1
|
Hu W, Zhou H, Li J, Yuan P, Zhang L, Liu X, Yan J. Visual identification for species and sex derived from bloodstain based on phosphate-mediated isothermal amplification colorimetric system. Talanta 2024; 275:126149. [PMID: 38678926 DOI: 10.1016/j.talanta.2024.126149] [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: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
Species and sex confirmation of the biological specimen play a crucial role in crime investigation. However, the specimen found in the scene is always trace quantity, which is hard to be analyzed by current methods. Moreover, the time-consuming DNA extraction, sophisticated apparatus, and complex data processing make it difficult to satisfy the demand of speediness and convenience for point-of-care tests. In this study, we first exhibit a phosphate-based visual system for field-based species and sex identification derived from trace bloodstain. By introducing phosphate ion-based colorimetry into loop-mediated isothermal amplification (LAMP) for result interpretation, not only the bloodstain can be directly submitted to mitochondrial variant amplification owing to the enhanced amplification efficiency by pyrophosphate ion hydrolyzation, but also the colorimetric signal can be recognized by the naked eye for result output within 30 min through molybdophosphate generation. Aerosol contamination, the major conflict of LAMP, has been solved once and for all by integrating uracil-DNA glycosylase into this system that still holds on a constant temperature. As a demonstration, cytochrome b and Y-chromosomal amelogenin are employed to identify species and sex respectively, which has achieved a highly sensitive and specific distinguishability under a strong interferential background. Accurate results can be obtained from both the simulative degraded and dated specimen, which indicates that this novel system may serve as a promising tool in forensic practice.
Collapse
Affiliation(s)
- Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Huyun Zhou
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China
| | - Xiaonan Liu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, China.
| |
Collapse
|
2
|
A novel fluorescence method based on loop-mediated isothermal amplification and universal molecular beacon in Mycobacterium tuberculosis detection. Talanta 2023. [DOI: 10.1016/j.talanta.2022.123996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
Selim K, Adel A, Eid S, Shahein M. Development of real time reverse transcription loop-mediated isothermal amplification assay for rapid detection of genotype VII of Newcastle disease viruses. Br Poult Sci 2022; 63:864-870. [DOI: 10.1080/00071668.2022.2094219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Karim Selim
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
| | - Amany Adel
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
| | - Samah Eid
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
| | - Momtaz Shahein
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
| |
Collapse
|
4
|
Chen Z, Zhao K, He Z, Luo X, Qin Z, Tan Y, Zheng X, Wu Z, Deng Y, Chen H, Guo Y, Li S. Development and evaluation of a thermostatic nucleic acid testing device based on magnesium pyrophosphate precipitation for detecting Enterocytozoon hepatopenaei. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.01.072] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
5
|
Graphene-based electrochemical genosensor incorporated loop-mediated isothermal amplification for rapid on-site detection of Mycobacterium tuberculosis. J Pharm Biomed Anal 2020; 186:113333. [DOI: 10.1016/j.jpba.2020.113333] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022]
|
6
|
Hua X, Yang E, Yang W, Yuan R, Xu W. LAMP-generated H + ions-induced dimer i-motif as signal transducer for ultrasensitive electrochemical detection of DNA. Chem Commun (Camb) 2019; 55:12463-12466. [PMID: 31576854 DOI: 10.1039/c9cc06738h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Herein, an ultrasensitive electrochemical biosensor is proposed for the quantification of the Flu A virus biomarker DNA (fDNA), and is based on loop-mediated isothermal amplification-generated hydrogen ions (LAMP-H+) which induce the formation of the dimer i-motif structure (DiMS) for signal transduction, coupled with exonuclease III (ExoIII)-assisted DNA walking for signal dual-amplification.
Collapse
Affiliation(s)
- Xiaoyu Hua
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Enfen Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Wenting Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| |
Collapse
|
7
|
Development of a point-of-care test to detect hepatitis B virus DNA threshold relevant for treatment indication. ASIAN BIOMED 2019. [DOI: 10.1515/abm-2019-0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
Background
Hepatitis B virus (HBV) has been the most prevalent blood-borne pathogen wherein utero transmission has still not been properly managed. Recent practice guidelines suggested that an antiviral drug should be administered to third-trimester pregnancies with significant viremia (>2 × 105 IU/mL).
Objectives
To develop a novel turbidity-based loop-mediated isothermal amplification (LAMP) coupled with heat treatment DNA extraction method that is a rapid, cost-effective, and feasible viral load assessment and could be applied to antenatal screening.
Methods
Primers and reagents were designed, turbidity-based platform and heat treatment method were added, and evaluated for optimal efficiency. Assay sensitivity was tested from serially diluted standard HBV DNA. Assay specificity was tested with six standard viral DNAs. Clinical samples were analyzed and the results were compared with those of quantitative polymerase chain reaction (qPCR) diagnostic records.
Results
The optimized condition was 60°C with no betaine, 1.4 mM deoxyribonucleotide triphosphates (dNTPs) and 6 mM of MgSO4 for 60 min. The assay accurately detected samples with standard HBV DNA at >2 × 105 IU/mL in both distilled water and spiked serum. Results can be interpreted within 31.48 ± 1.41 min in real-time turbidimeter. The amplification is exclusively specific to HBV, but not with the other six human-specific viruses. Moreover, the assay showed comparable performance within 95% confidence interval to the previously developed HBV LAMP toward clinical specimens.
Conclusions
This newly developed method was accurate, affordable, and flexible to further implementation to large-scale third-trimester pregnancy screening.
Collapse
|
8
|
Point-of-care rapid detection of Vibrio parahaemolyticus in seafood using loop-mediated isothermal amplification and graphene-based screen-printed electrochemical sensor. Biosens Bioelectron 2019; 132:271-278. [DOI: 10.1016/j.bios.2019.02.060] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
|
9
|
Jevtuševskaja J, Krõlov K, Tulp I, Langel Ü. The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification. Expert Rev Mol Diagn 2017; 17:403-410. [PMID: 28092481 DOI: 10.1080/14737159.2017.1283218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification Results: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. CONCLUSION These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.
Collapse
Affiliation(s)
- Jekaterina Jevtuševskaja
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia
| | - Katrin Krõlov
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia
| | - Indrek Tulp
- b SelfD Technologie GmbH , Leipzig , Germany.,c University of Tartu, Institute of Chemistry , Tartu , Estonia
| | - Ülo Langel
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia.,d Department of Neurochemistry , Stockholm University , Stockholm , Sweden
| |
Collapse
|
10
|
Xie S, Yuan Y, Chai Y, Yuan R. Tracing Phosphate Ions Generated during Loop-Mediated Isothermal Amplification for Electrochemical Detection of Nosema bombycis Genomic DNA PTP1. Anal Chem 2015; 87:10268-74. [DOI: 10.1021/acs.analchem.5b01858] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shunbi Xie
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yali Yuan
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yaqin Chai
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- State Key Laboratory of Silkworm
Genome Biology, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| |
Collapse
|
11
|
Demonstration of a very inexpensive, turbidimetric, real-time, RT-LAMP detection platform using shrimp Laem-Singh virus (LSNV) as a model. PLoS One 2014; 9:e108047. [PMID: 25255231 PMCID: PMC4177868 DOI: 10.1371/journal.pone.0108047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate detection of pathogens under field laboratory conditions is necessary for effective control of veterinary pathogens. Here we describe a prototype, portable, pathogen detection device developed for single tube, real-time, reverse transcription, loop-mediated isothermal amplification (RT-LAMP) using Laem-Singh virus (LSNV) as a model. LSNV is an RNA virus and a component cause of growth retardation in black tiger shrimp. We chose its RNA-dependent RNA polymerase (RdRp) gene as the target for our tests. The basis for detection was measurement of turbidity arising from formation of a white, insoluble magnesium pyrophosphate precipitate byproduct upon amplification of the RdRp target sequence from 100 ng template RNA extracted from shrimp. The measurement device consisted of a heating block to maintain constant temperature in the RT-LAMP reaction for 8 Eppindorf sample tubes, a light-emitting diode (LED) light source providing red light emission at 650 nm wavelength to pass through sample tubes, a light dependent resistance (LDR) photo-detector and a software program to report turbidity events and could potentially be marketed for under US$3000. The device was connected to a computer to display real-time results in a variety of formats. The optimized protocol for LSNV detection consisted of incubation of the sample tubes at 65 °C for 1 h during which turbidity was continuously measured, and quantitative results could be obtained by reaction time measurement. The sensitivity of detection was comparable to that of conventional nested RT-PCR and there was no cross reaction with other common shrimp viruses. The device was used for quantitative measurement of relative copy numbers of LSNV RdRp in 8 shrimp tissues and they were found to be highest in the gills followed in order by the lymphoid organ and hemolymph (p ≤ 0.05). This platform can be easily adapted for detection of other pathogens under field laboratory settings.
Collapse
|
12
|
Loop-mediated isothermal amplification (LAMP) assays for detection and identification of aquaculture pathogens: current state and perspectives. Appl Microbiol Biotechnol 2014; 98:2881-95. [DOI: 10.1007/s00253-014-5531-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 11/26/2022]
|
13
|
Salar R, Gahlawat S, Siwach P, Duhan J, Gahlawat SK. Rapid Detection of Viruses Using Loop-Mediated Isothermal Amplification (LAMP): A Review. BIOTECHNOLOGY: PROSPECTS AND APPLICATIONS 2013. [PMCID: PMC7122297 DOI: 10.1007/978-81-322-1683-4_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most of the diseases caused by viral infection are found to be fatal, and the diagnosis is difficult due to confusion with other causative agents. So, a highly efficient molecular-based advance detection technique, i.e., loop-mediated isothermal amplification (LAMP) method, is developed for diagnosis of viral infections by various workers. It is based on amplification of DNA at very low level under isothermal conditions, using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. This technique is found to be superior than most of the molecular techniques like PCR, RT-PCR, and real-time PCR due to its high specificity, sensitivity, and rapidity. Major advantage of LAMP method is its cost-effectiveness as it can be done simply by using water bath or dry bath. Here, in this review information regarding almost all the effective LAMP techniques which is developed so far for diagnosis of numerous viral pathogens is presented.
Collapse
Affiliation(s)
- R.K. Salar
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - S.K. Gahlawat
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - P. Siwach
- grid.448811.0Department of Biotechnology, Chaudhary Devi lal University, Sirsa, Haryana India
| | - J.S. Duhan
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | | |
Collapse
|
14
|
Arunrut N, Kampeera J, Suebsing R, Kiatpathomchai W. Rapid and sensitive detection of shrimp infectious myonecrosis virus using a reverse transcription loop-mediated isothermal amplification and visual colorogenic nanogold hybridization probe assay. J Virol Methods 2013; 193:542-7. [PMID: 23876366 DOI: 10.1016/j.jviromet.2013.07.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/01/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
This study reports a novel strategy for the detection of reverse transcription loop-mediated isothermal amplification (RT-LAMP) products derived from infectious myonecrosis virus (IMNV), causes a serious myonecrosis in Penaeus (Litopenaeus) vannamei, by using a ssDNA-labeled with gold nanoparticle (AuNP) probe. This technique relies on a self-aggregation method, when the AuNP aggregation is induced by an increasing of salt concentrations with visual detection. The presence of IMNV-LAMP target prevented an AuNP aggregation and a solution remained as pink color of AuNP, while non-complementary targets cannot prevent AuNP aggregation, resulting in a visible color change to purple color after addition of salt. By using the combination of LAMP and AuNP probe system, the total assay interval required approximately 50 min (exclude RNA preparation). Detection limit was 10 copies of IMNV RNA in vitro transcript that comparable to that of LAMP followed by LFD and nested RT-PCR, but it was 100-times more sensitive than RT-PCR methods. This assay can be adapted easily for rapid detection of other shrimp infectious diseases agents at low-cost with robust reagents and using a simple colorimetric detection method.
Collapse
Affiliation(s)
- Narong Arunrut
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | | | | | | |
Collapse
|
15
|
Rapid and sensitive detection of shrimp yellow head virus using loop-mediated isothermal amplification and a colorogenic nanogold hybridization probe. J Virol Methods 2012; 186:36-42. [DOI: 10.1016/j.jviromet.2012.08.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 07/30/2012] [Accepted: 08/21/2012] [Indexed: 02/06/2023]
|
16
|
Chang CC, Chen CC, Wei SC, Lu HH, Liang YH, Lin CW. Diagnostic devices for isothermal nucleic acid amplification. SENSORS (BASEL, SWITZERLAND) 2012; 12:8319-37. [PMID: 22969402 PMCID: PMC3436031 DOI: 10.3390/s120608319] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 05/29/2012] [Accepted: 06/07/2012] [Indexed: 11/23/2022]
Abstract
Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.
Collapse
Affiliation(s)
- Chia-Chen Chang
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | | | | | | | | | | |
Collapse
|