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Parker GD, Hanley L, Yu XY. Mass Spectral Imaging to Map Plant-Microbe Interactions. Microorganisms 2023; 11:2045. [PMID: 37630605 PMCID: PMC10459445 DOI: 10.3390/microorganisms11082045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Plant-microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.
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Affiliation(s)
- Gabriel D. Parker
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Luke Hanley
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xiao-Ying Yu
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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Razuvaeva AV, Ulyanova EG, Skolotneva ES, Andreeva IV. Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods. Vavilovskii Zhurnal Genet Selektsii 2023; 27:240-249. [PMID: 37293445 PMCID: PMC10244583 DOI: 10.18699/vjgb-23-30] [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: 07/14/2022] [Revised: 12/25/2022] [Accepted: 01/07/2022] [Indexed: 06/10/2023] Open
Abstract
Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agro- and biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed - from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region.
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Affiliation(s)
- A V Razuvaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Ulyanova
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
| | - E S Skolotneva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Andreeva
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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MALDI-TOF Mass Spectrometry for the Diagnosis of Citrus Canker Caused by Xanthomonas citri subsp. citri. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248947. [PMID: 36558076 PMCID: PMC9781495 DOI: 10.3390/molecules27248947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), is a disease that causes serious problems to the global citrus industry. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry (MS) has been used in human medicine to diagnose various diseases caused by both fungi and bacteria. In agriculture, this technique has potential for the diagnosis of diseases due to the low cost of large-scale analysis and quickness. This study showed that MALDI-TOF MS combined with chemometric analysis was effective for differentiating the macromolecule profile of orange leaves with canker lesions, healthy leaves, and leaves with phytotoxicity symptoms, proving that this technique may be used for the rapid diagnosis of citrus canker.
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A consolidative synopsis of the MALDI-TOF MS accomplishments for the rapid diagnosis of microbial plant disease pathogens. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Prudence Dlamini S, Olalekan Akanmu A, Emmanuel Fadiji A, Oluranti Babalola O. Maize rhizosphere modulates the microbiome diversity and community structure to enhance plant health. Saudi J Biol Sci 2022; 30:103499. [DOI: 10.1016/j.sjbs.2022.103499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
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Adedayo AA, Fadiji AE, Babalola OO. Plant Health Status Affects the Functional Diversity of the Rhizosphere Microbiome Associated With Solanum lycopersicum. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.894312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The microorganisms inhabiting soil perform unique functions in the growth and development of plants. However, little is known about how plant health status affects their potential functions. We examined the functional diversity of the microbiome inhabiting the rhizosphere of powdery mildew diseased and healthy tomato plants alongside the bulk soils in South Africa's Northwest Province employing a shotgun metagenomics approach. We envisaged that the functional categories would be abundant in the healthy rhizosphere (HR) of the tomato plant. We collected soil from the rhizosphere of healthy, powdery mildew diseased tomato plants (DR), and bulk soil (BR). After that, their DNA was extracted. The extracted DNA was subjected to shotgun metagenomic sequencing. Our result using the SEED subsystem revealed that a total of fifteen (15) functional categories dominated the healthy rhizosphere, seven (7) functional categories dominated the diseased rhizosphere. At the same time, six (6) functions dominated the bulk soil. Alpha (α) diversity assessment did not reveal a significant difference (p > 0.05) in all the soil samples, but a considerable difference was observed for beta (β) diversity (P = 0.01). The functional categories obtained in this research were highly abundant in HR. Therefore, this study shows that the functions groups of the rhizosphere microbiomes were more abundant in HR samples as compared to others. The high prevalence of functions groups associated with rhizobiomes in the tomato rhizosphere indicates the need for more research to establish the functional genes associated with these rhizosphere microbiomes.
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The Effects of Plant Health Status on the Community Structure and Metabolic Pathways of Rhizosphere Microbial Communities Associated with Solanum lycopersicum. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Powdery mildew disease caused by Oidium neolycopersici is one of the major diseases affecting tomato production in South Africa. Interestingly, limited studies exist on how this disease affects the community structure microbial communities associated with tomato plants employing shotgun metagenomics. In this study, we assess how the health status of a tomato plant affects the diversity of the rhizosphere microbial community. We collected soil samples from the rhizosphere of healthy (HR) and diseased (DR; powdery mildew infected) tomatoes, alongside bulk soil (BR), extracted DNA, and did sequencing using shotgun metagenomics. Our results demonstrated that the rhizosphere microbiome alongside some specific functions were abundant in HR followed by DR and bulk soil (BR) in the order HR > DR > BR. We found eighteen (18) bacterial phyla abundant in HR, including Actinobacteria, Acidobacteria, Aquificae, Bacteroidetes, etc. The dominant fungal phyla include; Ascomycota and Basidiomycota, while the prominent archaeal phyla are Thaumarchaeota, Crenarchaeota, and Euryarchaeota. Three (3) bacteria phyla dominated the DR samples; Bacteroidetes, Gemmatimonadetes, and Thermotoga. Our result also employed the SEED subsystem and revealed that the metabolic pathways involved were abundant in HR. The α-diversity demonstrates that there is no significant difference among the rhizosphere microbiomes across the sites, while β-diversity demonstrated a significant difference.
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Fasusi OA, Amoo AE, Babalola OO. Propagation and characterization of viable arbuscular mycorrhizal fungal spores within maize plant (Zea mays L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5834-5841. [PMID: 33788958 DOI: 10.1002/jsfa.11235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The harmful effect of chemical fertilizer application on human health and the environment as a modern method of meeting the food demand of the increasing world population demands an urgent alternative that is environmentally friendly, which will pose no harm to human health and the environment. Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms that provide various ecological functions in increasing soil fertility and enhancing plant growth. This present study aimed to propagate, characterize and examine the effect of viable arbuscular mycorrhizal fungal spores on maize (Zea mays L) hosts using molecular methods. The propagation of AMF in the host plant using sterile soil and vermiculite was conducted in the greenhouse. RESULT The effect of AMF inoculation revealed a significant difference (P > 0.05) in maize growth, root colonization and AMF spore count when compared with the control. In all the parameters measured in this study, all the AMF spores propagated had a positive effect on the maize plant over the control, with the highest value mostly recorded in Rhizophagus irregularis AOB1. The molecular characterization of the spore using a specific universal primer for Glomeromycota established the success of the propagation process, which enhanced the classification of the AMF species into Rhizophagus irregularis OAB1, Glomus mosseae OAB2 and Paraglomus occultum OAB3. CONCLUSION This finding will be a starting point in producing arbuscular mycorrhizal inoculum as a biofertilizer to enhance plant growth promotion. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Oluwaseun Adeyinka Fasusi
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
| | - Adenike Eunice Amoo
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
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Božik M, Mrázková M, Novotná K, Hrabětová M, Maršik P, Klouček P, Černý K. MALDI-TOF MS as a method for rapid identification of Phytophthora de Bary, 1876. PeerJ 2021; 9:e11662. [PMID: 34322319 PMCID: PMC8297470 DOI: 10.7717/peerj.11662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/01/2021] [Indexed: 12/25/2022] Open
Abstract
The number of described species of the oomycete genus Phytophthora is growing rapidly, highlighting the need for low-cost, rapid tools for species identification. Here, a collection of 24 Phytophthora species (42 samples) from natural as well as anthropogenic habitats were genetically identified using the internal transcribed spacer (ITS) and cytochrome c oxidase subunit I (COI) regions. Because genetic identification is time consuming, we have created a complementary method based on by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Both methods were compared and hypothesis that the MALDI-TOF MS method can be a fast and reliable method for the identification of oomycetes was confirmed. Over 3500 mass spectra were acquired, manually reviewed for quality control, and consolidated into a single reference library using the Bruker MALDI Biotyper platform. Finally, a database containing 144 main spectra (MSPs) was created and published in repository. The method presented in this study will facilitate the use of MALDI-TOF MS as a complement to existing approaches for fast, reliable identification of Phytophthora isolates.
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Affiliation(s)
- Matěj Božik
- Czech University of Life Sciences, Department of Food Science, Prague, Czech Republic
| | - Marcela Mrázková
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Pruhonice, Czech Republic
| | - Karolína Novotná
- Czech University of Life Sciences, Department of Food Science, Prague, Czech Republic
| | - Markéta Hrabětová
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Pruhonice, Czech Republic
| | - Petr Maršik
- Czech University of Life Sciences, Department of Food Science, Prague, Czech Republic
| | - Pavel Klouček
- Czech University of Life Sciences, Department of Food Science, Prague, Czech Republic
| | - Karel Černý
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Pruhonice, Czech Republic
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LaMontagne MG, Tran PL, Benavidez A, Morano LD. Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize. PeerJ 2021; 9:e11359. [PMID: 34123583 PMCID: PMC8166240 DOI: 10.7717/peerj.11359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.
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Affiliation(s)
- Michael G LaMontagne
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Phi L Tran
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Alexander Benavidez
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
| | - Lisa D Morano
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
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Nematode Identification Techniques and Recent Advances. PLANTS 2020; 9:plants9101260. [PMID: 32987762 PMCID: PMC7598616 DOI: 10.3390/plants9101260] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023]
Abstract
Nematodes are among the most diverse but least studied organisms. The classic morphology-based identification has proved insufficient to the study of nematode identification and diversity, mainly for lack of sufficient morphological variations among closely related taxa. Different molecular methods have been used to supplement morphology-based methods and/or circumvent these problems with various degrees of success. These methods range from fingerprint to sequence analyses of DNA- and/or protein-based information. Image analyses techniques have also contributed towards this success. In this review, we highlight what each of these methods entail and provide examples where more recent advances of these techniques have been employed in nematode identification. Wherever possible, emphasis has been given to nematodes of agricultural significance. We show that these alternative methods have aided nematode identification and raised our understanding of nematode diversity and phylogeny. We discuss the pros and cons of these methods and conclude that no one method by itself provides all the answers; the choice of method depends on the question at hand, the nature of the samples, and the availability of resources.
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Bredtmann CM, Krücken J, Murugaiyan J, Balard A, Hofer H, Kuzmina TA, von Samson-Himmelstjerna G. Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins. Proteomics 2020; 19:e1800290. [PMID: 30786147 DOI: 10.1002/pmic.201800290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/07/2018] [Indexed: 12/24/2022]
Abstract
Rapid, cost-effective, efficient, and reliable helminth species identification is of considerable importance to understand host-parasite interactions, clinical disease, and drug resistance. Cyathostomins (Nematoda: Strongylidae) are considered to be the most important equine parasites, yet research on this group is hampered by the large number of 50 morphologically differentiated species, their occurrence in mixed infections with often more than 10 species and the difficulties associated with conventional identification methods. Here, MALDI-TOF MS, previously successfully applied to identify numerous organisms, is evaluated and compared with conventional and molecular genetic approaches. A simple and robust protocol for protein extraction and subsequent DNA isolation allowing molecular confirmation of proteomic findings is developed, showing that MALDI-TOF MS can discriminate adult stages of the two closely related cyathostomin species Cylicostephanus longibursatus and Cylicostephanus minutus. Intraspecific variability of proteomic profiles within morphospecies demonstrated an identification of morphospecies with an accuracy of close to 100%. In contrast, three genospecies within C. minutus and sex-specific profiles within both morphospecies could not be reliably discriminated using MALDI-TOF MS. In conclusion, MALDI-TOF MS complemented by the molecular protocol is a reliable and efficient approach for cyathostomin species identification.
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Affiliation(s)
- Christina Maria Bredtmann
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Jayaseelan Murugaiyan
- Institute for Animal Hygiene and Environmental Health, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany.,Department of Biotechnology, SRM University AP, 522502, Amaravati, India
| | - Alice Balard
- Ecology and Evolution of Molecular Parasite Host Interactions, Molecular Parasitology, Institute for Biology, Humboldt University Berlin, 10115, Berlin, Germany.,Ecology and Evolution of Molecular Parasite Host Interactions, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - Heribert Hofer
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany.,Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tetiana A Kuzmina
- Department of Parasitology, I. I. Schmalhausen Institute of Zoology, 01030, Kiev, Ukraine
| | - Georg von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
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MALDI-TOF mass spectrometry as a diagnostic tool in human and veterinary helminthology: a systematic review. Parasit Vectors 2019; 12:245. [PMID: 31101120 PMCID: PMC6525464 DOI: 10.1186/s13071-019-3493-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022] Open
Abstract
Background Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a widely used technique for the rapid and accurate identification of bacteria, mycobacteria and certain fungal pathogens in the clinical microbiology laboratory. Thus far, only few attempts have been made to apply the technique in clinical parasitology, particularly regarding helminth identification. Methods We systematically reviewed the scientific literature on studies pertaining to MALDI-TOF MS as a diagnostic technique for helminths (cestodes, nematodes and trematodes) of medical and veterinary importance. Readily available electronic databases (i.e. PubMed/MEDLINE, ScienceDirect, Cochrane Library, Web of Science and Google Scholar) were searched from inception to 10 October 2018, without restriction on year of publication or language. The titles and abstracts of studies were screened for eligibility by two independent reviewers. Relevant articles were read in full and included in the systematic review. Results A total of 84 peer-reviewed articles were considered for the final analysis. Most papers reported on the application of MALDI-TOF for the study of Caenorhabditis elegans, and the technique was primarily used for identification of specific proteins rather than entire pathogens. Since 2015, a small number of studies documented the successful use of MALDI-TOF MS for species-specific identification of nematodes of human and veterinary importance, such as Trichinella spp. and Dirofilaria spp. However, the quality of available data and the number of examined helminth samples was low. Conclusions Data on the use of MALDI-TOF MS for the diagnosis of helminths are scarce, but recent evidence suggests a potential role for a reliable identification of nematodes. Future research should explore the diagnostic accuracy of MALDI-TOF MS for identification of (i) adult helminths, larvae and eggs shed in faecal samples; and (ii) helminth-related proteins that are detectable in serum or body fluids of infected individuals. Electronic supplementary material The online version of this article (10.1186/s13071-019-3493-9) contains supplementary material, which is available to authorized users.
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Galeano Garcia P, Neves Dos Santos F, Zanotta S, Eberlin MN, Carazzone C. Metabolomics of Solanum lycopersicum Infected with Phytophthora infestans Leads to Early Detection of Late Blight in Asymptomatic Plants. Molecules 2018; 23:E3330. [PMID: 30558273 PMCID: PMC6320815 DOI: 10.3390/molecules23123330] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 02/07/2023] Open
Abstract
Tomato crops suffer attacks of various pathogens that cause large production losses. Late blight caused by Phytophthora infestans is a devastating disease in tomatoes because of its difficultly to control. Here, we applied metabolomics based on liquid chromatography⁻mass spectrometry (LC-MS) and metabolic profiling by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) in combination with multivariate data analysis in the early detection of late blight on asymptomatic tomato plants and to discriminate infection times of 4, 12, 24, 36, 48, 60, 72 and 96 h after inoculation (hpi). MALDI-MS and LC-MS profiles of metabolites combined with multivariate data analysis are able to detect early-late blight-infected tomato plants, and metabolomics based on LC-MS discriminates infection times in asymptomatic plants. We found the metabolite tomatidine as an important biomarker of infection, saponins as early infection metabolite markers and isocoumarin as early and late asymptomatic infection marker along the post infection time. MALDI-MS and LC-MS analysis can therefore be used as a rapid and effective method for the early detection of late blight-infected tomato plants, offering a suitable tool to guide the correct management and application of sanitary defense approaches. LC-MS analysis also appears to be a suitable tool for identifying major metabolites of asymptomatic late blight-infected tomato plants.
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Affiliation(s)
- Paula Galeano Garcia
- Laboratory of Advanced Analytical Techniques in Natural Products, Universidad de los Andes, Bogotá 111711, Colombia.
- Bioprospección de los Productos Naturales Amazónicos, Facultad de Ciencias Básicas, Universidad de la Amazonia, Florencia 180002, Colombia.
- ThoMSon Mass Spectrometry Laboratory, University of Campinas, Institute of Chemistry, Campinas 13083-970, Brazil.
| | - Fábio Neves Dos Santos
- ThoMSon Mass Spectrometry Laboratory, University of Campinas, Institute of Chemistry, Campinas 13083-970, Brazil.
| | - Samantha Zanotta
- Laboratório de Diagnostico Fitopatológico, Instituto Biológico, São Paulo 04014-900, Brazil.
| | - Marcos Nogueira Eberlin
- ThoMSon Mass Spectrometry Laboratory, University of Campinas, Institute of Chemistry, Campinas 13083-970, Brazil.
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products, Universidad de los Andes, Bogotá 111711, Colombia.
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Kajiwara H, Hinomoto N, Gotoh T. Mass fingerprint analysis of spider mites (Acari) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid discrimination. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1037-1042. [PMID: 27003041 DOI: 10.1002/rcm.7534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/30/2015] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE Discrimination of spider mite species is still performed using morphological information, although DNA and other biological approaches have been attempted for identification purposes. These techniques need much time, are expensive, and require specialist staff. As an alternative, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis is applied for rapid discrimination of spider mite species. METHODS Spider mites were analyzed using MALDI-TOFMS after extraction with 70% formic acid and acetonitrile. A single spider mite was also analyzed directly on double-sided carbon tape. A dendrogram was compiled from the MS data. RESULTS Evolutionarily close and morphologically similar spider mites, the Kanzawa (Tetranychus kanzawai) and the two-spotted (T. urticae) spider mites, as well as three other related species of spider mites, could be discriminated by mass fingerprints. Although female adults were mainly used in this report, male adults and nymphs showed almost the same mass fingerprints and were not considered to affect discrimination capability. A single spider mite on double-sided carbon tape was analyzed directly by MALDI-TOFMS. CONCLUSIONS Spider mites could be analyzed directly by MALDI-TOFMS, with evolutionarily and morphologically closely related spider mites showing different mass fingerprints, allowing for their identification.
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Affiliation(s)
- Hideyuki Kajiwara
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Norihide Hinomoto
- Agriculture Research Center, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-1, Tsukuba, Ibaraki, 305-8666, Japan
| | - Tetsuo Gotoh
- Laboratory of Applied Entomology and Zoology, Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, 300-0393, Japan
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New Insights for Diagnosis of Pineapple Fusariosis by MALDI-TOF MS Technique. Curr Microbiol 2016; 73:206-13. [DOI: 10.1007/s00284-016-1041-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 04/07/2016] [Indexed: 10/21/2022]
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19
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Kajiwara H. Direct detection of the plant pathogens Burkholderia glumae, Burkholderia gladioli pv. gladioli, and Erwinia chrysanthemi pv. zeae in infected rice seedlings using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods 2016; 120:1-5. [DOI: 10.1016/j.mimet.2015.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 11/27/2022]
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20
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Šalplachta J, Kubesová A, Horký J, Matoušková H, Tesařová M, Horká M. Characterization of Dickeya and Pectobacterium species by capillary electrophoretic techniques and MALDI-TOF MS. Anal Bioanal Chem 2015; 407:7625-35. [PMID: 26229029 DOI: 10.1007/s00216-015-8920-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 11/27/2022]
Abstract
Dickeya and Pectobacterium species represent an important group of broad-host-range phytopathogens responsible for blackleg and soft rot diseases on numerous plants including many economically important plants. Although these species are commonly detected using cultural, serological, and molecular methods, these methods are sometimes insufficient to classify the bacteria correctly. On that account, this study was undertaken to investigate the feasibility of three individual analytical techniques, capillary zone electrophoresis (CZE), capillary isoelectric focusing (CIEF), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), for reliable classification of Dickeya and Pectobacterium species. Forty-three strains, representing different Dickeya and Pectobacterium species, namely Dickeya dianthicola, Dickeya dadantii, Dickeya dieffenbachiae, Dickeya chrysanthemi, Dickeya zeae, Dickeya paradisiaca, Dickeya solani, Pectobacterium carotovorum, and Pectobacterium atrosepticum, were selected for this purpose. Furthermore, the selected bacteria included one strain which could not be classified using traditional microbiological methods. Characterization of the bacteria was based on different pI values (CIEF), migration velocities (CZE), or specific mass fingerprints (MALDI-TOF MS) of intact cells. All the examined strains, including the undetermined bacterium, were characterized and classified correctly into respective species. MALDI-TOF MS provided the most reliable results in this respect.
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Affiliation(s)
- Jiří Šalplachta
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří 97, 602 00, Brno, Czech Republic.
| | - Anna Kubesová
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří 97, 602 00, Brno, Czech Republic
| | - Jaroslav Horký
- Division of Diagnostics, Central Institute for Supervising and Testing in Agriculture, Šlechtitelů 23, 77900, Olomouc, Czech Republic
| | - Hana Matoušková
- Division of Diagnostics, Central Institute for Supervising and Testing in Agriculture, Šlechtitelů 23, 77900, Olomouc, Czech Republic
| | - Marie Tesařová
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří 97, 602 00, Brno, Czech Republic
| | - Marie Horká
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří 97, 602 00, Brno, Czech Republic
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21
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Durmuş S, Çakır T, Özgür A, Guthke R. A review on computational systems biology of pathogen-host interactions. Front Microbiol 2015; 6:235. [PMID: 25914674 PMCID: PMC4391036 DOI: 10.3389/fmicb.2015.00235] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/10/2015] [Indexed: 12/27/2022] Open
Abstract
Pathogens manipulate the cellular mechanisms of host organisms via pathogen-host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein-protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature.
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Affiliation(s)
- Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, KocaeliTurkey
| | - Arzucan Özgür
- Department of Computer Engineering, Boǧaziçi University, IstanbulTurkey
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knoell-Institute, JenaGermany
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22
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Adaszek Ł, Banach T, Bartnicki M, Winiarczyk D, Łyp P, Winiarczyk S. Application the mass spectrometry MALDI-TOF technique for detection of Babesia canis canis infection in dogs. Parasitol Res 2014; 113:4293-5. [PMID: 25238794 PMCID: PMC4200353 DOI: 10.1007/s00436-014-4124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 08/29/2014] [Indexed: 12/01/2022]
Abstract
The aim of this study was to use rapid mass spectrometry (MS)-based proteomics analyses for diagnosis of Babesia canis canis infections in dogs. The study was conducted on two groups of dogs—healthy dogs and dogs infected with B. canis canis which demonstrated symptoms of babesiosis. The matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS technique revealed the presence of a protein fraction of 51–52 kDa in the blood serum of all the animals infected with the protozoa, which was not found in the serum of healthy dogs. The proteins are suspected to be disease markers, whereas the MALDI-TOF technique itself has high specificity and sensitivity and can be applied in analytical laboratories in the diagnosis of canine babesiosis.
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Affiliation(s)
- Łukasz Adaszek
- Department of Epizootiology and Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, 30 Głęboka St., 20-612, Lublin, Poland,
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Oliveira PM, Zannini E, Arendt EK. Cereal fungal infection, mycotoxins, and lactic acid bacteria mediated bioprotection: From crop farming to cereal products. Food Microbiol 2014; 37:78-95. [DOI: 10.1016/j.fm.2013.06.003] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 05/15/2013] [Accepted: 06/03/2013] [Indexed: 12/23/2022]
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24
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Horká M, Šalplachta J, Karásek P, Kubesová A, Horký J, Matoušková H, Šlais K, Roth M. Combination of Capillary Isoelectric Focusing in a Tapered Capillary with MALDI-TOF MS for Rapid and Reliable Identification of Dickeya Species from Plant Samples. Anal Chem 2013; 85:6806-12. [DOI: 10.1021/ac4009176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie Horká
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Jiří Šalplachta
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Pavel Karásek
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Anna Kubesová
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Jaroslav Horký
- Division of Diagnostics, State Phytosanitary Administration, Šlechtitelů
23, 779 00 Olomouc, Czech Republic
| | - Hana Matoušková
- Division of Diagnostics, State Phytosanitary Administration, Šlechtitelů
23, 779 00 Olomouc, Czech Republic
| | - Karel Šlais
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
| | - Michal Roth
- Institute of Analytical Chemistry of the ASCR, v. v. i., Veveří
97, 602 00 Brno, Czech Republic
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25
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Havlicek V, Lemr K, Schug KA. Current Trends in Microbial Diagnostics Based on Mass Spectrometry. Anal Chem 2012; 85:790-7. [DOI: 10.1021/ac3031866] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vladimir Havlicek
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Karel Lemr
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Kevin A. Schug
- The University of Texas at Arlington,
Department of Chemistry and Biochemistry, Arlington, Texas 76019-0065,
United States
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