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Macedo Rafael de Arruda J, da Silva Mendonça M, Maravilha Braga PV, Dos Santos Nascimento L, Burla Dias AJ, Lopes Rios ÁF, Magnelli Mangiavacchi P. Optimizing single-tube nested PCR for enhanced genotyping of single cells and in vitro produced bovine embryos. Gene 2024; 929:148838. [PMID: 39127412 DOI: 10.1016/j.gene.2024.148838] [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: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024]
Abstract
Single-tube nested PCR (STnPCR) is a technique that improves nested PCR, reducing potential contamination and false-positive results, enhancing the amplification sensitivity. Despite being commonly used for the detection of microorganisms, STnPCR can be a valuable tool for bovine genotyping, encompassing essential targets as ROSA26 and TSPY, pivotal in the fields of animal reproduction, genetic improvement, and transgenic research. The objective of this study was to improve and innovate STnPCR for gene detection in cattle. We aimed to detect the ROSA26 and TSPY genes using low-concentration DNA samples, including single cells, small cell groups (one to five cells), in vitro-produced embryos, and bovine tissue samples. Moreover, we refined STnPCR for gene detection in up to single cells by conducting sensitivity testing with different concentration ratios of internal and external primers. Successful amplification of the ROSA26 and TSPY genes was achieved across all tested primer concentrations, even in single cells, with more consistent results observed at lower primer concentrations. Additionally, simultaneous gene amplification was achieved through STnPCR multiplexing, representing the first study of multiplex STnPCR in cattle. These outcomes not only confirm its effectiveness in detecting genetic markers for animal genetic improvement and transgenic elements but also pave the way for its widespread adoption in reproductive studies in bovines.
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Affiliation(s)
- Jéssica Macedo Rafael de Arruda
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Mariana da Silva Mendonça
- Laboratório da Biologia do Reconhecer, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Paulo Vitor Maravilha Braga
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Leticia Dos Santos Nascimento
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Angelo José Burla Dias
- Laboratório de Reprodução e Melhoramento Genético Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Álvaro Fabrício Lopes Rios
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Paula Magnelli Mangiavacchi
- Laboratório de Reprodução e Melhoramento Genético Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil.
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Mohan S, Lavu V, Ajitkumar S, Balaji SK. Anti-biofilm activity of 445 nm and 970 nm diode laser on mixed species colonies of- aggregatibacter actinomycetemcomitans and porphyromonas gingivalis cultured on titanium discs -an in vitro study. Lasers Med Sci 2024; 39:206. [PMID: 39090348 DOI: 10.1007/s10103-024-04156-2] [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: 04/16/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
To assess and compare the anti-microbial efficacy of 445 nm and 970 nm diode laser on mixed species biofilm of Aggregatibacter actinomycetemcomitans [A.a] and Porphyromonas gingivalis [P.g] cultured on machined pure titanium discs. A total of 65 machined pure titanium discs with no surface modifications with a 10-mm diameter and a 2-mm height were sterilized by autoclaving at 121 °C for 15 min and incubated with the commercially available bacterial strains ATCC(American Type Culture Collection- P.g 33277 and A.a 29522)mixture of Aggregatibacter actinomycetemcomitans(A.a) and Porphyromonas gingivalis(P.g).After a 2-week incubation period with the mixture of bacteria to develop a mixed species biofilm, the discs were divided into three groups: (1) no treatment (control), (2) 445 nm laser (test), (3) 970 nm laser (test). For each laser wavelength (445 and 970 nm), the discs were exposed to 1.0 W and 2.0 W in continuous wave mode for the times points of 15, 30, and 60 s. The antimicrobial efficacy was assessed by qPCR. A significant reduction in the levels of both species of bacteria was observed between control and the laser intervention groups. A higher efficacy for the 445 nm diode laser against Porphyromonas gingivalis and a similar efficacy against Aggregatibacter actinomycetemcomitans was observed as compared to the 970 nm group. 445 nm wavelength represents a potential and effective laser wavelength which can be used for the management of peri-implant infection. The present study findings also need to be further validated through clinical interventional trials.
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Affiliation(s)
- Shylaja Mohan
- Department of Periodontology, Sri Ramachandra Dental College and Hospital, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, 600116, India
| | - Vamsi Lavu
- Department of Periodontology, Sri Ramachandra Dental College and Hospital, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, 600116, India.
| | - Supraja Ajitkumar
- Department of Periodontology, Sri Ramachandra Dental College and Hospital, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, 600116, India
| | - S K Balaji
- Department of Periodontology, Sri Ramachandra Dental College and Hospital, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, 600116, India
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Wang H. A Review of Nanotechnology in microRNA Detection and Drug Delivery. Cells 2024; 13:1277. [PMID: 39120308 PMCID: PMC11311607 DOI: 10.3390/cells13151277] [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: 06/17/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play a crucial role in regulating gene expression. Dysfunction in miRNAs can lead to various diseases, including cancers, neurological disorders, and cardiovascular conditions. To date, approximately 2000 miRNAs have been identified in humans. These small molecules have shown promise as disease biomarkers and potential therapeutic targets. Therefore, identifying miRNA biomarkers for diseases and developing effective miRNA drug delivery systems are essential. Nanotechnology offers promising new approaches to addressing scientific and medical challenges. Traditional miRNA detection methods include next-generation sequencing, microarrays, Northern blotting, and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Nanotechnology can serve as an effective alternative to Northern blotting and RT-qPCR for miRNA detection. Moreover, nanomaterials exhibit unique properties that differ from larger counterparts, enabling miRNA therapeutics to more effectively enter target cells, reduce degradation in the bloodstream, and be released in specific tissues or cells. This paper reviews the application of nanotechnology in miRNA detection and drug delivery systems. Given that miRNA therapeutics are still in the developing stages, nanotechnology holds great promise for accelerating miRNA therapeutics development.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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Hu K, Yin W, Bai Y, Zhang J, Yin J, Zhu Q, Mu Y. CRISPR-Based Biosensors for Medical Diagnosis: Readout from Detector-Dependence Detection Toward Naked Eye Detection. BIOSENSORS 2024; 14:367. [PMID: 39194596 DOI: 10.3390/bios14080367] [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: 05/31/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024]
Abstract
The detection of biomarkers (such as DNA, RNA, and protein) plays a vital role in medical diagnosis. The CRISPR-based biosensors utilize the CRISPR/Cas system for biometric recognition of targets and use biosensor strategy to read out biological signals without the employment of professional operations. Consequently, the CRISPR-based biosensors demonstrate great potential for the detection of biomarkers with high sensitivity and specificity. However, the signal readout still relies on specialized detectors, limiting its application in on-site detection for medical diagnosis. In this review, we summarize the principles and advances of the CRISPR-based biosensors with a focus on medical diagnosis. Then, we review the advantages and progress of CRISPR-based naked eye biosensors, which can realize diagnosis without additional detectors for signal readout. Finally, we discuss the challenges and further prospects for the development of CRISPR-based biosensors.
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Affiliation(s)
- Kai Hu
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Weihong Yin
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Yunhan Bai
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Jiarui Zhang
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Juxin Yin
- Academy of Edge Intelligence, Hangzhou City University, Hangzhou 310015, China
| | - Qiangyuan Zhu
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Ying Mu
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
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Liu Y, Hu Z, Yang S, Xu N, Song Q, Gao Y, Wen W. Fabrication of Cost-Effective Microchip-Based Device Using Sandblasting Technique for Real-Time Multiplex PCR Detection. MICROMACHINES 2024; 15:944. [PMID: 39203595 PMCID: PMC11356311 DOI: 10.3390/mi15080944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024]
Abstract
The combination of multiplex polymerase chain reaction (mPCR) and microfluidic technologies demonstrates great significance in biomedical applications. However, current microfluidics-based molecular diagnostics face challenges in multi-target detection due to their limited fluorescence channels, complicated fabrication process, and high cost. In this research, we proposed a cost-effective sandblasting method for manufacturing silicon microchips and a chip-based microdevice for field mPCR detection. The atomic force microscopy (AFM) images showed a rough surface of the sandblasted microchips, leading to poor biocompatibility. To relieve the inhibitory effect, we dip-coated a layer of bovine serum albumin (BSA) on the irregular substrate. The optimized coating condition was determined by scanning electron microscope (SEM) and energy-dispersive X-ray spectroscopy (EDS) (65 °C for 60 min). After sufficient coating, we performed on-chip PCR tests with 500 copies/mL Coronavirus Disease 2019 (COVID-19) standard sample within 20 min, and the sandblasted microchip displayed a higher amplification rate compared to dry etching chips. Finally, we achieved a 50 min mPCR for screening five resistance genes of the endophthalmitis pathogens on our microdevices, with strong specificity and reliability. Thus, this sandblasted microchip-based platform not only provides a rapid, accessible, and effective solution for multiplex molecular detection but also enables large-scale microfabrication in a low-cost and convenient way.
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Affiliation(s)
- Yiteng Liu
- Division of Emerging Interdisciplinary Areas, Academy of Interdisciplinary Studies, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China; (Y.L.)
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Zhiyang Hu
- Division of Emerging Interdisciplinary Areas, Academy of Interdisciplinary Studies, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China; (Y.L.)
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Siyu Yang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Na Xu
- Shenzhen Shineway Technology Corporation, Shenzhen 518048, China
| | - Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Yibo Gao
- Shenzhen Shineway Technology Corporation, Shenzhen 518048, China
| | - Weijia Wen
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
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Hassanain W, Johnson CL, Faulds K, Keegan N, Graham D. Ultrasensitive Dual ELONA/SERS-RPA Multiplex Diagnosis of Antimicrobial Resistance. Anal Chem 2024; 96:12093-12101. [PMID: 38975860 PMCID: PMC11270532 DOI: 10.1021/acs.analchem.4c02165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
Antimicrobial resistance (AMR) is a significant global health threat concern, necessitating healthcare practitioners to accurately prescribe the most effective antimicrobial agents with correct doses to combat resistant infections. This is necessary to improve the therapeutic outcomes for patients and prevent further increase in AMR. Consequently, there is an urgent need to implement rapid and sensitive clinical diagnostic methods to identify resistant pathogenic strains and monitor the efficacy of antimicrobials. In this study, we report a novel proof-of-concept magnetic scaffold-recombinase polymerase amplification (RPA) technique, coupled with an enzyme-linked oligonucleotide assay (ELONA) and surface-enhanced Raman scattering (SERS) detection, aimed at selectively amplifying and detecting the DNA signature of three resistant carbapenemase genes, VIM, KPC, and IMP. To achieve this, streptavidin-coated magnetic beads were functionalized with biotin-modified forward primers. RPA was conducted on the surface of the beads, resulting in an immobilized duplex amplicon featuring a single overhang tail specific to each gene. These tails were subsequently hybridized with recognition HRP probes conjugated to a complementary single-stranded oligonucleotide and detected colorimetrically. Additionally, they underwent hybridization with similar selective SERS probes and were measured using a handheld Raman spectrometer. The resulting quantification limits were at subpicomolar level for both assays, allowing the potential for early diagnosis. Moreover, we demonstrated the platform capability to conduct a multiplex RPA-SERS detection of the three genes in a single tube. Compared to similar approaches like PCR, RPA offers advantages of speed, affordability, and isothermal operation at 37 °C, eliminating the need for a thermal cycler. The whole assay was completed within <2 h. Therefore, this novel magnetic scaffold ELONA/SERS-RPA platform, for DNA detection, demonstrated excellent capability for the rapid monitoring of AMR in point-of-care applications, in terms of sensitivity, portability, and speed of analysis.
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Affiliation(s)
- Waleed
A. Hassanain
- Department
of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, U.K.
| | - Christopher L. Johnson
- Translational
and Clinical Research Institute, Newcastle
University, Newcastle-Upon-Tyne NE2 4HH, U.K.
| | - Karen Faulds
- Department
of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, U.K.
| | - Neil Keegan
- Translational
and Clinical Research Institute, Newcastle
University, Newcastle-Upon-Tyne NE2 4HH, U.K.
| | - Duncan Graham
- Department
of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, U.K.
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7
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Diez Benavente E, Sakkers TR, van der Harst P, den Ruijter HM. Atherosclerotic plaque-specific methylation biomarkers in plasma cell-free DNA of female and male patients with coronary artery disease. Eur Heart J 2024; 45:2468-2470. [PMID: 38685672 DOI: 10.1093/eurheartj/ehae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Affiliation(s)
- Ernest Diez Benavente
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Tim R Sakkers
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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Chi J, Ding L, Wang X, Chen X, Peng C, Xu J. A platform for precise quantification of gene editing products based on microfluidic chip-based digital PCR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4783-4793. [PMID: 38961688 DOI: 10.1039/d4ay00863d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The new generation of gene editing technologies, primarily based on CRISPR/Cas9 and its derivatives, allows for more precise editing of organisms. However, when the editing efficiency is low, only a small fraction of gene fragments is edited, leaving behind minimal traces and making it difficult to detect and evaluate the editing effects. Although a series of technologies and methods have been developed, they lack the ability for precise quantification and quantitative analysis of these products. Digital polymerase chain reaction (dPCR) offers advantages such as high precision and sensitivity, making it suitable for absolute quantification of nucleic acid samples. In the present study, we developed a novel platform for precise quantification of gene editing products based on microfluidic chip-based dPCR. The results indicated that our assay accurately identified different types of edited samples within a variety of different types, including more complex genomic crops such as tetraploid rapeseed and soybean (highly repetitive sequence). The sensitivity of this detection platform was as low as 8.14 copies per μL, with a detection limit of 0.1%. These results demonstrated the superior performance of the platform, including high sensitivity, low detection limit, and wide applicability, enabling precise quantification and assessment of gene editing efficiency. In conclusion, microfluidic chip-based dPCR was used as a powerful tool for precise quantification and assessment of gene editing products.
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Affiliation(s)
- Jingzheng Chi
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Lin Ding
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Moya Muñoz GG, Brix O, Klocke P, Harris PD, Luna Piedra JR, Wendler ND, Lerner E, Zijlstra N, Cordes T. Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573596. [PMID: 38234760 PMCID: PMC10793419 DOI: 10.1101/2023.12.29.573596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is,however, a growing gap between the state-of-the-art and what is accessible to biologists, biochemists, medical researchers or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed micro-spectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines are provided, to allow non-optics specialist to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and opensource Brick-MIC platform will be a valuable tool for many laboratories worldwide.
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Affiliation(s)
- Gabriel G. Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Oliver Brix
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Philipp Klocke
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Paul D. Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jorge R. Luna Piedra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Nicolas D. Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
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10
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Sugishita Y, Moriuchi R, Ishii Y. External quality assessment survey for SARS-CoV-2 nucleic acid amplification tests in clinical laboratories in Tokyo, 2021. J Infect Chemother 2024; 30:633-641. [PMID: 38325625 DOI: 10.1016/j.jiac.2024.01.016] [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: 11/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
INTRODUCTION Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests. METHODS In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan. In open testing, where the laboratories knew that the samples were intended for the survey, a simulated nasopharyngeal swab suspension sample was used, featuring a positive sample A with a viral concentration of 50 copies/μL, positive sample B with 5 copies/μL, and a negative sample. Laboratories employing real-time RT-PCR were required to report cycle threshold (Ct) values. In blind testing, where the samples were processed as normal test samples, a positive sample C with 50 copies/μL was prepared using a simulated saliva sample. RESULTS Of the 47 laboratories, 41 were engaged in open testing. For sample A, all 41 laboratories yielded positive results, whereas for sample B, 36 laboratories reported positive results, 3 laboratories reported "test decision pending", 1 laboratory reported "suspected positive", and 1 laboratory did not respond. All 41 laboratories correctly identified the negative samples as negative. The mean Ct values were 32.2 for sample A and 35.2 for sample B. In the blind test, six laboratories received samples. Sample C was identified as positive by five laboratories and negative by one laboratory. CONCLUSIONS The nature of the specimen, specifically the saliva, may have influenced the blind test outcomes. The identified issues must be meticulously investigated and rectified to ensure accurate results.
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Affiliation(s)
- Yoshiyuki Sugishita
- Quality Control Section, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan.
| | - Rie Moriuchi
- Quality Control Section, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan.
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan.
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11
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Rolando JC, Melkonian AV, Walt DR. The Present and Future Landscapes of Molecular Diagnostics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:459-474. [PMID: 38360553 DOI: 10.1146/annurev-anchem-061622-015112] [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: 02/17/2024]
Abstract
Nucleic acid testing is the cornerstone of modern molecular diagnostics. This review describes the current status and future directions of molecular diagnostics, focusing on four major techniques: polymerase chain reaction (PCR), next-generation sequencing (NGS), isothermal amplification methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods. We explore the advantages and limitations of each technique, describe how each overlaps with or complements other techniques, and examine current clinical offerings. This review provides a broad perspective into the landscape of molecular diagnostics and highlights potential future directions in this rapidly evolving field.
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Affiliation(s)
- Justin C Rolando
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Arek V Melkonian
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - David R Walt
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
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12
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Ang B, Jirapanjawat T, Tay KP, Ashtiani D, Greening C, Tuck KL, Neild A, Cadarso VJ. Rapid Concentration and Detection of Bacteria in Milk Using a Microfluidic Surface Acoustic Wave Activated Nanosieve. ACS Sens 2024; 9:3105-3114. [PMID: 38753893 DOI: 10.1021/acssensors.4c00291] [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: 05/18/2024]
Abstract
Rapid detection of microbes is a key feature for monitoring food quality. Unfortunately, current detection systems rely on labor-intensive and time-consuming lab-based processes that are not suitable for point-of-interest applications and typically require several days before results are available. Here, we demonstrate a microfluidic system capable of rapidly concentrating, fluorescent staining, and detecting bacteria in unprocessed complex biological media such as milk. This concentration is done using a surface acoustic wave-driven microfluidic device which operates based on the Bjerknes force, a force generated on one particle by another in its close proximity. We exploit this effect by exciting a tightly packed bed of 50 μm polystyrene microparticles temporarily with surface acoustic waves within a microfluidic device to capture and release bacterial cells on demand. The bacterial cells are fluorescently stained during capture and then detected using fluorescence microscopy upon release. This device offers a high capturing efficiency (>80%) and a 34 Colony Forming Units (CFU)/mL limit of detection, which is 1 order of magnitude below that of plate counting at 30 CFU per standard 100 μL plate (or 300 CFU/mL). This can be attained in just 1 h of processing at 10 μL/min. With this system, we demonstrate that bacterial detection from extremely low concentration samples down to the order of ∼10 CFU/mL is possible without requiring any additional external pre- or postprocessing.
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Affiliation(s)
- Bryan Ang
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3168, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton 3168, Victoria, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton 3168, Victoria, Australia
| | - Khai Ping Tay
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3168, Victoria, Australia
| | | | - Chris Greening
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton 3168, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton 3168, Victoria, Australia
| | - Kellie L Tuck
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia
| | - Adrian Neild
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3168, Victoria, Australia
| | - Victor J Cadarso
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3168, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton 3168, Victoria, Australia
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13
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Zhou H, Yang Y, Zhang Y, Li F, Shen Y, Qin L, Huang W. Current Status and Perspectives of Diagnosis and Treatment of Periprosthetic Joint Infection. Infect Drug Resist 2024; 17:2417-2429. [PMID: 38912221 PMCID: PMC11192293 DOI: 10.2147/idr.s457644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Periprosthetic joint infection (PJI) is a catastrophic complication following joint replacement surgery, posing significant challenges to orthopedic surgeons. Due to the lack of a definitive diagnostic gold standard, timely treatment initiation is problematic, resulting in substantial economic burdens on patients and society. In this review, we thoroughly analyze the complexities of PJI and emphasize the importance of accurate diagnosis and effective treatment. The article specifically focuses on the advancements in diagnostic techniques, ranging from traditional pathogen culture to advanced molecular diagnostics, and discusses their role in enhancing diagnostic accuracy. Additionally, we review the latest surgical management strategies, including everything from debridement to revision surgeries. Our summary aims to provide practical information for the diagnosis and treatment of PJI and encourages further research to improve diagnostic accuracy and treatment outcomes.
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Affiliation(s)
- Haotian Zhou
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yaji Yang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yanhao Zhang
- College of Pharmacy, Army Military Medical University, Chongqing, 400038, People’s Republic of China
| | - Feilong Li
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yidong Shen
- Department of Orthopaedics, The First People’s Hospital of Yancheng, Yancheng, 224000, People’s Republic of China
| | - Leilei Qin
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Wei Huang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
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14
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Saleh EAM, Ali E, Muxamadovna GM, Kassem AF, Kaur I, Kumar A, Jabbar HS, Alwaily ER, Elawady A, Omran AA. CRISPR/Cas-based colorimetric biosensors: a promising tool for the diagnosis of bacterial foodborne pathogens in food products. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3448-3463. [PMID: 38804827 DOI: 10.1039/d4ay00578c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Some physical phenomena and various chemical substances newly introduced in nanotechnology have allowed scientists to develop valuable devices in the field of food sciences. Regarding such progress, the identification of foodborne pathogenic microorganisms is an imperative subject nowadays. These bacterial species have been found to cause severe health impacts after food ingestion and can result in high mortality in acute cases. The rapid detection of foodborne bacterial species at low concentrations is in high demand in recent diagnostics. CRISPR/Cas-mediated biosensors possess the potential to overcome several challenges in classical assays such as complex pretreatments, long turnaround time, and insensitivity. Among them, colorimetric nanoprobes based on the CRISPR strategy afford promising devices for POCT (point-of-care testing) since they can be visualized with the naked eye and do not require diagnostic apparatus. In this study, we briefly classify and discuss the working principles of the different CRISPR/Cas protein agents that have been employed in biosensors so far. We assess the current status of the CRISPR system, specifically focusing on colorimetric biosensing platforms. We discuss the utilization of each Cas effector in the detection of foodborne pathogens and examine the restrictions of the existing technology. The challenges and future opportunities are also indicated and addressed.
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Affiliation(s)
- Ebraheem Abdu Musad Saleh
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia.
| | - Eyhab Ali
- Al-Zahraa University for Women, Karbala, Iraq
| | | | - Asmaa F Kassem
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka-560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan-303012, India
| | - Abhinav Kumar
- Department of Nuclear and Renewable Energy, Ural Federal University Named After the First President of Russia Boris Yeltsin, Yekaterinburg 620002, Russia
| | - Hijran Sanaan Jabbar
- Department of Chemistry, College of Science, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Enas R Alwaily
- Microbiology Research Group, College of Pharmacy, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Elawady
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- College of Technical Engineering, The Islamic University of Babylon, Babylon, Iraq
| | - Alaa A Omran
- Department of Engineering, AL-Nisour University College, Baghdad, Iraq
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15
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Frigoli M, Lowdon JW, Caldara M, Cleij TJ, Diliën H, Eersels K, van Grinsven B. Emerging Biomimetic Sensor Technologies for the Detection of Pathogenic Bacteria: A Commercial Viability Study. ACS OMEGA 2024; 9:23155-23171. [PMID: 38854523 PMCID: PMC11154936 DOI: 10.1021/acsomega.4c01478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/25/2024] [Accepted: 05/07/2024] [Indexed: 06/11/2024]
Abstract
Ensuring a rapid and accurate identification of harmful bacteria is crucial in various fields including environmental monitoring, food safety, and clinical diagnostics. Conventional detection methods often suffer from limitations such as long analysis time, complexity, and the need for qualified personnel. Therefore, a lot of research effort is devoted to developing technologies with the potential to revolutionize the detection of pathogenic bacteria by offering rapid, sensitive, and user-friendly platforms for point-of-care analysis. In this light, biosensors have gained significant commercial attention in recent years due to their simplicity, portability, and rapid analysis capabilities. The purpose of this review is to identify a trend by analyzing which biosensor technologies have become commercially successful in the field of bacteria detection. Moreover, we highlight the characteristics that a biosensor must possess to finally arrive in the market and therefore in the hands of the end-user, and we present critical examples of the market applications of various technologies. The aim is to investigate the reason why certain technologies have achieved commercial success and extrapolate these trends to the future economic viability of a new subfield in the world of biosensing: the development of biomimetic sensor platforms. Therefore, an overview of recent advances in the field of biomimetic bacteria detection will be presented, after which the challenges that need to be addressed in the coming years to improve market penetration will be critically evaluated. We will zoom into the current shortcomings of biomimetic sensors based on imprinting technology and aptamers and try to come up with a recommendation for further development based on the trends observed from previous commercial success stories in biosensing.
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Affiliation(s)
- Margaux Frigoli
- Sensor Engineering Department,
Faculty of Science and Engineering, Maastricht
University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Joseph W. Lowdon
- Sensor Engineering Department,
Faculty of Science and Engineering, Maastricht
University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Manlio Caldara
- Sensor Engineering Department,
Faculty of Science and Engineering, Maastricht
University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Thomas J. Cleij
- Sensor Engineering Department,
Faculty of Science and Engineering, Maastricht
University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Hanne Diliën
- Sensor Engineering Department,
Faculty of Science and Engineering, Maastricht
University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kasper Eersels
- Sensor Engineering Department,
Faculty of Science and Engineering, Maastricht
University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Bart van Grinsven
- Sensor Engineering Department,
Faculty of Science and Engineering, Maastricht
University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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16
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Kieffer C, Rondelez Y, Gines G. Coupling Exponential to Linear Amplification for Endpoint Quantitative Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309386. [PMID: 38593401 DOI: 10.1002/advs.202309386] [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: 12/03/2023] [Revised: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Exponential DNA amplification techniques are fundamental in ultrasensitive molecular diagnostics. These systems offer a wide dynamic range, but the quantification requires real-time monitoring of the amplification reaction. Linear amplification schemes, despite their limited sensitivity, can achieve quantitative measurement from a single end-point readout, suitable for low-cost, point-of-care, or massive testing. Reconciling the sensitivity of exponential amplification with the simplicity of end-point readout would thus break through a major design dilemma and open a route to a new generation of massively scalable quantitative bioassays. Here a hybrid nucleic acid-based circuit design is introduced to compute a logarithmic function, therefore providing a wide dynamic range based on a single end-point measurement. CELIA (Coupling Exponential amplification reaction to LInear Amplification) exploits a versatile biochemical circuit architecture to couple a tunable linear amplification stage - optionally embedding an inverter function - downstream of an exponential module in a one-pot format. Applied to the detection of microRNAs, CELIA provides a limit of detection in the femtomolar range and a dynamic range of six decades. This isothermal approach bypasses thermocyclers without compromising sensitivity, thereby opening the way to applications in various diagnostic assays, and providing a simplified, cost-efficient, and high throughput solution for quantitative nucleic acid analysis.
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Affiliation(s)
- Coline Kieffer
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Guillaume Gines
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, 10 rue Vauquelin, Paris, 75005, France
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17
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Ahmad S, Lohiya S, Taksande A, Meshram RJ, Varma A, Vagha K. A Comprehensive Review of Innovative Paradigms in Microbial Detection and Antimicrobial Resistance: Beyond Traditional Cultural Methods. Cureus 2024; 16:e61476. [PMID: 38952583 PMCID: PMC11216122 DOI: 10.7759/cureus.61476] [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: 05/22/2024] [Accepted: 06/01/2024] [Indexed: 07/03/2024] Open
Abstract
Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the efficacy of antimicrobial agents. While foundational in microbial identification, traditional cultural methods are often laborious, time-consuming, and limited in their ability to detect AMR markers. In response to these challenges, innovative paradigms have emerged, leveraging advances in molecular biology, genomics, proteomics, nanotechnology, and bioinformatics. This comprehensive review provides an overview of innovative approaches beyond traditional cultural methods for microbial detection and AMR surveillance. Molecular-based techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer enhanced sensitivity and specificity, enabling the rapid identification of microbial pathogens and AMR determinants. Mass spectrometry-based methods provide rapid and accurate detection of microbial biomarkers, including matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and biosensor technologies. Nanotechnology approaches, such as nanoparticle-based assays and nanopore sequencing, offer novel platforms for sensitive and label-free detection of pathogens and AMR markers. Embracing these innovative paradigms holds immense promise for improving disease diagnosis, antibiotic stewardship, and AMR containment efforts. However, challenges such as cost, standardization, and integration with existing healthcare systems must be addressed to realize the full potential of these technologies. By fostering interdisciplinary collaboration and innovation, we can strengthen our ability to detect, monitor, and combat AMR, safeguarding public health for generations.
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Affiliation(s)
- Shahzad Ahmad
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Sham Lohiya
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
- Pediatrics, Acharya Vinoba Bhave Rural Hospital, Wardha, IND
| | - Amar Taksande
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Revat J Meshram
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Ashish Varma
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Keta Vagha
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
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18
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Li Z, Zhang S, Zhang J, Avery L, Banach D, Zhao H, Liu C. Palm-Sized Lab-In-A-Magnetofluidic Tube Platform for Rapid and Sensitive Virus Detection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310066. [PMID: 38634211 PMCID: PMC11187901 DOI: 10.1002/advs.202310066] [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: 12/21/2023] [Revised: 03/12/2024] [Indexed: 04/19/2024]
Abstract
Simple, sensitive, and accurate molecular diagnostics are critical for preventing rapid spread of infection and initiating early treatment of diseases. However, current molecular detection methods typically rely on extensive nucleic acid sample preparation and expensive instrumentation. Here, a simple, fully integrated, lab-in-a-magnetofluidic tube (LIAMT) platform is presented for "sample-to-result" molecular detection of virus. By leveraging magnetofluidic transport of micro/nano magnetic beads, the LIAMT device integrates viral lysis, nucleic acid extraction, isothermal amplification, and CRISPR detection within a single engineered microcentrifuge tube. To enable point-of-care molecular diagnostics, a palm-sized processor is developed for magnetofluidic separation, nucleic acid amplification, and visual fluorescence detection. The LIAMT platform is applied to detect SARS-CoV-2 and HIV viruses, achieving a detection sensitivity of 73.4 and 63.9 copies µL-1, respectively. Its clinical utility is further demonstrated by detecting SARS-CoV-2 and HIV in clinical samples. This simple, affordable, and portable LIAMT platform holds promise for rapid and sensitive molecular diagnostics of infectious diseases at the point-of-care.
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Affiliation(s)
- Ziyue Li
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
- Department of Biomedical EngineeringUniversity of ConnecticutStorrsConnecticut06269USA
| | - Shuo Zhang
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
- Department of Biomedical EngineeringUniversity of ConnecticutStorrsConnecticut06269USA
| | - Jiongyu Zhang
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
- Department of Biomedical EngineeringUniversity of ConnecticutStorrsConnecticut06269USA
| | - Lori Avery
- Department of Pathology and Laboratory MedicineUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
| | - David Banach
- Department of MedicineDivision of Infectious DiseasesUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
| | - Hui Zhao
- Department of Mechanical EngineeringUniversity of NevadaLas VegasNevada89154USA
| | - Changchun Liu
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
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19
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Chen Z, Luo G, Ren J, Wang Q, Zhao X, Wei L, Wang Y, Liu Y, Deng Y, Li S. Recent Advances in and Application of Fluorescent Microspheres for Multiple Nucleic Acid Detection. BIOSENSORS 2024; 14:265. [PMID: 38920569 PMCID: PMC11201543 DOI: 10.3390/bios14060265] [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: 04/28/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Traditional single nucleic acid assays can only detect one target while multiple nucleic acid assays can detect multiple targets simultaneously, providing comprehensive and accurate information. Fluorescent microspheres in multiplexed nucleic acid detection offer high sensitivity, specificity, multiplexing, flexibility, and scalability advantages, enabling precise, real-time results and supporting clinical diagnosis and research. However, multiplexed assays face challenges like complexity, costs, and sample handling issues. The review explores the recent advancements and applications of fluorescent microspheres in multiple nucleic acid detection. It discusses the versatility of fluorescent microspheres in various fields, such as disease diagnosis, drug screening, and personalized medicine. The review highlights the possibility of adjusting the performance of fluorescent microspheres by modifying concentrations and carrier forms, allowing for tailored applications. It emphasizes the potential of fluorescent microsphere technology in revolutionizing nucleic acid detection and advancing health, disease treatment, and medical research.
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Affiliation(s)
- Zhu Chen
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Gaoming Luo
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Jie Ren
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Qixuan Wang
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xinping Zhao
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Linyu Wei
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China;
| | - Yuan Liu
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Yan Deng
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Song Li
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
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20
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Zhang H, Liu X, Wang X, Yan Z, Xu Y, Gaňová M, Řezníček T, Korabečná M, Neuzil P. SPEED: an integrated, smartphone-operated, handheld digital PCR Device for point-of-care testing. MICROSYSTEMS & NANOENGINEERING 2024; 10:62. [PMID: 38770032 PMCID: PMC11102901 DOI: 10.1038/s41378-024-00689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/14/2024] [Accepted: 03/04/2024] [Indexed: 05/22/2024]
Abstract
This study elaborates on the design, fabrication, and data analysis details of SPEED, a recently proposed smartphone-based digital polymerase chain reaction (dPCR) device. The dPCR chips incorporate partition diameters ranging from 50 μm to 5 μm, and these partitions are organized into six distinct blocks to facilitate image processing. Due to the superior thermal conductivity of Si and its potential for mass production, the dPCR chips were fabricated on a Si substrate. A temperature control system based on a high-power density Peltier element and a preheating/cooling PCR protocol user interface shortening the thermal cycle time. The optical design employs four 470 nm light-emitting diodes as light sources, with filters and mirrors effectively managing the light emitted during PCR. An algorithm is utilized for image processing and illumination nonuniformity correction including conversion to a monochromatic format, partition identification, skew correction, and the generation of an image correction mask. We validated the device using a range of deoxyribonucleic acid targets, demonstrating its potential applicability across multiple fields. Therefore, we provide guidance and verification of the design and testing of the recently proposed SPEED device.
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Affiliation(s)
- Haoqing Zhang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
- The Key Laboratory of Biomedical Information Engineering of the Ministry of Education; School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 PR China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049 PR China
| | - Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
| | - Xinlu Wang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
| | - Zhiqiang Yan
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 PR China
| | - Ying Xu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
| | - Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic
| | - Tomáš Řezníček
- ITD Tech S.R.O, Osvoboditelu, 1005, 735 81 Bohumín, Czech Republic
| | - Marie Korabečná
- Institute of Biology and Medical Genetics; First Faculty of Medicine, Charles University and General University Hospital of Prague, Albertov 4, 12800 Prague, Czech Republic
| | - Pavel Neuzil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
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21
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Zhao X, Bhat A, O’Connor C, Curtin J, Singh B, Tian F. Review of Detection Limits for Various Techniques for Bacterial Detection in Food Samples. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:855. [PMID: 38786811 PMCID: PMC11124167 DOI: 10.3390/nano14100855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024]
Abstract
Foodborne illnesses can be infectious and dangerous, and most of them are caused by bacteria. Some common food-related bacteria species exist widely in nature and pose a serious threat to both humans and animals; they can cause poisoning, diseases, disabilities and even death. Rapid, reliable and cost-effective methods for bacterial detection are of paramount importance in food safety and environmental monitoring. Polymerase chain reaction (PCR), lateral flow immunochromatographic assay (LFIA) and electrochemical methods have been widely used in food safety and environmental monitoring. In this paper, the recent developments (2013-2023) covering PCR, LFIA and electrochemical methods for various bacterial species (Salmonella, Listeria, Campylobacter, Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli)), considering different food sample types, analytical performances and the reported limit of detection (LOD), are discussed. It was found that the bacteria species and food sample type contributed significantly to the analytical performance and LOD. Detection via LFIA has a higher average LOD (24 CFU/mL) than detection via electrochemical methods (12 CFU/mL) and PCR (6 CFU/mL). Salmonella and E. coli in the Pseudomonadota domain usually have low LODs. LODs are usually lower for detection in fish and eggs. Gold and iron nanoparticles were the most studied in the reported articles for LFIA, and average LODs were 26 CFU/mL and 12 CFU/mL, respectively. The electrochemical method revealed that the average LOD was highest for cyclic voltammetry (CV) at 18 CFU/mL, followed by electrochemical impedance spectroscopy (EIS) at 12 CFU/mL and differential pulse voltammetry (DPV) at 8 CFU/mL. LOD usually decreases when the sample number increases until it remains unchanged. Exponential relations (R2 > 0.95) between LODs of Listeria in milk via LFIA and via the electrochemical method with sample numbers have been obtained. Finally, the review discusses challenges and future perspectives (including the role of nanomaterials/advanced materials) to improve analytical performance for bacterial detection.
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Affiliation(s)
- Xinyi Zhao
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, D07 ADY7 Dublin, Ireland; (X.Z.); (A.B.); (C.O.); (B.S.)
- FOCAS Research Institute, Technological University Dublin, Camden Row, D08 CKP1 Dublin, Ireland
| | - Abhijnan Bhat
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, D07 ADY7 Dublin, Ireland; (X.Z.); (A.B.); (C.O.); (B.S.)
- MiCRA Biodiagnostics Technology Gateway and Health, Engineering & Materials Sciences (HEMS) Research Hub, Technological University Dublin, D24 FKT9 Dublin, Ireland
| | - Christine O’Connor
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, D07 ADY7 Dublin, Ireland; (X.Z.); (A.B.); (C.O.); (B.S.)
| | - James Curtin
- Faculty of Engineering and Built Environment, Technological University Dublin, Bolton Street, D01 K822 Dublin, Ireland;
| | - Baljit Singh
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, D07 ADY7 Dublin, Ireland; (X.Z.); (A.B.); (C.O.); (B.S.)
- MiCRA Biodiagnostics Technology Gateway and Health, Engineering & Materials Sciences (HEMS) Research Hub, Technological University Dublin, D24 FKT9 Dublin, Ireland
| | - Furong Tian
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, D07 ADY7 Dublin, Ireland; (X.Z.); (A.B.); (C.O.); (B.S.)
- FOCAS Research Institute, Technological University Dublin, Camden Row, D08 CKP1 Dublin, Ireland
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22
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Son J, Kim SH, Cha BS, Lee ES, Kim S, Park KS. Primer exchange reaction-coupled transcription isothermal amplification as a sensitive biomolecular assay. Chem Commun (Camb) 2024; 60:4565-4568. [PMID: 38572617 DOI: 10.1039/d4cc00665h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
We devised a novel strategy that relies on a combination of the primer exchange reaction (PER) with transcription isothermal amplification, termed PER-Trap, for a sensitive biomolecular assay. Its design allowed light-up RNA aptamers to be produced as the final product, leading to the generation of an amplified fluorescence signal. The utility of PER-Trap was successfully demonstrated by the detection of exosomes.
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Affiliation(s)
- Jinseo Son
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
| | - Seok Hyeon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
| | - Byung Seok Cha
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
| | - Eun Sung Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
| | - Seokjoon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
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23
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Zhang L, Liu J, Huang S, Zeng W, Li L, Fan X, Lu Z. A high-throughput DNA analysis method based on isothermal amplification on a suspension microarray for detecting mpox virus and viruses with comparable symptoms. Anal Chim Acta 2024; 1299:342416. [PMID: 38499413 DOI: 10.1016/j.aca.2024.342416] [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: 12/21/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Mpox is a zoonotic disease caused by mpox virus (MPXV) infection. Since May 2022, there has been a marked increase in human mpox cases in different regions. Rash, fever, and sore throat are typical signs of mpox. However, other viruses, such as the B virus (BV), herpes simplex virus types 1 (HSV-1), herpes simplex virus types 2 (HSV-2), and varicella zoster virus (VZV), can also infect people and cause comparable symptoms. Therefore, clinical symptoms and signs alone make distinguishing MPXV from these viruses difficult. RESULTS In this study, we combined suspension microarray technology with recombinase-aided amplification technology (RAA) to establish a high-throughput, sensitive, and quantitative method for detecting MPXV and other viruses that can cause similar symptoms. The experimental results confirmed that the technique has outstanding sensitivity, with a minimum detection limit (LOD) of 0.1 fM and a linear range of 0.3 fM to 20 pM, spanning five orders of magnitude. The approach also exhibits exquisite selectivity, as the amplified signal can only be detected when the target virus nucleic acid is present. Additionally, serum recoveries ranging from 80.52% to 119.09% suggest that the detection outcomes are generally considered reliable. Moreover, the time required for detection using this high-throughput method is very short. After DNA extraction, the detection signal amplified by isothermal amplification on the bead array can be obtained in just 1 h. SIGNIFICANCE AND NOVELTY Our research introduces a new technique that utilizes suspension microarray technology and isothermal amplification to create a high-throughput nucleic acid assay. This innovative method offers multiple benefits compared to current techniques, such as being cost-effective, time-efficient, highly sensitive, and having high throughput capabilities. Furthermore, the assay is applicable not only for detecting MPXV and viruses with similar symptoms, but also for clinical diagnostics, food safety, and environmental monitoring, rendering it an effective tool for screening harmful microorganisms.
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Affiliation(s)
- Liming Zhang
- Key Laboratory of Tropical Molecular Pharmacology and Advanced Micro/Nano Diagnostic Technology, School of Tropical Medicine, Institute of Micro and Nanotechnology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China
| | - Jieyu Liu
- Key Laboratory of Tropical Molecular Pharmacology and Advanced Micro/Nano Diagnostic Technology, School of Tropical Medicine, Institute of Micro and Nanotechnology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China
| | - Shisi Huang
- Department of Medical Healthcare, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, 570208, China
| | - Wentao Zeng
- Key Laboratory of Tropical Molecular Pharmacology and Advanced Micro/Nano Diagnostic Technology, School of Tropical Medicine, Institute of Micro and Nanotechnology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China
| | - Li Li
- Key Laboratory of Tropical Molecular Pharmacology and Advanced Micro/Nano Diagnostic Technology, School of Tropical Medicine, Institute of Micro and Nanotechnology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China
| | - Xihao Fan
- Key Laboratory of Tropical Molecular Pharmacology and Advanced Micro/Nano Diagnostic Technology, School of Tropical Medicine, Institute of Micro and Nanotechnology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China
| | - Zhuoxuan Lu
- Key Laboratory of Tropical Molecular Pharmacology and Advanced Micro/Nano Diagnostic Technology, School of Tropical Medicine, Institute of Micro and Nanotechnology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China.
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24
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Yu Y, Ni W, Hu Q, Li H, Zhang Y, Gao X, Zhou L, Zhang S, Ma S, Zhang Y, Huang H, Li F, Han J. A Dual Fluorescence Turn-On Sensor Array Formed by Poly(para-aryleneethynylene) and Aggregation-Induced Emission Fluorophores for Sensitive Multiplexed Bacterial Recognition. Angew Chem Int Ed Engl 2024; 63:e202318483. [PMID: 38407995 DOI: 10.1002/anie.202318483] [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: 12/02/2023] [Revised: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Bacterial infections have emerged as the leading causes of mortality and morbidity worldwide. Herein, we developed a dual-channel fluorescence "turn-on" sensor array, comprising six electrostatic complexes formed from one negatively charged poly(para-aryleneethynylene) (PPE) and six positively charged aggregation-induced emission (AIE) fluorophores. The 6-element array enabled the simultaneous identification of 20 bacteria (OD600=0.005) within 30s (99.0 % accuracy), demonstrating significant advantages over the array constituted by the 7 separate elements that constitute the complexes. Meanwhile, the array realized different mixing ratios and quantitative detection of prevalent bacteria associated with urinary tract infection (UTI). It also excelled in distinguishing six simulated bacteria samples in artificial urine. Remarkably, the limit of detection for E. coli and E. faecalis was notably low, at 0.000295 and 0.000329 (OD600), respectively. Finally, optimized by diverse machine learning algorithms, the designed array achieved 96.7 % accuracy in differentiating UTI clinical samples from healthy individuals using a random forest model, demonstrating the great potential for medical diagnostic applications.
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Affiliation(s)
- Yang Yu
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Weiwei Ni
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Qin Hu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Huihai Li
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Yi Zhang
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Xu Gao
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Lingjia Zhou
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Shuming Zhang
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Shuoyang Ma
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Yanliang Zhang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing Research Center for Infectious Diseases of Integrated Traditional Chinese and Western Medicine, Nanjing, 210006, China
| | - Hui Huang
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Fei Li
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
| | - Jinsong Han
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing Department of Food Quality and Safety, College of Engineering, China, Pharmaceutical University, Nanjing, 211109, China
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25
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [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: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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26
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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [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: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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27
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Kumagai H, Furusawa H. Real-Time Monitoring of a Nucleic Acid Amplification Reaction Using a Mass Sensor Based on a Quartz-Crystal Microbalance. BIOSENSORS 2024; 14:155. [PMID: 38667148 PMCID: PMC11048521 DOI: 10.3390/bios14040155] [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: 01/29/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024]
Abstract
Nucleic acid amplification reactions such as polymerase chain reaction (PCR), which uses a DNA polymerase to amplify individual double-stranded DNA fragments, are a useful technique for visualizing the presence of specific genomes. Although the fluorescent labeling method is mainly used with DNA amplification, other detection methods should be considered for further improvements, such as miniaturization and cost reduction, of reaction-monitoring devices. In this study, the quartz-crystal microbalance (QCM) method, which can measure nanogram-order masses, was applied for the real-time detection of DNA fragments in a solution with nucleic acids. This was combined with an isothermal nucleic acid amplification reaction based on the recombinase polymerase amplification (RPA) method, which allowed DNA amplification at a constant temperature. When the DNA amplification reaction was initiated on a QCM sensor plate with an immobilized primer DNA strand, a significant increase in mass was observed compared to when the primer DNA was not immobilized. QCM was shown to be sufficiently sensitive for the in situ detection of amplified DNA fragments. Combining a portable QCM device and RPA offers a sensitive point-of-care method for detecting nucleic acids.
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Affiliation(s)
- Hideto Kumagai
- Graduate School of Organic Materials Science, Yamagata University, Yonezawa 992-8510, Japan
| | - Hiroyuki Furusawa
- Graduate School of Organic Materials Science, Yamagata University, Yonezawa 992-8510, Japan
- Institute for the Promotion of General Graduate Education (IPGE), Yamagata University, Yonezawa 992-8510, Japan
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28
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Liao C, Pan L, Tan M, Zhou Z, Long S, Yi X, Li X, Wei G, Liang L. A dual RPA-LFD assay for the simultaneous detection of Salmonella typhimurium and Salmonella enteritidis. Front Bioeng Biotechnol 2024; 12:1379939. [PMID: 38524195 PMCID: PMC10958489 DOI: 10.3389/fbioe.2024.1379939] [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: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction: Salmonella was one of the most common bacteria that caused foodborne illness, with S. typhimurium (Salmonella typhimurium) and S. enteritidis (Salmonella enteritidis) infections accounting for more than 75% of human salmonella infections. Methods: In this study, we developed a method of dual recombinase polymerase amplification (RPA) combined with a lateral flow dipstick for the rapid detection of S. typhimurium and S. enteritidis in clinical specimens (stool). Results: The entire reaction process, including amplification and result reading, could be completed within 65 min. The detection limits of S. typhimurium and S. enteritidis in pure culture samples were 5.23 × 101 CFU/mL and 3.59 × 101 CFU/mL, respectively. The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were 8.30 × 101 CFU/mL and 2.70 × 102 CFU/mL, respectively. In addition, the method had no cross-reaction with other pathogenic microorganisms. The results in clinical samples were fully consistent with those obtained using Bacterial Analysis Manual, with sensitivity and specificity were 100% (8/8) and 100% (17/17) for S. typhimurium and 100% (4/4) and 100% (21/21) for S. enteritidis, respectively. Discussion: The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were higher than those in pure culture samples, which might be attributed to the inherent complex composition of artificially contaminated samples. In addition, the detection limits of S. typhimurium and S. enteritidis in the same sample were also different, which might be attributed to different amplification efficiency of two target genes in the same reaction system. Conclusion: This assay had potential application outdoors, as it could be performed within 1 h at 38°C without a complex instrument, and the results could be observed with the naked eye. In conclusion, the dual RPA-LFD assay established in this study had practical significance for the rapid detection of S. typhimurium and S. enteritidis in the future.
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Affiliation(s)
- Chuan Liao
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Lele Pan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Meiying Tan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Zihan Zhou
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Shaoping Long
- Department of Clinical Laboratory, Baise People’s Hospital, Baise, China
| | - Xueli Yi
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Xuebin Li
- Department of Neurology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Guijiang Wei
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Lina Liang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
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29
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Zhang X, Zhao Y, Zhu X, Tian W, Zhang C. Rapid detection of four major HFMD-associated enteroviruses by multiplex HiFi-LAMP assays. Anal Bioanal Chem 2024; 416:1971-1982. [PMID: 38358534 DOI: 10.1007/s00216-024-05197-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: 11/15/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Hand, foot, and mouth disease (HFMD) caused by various enteroviruses is a major public health concern globally. Human enterovirus 71(EVA71), coxsackievirus A16 (CVA16), coxsackievirus A6 (CVA6), and coxsackievirus A10 (CVA10) are four major enteroviruses responsible for HFMD. Rapid, accurate, and specific point-of-care (POC) detection of the four enteroviruses is crucial for the prevention and control of HFMD. Here, we developed two multiplex high-fidelity DNA polymerase loop-mediated isothermal amplification (mHiFi-LAMP) assays for simultaneous detection of EVA71, CVA16, CVA6, and CVA10. The assays have good specificity and exhibit high sensitivity, with limits of detection (LOD) of 11.2, 49.6, 11.4, and 20.5 copies per 25 μL reaction for EVA71, CVA16, CVA6, and CVA10, respectively. The mHiFi-LAMP assays showed an excellent clinical performance (sensitivity 100.0%, specificity 83.3%, n = 47) when compared with four singleplex RT-qPCR assays (sensitivity 93.1%, specificity 100%). In particular, the HiFi-LAMP assays exhibited better performance (sensitivity 100.0%, specificity 100%) for CVA16 and CVA6 than the RT-qPCR assays (sensitivity 75.0-92.3%, specificity 100%). Furthermore, the mHiFi-LAMP assays detected all clinical samples positive for the four enteroviruses within 30 min, obviously shorter than about 1-1.5 h by the RT-qPCR assays. The new mHiFi-LAMP assays can be used as a robust point-of-care testing (POCT) tool to facilitate surveillance of HFMD at rural and remote communities and resource-limited settings.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Xiaoyi Zhu
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Weimin Tian
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China.
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30
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Li S, Huo X, Mu Y, Liu X, Wu J, Chen Y, Wang Y. TaqMan-based real-time polymerase chain reaction for the detection of feline chaphamaparvovirus. 3 Biotech 2024; 14:61. [PMID: 38344284 PMCID: PMC10850043 DOI: 10.1007/s13205-024-03917-8] [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: 03/20/2023] [Accepted: 01/03/2024] [Indexed: 03/10/2024] Open
Abstract
Feline chaphamaparvovirus (FeChPV) is a new viral strain detected in Chinese Mainland in recent years. The symptoms mainly include diarrhea and bloody stool in young cats, which can lead to death in severe cases. In this study, a TaqMan-based real-time quantitative PCR (qPCR) with specific primers and TaqMan probes based on the VP1 gene sequence of FeChPV was performed to detect the virus. The established qPCR indicated that there is no cross-reaction of FeChPV with other common feline viruses. The minimum detection limit of the established qPCR method is 3.75 × 10 copies/µL, while conventional PCR is 3.75 × 103 copies/µL. The result that the proposed qPCR protocol was shown to be 100 times more sensitive than conventional PCR. The correlation coefficients exceeded 0.995, and the amplification efficiency was 98%. The difference within and between groups is less than 5%, indicating that the established method has good repeatability. The results of clinical sample detection shown that 16 positive samples were detected from 45 stool samples by the established qPCR method. The conventional PCR method only detected 3 positive samples. In conclusion, the established qPCR method is fast and effective in identifying FeChPV, with higher specificity and sensitivity. It could be used as a diagnostic tool to quantitatively detect the virus content, which is conducive to disease monitoring and epidemiological investigation.
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Affiliation(s)
- Shuyan Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Xinrui Huo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Yuanyuan Mu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Xuan Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Jing Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Yumeng Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Yong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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Starolis MW, Zaydman MA, Liesman RM. Working with the Electronic Health Record and Laboratory Information System to Maximize Ordering and Reporting of Molecular Microbiology Results. Clin Lab Med 2024; 44:95-107. [PMID: 38280801 DOI: 10.1016/j.cll.2023.10.009] [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: 01/29/2024]
Abstract
Molecular microbiology assays have a higher cost of testing compared to traditional methods and need to be utilized appropriately. Results from these assays may also require interpretation and appropriate follow-up. Electronic tools available in the electronic health record and laboratory information system can be deployed both preanalytically and postanalytically to influence ordering behaviors and positively impact diagnostic stewardship. Next generation technologies, such as machine learning and artificial intelligence, have the potential to expand upon the capabilities currently available and warrant additional study and development but also require regulation around their use in health care.
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Affiliation(s)
- Meghan W Starolis
- Molecular Infectious Disease, Quest Diagnostics, 14225 Newbrook Drive, Chantilly, VA 20151, USA.
| | - Mark A Zaydman
- Department of Pathology & Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Rachael M Liesman
- Clinical Microbiology and Molecular Diagnostics Pathology, Department of Pathology, Medical College of Wisconsin, 9200 West Wisconsin, Milwaukee, WI 53226, USA
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Madadelahi M, Agarwal R, Martinez-Chapa SO, Madou MJ. A roadmap to high-speed polymerase chain reaction (PCR): COVID-19 as a technology accelerator. Biosens Bioelectron 2024; 246:115830. [PMID: 38039729 DOI: 10.1016/j.bios.2023.115830] [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: 06/07/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
The limit of detection (LOD), speed, and cost of crucial COVID-19 diagnostic tools, including lateral flow assays (LFA), enzyme-linked immunosorbent assays (ELISA), and polymerase chain reactions (PCR), have all improved because of the financial and governmental support for the epidemic. The most notable improvement in overall efficiency among them has been seen with PCR. Its significance for human health increased during the COVID-19 pandemic, when it emerged as the commonly used approach for identifying the virus. However, because of problems with speed, complexity, and expense, PCR deployment in point-of-care settings continues to be difficult. Microfluidic platforms offer a promising solution by enabling the development of smaller, more affordable, and faster PCR systems. In this review, we delve into the engineering challenges associated with the advancement of high-speed microfluidic PCR equipment. We introduce criteria that facilitate the evaluation and comparison of factors such as speed, LOD, cycling efficiency, and multiplexing capacity, considering sample volume, fluidics, PCR reactor geometry and materials, as well as heating/cooling methods. We also provide a comprehensive list of commercially available PCR devices and conclude with projections and a discussion regarding the current obstacles that need to be addressed in order to progress further in this field.
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Affiliation(s)
- Masoud Madadelahi
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, 64849, NL, Mexico; Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Rahul Agarwal
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, 64849, NL, Mexico
| | | | - Marc J Madou
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, 64849, NL, Mexico; Autonomous Medical Devices Incorporated (AMDI), Santa Ana, CA, 92704, USA.
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Zhou X, Liu X, Zhao H, Guo G, Jiang X, Liu S, Sun X, Yang H. Research advances in microfluidic collection and detection of virus, bacterial, and fungal bioaerosols. Mikrochim Acta 2024; 191:132. [PMID: 38351367 DOI: 10.1007/s00604-024-06213-7] [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: 09/20/2023] [Accepted: 01/14/2024] [Indexed: 02/16/2024]
Abstract
Bioaerosols are airborne suspensions of fine solid or liquid particles containing biological substances such as viruses, bacteria, cellular debris, fungal spores, mycelium, and byproducts of microbial metabolism. The global Coronavirus disease 2019 (COVID-19) pandemic and the previous emergence of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza have increased the need for reliable and effective monitoring tools for bioaerosols. Bioaerosol collection and detection have aroused considerable attention. Current bioaerosol sampling and detection techniques suffer from long response time, low sensitivity, and high costs, and these drawbacks have forced the development of novel monitoring strategies. Microfluidic technique is considered a breakthrough for high performance analysis of bioaerosols. In recent years, several emerging methods based on microfluidics have been developed and reported for collection and detection of bioaerosols. The unique advantages of microfluidic technique have enabled the integration of bioaerosol collection and detection, which has a higher efficiency over conventional methods. This review focused on the research progress of bioaerosol collection and detection methods based on microfluidic techniques, with special attention on virus aerosols and bacterial aerosols. Different from the existing reviews, this work took a unique perspective of the targets to be collected and detected in bioaerosols, which would provide a direct index of bioaerosol categories readers may be interested in. We also discussed integrated microfluidic monitoring system for bioaerosols. Additionally, the application of bioaerosol detection in biomedicine was presented. Finally, the current challenges in the field of bioaerosol monitoring are presented and an outlook given of future developments.
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Affiliation(s)
- Xinyue Zhou
- Department of Respiratory Medicine, The Fourth Hospital of China Medical University, No. 4, Chongshan East Road, Huanggu District, Shenyang, 110032, Liaoning, China
| | - Xin Liu
- Department of Respiratory Medicine, The Fourth Hospital of China Medical University, No. 4, Chongshan East Road, Huanggu District, Shenyang, 110032, Liaoning, China
| | - Haiyang Zhao
- Teaching Center for Basic Medical Experiment, China Medical University, No.77, Puhe Road, Shenyang, 110122, Liaoning Province, China
| | - Guanqi Guo
- Teaching Center for Basic Medical Experiment, China Medical University, No.77, Puhe Road, Shenyang, 110122, Liaoning Province, China
| | - Xiran Jiang
- School of Intelligent Medicine, China Medical University, No.77, Puhe Road, Shenyang, 110122, Liaoning Province, China.
| | - Shuo Liu
- Department of Respiratory Medicine, The Fourth Hospital of China Medical University, No. 4, Chongshan East Road, Huanggu District, Shenyang, 110032, Liaoning, China.
| | - Xiaoting Sun
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenyang, 110122, Liaoning Province, China.
| | - Huazhe Yang
- School of Intelligent Medicine, China Medical University, No.77, Puhe Road, Shenyang, 110122, Liaoning Province, China.
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Ergunay K, Bourke BP, Achee N, Jiang L, Grieco J, Linton YM. Vector-borne pathogen surveillance in a metagenomic world. PLoS Negl Trop Dis 2024; 18:e0011943. [PMID: 38386620 PMCID: PMC10883548 DOI: 10.1371/journal.pntd.0011943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Affiliation(s)
- Koray Ergunay
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, Maryland, United States of America
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, United States of America
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States of America
- Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Brian P. Bourke
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, Maryland, United States of America
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, United States of America
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States of America
| | - Nicole Achee
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Le Jiang
- Naval Medical Research Center (NMRC), Silver Spring, Maryland, United States of America
| | - John Grieco
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, Maryland, United States of America
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, United States of America
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, United States of America
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Ruhoff V, Arastoo MR, Moreno-Pescador G, Bendix PM. Biological Applications of Thermoplasmonics. NANO LETTERS 2024; 24:777-789. [PMID: 38183300 PMCID: PMC10811673 DOI: 10.1021/acs.nanolett.3c03548] [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: 09/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024]
Abstract
Thermoplasmonics has emerged as an extraordinarily versatile tool with profound applications across various biological domains ranging from medical science to cell biology and biophysics. The key feature of nanoscale plasmonic heating involves remote activation of heating by applying laser irradiation to plasmonic nanostructures that are designed to optimally convert light into heat. This unique capability paves the way for a diverse array of applications, facilitating the exploration of critical biological processes such as cell differentiation, repair, signaling, and protein functionality, and the advancement of biosensing techniques. Of particular significance is the rapid heat cycling that can be achieved through thermoplasmonics, which has ushered in remarkable technical innovations such as accelerated amplification of DNA through quantitative reverse transcription polymerase chain reaction. Finally, medical applications of photothermal therapy have recently completed clinical trials with remarkable results in prostate cancer, which will inevitably lead to the implementation of photothermal therapy for a number of diseases in the future. Within this review, we offer a survey of the latest advancements in the burgeoning field of thermoplasmonics, with a keen emphasis on its transformative applications within the realm of biosciences.
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Affiliation(s)
| | - Mohammad Reza Arastoo
- Niels
Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark
| | - Guillermo Moreno-Pescador
- Niels
Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark
- Copenhagen
Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Poul Martin Bendix
- Niels
Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark
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36
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Beler M, Cansız D, Ünal İ, Emekli-Alturfan E. Quantitative Real-Time PCR Method to Evaluate Gene Expression in Zebrafish Embryos. Methods Mol Biol 2024; 2753:553-561. [PMID: 38285367 DOI: 10.1007/978-1-0716-3625-1_36] [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: 01/30/2024]
Abstract
The fast zebrafish embryonic development offers an opportunity for the study of genes crucial for developmental processes. Several genes associated with human diseases have orthologs in zebrafish. Enhanced comprehension of a gene's function can be achieved by knowing when and where it is expressed. This knowledge also makes it possible to alter a gene-by-gene knockdown in a time- and place-specific manner. Moreover, gene expression analyses contribute greatly to teratogenicity studies in zebrafish embryos. Therefore, the importance of examining the differences between the expressions of these genes has increased day by day. The incorporation of reverse transcription (RT) as the initial step prior to thermal cycling in quantitative real-time polymerase chain reaction (RT-qPCR) has made a significant contribution to RNA research. RT-qPCR is the gold standard and an effective method for gene expression analysis. Quick readout, high sensitivity, reproducibility, as well as high potential throughput, along with reliable quantification, are just a few advantages of RT-qPCR. However, there are drawbacks to its application, such as RNA's inherent variability, impurities during RNA extraction, and variations in reverse transcription and PCR efficiencies. Implementing a precise normalization technique is crucial to account for these inaccuracies. In this chapter, the protocol for gene expression analysis by RT-qPCR for zebrafish embryos is explained.
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Affiliation(s)
- Merih Beler
- Department of Biochemistry, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Derya Cansız
- Department of Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - İsmail Ünal
- Department of Biochemistry, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Department of Basic Medical Sciences, Faculty of Dentistry, Marmara University, Istanbul, Turkey.
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Cardoso GC, Ganzella FADO, Miniskiskosky G, da Cunha RS, Ramos EADS. Digital methylation-specific PCR: New applications for liquid biopsy. Biomol Concepts 2024; 15:bmc-2022-0041. [PMID: 38345545 DOI: 10.1515/bmc-2022-0041] [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: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
Epigenetic analysis is a fundamental part of understanding pathophysiological processes with potential applications in diagnosis, prognosis, and assessment of disease susceptibility. Epigenetic changes have been widely studied in chronic obstructive pulmonary disease (COPD), but currently, there is no molecular marker used to improve the treatment of patients. Furthermore, this progressive disease is a risk factor for the development of more severe COVID-19. Methylation-specific polymerase chain reaction (MSP-PCR) plays an important role in the analysis of DNA methylation profiles, and it is one of the most widely used techniques. In this context, the combination of MSP-PCR with emerging PCR technologies, such as digital PCR (dPCR), results in more accurate analyses of the DNA methylation profile of the genes under study. In this study, we propose the application of the MSP-dPCR technique to evaluate the methylation profile of the ADAM33 gene from saliva samples and lung tissue biopsies of patients with COPD and COVID-19. MSP-dPCR generated a measurable prediction of gene methylation rate, with the potential application of this combined technology for diagnostic and prognostic purposes. It has also proven to be a powerful tool for liquid biopsy applications.
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Affiliation(s)
- Gabriela Casani Cardoso
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | | | - Guilherme Miniskiskosky
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Regiane Stafim da Cunha
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Edneia Amancio de Souza Ramos
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
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Domrazek K, Jurka P. Prevalence of Chlamydophila spp. and Canid herpesvirus-1 in Polish dogs. Vet World 2024; 17:226-232. [PMID: 38406369 PMCID: PMC10884577 DOI: 10.14202/vetworld.2024.226-232] [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: 09/18/2023] [Accepted: 01/08/2024] [Indexed: 02/27/2024] Open
Abstract
Background and Aim Chlamydophila spp. affect Leydig and Sertoli cells by dysregulating spermatogenesis, inducing apoptosis and sperm DNA fragmentation, as well as benign prostate hyperplasia. Canid herpes virus 1 (CHV-1) infection in male dogs is manifested by lesions on the base of the penis and foreskin. There is a lack of information on the influence of these microorganisms on the quality of canine semen. Seroprevalence of Chlamydophila spp. (55%-61%) and CHV-1 (22%-81%) in Europe is high. The prevalence of Chlamydophila spp. and CHV-1 has been evaluated using polymerase chain reaction (PCR) only in Sweden and Croatia, respectively. No positive samples were detected in either case. The aim of this study was to evaluate the epidemiological situation in Polish male dogs (PMDs) to provide a solution to limit the spread of these microorganisms using assisted reproduction techniques or elimination from the reproduction of CHV-1 carriers. In addition, we assessed the semen quality of Chlamydophila spp. carriers and CHV-1 carriers. Materials and Methods Cotton swabs were collected from prepuce or semen from each dog (n = 130). Real-time PCR for Chlamydophila spp. and CHV-1, as well as semen analysis, was performed using the computer-assisted semen analysis system. Results To the best of our knowledge, this is the first report of Chlamydophila spp. infection in PMD confirmed by real-time PCR. All parameters, except progressive movement in Chlamydophila semen carriers, were normal. Conclusion The average velocity values for a dog with Chlamydia are detailed. No CHV-1 was detected. The results achieved should be verified on the basis of a larger number of studies. However, the high prevalence of these pathogens in the PMD population has not been established.
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Affiliation(s)
- Kinga Domrazek
- Laboratory of Small Animal Reproduction, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159C Street, Warsaw 02-787, Poland
| | - Piotr Jurka
- Laboratory of Small Animal Reproduction, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159C Street, Warsaw 02-787, Poland
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Huang Q, Zhang Y, Hu W, Chen K, Zhang J, Luo Z, Lu C. Characterization of Heat-labile Uracil-DNA Glycosylase from Oncorhynchus mykiss and its Application for Carry-over Contamination Control in RT-qPCR. Protein Pept Lett 2024; 31:169-177. [PMID: 38343045 DOI: 10.2174/0109298665283737240122105923] [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: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 06/14/2024]
Abstract
BACKGROUND Heat-labile uracil-DNA glycosylase (HL-UDG) is commonly employed to eliminate carry-over contamination in DNA amplifications. However, the prevailing HL-UDG is markedly inactivated at 50°C, rendering it unsuitable for specific one-step RT-qPCR protocols utilizing reverse transcriptase at an optimal temperature of 42°C. OBJECTIVE This study aimed to explore novel HL-UDG with lower inactivation temperature and for recombinant expression. METHODS The gene encoding an HL-UDG was cloned from the cold-water fish rainbow trout (Oncorhynchus mykiss) and expressed in Escherichia coli with high yield. The thermostability of this enzyme and other enzymatic characteristics were thoroughly examined. The novel HL-UDG was then applied for controlling carry-over contamination in one-step RT-qPCR. RESULTS This recombinantly expressed truncated HL-UDG of rainbow trout (OmUDG) exhibited high amino acids similarity (84.1% identity) to recombinant Atlantic cod UDG (rcUDG) and was easily denatured at 40°C. The optimal pH of OmUDG was 8.0, and the optimal concentrations of both Na+ and K+ were 10 mM. Since its inactivation temperature was lower than that of rcUDG, the OmUDG could be used to eliminate carry-over contamination in one-step RT-qPCR with moderate reverse transcription temperature. CONCLUSION We successfully identified and recombinantly expressed a novel HL-UDG with an inactivation temperature of 40°C. It is suitable for eliminating carry-over contamination in one-step RT-qPCR.
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Affiliation(s)
- Qingyuan Huang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Yaqi Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Food & Pharmaceutical Science College, Huai'an 223023, China
| | - Wenhao Hu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Keqi Chen
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Best Enzymes Biotech Co., Ltd., Lianyungang, 222005, China
| | - Jian Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhidan Luo
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Chen Lu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Best Enzymes Biotech Co., Ltd., Lianyungang, 222005, China
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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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Laššáková S, Šenkyřík P, Pazourková E, Hořínek A, Calda P, Břešťák M, Světnicová K, Neužil P, Korabečná M. Rapid non-invasive prenatal screening test for trisomy 21 based on digital droplet PCR. Sci Rep 2023; 13:22948. [PMID: 38135736 PMCID: PMC10746715 DOI: 10.1038/s41598-023-50330-x] [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: 05/23/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
Non-invasive prenatal tests for the detection of fetal aneuploidies are predominantly based on the analysis of cell-free DNA (cfDNA) from the plasma of pregnant women by next-generation sequencing. The development of alternative tests for routine genetic laboratories is therefore desirable. Multiplex digital droplet PCR was used to detect 16 amplicons from chromosome 21 and 16 amplicons from chromosome 18 as the reference. Two fluorescently labeled lock nucleic acid probes were used for the detection of reaction products. The required accuracy was achieved by examining 12 chips from each patient using Stilla technology. The plasma cfDNA of 26 pregnant women with euploid pregnancies and 16 plasma samples from pregnancies with trisomy 21 were analyzed to determine the cutoff value for sample classification. The test was validated in a blind study on 30 plasma samples from pregnant patients with a risk for trisomy 21 ranging from 1:4 to 1:801. The results were in complete agreement with the results of the invasive diagnostic procedure (sensitivity, specificity, PPV, and NPV of 100%). Low cost, and speed of analysis make it a potential screening method for implementation into the clinical workflow to support the combined biochemical and ultrasound results indicating a high risk for trisomy 21.
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Affiliation(s)
- Soňa Laššáková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Pavel Šenkyřík
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Eva Pazourková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 499/2, 128 08, Prague 2, Czech Republic
| | - Aleš Hořínek
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- 3rd Department of Internal Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 1, 128 08, Prague 1, Czech Republic
| | - Pavel Calda
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Apolinarska 18, 128 51, Prague, Czech Republic
| | - Miroslav Břešťák
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Apolinarska 18, 128 51, Prague, Czech Republic
- Prenatal Diagnosis Center ProfiG2 S.R.O., Vajgarská, 1141, Prague, Czech Republic
| | | | - Pavel Neužil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, Shaanxi, People's Republic of China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
- Department of Laboratory Medicine, Faculty of Health Care and Social Work, University of Trnava in Trnava, Universitne Namestie 1, 918 43, Trnava, Slovak Republic.
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Zhao Y, Huang F, Wang W, Gao R, Fan L, Wang A, Gao SH. Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165867. [PMID: 37516185 DOI: 10.1016/j.scitotenv.2023.165867] [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: 07/01/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi, and protozoa, in urban water systems poses a significant risk to public health. The emergence of infectious waterborne diseases mediated by urban water systems has become one of the leading global causes of mortality. However, the detection and monitoring of these pathogenic microorganisms have been limited by the complexity and diversity in the environmental samples. Conventional methods were restricted by long assay time, high benchmarks of identification, and narrow application sceneries. Novel technologies, such as high-throughput sequencing technologies, enable potentially full-spectrum detection of trace pathogenic microorganisms in complex environmental matrices. This review discusses the current state of high-throughput sequencing technologies for identifying pathogenic microorganisms in urban water systems with a concise summary. Furthermore, future perspectives in pathogen research emphasize the need for detection methods with high accuracy and sensitivity, the establishment of precise detection standards and procedures, and the significance of bioinformatics software and platforms. We have compiled a list of pathogens analysis software/platforms/databases that boast robust engines and high accuracy for preference. We highlight the significance of analyses by combining targeted and non-targeted sequencing technologies, short and long reads technologies, sequencing technologies, and bioinformatic tools in pursuing upgraded biosafety in urban water systems.
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Affiliation(s)
- Yanmei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Fang Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Rui Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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Hu X, Feng S, Shi K, Shi Y, Yin Y, Long F, Wei X, Li Z. Development of a quadruplex real-time quantitative RT-PCR for detection and differentiation of PHEV, PRV, CSFV, and JEV. Front Vet Sci 2023; 10:1276505. [PMID: 38026635 PMCID: PMC10643766 DOI: 10.3389/fvets.2023.1276505] [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: 08/12/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV), porcine pseudorabies virus (PRV), classical swine fever virus (CSFV), and Japanese encephalitis virus (JEV) cause similar neurological symptoms in the infected pigs, and their differential diagnosis depends on laboratory testing. Four pairs of specific primers and probes were designed targeting the PHEV N gene, PRV gB gene, CSFV 5' untranslated region (5'UTR), and JEV NS1 gene, respectively, and a quadruplex real-time quantitative RT-PCR (qRT-PCR) was developed to detect and differentiate PHEV, PRV, CSFV, and JEV. The assay showed high sensitivity, with the limit of detection (LOD) of 1.5 × 101 copies/μL for each pathogen. The assay specifically detected only PHEV, PRV, CSFV, and JEV, without cross-reaction with other swine viruses. The coefficients of variation (CVs) of the intra-assay and the inter-assay were less than 1.84%, with great repeatability. A total of 1,977 clinical samples, including tissue samples, and whole blood samples collected from Guangxi province in China, were tested by the developed quadruplex qRT-PCR, and the positivity rates of PHEV, PRV, CSFV, and JEV were 1.57% (31/1,977), 0.35% (7/1,977), 1.06% (21/1,977), and 0.10% (2/1,977), respectively. These 1,977 samples were also tested by the previously reported qRT-PCR assays, and the coincidence rates of these methods were more than 99.90%. The developed assay is demonstrated to be rapid, sensitive, and accurate for detection and differentiation of PHEV, PRV, CSFV, and JEV.
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Affiliation(s)
- Xin Hu
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Shuping Feng
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Kaichuang Shi
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Yuwen Shi
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yanwen Yin
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Xiankai Wei
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Zongqiang Li
- College of Animal Science and Technology, Guangxi University, Nanning, China
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Escobar A, Diab-Liu A, Bosland K, Xu CQ. Microfluidic Device-Based Virus Detection and Quantification in Future Diagnostic Research: Lessons from the COVID-19 Pandemic. BIOSENSORS 2023; 13:935. [PMID: 37887128 PMCID: PMC10605122 DOI: 10.3390/bios13100935] [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: 07/19/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The global economic and healthcare crises experienced over the past three years, as a result of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted the commonplace habits of humans around the world. SARS-CoV-2, the virus responsible for the coronavirus 2019 (COVID-19) phenomenon, has contributed to the deaths of millions of people around the world. The potential diagnostic applications of microfluidic devices have previously been demonstrated to effectively detect and quasi-quantify several different well-known viruses such as human immunodeficiency virus (HIV), influenza, and SARS-CoV-2. As a result, microfluidics has been further explored as a potential alternative to our currently available rapid tests for highly virulent diseases to better combat and manage future potential outbreaks. The outbreak management during COVID-19 was initially hindered, in part, by the lack of available quantitative rapid tests capable of confirming a person's active infectiousness status. Therefore, this review will explore the use of microfluidic technology, and more specifically RNA-based virus detection methods, as an integral part of improved diagnostic capabilities and will present methods for carrying the lessons learned from COVID-19 forward, toward improved diagnostic outcomes for future pandemic-level threats. This review will first explore the context of the COVID-19 pandemic and how diagnostic technology was shown to have required even greater advancements to keep pace with the transmission of such a highly infectious virus. Secondly, the historical significance of integrating microfluidic technology in diagnostics and how the different types of genetic-based detection methods may vary in their potential practical applications. Lastly, the review will summarize the past, present, and future potential of RNA-based virus detection/diagnosis and how it might be used to better prepare for a future pandemic.
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Affiliation(s)
- Andres Escobar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Alex Diab-Liu
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Kamaya Bosland
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Chang-Qing Xu
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
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Liu CW, Tsutsui H. Sample-to-answer sensing technologies for nucleic acid preparation and detection in the field. SLAS Technol 2023; 28:302-323. [PMID: 37302751 DOI: 10.1016/j.slast.2023.06.002] [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: 03/23/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Efficient sample preparation and accurate disease diagnosis under field conditions are of great importance for the early intervention of diseases in humans, animals, and plants. However, in-field preparation of high-quality nucleic acids from various specimens for downstream analyses, such as amplification and sequencing, is challenging. Thus, developing and adapting sample lysis and nucleic acid extraction protocols suitable for portable formats have drawn significant attention. Similarly, various nucleic acid amplification techniques and detection methods have also been explored. Combining these functions in an integrated platform has resulted in emergent sample-to-answer sensing systems that allow effective disease detection and analyses outside a laboratory. Such devices have a vast potential to improve healthcare in resource-limited settings, low-cost and distributed surveillance of diseases in food and agriculture industries, environmental monitoring, and defense against biological warfare and terrorism. This paper reviews recent advances in portable sample preparation technologies and facile detection methods that have been / or could be adopted into novel sample-to-answer devices. In addition, recent developments and challenges of commercial kits and devices targeting on-site diagnosis of various plant diseases are discussed.
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Affiliation(s)
- Chia-Wei Liu
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA
| | - Hideaki Tsutsui
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA; Department of Bioengineering, University of California, Riverside, CA 92521, USA.
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Mohieldeen WA, Ahmed A, Elmosaad YM, Suliman RS, Alfahed A, Hjazi A, Al Shmrany H, Hakami N, Hakami MA, Almotiri A, Waggiallah HA. Detection of Methylene Tetrahydrofolate Reductase (MTHFR C677T) Mutation among Acute Lymphoblastic Leukemia in Sudanese Patients. Rep Biochem Mol Biol 2023; 12:458-464. [PMID: 38618256 PMCID: PMC11015921 DOI: 10.61186/rbmb.12.3.458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/02/2023] [Indexed: 04/16/2024]
Abstract
Background A genetic polymorphism that causes abnormal folate metabolism may lead to genomic instability and increase susceptibility to malignancies such as Acute Lymphoblastic leukemia (ALL). The purpose of this research is to identify methylene tetrahydrofolate reductase (MTHFR C677T) (NCBI ID: 4524) mutation in ALL patients. Methods The study was a descriptive case-control hospital-based study with one hundred Sudanese participants divided equally into fifty (50) Sudanese ALL diagnosed patients as cases and fifty (50) Sudanese individuals as controls. The MTHFR C677T mutant allele was detected using conventional PCR, with the primer sequence of MTHFR C677T F-TGAAGGAAGGTGTCTGCGGGA R-AGGACGGTGCGGTGAGAGTG. The study was conducted from January to March 2023, and samples were collected from the Radiation and Isotops Center at Khartoum Hospital. Results The investigation revealed that 12 of the 50 patients in the case group (24%) had the MTHFR C677T mutant allele, and the study also revealed that there is significant correlation with the control group. There is no significant relationship between socio-demographic variables and MTHFR mutation detection in ALL patients. Also, the sociodemographic variables predictors of MTHFR mutation among ALL patients adjusted for smoking habit revealed no significant relationship. Conclusion According to the findings of this study, the mutant allele of the Methylene Tetra Hydro Folate Reductase C677T was detected and demonstrated varying degrees of significance. It was concluded that the MTHFR C677T gene mutation was associated with acute lymphoblastic leukemia in Sudanese patients.
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Affiliation(s)
- Waad Almuatasem Mohieldeen
- Department of Hematology and Immunohematology, Faculty of Medical Laboratory, National University, Sudan.
| | - Albara Ahmed
- Department of Hematology, Medical Laboratory Program, Alfajr College for Sciences and Technology, Sudan.
| | - Yousif Mohammed Elmosaad
- Department of Public Health, College of Applied Medical Sciences, King Faisal University, Saudi Arabia.
| | - Rania Saad Suliman
- Department of Clinical Laboratory Sciences, Prince Sultan Military College for Health Sciences, Dhahran, Saudi Arabia.
| | - Abdulaziz Alfahed
- Department of Medical Laboratory, College of Applied Medical Science, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Science, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
| | - Humood Al Shmrany
- Department of Medical Laboratory, College of Applied Medical Science, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
| | - Nora Hakami
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia.
| | - Alhomidi Almotiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Dawadmi, Shaqra University, Riyadh, Saudi Arabia.
| | - Hisham Ali Waggiallah
- Department of Medical Laboratory, College of Applied Medical Science, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
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Kuznetsova AA, Kuznetsov NA. Direct Enzyme Engineering of B Family DNA Polymerases for Biotechnological Approaches. Bioengineering (Basel) 2023; 10:1150. [PMID: 37892880 PMCID: PMC10604792 DOI: 10.3390/bioengineering10101150] [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: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
DNA-dependent DNA polymerases have been intensively studied for more than 60 years and underlie numerous biotechnological and diagnostic applications. In vitro, DNA polymerases are used for DNA manipulations, including cloning, PCR, site-directed mutagenesis, sequencing, and others. Understanding the mechanisms of action of DNA polymerases is important for the creation of new enzymes possessing improved or modified properties. This review is focused on archaeal family B DNA polymerases. These enzymes have high fidelity and thermal stability and are finding many applications in molecular biological methods. Nevertheless, the search for and construction of new DNA polymerases with altered properties is constantly underway, including enzymes for synthetic biology. This brief review describes advances in the development of family B DNA polymerases for PCR, synthesis of xeno-nucleic acids, and reverse transcription.
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Affiliation(s)
- Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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Li HY, Chu YH. Expeditious Discovery of Small-Molecule Thermoresponsive Ionic Liquid Materials: A Review. Molecules 2023; 28:6817. [PMID: 37836660 PMCID: PMC10574798 DOI: 10.3390/molecules28196817] [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: 09/01/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Ionic liquids (ILs) are a class of low-melting molten salts (<100 °C) constituted entirely of ions, and their research has gained tremendous attention in line with their remarkably growing applications (>124,000 publications dated 30 August 2023 from the Web of ScienceTM). In this review, we first briefly discussed the recent developments and unique characteristics of ILs and zwitterionic liquids (ZILs). Compared to molecular solvents and other conventional organic compounds, (zwitter) ionic liquids carry negligible volatility and are potentially recyclable and reusable. For structures, both ILs and ZILs can be systematically tailor-designed and engineered and are synthetically fine-tunable. As such, ionic liquids, including chiral, supported, task-specific ILs, have been widely used as powerful ionic solvents as well as valuable additives and catalysts for many chemical reactions. Moreover, ILs have demonstrated their value for use as polymerase chain reaction (PCR) enhancers for DNA amplification, chemoselective artificial olfaction for targeted VOC analysis, and recognition-based affinity extraction. As the major focus of this review, we extensively discussed that small-molecule thermoresponsive ILs (TILs) and ZILs (zwitterionic TILs) are new types of smart materials and can be expeditiously discovered through the structure and phase separation (SPS) relationship study by the combinatorial approach. Using this SPS platform developed in our laboratory, we first depicted the rapid discovery of N,N-dialkylcycloammonium and 1,3,4-trialkyl-1,2,3-triazolium TILs that concomitantly exhibited LCST (lower critical solution temperature) phase transition in water and displayed biochemically attractive Tc values. Both smart IL materials were suited for applications to proteins and other biomolecules. Zwitterionic TILs are ZILs whose cations and anions are tethered together covalently and are thermoresponsive to temperature changes. These zwitterionic TIL materials can serve as excellent extraction solvents, through temperature change, for biomolecules such as proteins since they differ from the common TIL problems often associated with unwanted ion exchanges during extractions. These unique structural characteristics of zwitterionic TIL materials greatly reduce and may avoid the denaturation of proteins under physiological conditions. Lastly, we argued that both rational structural design and combinatorial library synthesis of small-molecule TIL materials should take into consideration the important issues of their cytotoxicity and biosafety to the ecosystem, potentially causing harm to the environment and directly endangering human health. Finally, we would concur that before precise prediction and quantitative simulation of TIL structures can be realized, combinatorial chemistry may be the most convenient and effective technology platform to discover TIL expeditiously. Through our rational TIL design and combinatorial library synthesis and screening, we have demonstrated its power to discover novel chemical structures of both TILs and zwitterionic TILs. Undoubtedly, we will continue developing new small-molecule TIL structures and studying their applications related to other thermoresponsive materials.
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Affiliation(s)
| | - Yen-Ho Chu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi 62102, Taiwan;
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Wei Y, Zhang S, Guan G, Wan Z, Wang R, Li P, Liu Y, Wang J, Jiao G, Wang H, Sun C. A specific and rapid method for detecting Bacillus and Acinetobacter species in Daqu. Front Bioeng Biotechnol 2023; 11:1261563. [PMID: 37818237 PMCID: PMC10561003 DOI: 10.3389/fbioe.2023.1261563] [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: 07/19/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Daqu is a spontaneous, solid-state cereal fermentation product used for saccharification and as a starter culture for Chinese Baijiu production. Bacillus and Acinetobacter, two dominant microbial genera in Daqu, produce enzymes and organic acids that influence the Daqu quality. However, there are no rapid analytical methods for detecting Bacillus and Acinetobacter. We designed primers specific to the genera Bacillus and Acinetobacter to perform genetic comparisons using the 16 S rRNA. After amplification of polymerase chain reaction using specific primers, high-throughput sequencing was performed to detect strains of Bacillus and Acinetobacter. The results showed that the effective amplification rates for Bacillus and Acinetobacter in Daqu were 86.92% and 79.75%, respectively. Thus, we have devised and assessed a method to accurately identify the species associated with Bacillus and Acinetobacter in Daqu, which can also hold significance for bacterial typing and identification.
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Affiliation(s)
- Yanwei Wei
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Shuyue Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Guikun Guan
- Lanling Meijiu Co., Ltd., Lanling, Shandong, China
| | - Ziran Wan
- Lanling Meijiu Co., Ltd., Lanling, Shandong, China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Yu Liu
- Lanling Meijiu Co., Ltd., Lanling, Shandong, China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Guanhua Jiao
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Hao Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Chuying Sun
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
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Danilevich VN, Kozlov SA, Sorokin VV, Mulyukin AL. Highly purified DNA-containing cell envelopes from fungi for direct use in PCR. Anal Chim Acta 2023; 1273:341528. [PMID: 37423662 DOI: 10.1016/j.aca.2023.341528] [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: 01/13/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Efficient DNA sample preparation from fungi with the rigid cell walls is still critical for successful polymerase chain reaction (PCR), one of the basic platforms in molecular diagnostics of fungi, especially in medical mycology. Common methods that involve different chaotropes to yield DNA samples have found a limited application for fungi. Here we describe a novel procedure for efficient production of permeable fungal cell envelopes with DNA inside as suitable templates for PCR. This procedure is facile, relies on boiling of fungal cells in aqueous solutions of selected chaotropic agents and additives and enables to remove RNA and proteins from PCR template samples. The use of chaotropic solutions containing 7 M urea, 1% sodium dodecyl sulfate (SDS), up to100 mM ammonia and/or 25 mM sodium citrate was the best option to yield highly purified DNA-containing cell envelopes from all fungal strains under study, including clinical Candida and Cryptococcusisolates. After treatment with the selected chaotropic mixtures, the fungal cell walls had undergone loosening and were no longer a barrier to release DNA in PCR as evident from electron microscopy examinations and successful target gene amplifications. Overall, the developed simple, fast, and low-cost approach to produce PCR-suitable templates in the form of DNA encased by permeable cell walls can find application in molecular diagnostics.
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Affiliation(s)
- Vasily N Danilevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Sergey A Kozlov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, Moscow, 117997, Russia.
| | - Vladimir V Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences. 33, Bld. 2 Leninsky Ave., Moscow, 119071, Russia
| | - Andrey L Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences. 33, Bld. 2 Leninsky Ave., Moscow, 119071, Russia
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