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Pecchia S, Da Lio D. Development of a rapid PCR-Nucleic Acid Lateral Flow Immunoassay (PCR-NALFIA) based on rDNA IGS sequence analysis for the detection of Macrophomina phaseolina in soil. J Microbiol Methods 2018; 151:118-128. [PMID: 29959955 DOI: 10.1016/j.mimet.2018.06.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 11/30/2022]
Abstract
The 'Nucleic Acid Lateral Flow Immunoassay' (NALFIA) using a generic 'Lateral Flow Device' (LFD), combined with PCR employing labelled primers (PCR-NALFIA), enables to circumvent the use of electrophoresis, making the diagnostic procedure more rapid and easier. If the specific amplicon is present in the sample, a coloured band, with an intensity proportional to the amplicon concentration, will develop on the LFD strip in addition to the control band. Species-specific primers for M. phaseolina based on the rDNA intergenic spacer (IGS) were developed and their specificity was checked and confirmed using 20 isolates of M. phaseolina and other 16 non-target fungi. A DNA extraction protocol based on a bead-beating technique using silica beads, skimmed milk and PVP was also developed. The M. phaseolina specific primers MP102F/MP102R, 5' labelled with biotin and FITC respectively, were used in the PCR-NALFIA assay to identify the pathogen starting from mycelium or microsclerotia. Microsclerotia of M. phaseolina (1, 10, 100 and 200) were manipulated under a stereomicroscope and their DNA was extracted using microsclerotia alone or mixed with different types of soil. The resulting DNA, used for the PCR-NALFIA assay, provided positive results for all the samples tested. A semi-quantitative grey-scale reference card based on the PCR-NALFIA assay using intervals corresponding to microsclerotia soil number was developed. For this purpose, the normalized pixel grey volumes obtained after a densitometric analysis of the test line intensity generated by the LFD dipsticks were used.
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Affiliation(s)
- Susanna Pecchia
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy.
| | - Daniele Da Lio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Ultrasensitive amperometric immunosensor for PSA detection based on Cu2O@CeO2-Au nanocomposites as integrated triple signal amplification strategy. Biosens Bioelectron 2017; 87:630-637. [DOI: 10.1016/j.bios.2016.09.018] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/31/2016] [Accepted: 09/05/2016] [Indexed: 11/23/2022]
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Diagnostics of Seed-Borne Plant Pathogens for Safe Introduction and Healthy Conservation of Plant Genetic Resources. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Pravi V, Jeeva ML, Archana PV. Nucleic acid spot hybridization based species-specific detection of Sclerotium rolfsii associated with collar rot disease of Amorphophallus paeoniifolius. World J Microbiol Biotechnol 2014; 31:315-20. [PMID: 25449141 DOI: 10.1007/s11274-014-1783-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/26/2014] [Indexed: 10/24/2022]
Abstract
Collar rot is one of the most destructive and prevalent disease of Amorphophallus paeoniifolius, resulting in heavy yield losses. The causative organism, Sclerotium rolfsii is a soil-borne polyphagous fungus characterized by prolific growth and ability to produce persistent sclerotia. The pathogen propagules surviving in soil and planting material are the major sources of inoculum. This study presents the suitability of DNA hybridization technique for species specific detection of S. rolfsii in soil and planting material. The detection limit of the probe was 10-15 pg of pure pathogen DNA. The developed probe was found to be highly specific and could be used for accurate identification of pathogen up to the species level. The protocol was standardized for detection of the pathogen in naturally infected field samples.
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Affiliation(s)
- V Pravi
- Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram, 695017, Kerala, India,
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Nagatani N, Yamanaka K, Ushijima H, Koketsu R, Sasaki T, Ikuta K, Saito M, Miyahara T, Tamiya E. Detection of influenza virus using a lateral flow immunoassay for amplified DNA by a microfluidic RT-PCR chip. Analyst 2012; 137:3422-6. [PMID: 22354200 DOI: 10.1039/c2an16294f] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Influenza virus RNA was amplified by a continuous-flow polydimethylsiloxane microfluidic RT-PCR chip within 15-20 min. The amplified influenza virus RNA was observed with the naked eye, as the red color at the test line, using a lateral flow immunoassay within 1 min.
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Affiliation(s)
- Naoki Nagatani
- Department of Applied Chemistry, Graduate School of Engineering, Okayama University of Science, Okayama-shi 700-0005, Japan.
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Halfpenny KC, Wright DW. Nanoparticle detection of respiratory infection. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2010; 2:277-90. [PMID: 20201109 PMCID: PMC7169802 DOI: 10.1002/wnan.83] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Respiratory viruses are a constant concern for all demographics. Examples include established viruses such as respiratory syncytial virus (RSV), the leading cause of respiratory infection in infants and young children, and emerging viruses such as severe acute respiratory syndrome (SARS), which reached near pandemic levels in 2003, or H1N1 (swine) influenza. Despite this prevalence, traditional methods of virus detection are typically labor intensive and require several days to successfully confirm infection. Recently, however, nanoparticle‐based detection strategies have been employed in an effort to develop detection assays that are both sensitive and expedient. Each of these platforms capitalizes on the unique properties of nanoparticles for the detection of respiratory viruses. In this article, several nanoparticle‐based scaffolds are discussed.Gold nanoparticles (AuNPs) have been functionalized with virus specific antibodies or oligonucleotides. In each of these constructs, AuNPs act as both an easily conjugated scaffolding system for biological molecules and a powerful fluorescence quencher. AuNPs have also been immobilized and used as electrochemical transducers. They efficiently serve as a conducting interface of electrocatalyic activity making them a powerful tool in this application. Quantum dots (QDs) posses unique fluorescence properties that have also been explored for their application to virus detection when combined with direct antibody conjugation or streptavidin‐biotin binding systems. QDs have an advantage over many traditional fluorophores because their fluorescence properties can be finely tuned and they are resistant to photobleaching. The development of these nanoparticle‐based detection strategies holds the potential to be a powerful method to quickly and easily confirm respiratory virus infection. WIREs Nanomed Nanobiotechnol 2010 2 277–290 This article is categorized under:
Diagnostic Tools > In Vitro Nanoparticle-Based Sensing Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease
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Niessen L. PCR-based diagnosis and quantification of mycotoxin-producing fungi. ADVANCES IN FOOD AND NUTRITION RESEARCH 2008; 54:81-138. [PMID: 18291305 DOI: 10.1016/s1043-4526(07)00003-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mycotoxins are secondary metabolites produced by filamentous fungi which have toxicologically relevant effects on vertebrates if administered in small doses via a natural route. In order to improve food safety and to protect consumers from harmful contaminants, the presence of fungi with the potential to produce such compounds must be checked at critical control points during the production of agricultural commodities as well as during the process of food and feed preparation. Polymerase chain reaction (PCR)-based diagnosis has been applied as an alternative assay replacing cumbersome and time-consuming microbiological and chemical methods for the detection and identification of the most serious toxin producers in the fungal genera Fusarium, Aspergillus, and Penicillium. The current chapter covers the numerous PCR-based assays which have been published since the first description of the use of this technology to detect Aspergillus flavus biosynthesis genes in 1996.
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Affiliation(s)
- Ludwig Niessen
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Weihenstephaner Steig 16, D-85350 Freising, Germany
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Terzi V, Morcia C, Faccioli P, Faccini N, Rossi V, Cigolini M, Corbellini M, Scudellari D, Delogu G. Fusarium DNA traceability along the bread production chain. Int J Food Sci Technol 2007. [DOI: 10.1111/j.1365-2621.2006.01344.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ikeda S, Fuji SI, Sato T, Furuya H, Naito H, Ytow N, Ezura H, Minamisawa K, Fujimura T. Microbial Diversity in Milled Rice as Revealed by Riosomal Intergenic Spacer Analysis. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.165] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Shin-ichi Fuji
- Faculty of Bioresource Sciences, Akita Prefectural University
| | - Toshiro Sato
- Faculty of Bioresource Sciences, Akita Prefectural University
| | | | - Hideki Naito
- Faculty of Bioresource Sciences, Akita Prefectural University
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Yuhi T, Nagatani N, Endo T, Kerman K, Takata M, Konaka H, Namiki M, Takamura Y, Tamiya E. Resin-based micropipette tip for immunochromatographic assays in urine samples. J Immunol Methods 2006; 312:54-60. [PMID: 16624320 DOI: 10.1016/j.jim.2006.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Revised: 02/13/2006] [Accepted: 02/15/2006] [Indexed: 11/19/2022]
Abstract
A novel bioanalysis system based on immunochromatography was developed in connection with a nitrocellulose resin modified micropipette tip, such as ZipTip. The sandwich-type immunoassay was applied to our bioanalysis system. The simple handling of the micropipette enabled us to increase the sample volume and detect low concentrations of target antigens in urine samples. In addition, the washing procedure could also be performed easily to reduce the background signal levels. For analytical evaluations, the color intensity was captured by a flatbed scanner, and processed by a software. We have achieved the detection of human chorionic gonadotropin (hCG) and prostate-specific antigen (PSA). The detection limit of hCG was 0.5 ng/ml (0.05 ng/tip), which is comparable to that of other conventional immunochromatographic systems. Moreover, the detection of PSA was greatly improved over the existing systems with the application of different sample volumes, such as 1 ng/ml (0.2 ng/tip) in a 200 microl sample volume, and 1 ng/ml (0.3 ng/tip) in 300 microl sample volume. Our bioanalysis system is a promising candidate for application to point-of-care tests with its simple handling and high sensitivity.
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Affiliation(s)
- Teruko Yuhi
- Japan Science and Technology Agency (JST) Innovation Plaza Ishikawa, 2-13 Asahidai, Nomi City, Ishikawa 923-1211, Japan
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Schmidt H, Bannier M, Vogel RF, Niessen L. Detection and quantification of Aspergillus ochraceus in green coffee by PCR. Lett Appl Microbiol 2004; 38:464-9. [PMID: 15130140 DOI: 10.1111/j.1472-765x.2004.01524.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to detect and quantify DNA of the ochratoxinogenic fungus Aspergillus ochraceus in green coffee and to compare the results with the ochratoxin A content of naturally contaminated samples. METHODS AND RESULTS A DNA extraction protocol based on a combination of ultrasonification and a commercial kit was tested for the recovery of fungal DNA. PCR and real-time PCR protocols were established for the detection of A. ochraceus. Sensitivity of the PCR was checked by the addition of inoculated green coffee and pure fungal DNA to uncontaminated green coffee samples. The A. ochraceus DNA content of 30 naturally contaminated green coffee samples was determined and compared with the ochratoxin A concentrations. CONCLUSIONS Aspergillus ochraceus can be rapidly and specifically detected in green coffee by PCR. A positive correlation between the ochratoxin A content and the DNA quantity was established. SIGNIFICANCE AND IMPACT OF THE STUDY This work offers a quick alternative to the conventional mycological detection and quantification of A. ochraceus in green coffee.
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Affiliation(s)
- H Schmidt
- TU München, Lehrstuhl für Technische Mikrobiologie, Freising, Germany
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Bluhm BH, Flaherty JE, Cousin MA, Woloshuk CP. Multiplex polymerase chain reaction assay for the differential detection of trichothecene- and fumonisin-producing species of Fusarium in cornmeal. J Food Prot 2002; 65:1955-61. [PMID: 12495016 DOI: 10.4315/0362-028x-65.12.1955] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The genus Fusarium comprises a diverse group of fungi including several species that produce mycotoxins in food commodities. In this study, a multiplex polymerase chain reaction (PCR) assay was developed for the group-specific detection of fumonisin-producing and trichothecene-producing species of Fusarium. Primers for genus-level recognition of Fusarium spp. were designed from the internal transcribed spacer regions (ITS1 and ITS2) of rDNA. Primers for group-specific detection were designed from the TRI6 gene involved in trichothecene biosynthesis and the FUM5 gene involved in fumonisin biosynthesis. Primer specificity was determined by testing for cross-reactivity against purified genomic DNA from 43 fungal species representing 14 genera, including 9 Aspergillus spp., 9 Fusarium spp., and 10 Penicillium spp. With purified genomic DNA as a template, genus-specific recognition was observed at 10 pg per reaction; group-specific recognition occurred at 100 pg of template per reaction for the trichothecene producer Fusarium graminearum and at 1 ng of template per reaction for the fumonisin producer Fusarium verticillioides. For the application of the PCR assay, a protocol was developed to isolate fungal DNA from cornmeal. The detection of F. graminearum and its differentiation from F. verticillioides were accomplished prior to visible fungal growth at <10(5) CFU/g of cornmeal. This level of detection is comparable to those of other methods such as enzyme-linked immunosorbent assay, and the assay described here can be used in the food industry's effort to monitor quality and safety.
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Affiliation(s)
- B H Bluhm
- Department of Botany and Plant Pathology, Purdue University, 1155 Lilly Hall, West Lafayette, Indiana 47907, USA
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