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Yuan G, Salalila A, Hwang S, Deng ZD, Deng S. An innovative high-throughput genome releaser for rapid and efficient PCR screening. Front Bioeng Biotechnol 2025; 13:1547909. [PMID: 40200958 PMCID: PMC11975962 DOI: 10.3389/fbioe.2025.1547909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 03/11/2025] [Indexed: 04/10/2025] Open
Abstract
High-throughput PCR screening is vital in synthetic biology and metabolic engineering, enabling rapid and precise analysis of genetic modifications. However, current methods face challenges including inefficient DNA extraction, high variability across sample types, scalability limitations, and the high cost of template DNA extraction. To address these common challenges, we developed a High-Throughput Genome Releaser (HTGR). This innovative device utilizes a squash-based method for rapid, cost-effective, and efficient DNA extraction, optimized for subsequent PCR reactions. After testing various synthetic materials, we selected a plastic that closely mimics the smooth surface and compression properties of microscope slides, ensuring reliable and consistent performance. The device comprises a 96-well plate and a Shear Applicator, designed for both manual and automated operation, and is compatible with standard liquid-handling robotic platforms. This compatibility simplifies integration into high-throughput PCR workflows. Additionally, we developed software to support its automated functions. Our results demonstrated that the specially engineered 96-well plate and HTGR effectively squash fungal spores, releasing sufficient genomic DNA for PCR screening with 100% efficiency. The genome releaser enables the preparation of PCR-ready genomic DNA from 96 samples within minutes, eliminating the need for an extraction buffer. Its adaptability to a wide range of microorganisms and cell types makes it a versatile tool that could significantly advance biomanufacturing processes.
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Affiliation(s)
- Guoliang Yuan
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Aljon Salalila
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sungjoo Hwang
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Zhiqun Daniel Deng
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- Department of Naval Architecture and Marine Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Shuang Deng
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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Gallardo V, Costa J, Sepúlveda M, Cayún Y, Santander C, Ponce E, Bittencourt J, Arriagada C, Soto J, Pedreschi R, Vicente VA, Cornejo P, Santos C. Lipid Production in Cultivable Filamentous Fungi Isolated from Antarctic Soils: A Comprehensive Study. Microorganisms 2025; 13:504. [PMID: 40142397 PMCID: PMC11944995 DOI: 10.3390/microorganisms13030504] [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: 01/28/2025] [Revised: 02/18/2025] [Accepted: 02/21/2025] [Indexed: 03/28/2025] Open
Abstract
Antarctic soil represents an important reservoir of filamentous fungi (FF) species with the ability to produce novel bioactive lipids. However, the lipid extraction method is still a bottleneck. The objective of the present work was to isolate and identify cultivable FF from Antarctic soils, to assess the most effective methods for fatty acid (FA) extraction, and to characterise the obtained lipids. A total of 18 fungal strains belonging to the Botrytis, Cladosporium, Cylindrobasidium, Mortierella, Penicillium, Pseudogymnoascus, and Talaromyces genera and the Melanommataceae family were isolated and identified. The Folch, Bligh and Dyer, and Lewis extraction methods were assessed, and methyl esters of FA (FAMEs) were obtained. The Lewis method was the best in recovering FAMEs from fungal biomass. A total of 17 FAs were identified, and their chemical compositions varied depending on fungal species and strain. Oleic, linoleic, stearic, and palmitic acids were predominant for all fungal strains in the three assessed methods. Among the analysed strains, Cylindrobasidium eucalypti, Penicillium miczynskii, P. virgatum, and Pseudogymnoascus pannorum produced high amounts of FA. This suggests that the soils of Antarctica Bay, as well as harbouring known oleaginous fungi, are also an important source of oleaginous filamentous fungi that remain poorly analysed.
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Affiliation(s)
- Victor Gallardo
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, Temuco 4811230, Chile; (V.G.); (M.S.)
- Postgraduate Program in Biotechnology, Federal University of Technology-Paraná, Ponta Grossa 84017-220, Brazil; (J.B.); (V.A.V.)
| | - Jéssica Costa
- Departamento de Biologia, Instituto de Ciências Biológicas—ICB, Universidade Federal do Amazonas, Manaus 69080-900, Brazil;
- Department of Chemical Science and Natural Resources, Universidad de La Frontera, Temuco 4811230, Chile; (Y.C.); (C.S.)
| | - Marcela Sepúlveda
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, Temuco 4811230, Chile; (V.G.); (M.S.)
- Postgraduate Program in Microbiology, Parasitology and Pathology, Federal University of Parana, Curitiba 80060-000, Brazil
| | - Yasna Cayún
- Department of Chemical Science and Natural Resources, Universidad de La Frontera, Temuco 4811230, Chile; (Y.C.); (C.S.)
| | - Christian Santander
- Department of Chemical Science and Natural Resources, Universidad de La Frontera, Temuco 4811230, Chile; (Y.C.); (C.S.)
| | - Excequel Ponce
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2340025, Chile; (E.P.); (R.P.)
| | - Juliana Bittencourt
- Postgraduate Program in Biotechnology, Federal University of Technology-Paraná, Ponta Grossa 84017-220, Brazil; (J.B.); (V.A.V.)
| | - César Arriagada
- Laboratorio Biorremediación, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile; (C.A.); (J.S.)
| | - Javiera Soto
- Laboratorio Biorremediación, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile; (C.A.); (J.S.)
| | - Romina Pedreschi
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2340025, Chile; (E.P.); (R.P.)
- Millennium Institute Center for Genome Regulation (CRG), Santiago 8331150, Chile
| | - Vania Aparecida Vicente
- Postgraduate Program in Biotechnology, Federal University of Technology-Paraná, Ponta Grossa 84017-220, Brazil; (J.B.); (V.A.V.)
- Postgraduate Program in Microbiology, Parasitology and Pathology, Federal University of Parana, Curitiba 80060-000, Brazil
- Postgraduate Program in Bioprocess Engineering and Biotechnology, Federal University of Parana, Curitiba 84017-220, Brazil
| | - Pablo Cornejo
- Plant Stress Physiology Laboratory, Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo 2940000, Chile
- Centro Tecnológico de Suelos y Cultivos (CTSyC), Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile
| | - Cledir Santos
- Postgraduate Program in Biotechnology, Federal University of Technology-Paraná, Ponta Grossa 84017-220, Brazil; (J.B.); (V.A.V.)
- Department of Chemical Science and Natural Resources, Universidad de La Frontera, Temuco 4811230, Chile; (Y.C.); (C.S.)
- Centro Regional de Investigación e Innovación para la Sostenibilidad de la Agricultura y los Territorios Rurales, CERES, La Palma, Quillota 2260000, Chile
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Abdelfattah MM, Hosny Y, Elkady NA, Abbas EM, Farahat IG, Hassan NHA, Helwa R. Back to Old Books Toward Affordable Research: Homemade Phenol-Based Reagent for Triphasic RNA Purification. Biochem Genet 2024; 62:1827-1839. [PMID: 37747532 PMCID: PMC11186942 DOI: 10.1007/s10528-023-10509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023]
Abstract
Covid-19 crisis did hit many socio-economic aspects in the whole world. In the scientific research, the problem is getting even worse, since most of materials and consumable are allocated to the health sector. Many research laboratories around the world have big delay in receiving their purchases to accomplish their research projects. In the developing countries, the situation is much more difficult, since most of the funding resources are directed to the Covid-19 crisis and there is a notable increase in reagents' prices. Therefore, the aim of the present study is to make a homemade reagents for RNA purification from eukaryotic cells/tissues. The homemade phenol-based RNA extraction reagents were prepared using saturated phenol pH 4.3 (adjusted by 0.5 M citrate buffer) and guanidine thiocyanate. To validate the phenol-based reagent, RNA was purified from different biological samples (cell line, tissues, and fungi) using homemade phenol-based versus a commercial one. Concentration of RNA samples extracted from the same number of cells were compared to assess the homemade preparation of phenol-based reagent. In conclusion, homemade phenol-based reagent is cost effective and comparable to the commercial one. Using homemade phenol-based, RNA extraction was successfully purified from different biological sources.
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Affiliation(s)
- Mahmoud M Abdelfattah
- Molecular Cancer Biology Group, Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Yasmine Hosny
- Vertebrate Biology Group, Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nadia A Elkady
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Eslam M Abbas
- Department of Chemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Iman G Farahat
- Department of Pathology- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Nagwa H A Hassan
- Molecular Cancer Biology Group, Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Reham Helwa
- Molecular Cancer Biology Group, Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt.
- Faculty of Advanced Basic Science, King Salman International University, South Sinai, Ras Sudr, Egypt.
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Possamai G, Dallemole-Giaretta R, Gomes-Laranjo J, Sampaio A, Rodrigues P. Chestnut Brown Rot and Gnomoniopsis smithogilvyi: Characterization of the Causal Agent in Portugal. J Fungi (Basel) 2023; 9:jof9040401. [PMID: 37108855 PMCID: PMC10143102 DOI: 10.3390/jof9040401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Sweet chestnut (Castanea sativa Miller) is a nutritious food with high social and economic impacts in Portugal. The fungus Gnomoniopsis smithogilvyi (syn. Gnomoniopsis castaneae) is the causal agent of chestnut brown rot, and is currently considered one of the major threats to the chestnut production chain worldwide. Considering the lack of knowledge on both the disease and the causal agent in Portugal, studies were conducted in an attempt to develop the necessary control strategies towards the mitigation of the disease in a timely way. Isolates of G. smithogilvyi were selected from three varieties of chestnut from the northeast of Portugal, and were characterized at the morphological, ecophysiological and molecular levels. Tests of pathogenicity and virulence were also developed. Gnomoniopsis smithogilvyi was confirmed as the causal agent of brown rot disease in Portuguese chestnut varieties, which showed high susceptibility. The fungus showed high adaptability to chestnut substrates. The Portuguese isolates of G. smithogilvyi are morphologically and genetically similar to those from other countries, even though some physiological variability was observed among them.
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Affiliation(s)
- Guilherme Possamai
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Campus de Pato Branco, UTFPR-Universidade Tecnológica Federal do Paraná, Pato Branco 85503-390, PR, Brazil
| | | | - José Gomes-Laranjo
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
- Laboratório Associado Instituto para a Inovação, Capacitação e Sustentabilidade da Produção Agroalimentar (Inov4Agro), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Ana Sampaio
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
- Laboratório Associado Instituto para a Inovação, Capacitação e Sustentabilidade da Produção Agroalimentar (Inov4Agro), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Paula Rodrigues
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
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Rodrigues P, Jelassi A, Kanoun E, Sulyok M, Correia P, Ramalhosa E, Pereira EL. Effect of different storage conditions on the stability and safety of almonds. J Food Sci 2023; 88:848-859. [PMID: 36633227 DOI: 10.1111/1750-3841.16453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/23/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Almond production in Portugal is of great importance for the economy of their main producing areas. However, the contamination of these nut fruits with fungi and mycotoxins poses a significant risk to food safety and security. This work intended to evaluate the influence of storage conditions on the microbial and mycotoxin stability and safety of almonds throughout long-term storage. Two almond varieties-Lauranne and Guara-were submitted to three different storage conditions, namely, 4°C with noncontrolled relative humidity (RH), 60% RH at 25°C, and 70% RH at 25°C, for a storage period of 9 months. Samples were collected after 0, 3, 6, and 9 months of storage and analyzed for microbial loads (aerobic mesophiles, yeasts, and molds), mold incidence and diversity, and mycotoxin contamination. In total, 26 species were identified belonging to 6 genera: Aspergillus, Cladosporium, Fusarium, Penicillium, Paecilomyces, and Talaromyces. For the variety Guara, mycotoxins related to Aspergillus sect. Flavi, such as aflatoxins, averufin, versicolorin C, and norsolorinic acid, were detected only after 9 months of storage at 70% and 60% RH. Penicillium mycotoxins, such as quinolactacin A and roquefortine C, were also detected. For the variety Lauranne, Penicillium mycotoxins were detected, such as citrinin, quinolactacins A and B, roquefortines C and D, cyclopenin, cyclopenol, penitrem A, viridicatin, and viridicatol. Mycotoxins related to Aspergillus, such as aspulvinone E, flavoglaucin, paspalin, asperglaucide, asperphenamate, cyclo(L-Pro-L-Tyr), and cyclo(L-Pro-L-Val), were also detected. PRACTICAL APPLICATION: (Optional, for JFS Research Articles ONLY) The quality of almonds depends on the storage period and the RH and temperature at which they are stored. Storage of almonds at 60% RH at 25°C is a good storage condition to maintain the stability and safety of nuts in terms of microbial and mycotoxin contaminations.
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Affiliation(s)
- Paula Rodrigues
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
| | - Arij Jelassi
- Ecole Polytechnique, Université Libre de Tunis, Tunis, Tunisia
| | - Elifa Kanoun
- Ecole Polytechnique, Université Libre de Tunis, Tunis, Tunisia
| | - Michael Sulyok
- Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paula Correia
- CERNAS Research Centre, Polytechnic Institute of Viseu, Viseu, Portugal
| | - Elsa Ramalhosa
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
| | - Ermelinda Lopes Pereira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
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Isa KNM, Jalaludin J, Hashim Z, Than LTL, Hashim JH, Norbäck D. Fungi composition in settled dust associated with fractional exhaled nitric oxide in school children with asthma. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158639. [PMID: 36089033 DOI: 10.1016/j.scitotenv.2022.158639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Fungi exposure has been significantly linked to respiratory illness. However, numerous fungi taxa that are potentially allergenic still undocumented and leave a barrier to establishing a clear connection between exposure and health risks. This study aimed to evaluate the association of fungi composition in settled dust with fractional exhaled nitric oxide (FeNO) levels among school children with doctor-diagnosed asthma. A cross-sectional study was undertaken among secondary school students in eight schools in the urban area of Hulu Langat, Selangor, Malaysia. A total of 470 school children (aged 14 years old) were randomly selected and their FeNO levels were measured and allergic skin prick tests were conducted. The settled dust samples were collected and analysed by using metagenomic technique to determine the fungi composition. The general linear regression with complex sampling was employed to determine the interrelationship. In total, 2645 fungal operational taxonomic units (OTUs) were characterised from the sequencing process which belongs to Ascomycota (60.7 %), Basidiomycota (36.4 %), Glomeromycota (2.9 %) and Chytridiomycota (0.04 %). The top five mostly abundance in all dust samples were Aspergillus clavatus (27.2 %), followed by Hyphoderma multicystidium (12.2 %), Verrucoconiothyrium prosopidis (9.4 %), Ganoderma tuberculosum (9.2 %), and Heterochaete shearii (7.2 %). The regression results indicated that A. clavatus, Brycekendrickomyces acaciae, Candida parapsilosis, Hazslinszkyomyces aloes, H. multicystidium, H. shearii, Starmerella meliponinorum, V. prosopidis were associated in increased of FeNO levels among the asthmatic group at 0.992 ppb (95 % CI = 0.34-1.68), 2.887 ppb (95 % CI = 2.09-3.76), 0.809 ppb (95 % CI = 0.14-1.49), 0.647 ppb (95 % CI = 0.36-0.94), 1.442 ppb (95 % CI = 0.29-2.61), 1.757 ppb (95 % CI = 0.59-2.87), 1.092 ppb (95 % CI = 0.43-1.75) and 1.088 ppb (95 % CI = 0.51-1.62), respectively. To our knowledge, this is a new finding. The findings pointed out that metagenomics profiling of fungi could enhance our understanding of a complex interrelation between rare and unculturable fungi with airway inflammation.
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Affiliation(s)
- Khairul Nizam Mohd Isa
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor, Malaysia; Environmental Health Research Cluster (EHRc), Environmental Healthcare Section, Institute of Medical Science Technology, Universiti Kuala Lumpur, 43000 Kajang, Selangor, Malaysia
| | - Juliana Jalaludin
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor, Malaysia.
| | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology & Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor, Malaysia
| | - Jamal Hisham Hashim
- Department of Health Sciences, Faculty of Engineering and Life Science, Universiti Selangor, Shah Alam Campus, Seksyen 7, 40000 Shah Alam, Selangor, Malaysia
| | - Dan Norbäck
- Department of Medical Science, Occupational and Environmental Medicine, Uppsala University Hospital, Uppsala University, 75185 Uppsala, Sweden
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Ongaro AE, Ndlovu Z, Sollier E, Otieno C, Ondoa P, Street A, Kersaudy-Kerhoas M. Engineering a sustainable future for point-of-care diagnostics and single-use microfluidic devices. LAB ON A CHIP 2022; 22:3122-3137. [PMID: 35899603 PMCID: PMC9397368 DOI: 10.1039/d2lc00380e] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Single-use, disposable, point-of-care diagnostic devices carry great promise for global health, including meeting urgent needs for testing and diagnosis in places with limited laboratory facilities. Unfortunately, the production and disposal of single-use devices, whether in lateral flow assay, cartridges, cassettes, or lab-on-chip microfluidic format, also poses significant challenges for environmental and human health. Point-of-care devices are commonly manufactured from unsustainable polymeric materials derived from fossil sources. Their disposal often necessitates incineration to reduce infection risk, thereby creating additional release of CO2. Many devices also contain toxic chemicals, such as cyanide derivatives, that are damaging to environmental and human health if not disposed of safely. Yet, in the absence of government regulatory frameworks, safe and sustainable waste management for these novel medical devices is often left unaddressed. There is an urgent need to find novel solutions to avert environmental and human harm from these devices, especially in low- and middle-income countries where waste management infrastructure is often weak and where the use of point-of-care tests is projected to rise in coming years. We review here common materials used in the manufacture of single-use point-of-care diagnostic tests, examine the risks they pose to environmental and human health, and investigate replacement materials that can potentially reduce the impact of microfluidic devices on the production of harmful waste. We propose solutions available to point-of-care test developers to start embedding sustainability at an early stage in their design, and to reduce their non-renewable plastic consumption in research and product development.
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Affiliation(s)
| | - Zibusiso Ndlovu
- Medecins Sans Frontières (MSF), Southern Africa Medical Unit (SAMU), Cape Town, South Africa
| | | | - Collins Otieno
- African Society for Laboratory Medicine (ASLM), Addis Ababa, Ethiopia
| | - Pascale Ondoa
- African Society for Laboratory Medicine (ASLM), Addis Ababa, Ethiopia
| | - Alice Street
- School of Social and Political Sciences, University of Edinburgh, Edinburgh, UK
| | - Maïwenn Kersaudy-Kerhoas
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK.
- Infection Medicine, College of Medicine and Veterinary Medicine University of Edinburgh, Edinburgh, UK
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Recent developments and trends of automatic nucleic acid detection systems. JOURNAL OF BIOSAFETY AND BIOSECURITY 2022; 4:54-58. [PMID: 35252802 PMCID: PMC8884274 DOI: 10.1016/j.jobb.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 11/21/2022] Open
Abstract
Nucleic acid detection, widely used in clinical diagnosis, biological analysis, and environmental monitoring, is of great significance for disease diagnosis and basic research. With the outbreak of COVID-19, the demand for fast and high-throughput nucleic acid detection from large numbers of samples has increased sharply. Automated nucleic acid detection systems can meet these needs, and also play important roles in disease screening and infectious disease prevention and control. In this review, we introduce and compare the current mainstream nucleic acid automatic detection instruments and equipment, then discuss the future demands of nucleic acid detection.
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Stefanova P, Brazkova M, Angelova G. Comparative study of DNA extraction methods for identification of medicinal mushrooms. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20224502007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The isolation of high quantity and intact DNA is of a great significance for molecular identification of higher fungi. The aim of this study was to compare two DNA extraction methods for isolation of DNA from medicinal mushrooms of Agaricomycetes class. A modified CTAB method and a modified SDS method were compared by the yield and purity of the extracted DNA, its fragmentation state and suitability for amplification. The results demonstrated high efficiency of both methods in regard to DNA yield (14.18 -144.28 ng DNA/mg biomass with CTAB method and 15.03 -108.34 ng DNA/mg biomass with SDS method). The CTAB method provided DNA extracts with higher purity (A260/A280 ranged from 1.83 to 1.99) in comparison with the SDS method (A260/A280 = 1.53 -1.86). The modified CTAB method produced amplifiable DNA from all mushroom isolates, while the SDS method demonstrated suitability for amplification only in 50% of the samples. Therefore, the modified CTAB method could be the method of choice for DNA extraction from medicinal mushrooms. The analyzed isolates were subjected to molecular identification by ITS1-5.8S-ITS2 rRNA gene sequence analysis and were identified as Ganoderma resinaceum, Trametes versicolor, Fomitopsis pinicola and Inonotus hispidus.
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Comprehensive Assessment of the Virulence Factors sub 3, sub 6 and mcpA in the Zoonotic Dermatophyte Trichophyton benhamiae Using FISH and qPCR. J Fungi (Basel) 2021; 8:jof8010024. [PMID: 35049964 PMCID: PMC8778074 DOI: 10.3390/jof8010024] [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: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Skin infections by keratinophilic fungi are commonly referred to as dermatophytosis and represent a major health burden worldwide. Although patient numbers are on the rise, data on virulence factors, their function and kinetics are scarce. We employed an ex vivo infection model based on guinea pig skin explants (GPSE) for the zoonotic dermatophyte Trichophyton (T.) benhamiae to investigate kinetics of the virulence factors subtilisin (sub) 3, sub 6, metallocarboxypeptidase A (mcpA) and isocitrate lyase (isol) at gene level for ten days. Fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR) were used to detect and quantify the transcripts, respectively. Kingdom-spanning, species-specific and virulence factor-specific probes were successfully applied to isolated fungal elements showing inhomogeneous fluorescence signals along hyphae. Staining results for inoculated GPSE remained inconsistent despite thorough optimization. qPCR revealed a significant increase of sub 3- and mcpA-transcripts toward the end of culture, sub 6 and isol remained at a low level throughout the entire culture period. Sub 3 is tightly connected to the de novo formation of conidia during culture. Since sub 6 is considered an in vivo disease marker. However, the presented findings urgently call for further research on the role of certain virulence factors during infection and disease.
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Carbajal-Valenzuela IA, Medina-Ramos G, Caicedo-Lopez LH, Jiménez-Hernández A, Ortega-Torres AE, Contreras-Medina LM, Torres-Pacheco I, Guevara-González RG. Extracellular DNA: Insight of a Signal Molecule in Crop Protection. BIOLOGY 2021; 10:biology10101022. [PMID: 34681122 PMCID: PMC8533321 DOI: 10.3390/biology10101022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary Agriculture systems use multiple chemical treatments to prevent pests and diseases, and to fertilize plants and eliminate weeds around the crop. These practices are less accepted by the consumers each day, mostly because of the associated environmental, health, and ecological impact; thus, new sustainable green technologies are being developed to replace the use of chemical products. Among green technologies for agriculture practices, the use of plant elicitors represents an alternative with great potential, and extracellular DNA has shown beneficial effects on important production traits such as defence mechanisms, plant growth and development, and secondary metabolites production that results in yield increment and better-quality food. In this review, we reunite experimental evidence of the natural effect that extracellular DNA has on plants. We also aim to contribute a step closer to the agricultural application of extracellular DNA. Additionally, we suggest that extracellular DNA can have a biostimulant effect on plants, and can be applied as a highly sustainable treatment contributing to the circular economy of primary production. Abstract Agricultural systems face several challenges in terms of meeting everyday-growing quantities and qualities of food requirements. However, the ecological and social trade-offs for increasing agricultural production are high, therefore, more sustainable agricultural practices are desired. Researchers are currently working on diverse sustainable techniques based mostly on natural mechanisms that plants have developed along with their evolution. Here, we discuss the potential agricultural application of extracellular DNA (eDNA), its multiple functioning mechanisms in plant metabolism, the importance of hormetic curves establishment, and as a challenge: the technical limitations of the industrial scale for this technology. We highlight the more viable natural mechanisms in which eDNA affects plant metabolism, acting as a damage/microbe-associated molecular pattern (DAMP, MAMP) or as a general plant biostimulant. Finally, we suggest a whole sustainable system, where DNA is extracted from organic sources by a simple methodology to fulfill the molecular characteristics needed to be applied in crop production systems, allowing the reduction in, or perhaps the total removal of, chemical pesticides, fertilizers, and insecticides application.
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Affiliation(s)
- Ireri Alejandra Carbajal-Valenzuela
- C. A. Biosystems Engineering, Campus Amazcala, Autonomous University of Queretaro, Carr. Chichimequillas-Amazcala Km 1 S/N, C.P., El Marques, Querétaro 76265, Mexico; (I.A.C.-V.); (L.H.C.-L.); (A.J.-H.); (A.E.O.-T.); (L.M.C.-M.); (I.T.-P.)
| | - Gabriela Medina-Ramos
- Molecular Plant Pathology Laboratory, Polytechnic University of Guanajuato, Cortazar 38496, Mexico
- Correspondence: (G.M.-R.); or (R.G.G.-G.); Tel.: +52-1-461-441-4300 (G.M.-R.); +52-1-442-192-1200 (ext. 6093) (R.G.G.-G.)
| | - Laura Helena Caicedo-Lopez
- C. A. Biosystems Engineering, Campus Amazcala, Autonomous University of Queretaro, Carr. Chichimequillas-Amazcala Km 1 S/N, C.P., El Marques, Querétaro 76265, Mexico; (I.A.C.-V.); (L.H.C.-L.); (A.J.-H.); (A.E.O.-T.); (L.M.C.-M.); (I.T.-P.)
| | - Alejandra Jiménez-Hernández
- C. A. Biosystems Engineering, Campus Amazcala, Autonomous University of Queretaro, Carr. Chichimequillas-Amazcala Km 1 S/N, C.P., El Marques, Querétaro 76265, Mexico; (I.A.C.-V.); (L.H.C.-L.); (A.J.-H.); (A.E.O.-T.); (L.M.C.-M.); (I.T.-P.)
| | - Adrian Esteban Ortega-Torres
- C. A. Biosystems Engineering, Campus Amazcala, Autonomous University of Queretaro, Carr. Chichimequillas-Amazcala Km 1 S/N, C.P., El Marques, Querétaro 76265, Mexico; (I.A.C.-V.); (L.H.C.-L.); (A.J.-H.); (A.E.O.-T.); (L.M.C.-M.); (I.T.-P.)
| | - Luis Miguel Contreras-Medina
- C. A. Biosystems Engineering, Campus Amazcala, Autonomous University of Queretaro, Carr. Chichimequillas-Amazcala Km 1 S/N, C.P., El Marques, Querétaro 76265, Mexico; (I.A.C.-V.); (L.H.C.-L.); (A.J.-H.); (A.E.O.-T.); (L.M.C.-M.); (I.T.-P.)
| | - Irineo Torres-Pacheco
- C. A. Biosystems Engineering, Campus Amazcala, Autonomous University of Queretaro, Carr. Chichimequillas-Amazcala Km 1 S/N, C.P., El Marques, Querétaro 76265, Mexico; (I.A.C.-V.); (L.H.C.-L.); (A.J.-H.); (A.E.O.-T.); (L.M.C.-M.); (I.T.-P.)
| | - Ramón Gerardo Guevara-González
- C. A. Biosystems Engineering, Campus Amazcala, Autonomous University of Queretaro, Carr. Chichimequillas-Amazcala Km 1 S/N, C.P., El Marques, Querétaro 76265, Mexico; (I.A.C.-V.); (L.H.C.-L.); (A.J.-H.); (A.E.O.-T.); (L.M.C.-M.); (I.T.-P.)
- Correspondence: (G.M.-R.); or (R.G.G.-G.); Tel.: +52-1-461-441-4300 (G.M.-R.); +52-1-442-192-1200 (ext. 6093) (R.G.G.-G.)
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Isa KNM, Jalaludin J, Elias SM, Than LTL, Jabbar MA, Saudi ASM, Norbäck D, Hashim JH, Hashim Z. Metagenomic characterization of indoor dust fungal associated with allergy and lung inflammation among school children. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 221:112430. [PMID: 34147866 DOI: 10.1016/j.ecoenv.2021.112430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 06/12/2023]
Abstract
The exposure of school children to indoor air pollutants has increased allergy and respiratory diseases. The objective of this study were to determine the toxicodynamic interaction of indoor pollutants exposure, biological and chemical with expression of adhesion molecules on eosinophil and neutrophil. A self-administered questionnaire, allergy skin test, and fractional exhaled nitric oxide (FeNO) analyser were used to collect information on health status, sensitization to allergens and respiratory inflammation, respectively among school children at age of 14 years. The sputum induced were analysed to determine the expression of CD11b, CD35, CD63 and CD66b on eosinophil and neutrophil by using flow cytometry technique. The particulate matter (PM2.5 and PM10), NO2, CO2, and formaldehyde, temperature, and relative humidity were measured inside the classrooms. The fungal DNA were extracted from settled dust collected from classrooms and evaluated using metagenomic techniques. We applied chemometric and regression in statistical analysis. A total of 1869 unique of operational taxonomic units (OTUs) of fungi were identified with dominated at genus level by Aspergillus (15.8%), Verrucoconiothyrium (5.5%), and Ganoderma (4.6%). Chemometric and regression results revealed that relative abundance of T. asahii were associated with down regulation of CD66b expressed on eosinophil, and elevation of FeNO levels in predicting asthmatic children with model accuracy of 63.6%. Meanwhile, upregulation of CD11b expressed on eosinophil were associated with relative abundance of A. clavatus and regulated by PM2.5. There were significant association of P. bandonii with upregulation of CD63 expressed on neutrophil and exposure to NO2. Our findings indicate that exposure to PM2.5, NO2, T. asahii, P.bandonii and A.clavatus are likely interrelated with upregulation of activation and degranulation markers on both eosinophil and neutrophil.
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Affiliation(s)
- Khairul Nizam Mohd Isa
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia; Environmental Health Research Cluster (EHRc), Environmental Healthcare Section, Institute of Medical Science Technology, Universiti Kuala Lumpur, Kajang, Selangor, Malaysia
| | - Juliana Jalaludin
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia.
| | - Saliza Mohd Elias
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor, Malaysia
| | - Mohammed Abdulrazzaq Jabbar
- Department of Population Medicine, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, Malaysia
| | - Ahmad Shakir Mohd Saudi
- Environmental Health Research Cluster (EHRc), Environmental Healthcare Section, Institute of Medical Science Technology, Universiti Kuala Lumpur, Kajang, Selangor, Malaysia
| | - Dan Norbäck
- Department of Medical Science, Occupational and Environmental Medicine, Uppsala University Hospital, Uppsala University, Uppsala, Sweden
| | - Jamal Hisham Hashim
- Department of Health Sciences, Faculty of Engineering and Life Science, Universiti Selangor, Shah Alam Campus, Seksyen 7, Shah Alam, Selangor, Malaysia
| | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
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Nikolchina I, Rodrigues P. A preliminary study on mycobiota and ochratoxin a contamination in commercial palm dates (Phoenix dactylifera). Mycotoxin Res 2021; 37:215-220. [PMID: 34018144 DOI: 10.1007/s12550-021-00432-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/20/2021] [Accepted: 05/12/2021] [Indexed: 11/27/2022]
Abstract
The occurrence of mycotoxins and mycotoxigenic fungi in palm dates has not been thoroughly documented. The aims of the present study were to identify the mycobiota present in commercial date samples (n = 19), to determine the ability of the isolated fungi to produce mycotoxins, and to determine and quantify the presence of OTA in date fruits. The majority of products originated from Tunisia (n = 14) and Algeria (n = 3). The dominant fungal species were Aspergillus niger, Aspergillus tubingensis and Aspergillus flavus which were most frequently found in premium quality and organic produce, produced without chemical preservatives. OTA was found in only one sample at a concentration of 0.75 µg/kg, as determined by HPLC with fluorescence detection. Although this preliminary study did not find elevated levels of OTA, its presence in one out of 19 samples indicates that palm dates for human consumption require continuous and stringent control, in order to prevent contaminated produce from entering the market.
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Affiliation(s)
- Iva Nikolchina
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Paula Rodrigues
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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Scharf S, Bartels A, Kondakci M, Pfeffer K, Henrich B, Haas R. Introduction of a bead beating step improves fungal DNA extraction from selected patient specimens. Int J Med Microbiol 2020; 310:151443. [PMID: 32862838 DOI: 10.1016/j.ijmm.2020.151443] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
In immunocompromised patients a colonisation with fungi carries the risk to develop serious invasive fungal infection. An early detection is therefore important, but not optimal hitherto. Fortunately, molecular genetic methods have increased the sensitivity of fungal detection and limited the time, until results are available. However, their success depends on an efficient extraction of genomic DNA from the fungal cell in the given diagnostic specimen. To improve the routine DNA preparation method for yeasts and moulds, the impact of bead beating on fungal DNA release was evaluated. PBS, blood and respiratory rinse were spiked with Candida glabrata or Aspergillus fumigatus. DNA was extracted by mechanical bead beating in addition to the different steps of the DNA preparation protocol, which comprised liquid nitrogen treatment, proteinase K digestion and DNA isolation using the EZ1 DNA Tissue Kit and Workstation. In every method variant tested, treatment with liquid nitrogen did not improve the DNA release. Bead beating once followed by proteinase K digestion and EZ1-work-up led to the highest DNA release from fungus, spiked in PBS, and increased the extracted DNA amount of C. glabrata about 100-fold and of A. fumigatus about 10-fold in relation to sole EZ1-work-up. In fungus-spiked respiratory rinse and blood, highest increase in DNA release was measured after triple bead beating with simultaneous proteinase K digestion. Fungal DNA release of C. glabrata increased for >100-fold in respiratory rinse and for >1000-fold in blood and of A. fumigatus for >10-fold in respiratory rinse and about 5- to 10-fold in blood. The data of this study clearly demonstrate that preparation of fungal DNA from human specimens is optimized by introduction of a bead beating step to the conventional DNA-preparation method without the necessity of a liquid nitrogen step.
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Affiliation(s)
- Sebastian Scharf
- Institute of Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Germany; Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Anna Bartels
- Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Mustafa Kondakci
- Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Germany.
| | - Rainer Haas
- Department of Haematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty, Duesseldorf, Germany
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Rodrigues P, Silva D, Costa P, Abrunhosa L, Venâncio A, Teixeira A. Mycobiota and mycotoxins in Portuguese pork, goat and sheep dry-cured hams. Mycotoxin Res 2019; 35:405-412. [PMID: 31494812 DOI: 10.1007/s12550-019-00374-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 11/27/2022]
Abstract
The objectives of the present work were to survey, for the first time, the contamination of Portuguese fresh and dry-cured meat products with ochratoxin A (OTA) and aflatoxin B1 (AFB1), and to determine the fungi potentially responsible for this contamination. A total of 128 samples including pork fresh legs, dry-cured legs and shoulders, as well as goat and sheep dry-cured legs were analysed. Mycological analysis of these samples yielded a total of 630 fungal isolates. Penicillium sp. was the dominant fungal genus in all products (66% of all isolates). Penicillium nordicum and Aspergillus westerdijkiae were only rarely isolated from pork ham samples. In fresh pork meat, 40% of the samples were contaminated with OTA at levels below 1 μg/kg. In pork dry-cured legs with 20 to 25 months of ripening, 43% of the samples showed detectable contamination, while 18% of the shoulder hams were contaminated. OTA was not detected in any of the goat and sheep samples. OTA contamination does not seem to be a risk in small-piece and short-ripe products like goat and sheep legs, but affects longer ripe products like pork legs and shoulders. Although aflatoxigenic fungi were identified, AFB1 was not detected in any sample, and it should not be considered a risk in dry-cured hams.
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Affiliation(s)
- Paula Rodrigues
- Centro de Investigação de Montanha (CIMO), ESA, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
| | - Diana Silva
- Centro de Investigação de Montanha (CIMO), ESA, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Pedro Costa
- Centro de Investigação de Montanha (CIMO), ESA, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Luís Abrunhosa
- CEB - Centre for Biological Engineering, Universidade do Minho, 4710-057, Braga, Portugal
| | - Armando Venâncio
- CEB - Centre for Biological Engineering, Universidade do Minho, 4710-057, Braga, Portugal
| | - Alfredo Teixeira
- Centro de Investigação de Montanha (CIMO), ESA, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
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Barbier FF, Chabikwa TG, Ahsan MU, Cook SE, Powell R, Tanurdzic M, Beveridge CA. A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing. PLANT METHODS 2019; 15:62. [PMID: 31171930 PMCID: PMC6549277 DOI: 10.1186/s13007-019-0447-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/27/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Woody tropical plants contain high levels of complex organic compounds that inhibit the chemical procedures needed to extract RNA or DNA, thus compromising downstream applications such as RNA sequencing and analysis of gene expression. To overcome this issue, researchers must use extraction protocols using CTAB/PVP buffer instead of commercially available DNA/RNA extraction kits. However, these protocols are time-consuming, use toxic chemicals like phenol and chloroform, and can only be used to process a small number of samples at a time. To overcome these issues, we developed a new CTAB/PVP based protocol for RNA or DNA extraction that eliminates the traditional phenol/chloroform step. Furthermore, the protocol was developed for 96-well plates to speed up processing. RESULTS Our new protocol enabled us to successfully extract RNA from macadamia, avocado, and mango tissues that are traditionally difficult to work with. This RNA was then successfully used to synthesise cDNA for real-time quantitative PCR and to generate good quality RNA-Seq libraries. Our protocol can be easily converted for rapid DNA extraction from different tropical and sub-tropical tree species. CONCLUSION This method enables safer and faster DNA and RNA extraction from recalcitrant species, thus facilitating future work on tropical trees.
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Affiliation(s)
- François F. Barbier
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Tinashe G. Chabikwa
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Muhammad U. Ahsan
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Stacey E. Cook
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Rosanna Powell
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Milos Tanurdzic
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Christine A. Beveridge
- School of Biological Sciences, and The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072 Australia
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