1
|
Poles M, Meggiolaro A, Cremaschini S, Marinello F, Filippi D, Pierno M, Mistura G, Ferraro D. Shaking Device for Homogeneous Dispersion of Magnetic Beads in Droplet Microfluidics. SENSORS (BASEL, SWITZERLAND) 2023; 23:5399. [PMID: 37420565 DOI: 10.3390/s23125399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Magnetic beads (or particles) having a size between 1 and 5 µm are largely used in many biochemical assays devoted to both purification and quantification of cells, nucleic acids, or proteins. Unfortunately, the use of these beads within microfluidic devices suffers from natural precipitation because of their size and density. The strategies applied thus far to cells or polymeric particles cannot be extended to magnetic beads, mainly due to their magnetization and their higher densities. We report an effective shaking device capable of preventing the sedimentation of beads that are stored in a custom PCR tube. After the characterization of the operating principle, the device is validated for magnetic beads in droplets, leading to an equal distribution between the droplets, barely affecting their generation.
Collapse
Affiliation(s)
- Maria Poles
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Alessio Meggiolaro
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Sebastian Cremaschini
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Filippo Marinello
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Daniele Filippi
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Matteo Pierno
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Giampaolo Mistura
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Davide Ferraro
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| |
Collapse
|
2
|
Zhang G, Li B, Raghwani J, Vrancken B, Jia R, Hill SC, Fournié G, Cheng Y, Yang Q, Wang Y, Wang Z, Dong L, Pybus OG, Tian H. Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020. Mol Biol Evol 2023; 40:msad019. [PMID: 36703230 PMCID: PMC9922686 DOI: 10.1093/molbev/msad019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023] Open
Abstract
Migratory birds play a critical role in the rapid spread of highly pathogenic avian influenza (HPAI) H5N8 virus clade 2.3.4.4 across Eurasia. Elucidating the timing and pattern of virus transmission is essential therefore for understanding the spatial dissemination of these viruses. In this study, we surveyed >27,000 wild birds in China, tracked the year-round migration patterns of 20 bird species across China since 2006, and generated new HPAI H5N8 virus genomic data. Using this new data set, we investigated the seasonal transmission dynamics of HPAI H5N8 viruses across Eurasia. We found that introductions of HPAI H5N8 viruses to different Eurasian regions were associated with the seasonal migration of wild birds. Moreover, we report a backflow of HPAI H5N8 virus lineages from Europe to Asia, suggesting that Europe acts as both a source and a sink in the global HPAI virus transmission network.
Collapse
Affiliation(s)
- Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Jayna Raghwani
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Ru Jia
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Guillaume Fournié
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Yanchao Cheng
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuxin Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| |
Collapse
|
3
|
Lin YH, Shen SM, Wen CJ, Lin YJ, Chang TD, Chu SC. Molecular Detection Assays for Rapid Field-Detection of Rice Sheath Blight. FRONTIERS IN PLANT SCIENCE 2021; 11:552916. [PMID: 33505407 PMCID: PMC7829186 DOI: 10.3389/fpls.2020.552916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Rhizoctonia solani (Rs), a soil-borne fungal pathogen, can result in rice sheath blight (ShB), which causes yield loss. To prevent outbreaks of ShB and enhance the sustainability of rice production, it is critical to develop a rapid ShB detection method for specific, fast, and on-site disease management. In this study, a reagent for the rapid extraction of this pathogen was developed for on-site detection. The specificity and sensitivity of a novel SMS RS1-F/SMS RS1-R primer set and a ITS1/GMRS-3 reference primer set were tested, while four different extraction protocols for ShB were developed. Moreover, intraday and interday assays were performed to evaluate the reproducibility of the detection methods developed. The results indicated that all of the developed protocols are suitable for use in detecting ShB. In addition, all the samples of infected rice yielded positive Rs detection results when subjected to TaqMan probe-based real-time PCR and SYBR green-based real-time PCR (SMS RS1-F/SMS RS1-R) tests in which automatic magnetic bead-based DNA extraction was performed. These results indicated that the two molecular detection protocols were suitable for the field diagnosis of ShB for all asymptomatic and symptomatic rice samples.
Collapse
Affiliation(s)
- Ying-Hong Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Plant Medicine Teaching Hospital, General Research Service Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Mao Shen
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chen-Jie Wen
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yi-Jia Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Tsai-De Chang
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Sheng-Chi Chu
- Biological Control Branch Station, Miaoli District Agricultural Research and Extension Station, Council of Agriculture, Miaoli, Taiwan
| |
Collapse
|
4
|
Kim S, Mertens-Talcott SU, Vaidya B, Venancio VP, Cho SY, Song JA, Chew BP, Kwon J, Kim D. Performance of concanavalin A-immobilized on polyacrylate beads for the detection of human norovirus and hepatitis A virus in fecal specimens. Food Sci Biotechnol 2020; 29:1727-1733. [PMID: 33282439 PMCID: PMC7708564 DOI: 10.1007/s10068-020-00833-4] [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: 06/15/2020] [Revised: 09/15/2020] [Accepted: 09/25/2020] [Indexed: 11/30/2022] Open
Abstract
Quantitative reverse transcription PCR (qRT-PCR) is a sensitive method for the detection of foodborne viruses in fecal samples. However, the performance of qRT-PCR depends on the efficiency of virus concentration methods. In this study, the effect of Concanavalin A (Con A)-immobilized on polyacrylate beads (Con A-PAB) on the qRT-PCR performance, in terms of sensitivity and specificity to detect foodborne viruses in human fecal specimens was compared with commercial viral RNA extraction kit (VRNA). The detection of foodborne viruses by qRT-PCR was validated by viral genome sequencing. Both Con A-PAB and VRNA methods were equally sensitive and specific for detecting hepatitis A virus in fecal specimens. Even though both methods showed high specificity (100% vs. 100%) for detecting human norovirus (HuNoV), Con A-PAB method exhibited higher sensitivity (100% vs. 42.9%) and accuracy (100% vs. 73.3%) compared to VRNA method. In conclusion, the application of Con A-PAB would improve the performance of qRT-PCR for the detection of HuNoV in fecal samples.
Collapse
Affiliation(s)
- Songhak Kim
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju, 61186 Republic of Korea
| | | | - Bipin Vaidya
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Vinicius Paula Venancio
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843-2252 USA
| | - Se-Young Cho
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Jong-Am Song
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 34133 Republic of Korea
| | - Boon P. Chew
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843-2252 USA
| | - Joseph Kwon
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 34133 Republic of Korea
| | - Duwoon Kim
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju, 61186 Republic of Korea
| |
Collapse
|
5
|
Comparison of nucleic acid extraction methods for next-generation sequencing of avian influenza A virus from ferret respiratory samples. J Virol Methods 2019; 270:95-105. [DOI: 10.1016/j.jviromet.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/13/2019] [Accepted: 04/15/2019] [Indexed: 11/13/2022]
|
6
|
Kang J, Park C, Lee J, Namkung J, Hwang SY, Kim YS. Automated nucleic acids purification from fecal samples on a microfluidic cartridge. BIOCHIP JOURNAL 2017. [DOI: 10.1007/s13206-016-1205-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|