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Syed RU, Afsar S, Aboshouk NAM, Salem Alanzi S, Abdalla RAH, Khalifa AAS, Enrera JA, Elafandy NM, Abdalla RAH, Ali OHH, Satheesh Kumar G, Alshammari MD. LncRNAs in necroptosis: Deciphering their role in cancer pathogenesis and therapy. Pathol Res Pract 2024; 256:155252. [PMID: 38479121 DOI: 10.1016/j.prp.2024.155252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 04/14/2024]
Abstract
Necroptosis, a controlled type of cell death that is different from apoptosis, has become a key figure in the aetiology of cancer and offers a possible target for treatment. A growing number of biological activities, including necroptosis, have been linked to long noncoding RNAs (lncRNAs), a varied family of RNA molecules with limited capacity to code for proteins. The complex interactions between LncRNAs and important molecular effectors of necroptosis, including mixed lineage kinase domain-like pseudokinase (MLKL) and receptor-interacting protein kinase 3 (RIPK3), will be investigated. We will explore the many methods that LncRNAs use to affect necroptosis, including protein-protein interactions, transcriptional control, and post-transcriptional modification. Additionally, the deregulation of certain LncRNAs in different forms of cancer will be discussed, highlighting their dual function in influencing necroptotic processes as tumour suppressors and oncogenes. The goal of this study is to thoroughly examine the complex role that LncRNAs play in controlling necroptotic pathways and how that regulation affects the onset and spread of cancer. In the necroptosis for cancer treatment, this review will also provide insight into the possible therapeutic uses of targeting LncRNAs. Techniques utilising LncRNA-based medicines show promise in controlling necroptotic pathways to prevent cancer from spreading and improve the effectiveness of treatment.
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Affiliation(s)
- Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, Hail 81442, Saudi Arabia.
| | - S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh 517502, India.
| | - Nayla Ahmed Mohammed Aboshouk
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | | | | | - Amna Abakar Suleiman Khalifa
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Jerlyn Apatan Enrera
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Nancy Mohammad Elafandy
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Randa Abdeen Husien Abdalla
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Omar Hafiz Haj Ali
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - G Satheesh Kumar
- Department of Pharmaceutical Chemistry, College of Pharmacy, Seven Hills College of Pharmacy, Venkataramapuram, Tirupati, India
| | - Maali D Alshammari
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
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Zhang X, Li J, Yang M, Huang H, Wang H, Zhang H. Accurate and sensitive low-density lipoprotein (LDL) detection based on the proximity ligation assisted rolling circle amplification (RCA). ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1894-1900. [PMID: 38482952 DOI: 10.1039/d4ay00070f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Metabolic-associated fatty liver disease (MAFLD) is one of the leading causes of mortality from chronic diseases worldwide, and it is strongly linked to dyslipidemia. Dyslipidemia typically presents as an elevated concentration of low density lipoprotein (LDL). Hence, accurate quantification of LDL particles is crucial for predicting the risks of cardiovascular illnesses. Nevertheless, conventional techniques can merely provide indirect measurements of LDL particle concentrations through the detection of cholesterol or proteins within LDL particles, and they often require significant effort and time. Therefore, an accurate and effective method for identifying intact LDL particles is highly desired. We have devised a method that allows for the measurement of LDL concentration without the need for isolation. This method relies on proximity ligation rolling circle amplification (RCA). This technique enables the direct and precise measurement of the concentration of "actual" LDL particles, rather than measuring the cholesterol content inside LDL. It has a detection limit of 7.3 μg dL-1, which also meets the requirements for analyzing lipoproteins in clinical samples. Hence, this platform exhibits immense potential in clinical applications and health management.
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Affiliation(s)
- Xingyu Zhang
- Department of Endocrinology, People's Hospital of Chongqing Liang Jiang New Area, No. 199, Renxing Road, Chongqing, China 401121.
| | - Jie Li
- Department of Clinical Biochemistry, The Key Laboratory of Laboratory Medical Diagnostics in the Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing, China 400016
| | - Mei Yang
- Department of Endocrinology, People's Hospital of Chongqing Liang Jiang New Area, No. 199, Renxing Road, Chongqing, China 401121.
| | - Hong Huang
- Department of Clinical Laboratory, People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China 401121
| | - Hao Wang
- Department of Endocrinology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China 400016
| | - Hongmin Zhang
- Department of Endocrinology, People's Hospital of Chongqing Liang Jiang New Area, No. 199, Renxing Road, Chongqing, China 401121.
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Zhou Q, Ding X, Du W, Wang H, Wu S, Li J, Yang S. Multi-enzymatic systems synergize new RCA technique amplified super-long dsDNA from DNA circle. Anal Chim Acta 2024; 1291:342220. [PMID: 38280785 DOI: 10.1016/j.aca.2024.342220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND In the field of DNA amplification, there are great challenges in the effectively amplify of long-chain amplification, especially amplification up to several hundred kb level. RESULTS A novel technique for the unbiased whole genome amplification from a thimbleful of DNA circles, such as low as 10 ng/ 10 μL of the circular cpDNA or low as 5 ng/ 10 μL of the plasmid, is developed, which can amplify an abundance of the whole genome sequences. Specifically, the new technique that combines rolling-amplification and triple-enzyme system presents a tightly controlled process of a series of buffers/reactions and optimized procedures, that applies from the primer-template duplexes to the Elution step. The result of this technique provides a new approach for extending RCA capacity, where it can reach 200 kb from the circular cpDNA amplification and 150 kb from the plasmid DNA amplification, that demonstrates superior breadth and evenness of genome coverage, high reproducibility, small amplification bias with the amplification efficiency. SIGNIFICANCE AND NOVELTY This new technique will develop into one of the powerful tools for isothermal DNA amplification in vitro, genome sequencing/analysis, phylogenetic analysis, physical mapping, and other molecular biology applications.
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Affiliation(s)
- Qiang Zhou
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Xianlong Ding
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Wanqing Du
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Hongjie Wang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Shuo Wu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Jun Li
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Shouping Yang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Tian Y, Chen X, Xu P, Wang Y, Wu X, Wu K, Fu X, Chin Y, Liao Y. Rapid Visual Detection of Elite Erect Panicle Dense and Erect Panicle 1 Allele for Marker-Assisted Improvement in Rice ( Oryza sativa L.) Using the Loop-Mediated Isothermal Amplification Method. Curr Issues Mol Biol 2024; 46:498-512. [PMID: 38248334 PMCID: PMC10814556 DOI: 10.3390/cimb46010032] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa L.) breeding. In this study, a colorimetric LAMP (loop-mediated isothermal amplification) assay was developed for the detection of the dep1 allele and tested for the screening and selection of the heavy-panicle hybrid rice elite restorer line SHUHUI498, modified with the allele. InDel (Insertion and Deletion) primers (DEP1_F and DEP1_R) and LAMP primers (F3, B3, FIP, and BIP) for genotyping were designed using the Primer3 Plus (version 3.3.0) and PrimerExplore (version 5) software. Our results showed that both InDel and LAMP markers could be used for accurate genotyping. After incubation at a constant temperature of 65 °C for 60 min with hydroxynaphthol blue (HNB) as a color indicator, the color of the LAMP assay containing the dep1 allele changed to sky blue. The SHUHUI498 rice line that was detected in our LAMP assay displayed phenotypes consistent with the dep1 allele such as having a more compact plant architecture, straight stems and leaves, and a significant increase in the number of effective panicles and spikelets, demonstrating the effectiveness of our method in screening for the dep1 allele in rice breeding.
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Affiliation(s)
- Yonghang Tian
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Xiyi Chen
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Kun Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
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Sciaudone M, Carpena R, Calderón M, Sheen P, Zimic M, Coronel J, Gilman RH, Bowman NM. Rapid detection of Mycobacterium tuberculosis using recombinase polymerase amplification: A pilot study. PLoS One 2023; 18:e0295610. [PMID: 38064441 PMCID: PMC10707601 DOI: 10.1371/journal.pone.0295610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Tuberculosis remains one of the leading causes of death worldwide, especially in low- and middle-income countries. Tuberculosis treatment and control efforts are hindered by the difficulty in making the diagnosis, as currently available diagnostic tests are too slow, too expensive, or not sufficiently sensitive. Recombinase polymerase amplification (RPA) is a novel technique that allows for the amplification of DNA rapidly, at constant temperature, and with minimal expense. We calculated and compared the limit of detection, sensitivity, and specificity of two RPA-based assays for the diagnosis of pulmonary tuberculosis, using two sets of published primers. We also calculated and compared the assays' limits of detection and compared their performance using two different DNA extraction methods prior to amplification (a commercially available DNA extraction kit vs. the chelex method). The RPA-lateral flow assay had a limit of detection of 5 fg/μL of DNA, a sensitivity of 53.2%, and a specificity of 93.3%, while the real time-RPA assay had a limit of detection of 25 fg/μL of DNA, a sensitivity of 85.1%, and a specificity of 93.3%. There was no difference in assay performance when DNA extraction was carried out using the commercial kit vs. the chelex method. The real-time RPA assay has adequate sensitivity and specificity for the diagnosis of pulmonary tuberculosis and could be a viable diagnostic tool in resource-limited settings, but the lateral flow assay did not perform as well, perhaps due to the fact we used stored sputum specimens from a biorepository. More work is needed to optimize the RPA-lateral flow assay, to get a more accurate estimate of its specificity and sensitivity using prospectively collected specimens, and to develop both assays into point-of-care tests that can be easily deployed in the field.
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Affiliation(s)
- Michael Sciaudone
- Department of Medicine, Section of Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
- Center for Intelligent Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Renzo Carpena
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maritza Calderón
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Patricia Sheen
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jorge Coronel
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Natalie M. Bowman
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
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Tian Y, Ye W, Liang X, Xu P, Wu X, Fu X, Chin Y, Liao Y. Rapid Visual Detection of High Nitrogen-Use Efficiency Gene OsGRF4 in Rice ( Oryza sativa L.) Using Loop-Mediated Isothermal Amplification Method. Genes (Basel) 2023; 14:1850. [PMID: 37895199 PMCID: PMC10606894 DOI: 10.3390/genes14101850] [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: 09/03/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The GROWTH-REGULATING FACTOR4 (OsGRF4) allele is an important target for the development of new high nitrogen-use efficiency (NUE) rice lines that would require less fertilizers. Detection of OsGRF4 through PCR (polymerase chain reaction)-based assay is cumbersome and needs advanced laboratory skills and facilities. Hence, a method for conveniently and rapidly detecting OsGRF4 on-field is a key requirement for further research and applications. In this study, we employed cleaved amplified polymorphic sequences (CAPs) and loop-mediated isothermal amplification (LAMP) techniques to develop a convenient visual detection method for high NUE gene OsGRF4NM73 (OsGRF4 from the rice line NM73). The TC→AA mutation at 1187-1188 bp loci was selected as the target sequence for the OsGRF4NM73 allele. We further employed this method of identification in 10 rice varieties that carried the OsGRF4 gene and results revealed that one variety (NM73) carries the target OsGRF4NM73 allele, while other varieties did not possess the osgrf4 genotype. The optimal LAMP reaction using hydroxynaphthol blue (HNB), a chromogenic indicator, was carried out at 65 °C for 60 min, and the presence of OsGRF4NM73 allele was confirmed by color changes from violet to sky blue. The results of this study showed that the LAMP method can be conveniently and accurately used to detect the OsGRF4NM73 gene in rice.
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Affiliation(s)
- Yonghang Tian
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (X.L.); (Y.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Wenwei Ye
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
| | - Xiangshuai Liang
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (X.L.); (Y.C.)
| | - Peizhou Xu
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
| | - Xianjun Wu
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China;
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (X.L.); (Y.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Yongxiang Liao
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
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Xue Q, Sheng L, Guo J, Zou M, Teng Q, Xu S, Li Y, Zhao J. Rapid visual detection of the allergen Dermatophagoides farinae in house dust by loop-mediated isothermal amplification. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:84674-84685. [PMID: 37368209 DOI: 10.1007/s11356-023-28398-9] [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: 02/22/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023]
Abstract
Dermatophagoides farinae is considered to be an important factor causing some allergic diseases, such as urticaria, allergic rhinitis, asthma, and other interrelated diseases. Avoiding exposure to allergens is the most effective way to reduce allergic reactions. In this study, we successfully established a loop-mediated isothermal amplification (LAMP) method for the detection of D. farinae DNA target internal transcribed spacer (ITS) and D. farinae 1 allergen (Der f 1) genes. The turbidity-monitoring system and visual fluorescent reagents were used to verify the test results of LAMP assay. Following optimization of the primers and reaction temperatures, the amplification sensitivity, specificity, and efficiency of the method for detecting D. farinae were assessed. There was no cross-reaction with other arthropod species that are commonly found in indoor environmental dust, such as Dermatophagoides pteronyssinus, Alophagoides ovatus, Periplaneta americana, Anopheles sinensis, and Musca domestica. Furthermore, the sensitivity of LAMP assay for detecting D. farinae DNA was 10 times greater than that of conventional PCR. The positive detection rate by the LAMP method was greater than the conventional PCR for both single D. farinae mites and D. farinae mites in indoor dust. A new type of LAMP method for D. farinae based on the Der f 1 and ITS genes was, therefore, successfully established. This study is the first time to detect the D. farinae allergen using LAMP assay. This assay could be useful as a model for the rapid detection of allergens produced by other house dust mites in the future.
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Affiliation(s)
- Qiqi Xue
- Department of Medical Parasitology, Wannan Medical College, Wuhu, 241002, Anhui, China
| | - Lingwei Sheng
- Medical Laboratory Science, Wannan Medical College, Wuhu, 241002, Anhui, China
| | - Junjie Guo
- Department of Medical Parasitology, Qiqihaer Medical College, Qiqihaer, 161000, Heilongjiang, China
| | - Minghui Zou
- Department of Medical Parasitology, Wannan Medical College, Wuhu, 241002, Anhui, China
| | - Qiao Teng
- Department of Medical Parasitology, Wannan Medical College, Wuhu, 241002, Anhui, China
| | - Sijia Xu
- Medical Laboratory Science, Wannan Medical College, Wuhu, 241002, Anhui, China
| | - Yuanyuan Li
- Department of Medical Parasitology, Wannan Medical College, Wuhu, 241002, Anhui, China
| | - Jinhong Zhao
- Department of Medical Parasitology, Wannan Medical College, Wuhu, 241002, Anhui, China.
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, 241002, Anhui, China.
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Meng J, Li C, Wang Y, Bian Z, Chu P, Zhai S, Yang D, Song S, Li Y, Jiang Z, Zhang K, Li Y, Gou H. Accelerated loop-mediated isothermal amplification method for the rapid detection of Streptococcus suis serotypes 2 and 14 based on single nucleotide polymorphisms. Front Cell Infect Microbiol 2022; 12:1034762. [PMID: 36439234 PMCID: PMC9691836 DOI: 10.3389/fcimb.2022.1034762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022] Open
Abstract
Streptococcus suis serotypes 2 and 14 are the most prevalent zoonotic strains. The establishment of a sensitive and extremely accurate method for point-of-care testing for Streptococcus suis serotype 2 and 14 strains is highly desirable. In this study, a loop primer probe-introduced loop-mediated isothermal amplification assay was developed to differentiate Streptococcus suis serotypes 2 and 14 based on SNP (single nucleotide polymorphism). The specific fluorescent probes were designed for the SNP site specific for serotype 2 and 14 Streptococcus suis cpsK genes, and the loop primer probe-introduced loop-mediated isothermal amplification (LAMP) assay was developed using the specific cleavage properties of the RNase H2 enzyme. Rapid and efficient LAMP assays were realized through the use of loop forward primers and stem forward primers. The results showed that the amplification reaction can be performed efficiently at 59°C. The results can be real-time detected or judged using a smartphone and a 3D-printed visualization cassette. The sensitivity of the LAMP assay can reach 18.4 CFU within 40 minutes. The detection rate of the assay system was evaluated using 19 clinical samples with suspected Streptococcus suis infection, and the detection rate was consistent with the sequencing method, suggesting that the test is highly practical. The LAMP assay for Streptococcus suis serotypes 2 and 14 established in this study has strong specificity, high sensitivity, and simple operation, while the reaction can be performed at an isothermal temperature and is not dependent on complex instruments or professional operators, making it suitable for field testing.
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Affiliation(s)
- Jiajia Meng
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chunling Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yu Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhibiao Bian
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Pinpin Chu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Shaolun Zhai
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Dongxia Yang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yan Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Zhiyong Jiang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Kunli Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yugu Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- *Correspondence: Yugu Li, ; Hongchao Gou,
| | - Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
- *Correspondence: Yugu Li, ; Hongchao Gou,
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9
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Wu Y, Zhang Y, Zhu ZW, Xue QQ, Zou MH, Sun M, Li YY, Zhao JH. Rapid and Visual Detection of Toxoplasma gondii in Blood Samples from Pet Cats and Dogs by Loop-Mediated Isothermal Amplification. Vector Borne Zoonotic Dis 2022; 22:512-519. [PMID: 36201229 DOI: 10.1089/vbz.2022.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Toxoplasma gondii is an obligate intracellular parasite that invades nearly all nucleated cells of a broad spectrum of vertebrate hosts, and which may cause serious disease in immunocompromised patients, as well as in the immunologically incompetent fetus. This study aimed to establish a loop-mediated isothermal amplification (LAMP) technique to rapidly detect T. gondii in the blood infection by targeting the 529 bp repeat element of T. gondii. Methods: A turbidity monitoring system, together with visual reagent, was used to test the amplification result of the LAMP assay. In addition, the specificity and sensitivity of the LAMP assay were measured. Results: The results suggest that the successfully established LAMP assay profile can detect the DNA of T. gondii at 67°C within 40 min. The limit of detection of the LAMP assay was 101 copies/μL. No cross reaction occurred with Plasmodium vivax, Toxocara cati, Clonorchis sinensi, Spirometra mansoni or Cryptosporidium parvum. We validated the developed LAMP assay by detecting T. gondii in DNA extracted from 353 blood samples collected from domestic cats and dogs. The percentages of positive results in detecting these blood samples by LAMP and conventional PCR were 5.38% and 2.83%, respectively. Conclusions: Our findings show that the developed LAMP assay offers higher analytical sensitivity than conventional PCR and good analytical specificity, minimizes aerosol contamination, and can be applied to on-site rapid detection of T. gondii.
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Affiliation(s)
- Yan Wu
- School of Medical Laboratory Science, Wannan Medical College, Wuhu, China
| | - Yan Zhang
- School of Medical Laboratory Science, Wannan Medical College, Wuhu, China
| | - Zhi-Wei Zhu
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China
| | - Qi-Qi Xue
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China
| | - Ming-Hui Zou
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China
| | - Ming Sun
- Tiantian Pet Hospital, Wuhu, China
| | - Yuan-Yuan Li
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China
| | - Jin-Hong Zhao
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China.,Anhui Provincial Key Laboratory of Biological Macromolecules, Wuhu, China
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10
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Zhang X, Zhao Y, Ma C, Wu W, Dong M, You J, Liu J, Yun S. An Optimized Visual Loop Mediated Isothermal Amplification Assay for Efficient Detection of Minute Virus of Mice With Hydroxynaphthol Blue Dye. J Virol Methods 2022; 308:114575. [DOI: 10.1016/j.jviromet.2022.114575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/26/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022]
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11
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Yasui R, Matsui A, Sekine K, Okamoto S, Taniguchi H. Highly Sensitive Detection of Human Pluripotent Stem Cells by Loop-Mediated Isothermal Amplification. Stem Cell Rev Rep 2022; 18:2995-3007. [PMID: 35661077 PMCID: PMC9622575 DOI: 10.1007/s12015-022-10402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2022] [Indexed: 11/24/2022]
Abstract
For safe regenerative medicines, contaminated or remaining tumorigenic undifferentiated cells in cell-derived products must be rigorously assessed through sensitive assays. Although in vitro nucleic acid tests offer particularly sensitive tumorigenicity-associated assays, the human pluripotent stem cell (hPSC) detectability is partly constrained by the small input amount of RNA per test. To overcome this limitation, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays that are highly gene specific and robust against interfering materials. LAMP could readily assay microgram order of input sample per test and detected an equivalent model of 0.00002% hiPSC contamination in a simple one-pot reaction. For the evaluation of cell-derived total RNA, RT-LAMP detected spiked-in hPSCs among hPSC-derived trilineage cells utilizing multiple pluripotency RNAs. We also developed multiplex RT-LAMP assays and further applied for in situ cell imaging, achieving specific co-staining of pluripotency proteins and RNAs. Our attempts uncovered the utility of RT-LAMP approaches for tumorigenicity-associated assays, supporting practical applications of regenerative medicine.
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Affiliation(s)
- Ryota Yasui
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
- Fundamental Research Laboratory, Eiken Chemical Co., Ltd., Nogi, Tochigi, 329-0114, Japan
| | - Atsuka Matsui
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Ohtawara, Tochigi, 324-0036, Japan
| | - Keisuke Sekine
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Satoshi Okamoto
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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12
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Chen D, Liang Z, Ren S, Alali W, Chen L. Rapid and Visualized Detection of Virulence-Related Genes of Vibrio cholerae in Water and Aquatic Products by Loop-Mediated Isothermal Amplification. J Food Prot 2022; 85:44-53. [PMID: 34436566 DOI: 10.4315/jfp-21-182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/20/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Vibrio cholerae can cause pandemic cholera in humans. The bacterium resides in aquatic environments worldwide. Continuous testing of V. cholerae contamination in water and aquatic products is imperative for food safety control and human health. In this study, a rapid and visualized method was developed for the first time based on loop-mediated isothermal amplification (LAMP) for detection of the important virulence-related genes ace, zot, cri, and nanH for toxins and the infectious process of V. cholerae. Three pairs of molecular probes targeting each of these genes were designed and synthesized. The one-step LAMP reaction was conducted at 65°C for 40 min. Positive results were inspected by the production of a light green color under visible light or green fluorescence under UV light (302 nm). Limit of detection of the LAMP method ranged from 1.85 to 2.06 pg per reaction of genomic DNA or 2.50 × 100 to 4.00 × 102 CFU per reaction for target genes of cell culture of V. cholerae, which was more sensitive than standard PCR. Inclusivity and exclusivity of the LAMP method were 100% for all target genes. The method showed similar high efficiency to a certain extent in rapid testing of spiked or collected specimens of water and aquatic products. Target genes were detected by absence from all water samples from various sources. However, high occurrences of the nanH gene were observed in intestinal samples derived from four species of fish and one species of shellfish, indicating a risk of potentially toxic V. cholerae in commonly consumed aquatic products. The results in this study provide a potential tool for rapid and visualized detection of V. cholerae in water and aquatic products. HIGHLIGHTS
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Affiliation(s)
- Dailing Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of the People's Republic of China, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, People's Republic of China
| | - Zhili Liang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of the People's Republic of China, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, People's Republic of China
| | - Shunlin Ren
- Department of Internal Medicine, Virginia Commonwealth University/McGuire VA Medical Centre, Richmond, Virginia 23249, USA
| | - Walid Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, Kuwait City, Kuwait
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of the People's Republic of China, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, People's Republic of China
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13
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Huang Q, Shan X, Cao R, Jin X, Lin X, He Q, Zhu Y, Fu R, Du W, Lv W, Xia Y, Huang G. Microfluidic Chip with Two-Stage Isothermal Amplification Method for Highly Sensitive Parallel Detection of SARS-CoV-2 and Measles Virus. MICROMACHINES 2021; 12:mi12121582. [PMID: 34945432 PMCID: PMC8705924 DOI: 10.3390/mi12121582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/11/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023]
Abstract
A two-stage isothermal amplification method, which consists of a first-stage basic recombinase polymerase amplification (RPA) and a second-stage fluorescence loop-mediated isothermal amplification (LAMP), as well as a microfluidic-chip-based portable system, were developed in this study; these enabled parallel detection of multiplex targets in real time in around one hour, with high sensitivity and specificity, without cross-contamination. The consumption of the sample and the reagent was 2.1 μL and 10.6 μL per reaction for RPA and LAMP, respectively. The lowest detection limit (LOD) was about 10 copies. The clinical amplification of about 40 nasopharyngeal swab samples, containing 17 SARS-CoV-2 (severe acute respiratory syndrome coronavirus) and 23 measles viruses (MV), were parallel tested by using the microfluidic chip. Both clinical specificity and sensitivity were 100% for MV, and the clinical specificity and sensitivity were 94.12% and 95.83% for SARS-CoV-2, respectively. This two-stage isothermal amplification method based on the microfluidic chip format offers a convenient, clinically parallel molecular diagnostic method, which can identify different nucleic acid samples simultaneously and in a timely manner, and with a low cost of the reaction reagent. It is especially suitable for resource-limited areas and point-of-care testing (POCT).
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Affiliation(s)
- Qin Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Xiaohui Shan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Ranran Cao
- Sichuan Center for Disease Control and Prevention, Chengdu 610041, China;
| | - Xiangyu Jin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Xue Lin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Qiurong He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.Z.)
| | - Yulei Zhu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.Z.)
| | - Rongxin Fu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Wenli Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Wenqi Lv
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Ying Xia
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.Z.)
- Correspondence: (Y.X.); (G.H.); Tel.: +86-(010)-62797213 (G.H.)
| | - Guoliang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
- Correspondence: (Y.X.); (G.H.); Tel.: +86-(010)-62797213 (G.H.)
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14
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Chu J, Shin J, Kang S, Shin S, Chung YJ. Rapid and sensitive detection of Salmonella species targeting the hilA gene using a loop-mediated isothermal amplification assay. Genomics Inform 2021; 19:e30. [PMID: 34638177 PMCID: PMC8510866 DOI: 10.5808/gi.21048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022] Open
Abstract
Salmonella species are among the major pathogens that cause foodborne illness outbreaks. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid and sensitive detection of Salmonella species. We designed LAMP primers targeting the hilA gene as a universal marker of Salmonella species. A total of seven Salmonella species strains and 11 non-Salmonella pathogen strains from eight different genera were used in this study. All Salmonella strains showed positive amplification signals with the Salmonella LAMP assay; however, there was no non-specific amplification signal for the non-Salmonella strains. The detection limit was 100 femtograms (20 copies per reaction), which was ~1,000 times more sensitive than the detection limits of the conventional polymerase chain reaction (PCR) assay (100 pg). The reaction time for a positive amplification signal was less than 20 minutes, which was less than one-third the time taken while using conventional PCR. In conclusion, our Salmonella LAMP assay accurately detected Salmonella species with a higher degree of sensitivity and greater rapidity than the conventional PCR assay, and it may be suitable for point-of-care testing in the field.
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Affiliation(s)
- Jiyon Chu
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, College of Medicine, Seoul 06591, Korea
| | | | - Shinseok Kang
- Chungbuk Veterinary Services Laboratory, Chungju 27336, Korea
| | - Sun Shin
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, College of Medicine, Seoul 06591, Korea
| | - Yeun-Jun Chung
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, College of Medicine, Seoul 06591, Korea
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15
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Huang Z, Yu X, Yang Q, Zhao Y, Wu W. Aptasensors for Staphylococcus aureus Risk Assessment in Food. Front Microbiol 2021; 12:714265. [PMID: 34603242 PMCID: PMC8483178 DOI: 10.3389/fmicb.2021.714265] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is the top ordinary pathogen causing epidemic and food poisoning. The authentication of S. aureus has great significance for pathologic diagnosis and food hygiene supervision. Various biosensor methods have been established for identification. This paper reviews the research progress of aptasensors for S. aureus detection, focusing on the classification of aptamer technologies, including optical aptasensors and electrochemical aptasensors. Furthermore, the feasibility and future challenges of S. aureus detection for aptamer assays are discussed. Combining aptasensors with nanomaterials appears to be the developing trend in aptasensors.
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Affiliation(s)
- Ziqian Huang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xin Yu
- Qingdao Municipal Hospital, Qingdao, China
| | - Qingli Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Ying Zhao
- Department of Anesthesiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
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16
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Costa-Junior LM, Chaudhry UN, Skuce PJ, Stack S, Sargison ND. A loop-mediated isothermal amplification (LAMP) assay to identify isotype 1 β-tubulin locus SNPs in synthetic double-stranded Haemonchus contortus DNA. J Parasit Dis 2021; 46:47-55. [PMID: 35295940 PMCID: PMC8901900 DOI: 10.1007/s12639-021-01414-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/21/2021] [Indexed: 11/27/2022] Open
Abstract
Development of sustainable gastrointestinal nematode (GIN) control strategies depends on the ability to identify the frequencies of drug-susceptible and resistant genotypes in GIN populations arising from management practices undertaken on individual farms. Resistance to BZ drugs in GINs has been shown to be conferred by the presence of defined SNPs in the isotype 1 β-tubulin locus. Loop-mediated isothermal amplification (LAMP) assays are amenable to use on a range of DNA templates and are potentially adaptable to use in practical, cost-effective, pen-side diagnostic platforms that are needed to detect anthelmintic resistance in the field. In this study, we designed primers and examined LAMP assays to detect each of the three major isotype 1 β-tubulin SNPs conferring genetic susceptibility to BZ drugs. We used artificial pools of synthetic DNA, containing different proportions of susceptible and resistant SNPs to determine reproducibility of the assays. We demonstrated the detection of each of the isotype 1 β-tubulin SNPs conferring susceptibility to BZ drugs using the optimal LAMP assay. Isotype 1 β-tubulin SNP typing was effective in detecting BZ susceptibility, but the accuracy was reduced in samples with less than 60 % susceptible DNA. Our results show the potential for LAMP SNP typing to detect genetic susceptibility or resistance to anthelmintic drugs in livestock GINs, and some of the limitations in our approach that will need to be overcome in order to evaluate this assay using field samples.
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Affiliation(s)
| | - Umer N. Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9RG UK
| | - Philip J. Skuce
- Moredun Research Institute, Pentlands Science Park, Edinburgh, Midlothian, EH26 0PZ Scotland, UK
| | - Seamus Stack
- Mast Group, Mast House, Derby Road, Bootle Merseyside, L20 1EA UK
| | - Neil D. Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9RG UK
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17
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Fan S, Ma C, Tian X, Ma X, Qin M, Wu H, Tian X, Lu J, Lyu M, Wang S. Detection of Vibrio vulnificus in Seafood With a DNAzyme-Based Biosensor. Front Microbiol 2021; 12:655845. [PMID: 34149642 PMCID: PMC8213197 DOI: 10.3389/fmicb.2021.655845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022] Open
Abstract
Vibrio vulnificus is an important pathogenic bacterium that is often associated with seafood-borne illnesses. Therefore, to detect this pathogen in aquatic products, a DNAzyme-based fluorescent sensor was developed for the in vitro detection of V. vulnificus. After screening and mutation, a DNAzyme that we denominated “RFD-VV-M2” exhibited the highest activity, specificity, and sensitivity. The limit of detection was 2.2 × 103 CFU/ml, and results could be obtained within 5–10 min. Our findings suggested that the target of DNAzyme RFD-VV-M2 was a protein with a molecular weight between 50 and 100 kDa. The proposed biosensor exhibited an excellent capacity to detect marine products contaminated with V. vulnificus. Therefore, our study established a rapid, simple, sensitive, and highly specific detection method for V. vulnificus in aquatic products.
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Affiliation(s)
- Shihui Fan
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Chao Ma
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Xiaopeng Tian
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Xiaoyi Ma
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Mingcan Qin
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Hangjie Wu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Xueqing Tian
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Jing Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Lianyungang, China
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Arjuna S, Venkataram R, Dechamma PN, Chakraborty G, Babu N, D'Cruz A, Hosmane GB, Chakraborty A. Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP). Sci Rep 2020; 10:17559. [PMID: 33067539 PMCID: PMC7568567 DOI: 10.1038/s41598-020-74689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022] Open
Abstract
Targeting epidermal growth factor receptor (EGFR) through tyrosine kinase inhibitors (TKI) is a successful therapeutic strategy in non-small cell lung cancer. However, the response to TKI therapy depends on specific activating and acquired mutations in the tyrosine kinase domain of the EGFR gene. Therefore, confirming the EGFR status of patients is crucial, not only for determining the eligibility, but also for monitoring the emergence of mutations in patients under TKI therapy. In this study, our aim was to develop a cost effective, yet sensitive, technique that allows the detection of therapeutically-relevant EGFR hotspot mutations at isothermal conditions in a non-invasive manner. Previously, we developed an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for screening germline and somatic de novo T790M EGFR mutation in lung cancer patients. In this study, we used cell free DNA as a template in AS-LAMP assay (CF-LAMP) for non-invasive detection of two hotspot EGFR mutations (T790M, and L858R) and compared its efficiency with ultrasensitive droplet digital PCR (ddPCR) assay. The results of CF-LAMP assay were consistent with those obtained in ddPCR assay, indicating the robustness of the method. CF-LAMP may serve as a valuable and cost-effective alternative for liquid biopsy techniques used in molecular diagnosis of non-small cell lung cancer.
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Affiliation(s)
- Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Rajesh Venkataram
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Pandyanda Nanjappa Dechamma
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Gunimala Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Audrey D'Cruz
- Department of Health Dentistry, A B Shetty Memorial Institute of Dental Sciences, Nitte (Deemed to be University), Mangaluru, India
| | - Giridhar Belur Hosmane
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India.
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19
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Shen H, Wen J, Liao X, Lin Q, Zhang J, Chen K, Wang S, Zhang J. A Sensitive, Highly Specific Novel Isothermal Amplification Method Based on Single-Nucleotide Polymorphism for the Rapid Detection of Salmonella Pullorum. Front Microbiol 2020; 11:560791. [PMID: 33117307 PMCID: PMC7575712 DOI: 10.3389/fmicb.2020.560791] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/03/2020] [Indexed: 11/30/2022] Open
Abstract
S. Pullorum (Salmonella enterica serovar Gallinarum biovars Pullorum) is an infectious pathogen that causes the acute systemic disease called Pullorum disease in poultry. This disease causes huge losses to the poultry industry and seriously affects the yield and quality of the chicken product. It is not easily distinguishable with fowl typhoid caused by S. Gallinarum (Salmonella enterica serovar Gallinarum biovars Gallinarum), hence the development of a specific and rapid detection method for this pathogen is highly desired. In this study, we propose a novel single-nucleotide polymorphism (SNP) detection strategy termed loop primer probe-introduced loop-mediated isothermal amplification (LP-LAMP) for S. Pullorum detection. Based on the original primer sets, we targeted the nucleotide position 237 of the rfbS gene sequence to design a new modified loop-primer probe with a ribonucleotide insertion, where activity of the enzyme ribonuclease H2 (RNase H2) is only activated when the probe is perfectly complementary, leading to the hydrolytic release of a quencher moiety and thus an amplified signal. The method exhibits robust specificity and a low detection limit as the copy number and genomic DNA is 21 copies/μL and 4.92 pg/μL, respectively. This method showed great performance in real sample testing of 130 samples of embryos, livers, and anal swabs from chickens in poultry farms. The experimental results are mainly consistent with traditional identification methods and a PCR method reported in the past. However, the other two methods still contain some false negative results, while our method is without miss detection. The entire closed-tube reaction process can be accomplished within 40 min at a constant temperature (61°C) without the need for expensive instruments or a complicated operation. The LP-LAMP strategy established in this study not only overcomes the existing difficulties of S. Pullorum rapid detection, it also provides a novel, sensitive, and highly specific detection platform for SNPs that is suitable for clinical use.
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Affiliation(s)
- Haiyan Shen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China; Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Guangdong, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, China
| | - Junping Wen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture; Guangdong Laboratory for Lingnan Modern Agriculture; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xinmeng Liao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Qijie Lin
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture; Guangdong Laboratory for Lingnan Modern Agriculture; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jianfeng Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China; Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Guangdong, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, China
| | - Kaifeng Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture; Guangdong Laboratory for Lingnan Modern Agriculture; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shaojun Wang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture; Guangdong Laboratory for Lingnan Modern Agriculture; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture; Guangdong Laboratory for Lingnan Modern Agriculture; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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20
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Garafutdinov RR, Gilvanov AR, Kupova OY, Sakhabutdinova AR. Effect of metal ions on isothermal amplification with Bst exo- DNA polymerase. Int J Biol Macromol 2020; 161:1447-1455. [DOI: 10.1016/j.ijbiomac.2020.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 01/28/2023]
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21
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Arjuna S, Chakraborty G, Venkataram R, Dechamma PN, Chakraborty A. Detection of epidermal growth factor receptor T790M mutation by allele-specific loop mediated isothermal amplification. J Carcinog 2020; 19:3. [PMID: 32684851 PMCID: PMC7363156 DOI: 10.4103/jcar.jcar_6_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Targeted therapy using specific inhibitors against tyrosine kinases (TKs) is a paradigm in non-small-cell lung cancer management. However, the success of TK inhibitor (TKI) therapy depends on certain activating or acquired mutations, which render sensitivity or resistance to TKIs in the patients. The acquisition of epidermal growth factor receptor (EGFR) T790M point mutation is the most common mechanism of resistance to TKI in non-small cell lung cancer. A number of molecular strategies are now available for molecular testing of non-small cell lung cancers. However, almost all of them are cost-intensive and laborious and require high-end advanced equipment. Thus, assays that are rapid, simple, and cost-effective, yet sensitive, are most ideal in clinical settings for screening such therapeutically relevant mutations. MATERIALS AND METHODS Allele-specific loop-mediated isothermal amplification assay (AS-LAMP), which is a variant of the original LAMP assay, is a promising diagnostic technique for screening single-nucleotide polymorphisms. Using commercially available plasmid constructs as template DNA, AS-LAMP assay for EGFR T790M mutation was optimized with six different sets of reaction mixture containing varying concentrations of buffer and primers. The results of AS-LAMP assay were further validated by ultrasensitive droplet digital polymerase chain reaction. RESULTS Only one of the six sets of reaction mixture could accurately distinguish between wild type and mutated DNA, indicating that the primers and buffer are the two most critical components that determine the accuracy of AS-LAMP. The optimized AS-LAMP assay was further used to screen germ line and somatic T790M mutations in non-small cell lung cancer using blood and tissue samples collected from patients. CONCLUSION Development of an accurate and rapid diagnostic assay that can detect resistant mutations without the need for sequencing is highly useful for clinicians in deciding on the eligibility of patients for TKI therapy. Considering its several inherent advantages, AS-LAMP assay could become an effective molecular tool for screening baseline or acquired EGFR T790M mutations in non-small cell lung cancer patients.
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Affiliation(s)
- Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Gunimala Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Rajesh Venkataram
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Pandyanda Nanjappa Dechamma
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
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22
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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23
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Wang WH, Lin M, Li HL, Huang JY, Chen JT, Fang XS, Huang DM, Xi XX, Zhao QF, Song FL, Huang S, Zhong TY. <p>Establishment and Evaluation of a Novel Method Based on Loop-Mediated Isothermal Amplification for the Rapid Diagnosis of Thalassemia Genes</p>. Healthc Policy 2020; 13:303-311. [PMID: 32308513 PMCID: PMC7147610 DOI: 10.2147/rmhp.s241399] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 03/21/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose Currently, thalassemia is commonly detected using gap-polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) reverse dot blot, which have high requirements of space, instruments, and personnel. Therefore, it is necessary to develop a new method for thalassemia detection with high sensitivity, low cost, and simple and fast operation. In this study, we aimed to design and evaluate a new method for detecting three α-thalassemia genes including –Southeast Asian (SEA), -α3.7, and -α4.2 and five β-thalassemia genes including 654M, 41/42M, −28M, 17M, and 27/28M based on loop-mediated isothermal amplification (LAMP). Methods Primer sequences were designed using Primer Explorer V4 software. Blood samples (5 mL) were collected from all participants in EDTA. DNA was extracted using Chelex 100 and was subjected to LAMP. LAMP products were detected by fluorescence development in ultraviolet light. Results We found that LAMP assays for positive samples of thalassemia reached a plateau before 60 minutes, whereas the negative control samples entered the plateau after 70 minutes or showed no amplification. The concentration range of positive reactions was between 20–60 pg/μL and 20–60 ng/μL. Additionally, there were no cross-reactivities among 8 thalassemia subtypes. For clinical samples, the positive sample tube showed strong green fluorescence, whereas the negative tube showed light green fluorescence. According to these results, the LAMP method has high sensitivity for detecting thalassemia (252/254). However, 43 false-positive results were obtained in the LAMP test. The LAMP assay was also of low cost and with simple and fast operation. Conclusion The novel LAMP assay can be completed within 60 min using a heating block or a water bath, and the result can be read visually based on color change to detect thalassemia. The LAMP assay fulfills the requirements of field application and resource-limited areas, especially those with primary hospitals and rural areas.
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Affiliation(s)
- Wei-hua Wang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, People’s Republic of China
| | - Hai-liang Li
- Department of Hematology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Jun-yun Huang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Jiang-tao Chen
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou, Guangdong Province, People’s Republic of China
- Department of Medical Laboratory, Huizhou Central Hospital, Huizhou, Guangdong Province, People’s Republic of China
| | - Xian-song Fang
- Department of Blood Transfusion, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Dong-mei Huang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Xu-xiang Xi
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Qing-fei Zhao
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Fang-li Song
- Jiangxi Shiningmed Medical Technology Ltd, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Shao Huang
- Jiangxi Shiningmed Medical Technology Ltd, Ganzhou, Jiangxi Province, People’s Republic of China
- Correspondence: Shao Huang Jiangxi Shiningmed Medical Technology Ltd, Ganzhou, Jiangxi Province, People’s Republic of ChinaTel +86-18602004914 Email
| | - Tian-yu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
- Tian-yu Zhong Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou341000, Jiangxi, People’s Republic of ChinaTel +86-797-8680632 Email
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