14/2020] [Indexed: 12/22/2022] Open
Abstract
The rise in carbapenem-resistant Enterobacteriaceae (CRE) infections has created a global health emergency, underlining the critical need to develop faster diagnostics to treat swiftly and correctly. Although rapid pathogen-identification (ID) tests are being developed, gold-standard antibiotic susceptibility testing (AST) remains unacceptably slow (1-2 d), and innovative approaches for rapid phenotypic ASTs for CREs are urgently needed. Motivated by this need, in this manuscript we tested the hypothesis that upon treatment with β-lactam antibiotics, susceptible Enterobacteriaceae isolates would become sufficiently permeabilized, making some of their DNA accessible to added polymerase and primers. Further, we hypothesized that this accessible DNA would be detectable directly by isothermal amplification methods that do not fully lyse bacterial cells. We build on these results to develop the polymerase-accessibility AST (pol-aAST), a new phenotypic approach for β-lactams, the major antibiotic class for gram-negative infections. We test isolates of the 3 causative pathogens of CRE infections using ceftriaxone (CRO), ertapenem (ETP), and meropenem (MEM) and demonstrate agreement with gold-standard AST. Importantly, pol-aAST correctly categorized resistant isolates that are undetectable by current genotypic methods (negative for β-lactamase genes or lacking predictive genotypes). We also test contrived and clinical urine samples. We show that the pol-aAST can be performed in 30 min sample-to-answer using contrived urine samples and has the potential to be performed directly on clinical urine specimens.
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Affiliation(s)
- Nathan G. Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Eric J. Liaw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Alexander Winnett
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Emily S. Savela
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Omai B. Garner
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, United States of America
| | - Rustem F. Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
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Zhou R, Li Y, Dong T, Tang Y, Li F. A sequence-specific plasmonic loop-mediated isothermal amplification assay with orthogonal color readouts enabled by CRISPR Cas12a. Chem Commun (Camb) 2020; 56:3536-3538. [PMID: 32103228 DOI: 10.1039/d0cc00397b] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Herein, we introduce a sequence-specific plasmonic loop-mediated isothermal amplification (LAMP) assay with dual, complementary color readouts enabled by CRISPR Cas12a. Using this assay, any double-stranded LAMP amplicon containing a 5'-TTN PAM sequence can be recognized by Cas12a through a specific CRISPR RNA. The signal transduction is achieved using two orthogonal plasmonic systems mediated by Cas12a.
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Affiliation(s)
- Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan, China
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53
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Liu X, Silverman AD, Alam KK, Iverson E, Lucks JB, Jewett MC, Raman S. Design of a Transcriptional Biosensor for the Portable, On-Demand Detection of Cyanuric Acid. ACS Synth Biol 2020; 9:84-94. [PMID: 31825601 PMCID: PMC7372534 DOI: 10.1021/acssynbio.9b00348] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid molecular biosensing is an emerging application area for synthetic biology. Here, we engineer a portable biosensor for cyanuric acid (CYA), an analyte of interest for human and environmental health, using a LysR-type transcription regulator (LTTR) from Pseudomonas within the context of Escherichia coli gene expression machinery. To overcome cross-host portability challenges of LTTRs, we rationally engineered hybrid Pseudomonas-E. coli promoters by integrating DNA elements required for transcriptional activity and ligand-dependent regulation from both hosts, which enabled E. coli to function as a whole-cell biosensor for CYA. To alleviate challenges of whole-cell biosensing, we adapted these promoter designs to function within a freeze-dried E. coli cell-free system to sense CYA. This portable, on-demand system robustly detects CYA within an hour from laboratory and real-world samples and works with both fluorescent and colorimetric reporters. This work elucidates general principles to facilitate the engineering of a wider array of LTTR-based environmental sensors.
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Affiliation(s)
- Xiangyang Liu
- Biophysics Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Erik Iverson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
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Thavarajah W, Verosloff MS, Jung JK, Alam KK, Miller JD, Jewett MC, Young SL, Lucks JB. A Primer on Emerging Field-Deployable Synthetic Biology Tools for Global Water Quality Monitoring. NPJ CLEAN WATER 2020; 3:18. [PMID: 34267944 PMCID: PMC8279131 DOI: 10.1038/s41545-020-0064-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 05/22/2023]
Abstract
Tracking progress towards Target 6.1 of the United Nations Sustainable Development Goals, "achieving universal and equitable access to safe and affordable drinking water for all", necessitates the development of simple, inexpensive tools to monitor water quality. The rapidly growing field of synthetic biology has the potential to address this need by taking DNA-encoded sensing elements from nature and reassembling them to create field-deployable 'biosensors' that can detect pathogenic or chemical water contaminants. Here we describe water quality monitoring strategies enabled by synthetic biology and compare them to previous approaches used to detect three priority water contaminants: fecal pathogens, arsenic, and fluoride in order to explain the potential for engineered biosensors to simplify and decentralize water quality monitoring. We also briefly discuss expanding biosensors to detect emerging contaminants including metals and pharmaceuticals. We conclude with an outlook on the future of biosensor development, in which we discuss adaptability to emerging contaminants, outline current limitations, and propose steps to overcome the field's outstanding challenges to facilitate global water quality monitoring.
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Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2204 Tech Drive, Evanston, IL, 60208, USA
| | - Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Joshua D. Miller
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Sera L. Young
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
- Institute for Policy Research, Northwestern University, 2040 Sheridan Rd, Evanston, IL, 60208 USA
- To whom correspondence should be addressed, ,
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- To whom correspondence should be addressed, ,
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Li J, Ma B, Fang J, Zhi A, Chen E, Xu Y, Yu X, Sun C, Zhang M. Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow Immunoassay for Rapid Detection of Salmonella in Food. Foods 2019; 9:foods9010027. [PMID: 31887998 PMCID: PMC7022641 DOI: 10.3390/foods9010027] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Salmonella can cause serious foodborne diseases. We have developed a lateral flow immunoassay combined with recombinase polymerase amplification (LFD-RPA) for detection of Salmonella in food. The conserved fragment (fimY) was selected as the target gene. Under an optimal condition (37 °C, 10 min), the sensitivity was 12 colony-forming units (CFU)/mL in a pure culture. Testing with 16 non-Salmonella strains as controls revealed that LFD-RPA was specific to the fimY gene of Salmonella. The established assay could detect Salmonella at concentrations as low as 1.29 × 102 CFU/mL in artificially contaminated samples. This detection was at a slightly higher level than that for a pure bacterial culture. Combined with the test strip reader, the LFD-RPA is a feasible method for quantitative detection of Salmonella based on the test line intensity, which was the ratio for the test line and control line of the reflected light. The method could be a potential point-of-care test in limited resource areas and provides a new approach and technical support for the diagnosis of food safety.
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Affiliation(s)
- Jiali Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Biao Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Jiehong Fang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Antong Zhi
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Erjing Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Ying Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Science (SLU), P.O. Box 7080, SE-75007 Uppsala, Sweden;
| | - Mingzhou Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
- Correspondence: ; Tel.: +86-571-86914476
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56
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Xu M, Fu H, Chen D, Shao Z, Zhu J, Alali WQ, Chen L. Simple Visualized Detection Method of Virulence-Associated Genes of Vibrio cholerae by Loop-Mediated Isothermal Amplification. Front Microbiol 2019; 10:2899. [PMID: 31921074 PMCID: PMC6932958 DOI: 10.3389/fmicb.2019.02899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Vibrio cholerae is a leading waterborne pathogenic bacterium worldwide. It can cause human cholera that is still pandemic in developing nations. Detection of V. cholerae contamination in drinking water and aquatic products is imperative for assuring food safety. In this study, a simple, sensitive, specific, and visualized method was developed based on loop-mediated isothermal amplification (LAMP) (designated sssvLAMP) to detect virulence-associated (ctxA, tcpA, hapA, mshA, pilA, and tlh) and species-specific (lolB) genes of V. cholerae. Three pairs of oligonucleotide primers (inner, outer, and loop primers) were designed and or synthesized to target each of these genes. The optimal conditions of the sssvLAMP method was determined, and one-step sssvLAMP reaction was performed at 65°C for 40 min. Positive results were simply read by the naked eye via color change (from orange to light green) under the visible light, or by the production of green fluorescence under the UV light (260 nm). The sssvLAMP method was more efficient in detecting 6.50 × 101-6.45 × 104-fold low number of V. cholerae cells, and more sensitive in V. cholerae genomic DNA (1.36 × 10-2-4.42 × 10-6 ng/reaction) than polymerase chain reaction (PCR) method. Among 52 strains of V. cholerae and 50 strains of non-target species (e.g., other Vibrios and common pathogens) examined, the sensitivity and specificity of the sssvLAMP method were 100% for all the target genes. Similar high efficiency of the method was observed when tested with spiked samples of water and aquatic products, as well as human stool specimens. Water from various sources and commonly consumed fish samples were promptly screened by this simple and efficient visualized method and diversified variation in the occurrence of the target genes was observed. V. cholerae strains could be mostly detected by the presence of hapA and tlh alone or in combination with other genes, indicating a variable risk of potentially pathogenic non-O1/O139 strains in edible food products. This novel LAMP method can be a promising tool to address the increasing need of food safety control of aquatic products.
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Affiliation(s)
- Mengjie Xu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Huiyu Fu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Dailing Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zehuai Shao
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jun Zhu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Walid Q. Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, Safat, Kuwait
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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57
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Cheng N, Yang Z, Wang W, Wang X, Xu W, Luo Y. A Variety of Bio-nanogold in the Fabrication of Lateral Flow Biosensors for the Detection of Pathogenic Bacteria. Curr Top Med Chem 2019; 19:2476-2493. [DOI: 10.2174/1568026619666191023125020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/15/2019] [Accepted: 09/13/2019] [Indexed: 12/19/2022]
Abstract
Pathogenic bacteria constitute one of the most serious threats to human health. This has led
to the development of technologies for the rapid detection of bacteria. Bio-nanogold-based lateral flow
biosensors (LFBs) are a promising assay due to their low limit of detection, high sensitivity, good selectivity,
robustness, low cost, and quick assay performance ability. The aim of this review is to provide
a critical overview of the current variety of bio-nanogold LFBs and their targets, with a special focus on
whole-cell and DNA detection of pathogenic bacteria. The challenges of bio-nanogold-based LFBs in
improving their performance and accessibility are also comprehensively discussed.
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Affiliation(s)
- Nan Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhansen Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Weiran Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinxian Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
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58
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Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
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59
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Dong X, Gao Y, Zhang X, Yuan J, Li P, Xing C, Yan W. Multiplex europium (III) nanoparticles immunochromatographic assay method for the detection of four nitrofuran metabolites in fish sample. Microchem J 2019. [DOI: 10.1016/j.microc.2019.104207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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60
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Phillips EA, Moehling TJ, Ejendal KFK, Hoilett OS, Byers KM, Basing LA, Jankowski LA, Bennett JB, Lin LK, Stanciu LA, Linnes JC. Microfluidic rapid and autonomous analytical device (microRAAD) to detect HIV from whole blood samples. LAB ON A CHIP 2019; 19:3375-3386. [PMID: 31539001 PMCID: PMC7384476 DOI: 10.1039/c9lc00506d] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While identifying acute HIV infection is critical to providing prompt treatment to HIV-positive individuals and preventing transmission, existing laboratory-based testing methods are too complex to perform at the point of care. Specifically, molecular techniques can detect HIV RNA within 8-10 days of transmission but require laboratory infrastructure for cold-chain reagent storage and extensive sample preparation performed by trained personnel. Here, we demonstrate our point-of-care microfluidic rapid and autonomous analysis device (microRAAD) that automatically detects HIV RNA from whole blood. Inside microRAAD, we incorporate vitrified amplification reagents, thermally-actuated valves for fluidic control, and a temperature control circuit for low-power heating. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized using a lateral flow immunoassay (LFIA), resulting in an assay limit of detection of 100 HIV-1 RNA copies when performed as a standard tube reaction. Even after three weeks of room-temperature reagent storage, microRAAD automatically isolates the virus from whole blood, amplifies HIV-1 RNA, and transports amplification products to the internal LFIA, detecting as few as 3 × 105 HIV-1 viral particles, or 2.3 × 107 virus copies per mL of whole blood, within 90 minutes. This integrated microRAAD is a low-cost and portable platform to enable automated detection of HIV and other pathogens at the point of care.
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Affiliation(s)
- Elizabeth A Phillips
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA.
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Deng HM, Zhu MH, Huang LJ, Chai YQ, Liu XR, Yuan R, Yuan YL. Novel D-A-D-Type Supramolecular Aggregates with High Photoelectric Activity for Construction of Ultrasensitive Photoelectrochemical Biosensor. Anal Chem 2019; 91:12468-12475. [DOI: 10.1021/acs.analchem.9b03151] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Han-Mei Deng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ming-Hui Zhu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Liao-Jing Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Xiao-Rui Liu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ya-Li Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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62
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Catalytic hairpin assembly-assisted lateral flow assay for visual determination of microRNA-21 using gold nanoparticles. Mikrochim Acta 2019; 186:661. [DOI: 10.1007/s00604-019-3743-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/10/2019] [Indexed: 01/25/2023]
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63
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Real-time fluorescence loop-mediated isothermal amplification assay for rapid and sensitive detection of Streptococcus gallolyticus subsp. gallolyticus associated with colorectal cancer. Anal Bioanal Chem 2019; 411:6877-6887. [PMID: 31388715 DOI: 10.1007/s00216-019-02059-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022]
Abstract
The increasing threat of Streptococcus gallolyticus subsp. gallolyticus (SGG) infections has gained considerable attention for its strong association with colorectal cancer (CRC). Herein, we proposed real-time fluorescence loop-mediated isothermal amplification (LAMP) as a novel, simple, rapid, and highly sensitive assay for identifying SGG for the first time. This assay was capable of detecting SGG with initial DNA concentrations ranging from 102 to 108 copies per microliter, under isothermal conditions within 30 min via real-time fluorescence monitoring. Our method was tested for specific identification of SGG strains without cross-reaction with other Streptococcus gallolyticus subspecies and Escherichia coli. The developed LAMP shows a superior performance with shorter time and higher sensitivity compared with conventional polymerase chain reaction (PCR). Significantly, this proposed approach was successfully applied for detecting SGG in clinical urine samples, which is non-invasive diagnosis, showing excellent accuracy and reliability to discriminate healthy controls and CRC patients. For comparison, these samples were also tested against PCR assay. These results yielded an analytical sensitivity of 100% and a specificity of 100% for SGG testing using LAMP. The findings suggest LAMP can be employed for detecting SGG infections which is useful for diagnosis and screening of CRC.
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64
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Liu L, Yang D, Liu G. Signal amplification strategies for paper-based analytical devices. Biosens Bioelectron 2019; 136:60-75. [DOI: 10.1016/j.bios.2019.04.043] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/26/2022]
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65
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Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
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66
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Cai R, Yin F, Zhang Z, Tian Y, Zhou N. Functional chimera aptamer and molecular beacon based fluorescent detection of Staphylococcus aureus with strand displacement-target recycling amplification. Anal Chim Acta 2019; 1075:128-136. [PMID: 31196418 DOI: 10.1016/j.aca.2019.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/17/2019] [Accepted: 05/05/2019] [Indexed: 01/09/2023]
Abstract
A fluorescent detection of Staphylococcus aureus (S. aureus) is established based on a finely designed functional chimera sequence, a molecular beacon (MB), and strand displacement target recycling. The chimera sequence, which consists of the aptamer sequence of S. aureus and the complementary sequence of MB, can form a hairpin structure due to the existence of intramolecular complementary regions. When S. aureus is present, it binds to the aptamer region of the chimera, opens the hairpin and unlocks the complementary sequence of MB. Subsequently, the MB is opened and intensive fluorescence signal is restored. To increase the sensitivity of the detection, signal amplification is achieved through strand displacement-based target recycling. With the catalysis of Nb. Bpu10I nicking endonuclease and Bsm DNA polymerase, the MB sequence can be cleaved and then elongated to form a complete duplex with the chimera, during which S. aureus is displaced from the chimera and proceeded to the next round of the reaction. This assay displays a linear correlation between the fluorescence intensity and the logarithm of the concentration of S. aureus within a broad concentration range from 80 CFU/mL to 8 × 106 CFU/mL. The detection limit of 39 CFU/mL can be derived. The assay was applied to detect S. aureus in different water samples, and satisfactory recovery and repeatability were achieved. Hence the designed chimera sequence and established assay have potential application in environmental pollution monitoring.
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Affiliation(s)
- Rongfeng Cai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Fan Yin
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhongwen Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yaping Tian
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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67
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T4 DNA polymerase-assisted upgrade of a nicking/polymerization amplification strategy for ultrasensitive electrochemical detection of Watermelon mosaic virus. Anal Bioanal Chem 2019; 411:2915-2924. [DOI: 10.1007/s00216-019-01737-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/24/2019] [Accepted: 02/28/2019] [Indexed: 01/16/2023]
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68
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Dong T, Wang GA, Li F. Shaping up field-deployable nucleic acid testing using microfluidic paper-based analytical devices. Anal Bioanal Chem 2019; 411:4401-4414. [DOI: 10.1007/s00216-019-01595-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/31/2018] [Accepted: 01/09/2019] [Indexed: 12/28/2022]
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69
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Shang Y, Sun J, Ye Y, Zhang J, Zhang Y, Sun X. Loop-mediated isothermal amplification-based microfluidic chip for pathogen detection. Crit Rev Food Sci Nutr 2018; 60:201-224. [DOI: 10.1080/10408398.2018.1518897] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yuting Shang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiadi Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Yongli Ye
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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70
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Chen J, Chen S, Li F. DNA Probes for Implementation of Multiple Molecular Computations Using a Lateral Flow Strip Biosensor as the Sensing Platform. Anal Chem 2018; 90:10311-10317. [DOI: 10.1021/acs.analchem.8b02103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Junhua Chen
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Shu Chen
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Fengling Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
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71
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Ye X, Li Y, Wang L, Fang X, Kong J. A novel exonuclease-assisted isothermal nucleic acid amplification with ultrahigh specificity mediated by full-length Bst DNA polymerase. Chem Commun (Camb) 2018; 54:10562-10565. [PMID: 30065993 DOI: 10.1039/c8cc04577a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Here, we introduced a novel exonuclease-assisted isothermal nucleic acid amplification (Exo-NAT) utilizing the full-length Bst DNA polymerase combined with a melting curve analysis. This method achieved an ultrahigh specificity with a good detection limit (102 copies) in both singleplex and multiplex detection, which was validated by detecting three diarrhea-inducing pathogens, rotavirus A, astrovirus, and adenovirus, in 42 clinical samples.
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Affiliation(s)
- Xin Ye
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China.
| | - Yang Li
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318, P. R. China and Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318, P. R. China
| | - Lijuan Wang
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318, P. R. China and Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318, P. R. China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China.
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China.
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