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Changtor P, Rodriguez-Mateos P, Buddhachat K, Wattanachaiyingcharoen W, Iles A, Kerdphon S, Yimtragool N, Pamme N. Integration of IFAST-based nucleic acid extraction and LAMP for on-chip rapid detection of Agroathelia rolfsii in soil. Biosens Bioelectron 2024; 250:116051. [PMID: 38301544 DOI: 10.1016/j.bios.2024.116051] [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: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
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.
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Affiliation(s)
- Phanupong Changtor
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden; Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Pablo Rodriguez-Mateos
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Wandee Wattanachaiyingcharoen
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand; Center of Excellence for Biodiversity, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Alexander Iles
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Sutthichat Kerdphon
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Nonglak Yimtragool
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand; Center of Excellence for Biodiversity, Faculty of Science, Naresuan University, Phitsanulok, Thailand.
| | - Nicole Pamme
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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Qi S, Xu X, Liu L, Wang G, Bao Q, Zhang Y, Zhang Y, Zhang Y, Xu Q, Zhao W, Chen G. The development rule of feathers and application of hair root tissue in sex identification of Yangzhou geese. Poult Sci 2024; 103:103529. [PMID: 38350388 PMCID: PMC10875616 DOI: 10.1016/j.psj.2024.103529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/06/2024] [Accepted: 01/28/2024] [Indexed: 02/15/2024] Open
Abstract
Accurate gender identification is crucial for the study of bird reproduction and evolution. The current study aimed to explore and evaluate the effectiveness of a noninvasive method for gender identification in Yangzhou geese. In this experiment, 600 goose eggs were collected. Hair root tissues were used for PCR amplification, molecular sequencing, and anal inversion for early sex recognition in goslings. According to the DNA amplification results for the feather pulp tissue of 2-wk-old geese, bands appeared at 436 bp (CHD1-Z) and 330 bp (CHD1-W) upon gel electrophoresis. This method considered the base of goose feathers to accelerate the process of gender recognition. By examining the sex of anatomized poultry for verification, the accuracy rate of PCR gel electrophoresis and molecular sequencing sex identification was 100%, whereas the average accuracy rate of anal inversion was 97.41%. In the comparison of feather growth trends at 0 to 18 wk of age, the feather root weight (FRW), feather root length (FRL), feather branch length (FBL), and feather shaft diameter (FSD) of Yangzhou goose of the same age were not significantly different between males and females (P > 0.05). At 6 wk of age, the FRW, FRL, and FSD in males and FRL in females increased rapidly; their growth increased by 84.43, 67.58, 45.10, and 69.42%, respectively. At 10 wk of age, the male FRL, male FBL, and female FBL increased by 37.31, 34.81, and 21.72, respectively. The Boltzmann model was found to be the best-fitting model for the feathers of male Yangzhou geese. Early sex identification based on feather growth trends between the sexes is not feasible. This study provides a convenient and reliable technical means for early sex identification of waterfowl and serves as an ecological strategy for protecting the reproduction of poultry populations.
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Affiliation(s)
- Shangzong Qi
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Xinlei Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Linyu Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Guoyao Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Qiang Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Yong Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Jiangsu Yangzhou 225009, China
| | - Yu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Yang Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Qi Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Wenming Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China.
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China; Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, P.R. China
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