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Habibi S, Bautista MA, Bryant SL, Shor RJ, Natale G. A novel synthesis method of magnetic Janus particles for wastewater applications. J Colloid Interface Sci 2024; 669:952-964. [PMID: 38759594 DOI: 10.1016/j.jcis.2024.05.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
HYPOTHESIS Magnetic particles are widely used in many adsorption and removal processes. Among the many types of magnetic colloids, magnetic Janus particles offer significant possibilities for the effective removal of several components from aqueous solutions. Nevertheless, the synthesis of structures integrating different types of materials requires scalable fabrication processes to overcome the limitations of the available methodologies. Herein, we hypothesized a fabrication process for dual-surface functionalized magnetic Janus particles. EXPERIMENTS The primary silica particles with surface-attached amine groups are further asymmetrically modified by iron oxide nanoparticles, exploiting Pickering emulsion and electroless deposition techniques. The dual surface functionality of the particles is designed for its versatility and demonstrated in two wastewater-related applications. FINDINGS We show that our design can simultaneously remove chromium (VI) and phenol from aqueous solution. The fabricated magnetic-responsive Janus particles are also an effective adsorbent for genomic Deoxyribonucleic acid (DNA) and show superior performance to commercial magnetic beads. Thus, this study provides a novel platform for designing magnetic Janus particles with multifunctional surfaces for wastewater treatment applications.
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Affiliation(s)
- Samin Habibi
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Maria A Bautista
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Steven L Bryant
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Roman J Shor
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Giovanniantonio Natale
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
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Costa-Ribeiro A, Lamas A, Mora A, Prado M, Garrido-Maestu A. Moving towards on-site detection of Shiga toxin-producing Escherichia coli in ready-to-eat leafy greens. Curr Res Food Sci 2024; 8:100716. [PMID: 38511154 PMCID: PMC10950744 DOI: 10.1016/j.crfs.2024.100716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Rapid identification of Shiga toxin-producing Escherichia coli, or STEC, is of utmost importance to assure the innocuousness of the foodstuffs. STEC have been implicated in outbreaks associated with different types of foods however, among them, ready-to-eat (RTE) vegetables are particularly problematic as they are consumed raw, and are rich in compounds that inhibit DNA-based detection methods such as qPCR. In the present study a novel method based on Loop-mediated isothermal amplification (LAMP) to overcome the limitations associated with current molecular methods for the detection of STEC in RTE vegetables targeting stx1 and stx2 genes. In this sense, LAMP demonstrated to be more robust against inhibitory substances in food. In this study, a comprehensive enrichment protocol was combined with four inexpensive DNA extraction protocols. The one based on silica purification enhanced the performance of the method, therefore it was selected for its implementation in the final method. Additionally, three different detection chemistries were compared, namely real-time fluorescence detection, and two end-point colorimetric strategies, one based on the addition of SYBR Green, and the other based on a commercial colorimetric master mix. After optimization, all three chemistries demonstrated suitable for the detection of STEC in spiked RTE salad samples, as it was possible to reach a LOD50 of 0.9, 1.4, and 7.0 CFU/25 g for the real-time, SYBR and CC LAMP assays respectively. All the performance parameters reached values higher than 90 %, when compared to a reference method based on multiplex qPCR. More specifically, the analytical sensitivity was 100, 90.0 and 100 % for real-time, SYBR and CC LAMP respectively, the specificity 100 % for all three assays, and accuracy 100, 96 and 100 %. Finally, a high degree of concordance was also obtained (1, 0.92 and 1 respectively). Considering the current technological advances, the method reported, using any of the three detection strategies, demonstrated suitable for their implementation in decentralized settings, with low equipment resources.
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Affiliation(s)
- Ana Costa-Ribeiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition, and Bromatology, Veterinary School, Campus Terra, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition, and Bromatology, Veterinary School, Campus Terra, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Laboratory of Microbiology and Technology of Marine Products (MicroTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello, 6, 36208, Vigo, Spain
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Ramos-Mandujano G, Grünberg R, Zhang Y, Bi C, Guzmán-Vega FJ, Shuaib M, Gorchakov RV, Xu J, Tehseen M, Takahashi M, Takahashi E, Dada A, Ahmad AN, Hamdan SM, Pain A, Arold ST, Li M. An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing. Sci Rep 2023; 13:20349. [PMID: 37990068 PMCID: PMC10663496 DOI: 10.1038/s41598-023-47190-w] [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: 05/09/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use-with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.
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Affiliation(s)
- Gerardo Ramos-Mandujano
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Raik Grünberg
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Yingzi Zhang
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Francisco J Guzmán-Vega
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Shuaib
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Rodion V Gorchakov
- Health, Safety and Environment Department, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Jinna Xu
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Etsuko Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
- College of Medicine, Al Faisal University, Riyadh, Kingdom of Saudi Arabia
| | - Adeel Nazir Ahmad
- KAUST Health, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Stefan T Arold
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
| | - Mo Li
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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Page R, Scourfield E, Ficarelli M, McKellar SW, Lee KL, Maguire TJ, Bouton C, Lista MJ, Neil SJ, Malim MH, Zuckerman M, Mischo HE, Martinez-Nunez RT. Homebrew: Protocol for glassmilk-based nucleic-acid extraction for SARS-CoV-2 diagnostics. STAR Protoc 2022; 3:101300. [PMID: 35479118 PMCID: PMC8938258 DOI: 10.1016/j.xpro.2022.101300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The gold standard protocol for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection detection remains reverse transcription quantitative polymerase chain reaction (qRT-PCR), which detects viral RNA more sensitively than any other approach. Here, we present Homebrew, a low-cost protocol to extract RNA using widely available reagents. Homebrew is as sensitive as commercially available RNA extraction kits. Homebrew allows for sample pooling and can be adapted for automation in high-throughput settings. For complete details on the use and execution of this protocol, please refer to Page et al. (2022).
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Affiliation(s)
- Robert Page
- ImmunoEngineering Lab, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Great Maze Pond, London SE1 9RT, UK
| | - Edward Scourfield
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mattia Ficarelli
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart W. McKellar
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Kwok Leung Lee
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Thomas J.A. Maguire
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Clement Bouton
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Maria Jose Lista
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart J.D. Neil
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Michael H. Malim
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mark Zuckerman
- South London Specialist Virology Centre, King’s College Hospital, London, UK
| | - Hannah E. Mischo
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Rocio T. Martinez-Nunez
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
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