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Integration of IFAST-based nucleic acid extraction and LAMP for on-chip rapid detection of Agroathelia rolfsii in soil
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Naresuan University, Thailand.ORCID iD: 0000-0003-2715-0570
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).ORCID iD: 0000-0002-7102-5024
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Number of Authors: 82024 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 250, article id 116051Article in journal (Refereed) Published
Abstract [en]

Agroathelia rolfsii (A. rolfsii) is a fungal infection and poses a significant threat to over 500 plant species worldwide. It can reduce crop yields drastically resulting in substantial economic losses. While conventional detection methods like PCR offer high sensitivity and specificity, they require specialized and expensive equipment, limiting their applicability in resource -limited settings and in the field. Herein, we present an integrated workflow with nucleic acid extraction and isothermal amplification in a lab -on -a -chip cartridge based on immiscible filtration assisted by surface tension (IFAST) to detect A. rolfsii fungi in soil for point -of -need application. Our approach enabled both DNA extraction of A. rolfsii from soil and subsequent colorimetric loop -mediated isothermal amplification (LAMP) to be completed on a single chip, termed IFAST-LAMP. LAMP primers targeting ITS region of A. rolfsii were newly designed and tested. Two DNA extraction methods based on silica paramagnetic particles (PMPs) and three LAMP assays were compared. The best -performing assay was selected for on -chip extraction and detection of A. rolfsii from soil samples inoculated with concentrations of 3.75, 0.375 and 0.0375 mg fresh weight per 100-g soil (%FW). The full on -chip workflow was achieved within a 1-h turnaround time. The platform was capable of detecting as low as 3.75 %FW at 2 days after inoculation and down to 0.0375 %FW at 3 days after inoculation. The IFAST-LAMP could be suitable for field -applicability for A. rolfsii detection in low -resource settings.

Place, publisher, year, edition, pages
2024. Vol. 250, article id 116051
Keywords [en]
Agroathelia rolfsii, DNA extraction, Immiscible filtration, LAMP, Magnetic particle
National Category
Analytical Chemistry Other Industrial Biotechnology
Identifiers
URN: urn:nbn:se:su:diva-228127DOI: 10.1016/j.bios.2024.116051ISI: 001179335400001PubMedID: 38301544Scopus ID: 2-s2.0-85183981099OAI: oai:DiVA.org:su-228127DiVA, id: diva2:1850413
Available from: 2024-04-10 Created: 2024-04-10 Last updated: 2024-04-10Bibliographically approved

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Changtor, PhanupongRodriguez Mateos, PabloIles, AlexanderPamme, Nicole

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