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Rioboó-Legaspi P, Costa-Rama E, Fernández-Abedul MT. ElectrochemCap: an integrated detection for loop-mediated isothermal amplification reactions. LAB ON A CHIP 2024; 24:4085-4095. [PMID: 39082091 DOI: 10.1039/d4lc00395k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) of genetic materials has emerged as a powerful molecular biology technique with great potential to be a standard point-of-care (POC) technique. This method has found several applications, but it still presents challenges for its direct on-site application, particularly in terms of integrated reaction and detection systems and the risk of carryover contamination. In this work, we propose an innovative solution - an electrochemical microcentrifuge tube cap (ElectrochemCap) based on a screen-printed electrode, a 3D printed adapter and an adhesive layer - which integrates the amplification reaction and its subsequent electrochemical detection in a single device. The design, fabrication, and electrochemical characterization of the ElectrochemCap are reported here, demonstrating its suitability for LAMP detection. Rapidly emerging technologies, such as 3D printing or xurography, are the basis of a prototype that has been validated for the detection of SARS-CoV-2 using reverse transcription LAMP (RT-LAMP), achieving results comparable to those obtained by gold-standard RT-qPCR. Moreover, we have explored the versatility of the ElectrochemCap presenting several additional designs (for containers with different volumes, shapes and materials, as well as multiplexed approaches), expanding its potential applications. Overall, the ElectrochemCap represents an affordable, versatile, and marketable innovation for integrated quantitative electrochemical detection, with enormous possibilities in bioelectroanalytical procedures and portable laboratory setups.
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Affiliation(s)
- P Rioboó-Legaspi
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain.
| | - E Costa-Rama
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain.
| | - M T Fernández-Abedul
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain.
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Wang J, Cui X, Liang L, Li J, Pang B, Li J. Advances in DNA-based electrochemical biosensors for the detection of foodborne pathogenic bacteria. Talanta 2024; 275:126072. [PMID: 38615455 DOI: 10.1016/j.talanta.2024.126072] [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: 01/16/2024] [Revised: 03/18/2024] [Accepted: 04/06/2024] [Indexed: 04/16/2024]
Abstract
The detection of foodborne pathogenic bacteria is critical in preventing foodborne diseases. DNA-based electrochemical biosensors, with the merits of high sensitivity and short detection time, provide an effective detecting method for foodborne pathogens, attracting significant interest for the past few years. This review mainly describes the important research progress of DNA-based electrochemical biosensors for the detection of foodborne pathogenic bacteria through four perspectives: representative foodborne pathogens detection using electrochemical approaches, DNA immobilization strategies of aptamers, DNA-based signal amplification strategies used in electrochemical DNA sensors, and functional DNA used in electrochemical DNA sensors. Finally, perspectives and challenges are presented in this field. This review will contribute to DNA-based electrochemical biosensor in enhancing the nucleic acid signal amplification.
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Affiliation(s)
- Jun Wang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, China
| | - Xueting Cui
- School of Public Health, Jilin University, Changchun, Jilin, 130021, China
| | - Lanqian Liang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, China
| | - Juan Li
- School of Public Health, Jilin University, Changchun, Jilin, 130021, China.
| | - Bo Pang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, China.
| | - Jinhua Li
- School of Public Health, Jilin University, Changchun, Jilin, 130021, China.
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Yang N, Zhang H, Han X, Liu Z, Lu Y. Advancements and applications of loop-mediated isothermal amplification technology: a comprehensive overview. Front Microbiol 2024; 15:1406632. [PMID: 39091309 PMCID: PMC11292733 DOI: 10.3389/fmicb.2024.1406632] [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: 03/25/2024] [Accepted: 07/04/2024] [Indexed: 08/04/2024] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a novel method for nucleic acid detection known for its isothermal properties, high efficiency, sensitivity, and specificity. LAMP employs 4 to 6 primers targeting 6 to 8 regions of the desired sequence, allowing for amplification at temperatures between 60 and 65°C and the production of up to 109 copies within a single hour. The product can be monitored by various methods such as turbidimetry, fluorometry, and colorimetry. However, it faces limitations such as the risk of non-specific amplification, challenges in primer design, unsuitability for short gene sequences, and difficulty in multiplexing. Recent advancements in polymerase and primer design have enhanced the speed and convenience of the LAMP reaction. Additionally, integrating LAMP with technologies like rolling circle amplification (RCA), recombinase polymerase amplification (RPA), and CRISPR-Cas systems has enhanced its efficiency. The combination of LAMP with various biosensors has enabled real-time analysis, broadening its application in point-of-care testing (POCT). Microfluidic technology has further facilitated the automation and miniaturization of LAMP assays, allowing for the simultaneous detection of multiple targets and preventing contamination. This review highlights advancements in LAMP, focusing on primer design, polymerase engineering, and its integration with other technologies. Continuous improvements and integration of LAMP with complementary technologies have significantly enhanced its diagnostic capabilities, making it a robust tool for rapid, sensitive, and specific nucleic acid detection with promising implications for healthcare, agriculture, and environmental monitoring.
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Affiliation(s)
- Nan Yang
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Han Zhang
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Xiu Han
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Zhifeng Liu
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Lu
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
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Wang Y, Qian J, Shi T, Wang Y, Ding Q, Ye C. Application of extremophile cell factories in industrial biotechnology. Enzyme Microb Technol 2024; 175:110407. [PMID: 38341913 DOI: 10.1016/j.enzmictec.2024.110407] [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: 12/15/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/13/2024]
Abstract
Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.
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Affiliation(s)
- Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China; Ministry of Education Key Laboratory of NSLSCS.
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Rivas-Macho A, Eletxigerra U, Diez-Ahedo R, Barros Á, Merino S, Goñi-de-Cerio F, Olabarria G. Development of an Electrochemical Sensor for SARS-CoV-2 Detection Based on Loop-Mediated Isothermal Amplification. BIOSENSORS 2023; 13:924. [PMID: 37887117 PMCID: PMC10605850 DOI: 10.3390/bios13100924] [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: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused more than 6 million deaths all over the world, demonstrating the need for a simple, fast and cost-effective point-of-care (POC) test for the detection of the virus. In this work, we developed an electrochemical sensor for SARS-CoV-2 virus detection on clinical samples based on loop-mediated isothermal amplification (LAMP). With the development of this novel sensor, the time of each measurement is significantly reduced by avoiding the DNA extraction step and replacing it with inactivation of the sample by heating it at 95 °C for 10 min. To make the reaction compatible with the sample pre-treatment, an RNase inhibitor was added directly to the premix. The LAMP product was measured in a novel, easy-to-use manufactured sensor containing a custom-made screen-printed carbon electrode. Electrochemical detection was performed with a portable potentiostat, and methylene blue was used as the redox-transducing molecule. The developed sensor achieved a limit of detection of 62 viral copies and was 100% specific for the detection of the SARS-CoV-2 virus. The performance of the electrochemical sensor was validated with nasopharyngeal samples, obtaining a sensibility and specificity of 100% compared to the gold standard RT-PCR method.
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Affiliation(s)
- Ane Rivas-Macho
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
- Molecular Biology and Biomedicine PhD Program, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Unai Eletxigerra
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Ruth Diez-Ahedo
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Ángela Barros
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Santos Merino
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
- Electricity and Electronics Department, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Felipe Goñi-de-Cerio
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
| | - Garbiñe Olabarria
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
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Yedire SG, Hosseini II, Shieh H, Khorrami Jahromi A, AbdelFatah T, Jalali M, Mahshid S. Additive manufacturing leveraged microfluidic setup for sample to answer colorimetric detection of pathogens. LAB ON A CHIP 2023; 23:4134-4145. [PMID: 37656450 DOI: 10.1039/d3lc00429e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Colorimetric readout for the detection of infectious diseases is gaining traction at the point of care/need owing to its ease of analysis and interpretation, and integration potential with highly specific loop-mediated amplification (LAMP) assays. However, coupling colorimetric readout with LAMP is rife with challenges including, rapidity, inter-user variability, colorimetric signal quantification, and user involvement in sequential steps of the LAMP assay, hindering its application. To address these challenges, for the first time, we propose a remotely smartphone-operated automated setup consisting of (i) an additively manufactured microfluidic cartridge, (ii) a portable reflected-light imaging setup with controlled epi-illumination (PRICE) module, and (iii) a control and data analysis module. The microfluidic cartridge facilitates sample collection, lysis, mixing of amplification reagents stored on-chip, and subsequent isothermal heating for initiation of amplification in a novel way by employing tunable elastomeric chambers and auxiliary components (heaters and linear actuators). PRICE offers a new imaging setup that captures the colorimetric change of the amplification media over a plasmonic nanostructured substrate in a controlled and noise-free environment for rapid minute-scale nucleic acid detection. The control and data analysis module employs microprocessors to automate cartridge operation in tandem with the imaging module. The different device components were characterized individually and finally, as a proof of concept, SARS-CoV-2 wild-type RNA was detected with a turnaround time of 13 minutes, showing the device's clinical feasibility. The suggested automated device can be adopted in future iterations for other detection and molecular assays that require sequential fluid handling steps.
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Affiliation(s)
| | | | - Hamed Shieh
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0C3, Canada.
| | | | - Tamer AbdelFatah
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0C3, Canada.
| | - Mahsa Jalali
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0C3, Canada.
| | - Sara Mahshid
- Department of Bioengineering, McGill University, Montréal, QC, H3A 0C3, Canada.
- Division of Experimental Medicine, McGill University, Montréal, QC, H3A 0C3, Canada
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Rivas-Macho A, Sorarrain A, Marimón JM, Goñi-de-Cerio F, Olabarria G. Extraction-Free Colorimetric RT-LAMP Detection of SARS-CoV-2 in Saliva. Diagnostics (Basel) 2023; 13:2344. [PMID: 37510088 PMCID: PMC10377860 DOI: 10.3390/diagnostics13142344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The pandemic situation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need of fast, simple, and cost-effective tests for the diagnosis of emerging pathogens. RT-qPCR has been established as the reference technique for the diagnosis of SARS-CoV-2 infections. This method requires a time-consuming protocol for the extraction of the nucleic acids present in the sample. A colorimetric reverse transcription loop-mediated isothermal amplification using the calcein molecule combined with a simple extraction-free method for saliva samples (calcein RT-LAMP) has been developed. Samples are heated 95 °C for 10 min before amplification at 63 °C for 40 min. The results can be observed by fluorescence or by the naked eye with a color change from orange to green. The method was compared with commercialized available colorimetric and fluorescent RT-LAMP kits. The developed method shows better sensitivity and specificity than the colorimetric commercial RT-LAMP and the same as the fluorescent RT-LAMP, without the need of a fluorescent reader. Moreover, the calcein RT-LAMP has, compared to RT-qPCR, a sensitivity of 90% and a specificity of 100% for saliva samples with a Ct ≤ 34, without the need for expensive RT-qPCR instruments, demonstrating the potential of this method for population screening.
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Affiliation(s)
- Ane Rivas-Macho
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
- Molecular Biology and Biomedicine PhD Program, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Ane Sorarrain
- Biodonostia Health Research Institute, Infectious Diseases Area, Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain
| | - José M Marimón
- Biodonostia Health Research Institute, Infectious Diseases Area, Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain
| | - Felipe Goñi-de-Cerio
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
| | - Garbiñe Olabarria
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
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Liustrovaite V, Pogorielov M, Boguzaite R, Ratautaite V, Ramanaviciene A, Pilvenyte G, Holubnycha V, Korniienko V, Diedkova K, Viter R, Ramanavicius A. Towards Electrochemical Sensor Based on Molecularly Imprinted Polypyrrole for the Detection of Bacteria- Listeria monocytogenes. Polymers (Basel) 2023; 15:polym15071597. [PMID: 37050211 PMCID: PMC10097406 DOI: 10.3390/polym15071597] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Detecting bacteria-Listeria monocytogenes-is an essential healthcare and food industry issue. The objective of the current study was to apply platinum (Pt) and screen-printed carbon (SPCE) electrodes modified by molecularly imprinted polymer (MIP) in the design of an electrochemical sensor for the detection of Listeria monocytogenes. A sequence of potential pulses was used to perform the electrochemical deposition of the non-imprinted polypyrrole (NIP-Ppy) layer and Listeria monocytogenes-imprinted polypyrrole (MIP-Ppy) layer over SPCE and Pt electrodes. The bacteria were removed by incubating Ppy-modified electrodes in different extraction solutions (sulphuric acid, acetic acid, L-lysine, and trypsin) to determine the most efficient solution for extraction and to obtain a more sensitive and repeatable design of the sensor. The performance of MIP-Ppy- and NIP-Ppy-modified electrodes was evaluated by pulsed amperometric detection (PAD). According to the results of this research, it can be assumed that the most effective MIP-Ppy/SPCE sensor can be designed by removing bacteria with the proteolytic enzyme trypsin. The LOD and LOQ of the MIP-Ppy/SPCE were 70 CFU/mL and 210 CFU/mL, respectively, with a linear range from 300 to 6700 CFU/mL.
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Affiliation(s)
- Viktorija Liustrovaite
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania
| | - Maksym Pogorielov
- Biomedical Research Centre, Sumy State University, R-Korsakova Street, 40007 Sumy, Ukraine
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Jelgavas iela 3, LV-1004 Riga, Latvia
| | - Raimonda Boguzaite
- Department of Nanotechnology, State Research Institute Center for Physical Sciences and Technology, Saulėtekio Av. 3, LT-10257 Vilnius, Lithuania
- NanoTechnas-Center of Nanotechnology and Materials Science, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania
| | - Vilma Ratautaite
- Department of Nanotechnology, State Research Institute Center for Physical Sciences and Technology, Saulėtekio Av. 3, LT-10257 Vilnius, Lithuania
- NanoTechnas-Center of Nanotechnology and Materials Science, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania
| | - Almira Ramanaviciene
- NanoTechnas-Center of Nanotechnology and Materials Science, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania
| | - Greta Pilvenyte
- Department of Nanotechnology, State Research Institute Center for Physical Sciences and Technology, Saulėtekio Av. 3, LT-10257 Vilnius, Lithuania
| | - Viktoriia Holubnycha
- Biomedical Research Centre, Sumy State University, R-Korsakova Street, 40007 Sumy, Ukraine
| | - Viktoriia Korniienko
- Biomedical Research Centre, Sumy State University, R-Korsakova Street, 40007 Sumy, Ukraine
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Jelgavas iela 3, LV-1004 Riga, Latvia
| | - Kateryna Diedkova
- Biomedical Research Centre, Sumy State University, R-Korsakova Street, 40007 Sumy, Ukraine
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Jelgavas iela 3, LV-1004 Riga, Latvia
| | - Roman Viter
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Jelgavas iela 3, LV-1004 Riga, Latvia
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania
- Department of Nanotechnology, State Research Institute Center for Physical Sciences and Technology, Saulėtekio Av. 3, LT-10257 Vilnius, Lithuania
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