1
|
Alič Š, Dermastia M, Burger J, Dickinson M, Pietersen G, Pietersen G, Dreo T. Genome-Informed Design of a LAMP Assay for the Specific Detection of the Strain of ' Candidatus Phytoplasma asteris' Phytoplasma Occurring in Grapevines in South Africa. PLANT DISEASE 2022; 106:2927-2939. [PMID: 35380469 DOI: 10.1094/pdis-10-21-2312-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine 'Candidatus Phytoplasma asteris' that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Špela Alič
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Marina Dermastia
- National Institute of Biology, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
| | - Johan Burger
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Matthew Dickinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Gerhard Pietersen
- Department of Microbiology and Plant Pathology, University of Pretoria, Hatfield 0028, South Africa
| | | | - Tanja Dreo
- National Institute of Biology, 1000 Ljubljana, Slovenia
| |
Collapse
|
2
|
Brandão WQ, da Silva RJ, Mojica-Sánchez LC, Maciel BG, Ratkovski GP, de Melo CP. Use of polypyrrole-polystyrene membranes for extracting DNA from plant tissues. BIOMATERIALS AND BIOSYSTEMS 2022; 7:100060. [PMID: 36824490 PMCID: PMC9934434 DOI: 10.1016/j.bbiosy.2022.100060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 10/16/2022] Open
Abstract
We describe the preparation of a membrane composed of polypyrrole-polystyrene (PPy-PS) and its application in DNA extraction. We adopted the electrospinning technique to prepare polystyrene (PS) membranes, which we used as substrates for incorporating polypyrrole chains through an in situ chemical procedure. As a model system, we initially investigated the use of PPy-PS membranes for the extraction of salmon sperm DNA from aqueous solutions. These studies have shown that the PPy-PS membrane has a maximum adsorption capacity of 236.0 mg of DNA per gram of PPy after 30 min of exposure to a DNA solution (100 mg/L). We incorporated the PPy-PS membranes into centrifugation columns, which we used to carry out experiments for extracting and purification of DNA from curly lettuce leaves. The protocol was initially optimized by first examining the most appropriate concentration of the three components of the lysis buffer (Tris/HCl, NaCl, and EDTA-Na). We then investigated the most adequate volumes of the concentrated surfactant solution (SDS 20%) and that used in the protein and polysaccharide precipitation step (5 M potassium acetate, pH 6.3), factors that directly influence the quality and quantity of the fraction of DNA obtained. For curly lettuce leaves, both in their mature and young stages, the yield and purity of the DNA purified using the PPy-PS membrane were comparable to those obtained using a commercial kit. In both cases, the collected DNA samples presented excellent integrity and quality. These results are suggestive that these composite membranes are competitive with the commercial kits available for the extraction and purification of DNA from plants.
Collapse
Affiliation(s)
| | - Romário J da Silva
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | | | | | - Gabriela P Ratkovski
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Celso P de Melo
- Pós-Graduação em Ciência de Materiais, Brazil
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| |
Collapse
|
3
|
Yin K, Ding X, Xu Z, Li Z, Wang X, Zhao H, Otis C, Li B, Liu C. Multiplexed colorimetric detection of SARS-CoV-2 and other pathogens in wastewater on a 3D printed integrated microfluidic chip. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 344:130242. [PMID: 34121812 PMCID: PMC8183101 DOI: 10.1016/j.snb.2021.130242] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has become a global public health emergency. The detection of SARS-CoV-2 and human enteric pathogens in wastewater can provide an early warning of disease outbreak. Herein, a sensitive, multiplexed, colorimetric detection (termed "SMCD") method was established for pathogen detection in wastewater samples. The SMCD method integrated on-chip nucleic acid extraction, two-stage isothermal amplification, and colorimetric detection on a 3D printed microfluidic chip. The colorimetric signal during nucleic acid amplification was recorded in real-time and analyzed by a programmed smartphone without the need for complicated equipment. By combining two-stage isothermal amplification assay into the integrated microfluidic platform, we detected SARS-CoV-2 and human enteric pathogens with sensitivities of 100 genome equivalent (GE)/mL and 500 colony-forming units (CFU)/mL, respectively, in wastewater within one hour. Additionally, we realized smart, connected, on-site detection with a reporting framework embedded in a portable detection platform, which exhibited potential for rapid spatiotemporal epidemiologic data collection regarding the environmental dynamics, transmission, and persistence of infectious diseases.
Collapse
Affiliation(s)
- Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Zhiheng Xu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xingyu Wang
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, 89154, USA
| | - Clifford Otis
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Baikun Li
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| |
Collapse
|
4
|
A practical, low-cost, short-term storage method for genomic DNA. Biotechniques 2021; 70:194-201. [PMID: 33749333 DOI: 10.2144/btn-2020-0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to assess the DNA preservation capability of cellulose paper towel and blotting paper as low-cost alternatives to commercial DNA preservation products. Chicken blood was applied as DNA source to each paper towel, blotting paper, FTA® cards and DNA/RNA Shield™. All samples were stored at room temperature for 130 days. DNA extraction from dried blood spots was performed after various time periods using Tris-EDTA and NaOH protocols. PCR activity and the mean amount of DNA isolated from paper towels were reliable. The results of this study demonstrated that cellulose-based blotting paper and especially paper towel had considerable DNA binding and preservation capacity for at least 130 days at room temperature without DNA degradation.
Collapse
|
5
|
Miyama T, Byaruhanga J, Okamura I, Uchida L, Muramatsu Y, Mwebembezi W, Vudriko P, Makita K. Effect of chemical tick control practices on tick infestation and Theileria parva infection in an intensive dairy production region of Uganda. Ticks Tick Borne Dis 2020; 11:101438. [PMID: 32299787 DOI: 10.1016/j.ttbdis.2020.101438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
Chemical tick control is a major means of preventing East Coast fever (ECF), especially in sub-Saharan Africa. However, in southwestern Uganda, improper tick control practices have led to severe acaricide resistance. The objectives of this study were to determine the risk factors associated with tick infestation in dairy cattle and Theileria parva infection, and to generate evidence for the prioritization of effective countermeasures for tick control. A cross-sectional study was conducted in 30 farms in Mbarara District, and information on tick control practices and tick infestation were collected. Tick samples were collected from 13 farms to test tick acaricide efficacy. A total of 420 blood samples from calves to adults of exotic- and cross-breed dairy cattle were collected, and T. parva diagnosis via polymerase chain reaction was performed. All the 13 tick populations tested were resistant to deltamethrin (synthetic pyrethroid). Resistance to single-formulation organophosphate-chlorfenvinphos was 39 % (5/13); co-formulations (chlorpyrifos + cypermethrin), 69 % (9/13); and amitraz (amidine), 85 % (11/13). The overall prevalence of T. parva infection at the individual-level was 45.2 % (190/420, 95 % confidence interval (CI): 40.4-50.1), and that at the farm-level was 83 % (25/30, 95 %CI: 65-94). A good quality cattle crush was a preventive factor for tick infestation (odds ratio (OR): 0.32, 95 %CI: 0.15-0.63, p = 0.001). Well-managed acaricide storage (OR: 0.36, 95 %CI: 0.17-0.76, p = 0.008), and a good quality measuring cylinder for acaricide were preventive factors (OR: 0.32, 95 %CI: 0.11-0.93, p = 0.036) for T. parva infection. The risk factors for T. parva infection were a longer period of acaricide use of the same brand (OR: 1.06, 95 %CI: 1.01-1.10, p = 0.012), and a higher frequency (twice a week) of acaricide use rather than once a week (OR: 11.70, 95 %CI: 1.95-70.13, p = 0.007). These risk factors should be given high intervention priority in order to effectively control ticks and prevent T. parva infections in dairy farms. Teaching proper practices to dairy farmers and to technical staff should be used to overcome the severe challenge of acaricide resistance in Mbarara District.
Collapse
Affiliation(s)
- Takeshi Miyama
- Graduate School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan.
| | - Joseph Byaruhanga
- Research Center for Tropical Diseases and Vector Control, Department of Veterinary Pharmacy, Clinical and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda; Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, Hokkaido 069-8501, Japan.
| | - Ikuo Okamura
- Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, Hokkaido 069-8501, Japan.
| | - Leo Uchida
- Zoonotic Diseases Unit, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, 069-8501, Japan.
| | - Yasukazu Muramatsu
- Zoonotic Diseases Unit, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, 069-8501, Japan.
| | - William Mwebembezi
- Mbarara District Veterinary Office, Mbarara District Local Government, Galt Road plot 5 Boma Hill, P.O. Box 1, Mbarara, Uganda.
| | - Patrick Vudriko
- Research Center for Tropical Diseases and Vector Control, Department of Veterinary Pharmacy, Clinical and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.
| | - Kohei Makita
- Graduate School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, Hokkaido, 069-8501, Japan.
| |
Collapse
|
6
|
Uchida L, Byaruhanga J, Okamura I, Miyama T, Muramatsu Y, Vudriko P, Makita K. FTA-Sodium hydroxide-based polymerase chain reaction (PCR): An efficient and cheaper option for Theileria parva detection in dairy cattle in Mbarara, Uganda. J Vet Med Sci 2019; 82:188-192. [PMID: 31875599 PMCID: PMC7041997 DOI: 10.1292/jvms.19-0521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
East Coast fever is caused by Theileria parva, and poses serious
concerns for dairy farmers owing to massive economic losses. In the current study, we
compared three methods (DNA extraction kits, FTA-NaOH and FTA-TENT) of DNA extraction to
identify the most economical and reliable method. A survey for T. parva
prevalence was conducted in dairy cattle in Mbarara, Uganda. Cytochrome C oxidase
subunit I (COI) and T.
parva-p104 genes were amplified to compare the methods.
FTA-NaOH-based polymerase chain reaction (PCR) yielded the best detection rate for both
COI gene and p104 gene. Prevalence of T.
parva was 45.0% and 83.3% at animal and farm-level, respectively. FTA-NaOH
based-PCR is simple, highly sensitive and cost-effective tool for T.
parva diagnosis in resource constrained settings.
Collapse
Affiliation(s)
- Leo Uchida
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501, Japan
| | - Joseph Byaruhanga
- Research Center for Tropical Diseases and Vector Control, Department of Veterinary Pharmacy, Clinical and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, PO BOX 7062, Kampala, Uganda
| | - Ikuo Okamura
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501, Japan
| | - Takeshi Miyama
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501, Japan
| | - Yasukazu Muramatsu
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501, Japan
| | - Patrick Vudriko
- Research Center for Tropical Diseases and Vector Control, Department of Veterinary Pharmacy, Clinical and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, PO BOX 7062, Kampala, Uganda
| | - Kohei Makita
- School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501, Japan
| |
Collapse
|