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Sliwinska E, Loureiro J, Leitch IJ, Šmarda P, Bainard J, Bureš P, Chumová Z, Horová L, Koutecký P, Lučanová M, Trávníček P, Galbraith DW. Application-based guidelines for best practices in plant flow cytometry. Cytometry A 2021; 101:749-781. [PMID: 34585818 DOI: 10.1002/cyto.a.24499] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/10/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022]
Abstract
Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.
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Affiliation(s)
- Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ilia J Leitch
- Kew Science Directorate, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jillian Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - David W Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Kaifeng, China
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Transmission Electron Microscopy Imaging to Analyze Chromatin Density Distribution at the Nanoscale Level. Methods Mol Biol 2018; 1675:633-651. [PMID: 29052215 DOI: 10.1007/978-1-4939-7318-7_34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transmission electron microscopy (TEM) is used to study the fine ultrastructural organization of cells. Delicate specimen preparation is required for results to reflect the "native" ultrastructural organization of subcellular features such as the nucleus. Despite the advent of high-resolution, fluorescent imaging of chromatin components, TEM still provides a unique and complementary level of resolution capturing chromatin organization at the nanoscale level. Here, we describe the workflow, from tissue preparation, TEM image acquisition and image processing, for obtaining a quantitative description of chromatin density distribution in plant cells, informing on local fluctuations and periodicity. Comparative analyses then allow to elucidate the structural changes induced by developmental or environmental cues, or by mutations affecting specific chromatin modifiers at the nanoscale level. We argue that this approach remains affordable and merits a renewed interest by the plant chromatin community.
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Goga M, Ručová D, Kolarčik V, Sabovljević M, Bačkor M, Lang I. Usnic acid, as a biotic factor, changes the ploidy level in mosses. Ecol Evol 2018; 8:2781-2787. [PMID: 29531694 PMCID: PMC5838065 DOI: 10.1002/ece3.3908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/04/2017] [Accepted: 01/14/2018] [Indexed: 11/09/2022] Open
Abstract
Lichens and mosses often share the same environmental conditions where they compete for substrate and other essential factors. Lichens use secondary metabolites as allelochemicals to repel surrounding plants and potential rivals. In mosses, endoreduplication leads to the occurrence of various ploidy levels in the same individual and has been suggested as an adaptation to abiotic stresses. Here, we show that also biotic factors such as usnic acid, an allelochemical produced by lichens, directly influenced the level of ploidy in mosses. Application of usnic acid changed the nuclei proportion and significantly enhanced the endoreduplication index in two moss species, Physcomitrella patens and Pohlia drummondii. These investigations add a new aspect on secondary metabolites of lichens which count as biotic factors and affect ploidy levels in mosses.
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Affiliation(s)
- Michal Goga
- Core Facility Cell Imaging and Ultrastructure ResearchUniversity of ViennaViennaAustria
- Department of BotanyFaculty of ScienceInstitute of Biology and EcologyPavol Jozef Šafárik UniversityKošiceSlovakia
| | - Dajana Ručová
- Department of BotanyFaculty of ScienceInstitute of Biology and EcologyPavol Jozef Šafárik UniversityKošiceSlovakia
| | - Vladislav Kolarčik
- Department of BotanyFaculty of ScienceInstitute of Biology and EcologyPavol Jozef Šafárik UniversityKošiceSlovakia
| | - Marko Sabovljević
- Faculty of BiologyInstitute of Botany and Botanical GardenUniversity of BelgradeBelgradeSerbia
| | - Martin Bačkor
- Department of BotanyFaculty of ScienceInstitute of Biology and EcologyPavol Jozef Šafárik UniversityKošiceSlovakia
| | - Ingeborg Lang
- Core Facility Cell Imaging and Ultrastructure ResearchUniversity of ViennaViennaAustria
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Bainard LD, Bainard JD, Newmaster SG, Klironomos JN. Mycorrhizal symbiosis stimulates endoreduplication in angiosperms. PLANT, CELL & ENVIRONMENT 2011; 34:1577-85. [PMID: 21707648 DOI: 10.1111/j.1365-3040.2011.02354.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Symbiotic and parasitic relationships can alter the degree of endoreduplication in plant cells, and a limited number of studies have documented this occurrence in root cells colonized by arbuscular mycorrhizal (AM) fungi. However, this phenomenon has not been tested in a wide range of plant species, including species that are non-endopolyploid and those that do not associate with AM fungi. We grew 37 species belonging to 16 plant families, with a range of genome sizes and a range in the degree of endopolyploidy. The endoreduplication index (EI) was compared between plants that were inoculated with Glomus irregulare and plants that were not inoculated. Of the species colonized with AM fungi, 22 of the 25 species had a significant increase in endopolyploid root nuclei over non-mycorrhizal plants, including species that do not normally exhibit endopolyploidy. Changes in the EI were strongly correlated (R(2) = 0.619) with the proportion of root length colonized by arbuscules. No change was detected in the EI for the 12 non-mycorrhizal species. This work indicates that colonization by symbiotic fungi involves a mechanism to increase nuclear DNA content in roots across many angiosperm groups and is likely linked to increased metabolism and protein production.
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Affiliation(s)
- L D Bainard
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
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Kamińska M, Klamkowski K, Berniak H, Sowik I. Response of mycorrhizal periwinkle plants to aster yellows phytoplasma infection. MYCORRHIZA 2010; 20:161-166. [PMID: 19756778 DOI: 10.1007/s00572-009-0276-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 08/25/2009] [Indexed: 05/28/2023]
Abstract
The objective of our research was to assess if arbuscular mycorrhizal (AM) fungal colonization can modify the effect of infection by two aster yellows phytoplasma strains (AY1, AYSim) in Catharanthus roseus plants. Both phytoplasma strains had a negative effect on the root fresh weight, but they differed in symptoms appearance and in their influence on photosynthetic and transpiration rates of the periwinkle plants. AM plants showed significantly reduced shoot fresh weight, while the transpiration rate was significantly increased. AM fungal colonization significantly affected shoot height and fresh weight of the plants infected by each phytoplasma strains as well as the root system of plants infected with the more aggressive AYSim phytoplasma strain. Double inoculation did not reduce the negative effects induced with phytoplasma alone on the photosynthetic activity of phytoplasma-infected plants.
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Affiliation(s)
- Maria Kamińska
- Department of Plant Protection, Research Institute of Pomology and Floriculture, 96-100 Skierniewice, Poland.
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Semenzin E, Critto A, Rutgers M, Marcomini A. Integration of bioavailability, ecology and ecotoxicology by three lines of evidence into ecological risk indexes for contaminated soil assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2008; 389:71-86. [PMID: 17904618 DOI: 10.1016/j.scitotenv.2007.08.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 08/09/2007] [Accepted: 08/12/2007] [Indexed: 05/17/2023]
Abstract
A Weight of Evidence approach was applied to define three integrated effect indexes estimating the impairment on terrestrial ecosystems caused by the stressor(s) of concern. According to a Triad approach, the integrated effect indexes combined the information provided by the measurement endpoints of each line of evidence (chemistry/bioavailability, ecology and ecotoxicology) and allowed to analyse the impairment degree highlighted by each measurement endpoint as difference from the reference condition. Multi-Criteria Decision Analysis (MCDA) was used for the aggregation of the complementary Triad information, including expert judgement and a weighted procedure based on the endpoint sensitivity and the sensitivity of the test for ecosystem effects. The developed methodology was implemented in the DSS-ERAMANIA, Module 2, and is presented in this paper as "Integrated Effect Indexes" (IEI) sub-module. The latter has been preliminary applied to the Acna di Cengio (Italy) contaminated site; the results of this application are presented and discussed.
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Affiliation(s)
- Elena Semenzin
- Department of Environmental Sciences and Centre IDEAS, University Ca' Foscari, Venice, Italy
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Repetto O, Massa N, Gianinazzi-Pearson V, Dumas-Gaudot E, Berta G. Cadmium effects on populations of root nuclei in two pea genotypes inoculated or not with the arbuscular mycorrhizal fungus Glomus mosseae. MYCORRHIZA 2007; 17:111-120. [PMID: 17109143 DOI: 10.1007/s00572-006-0082-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 08/26/2006] [Indexed: 05/12/2023]
Abstract
Plants possess a broad range of strategies to cope with cadmium (Cd) stress, including the arbuscular mycorrhizal (AM) symbiosis. In cell responses towards Cd, the contribution of changes in ploidy levels is still unclear. We used flow cytometry to investigate if nuclear ploidy changes are involved in response mechanisms toward Cd and to analyze the effect of the symbiotic status on populations of nuclei. The impact of Cd was investigated in roots of two pea (Pisum sativum L.) genotypes differing in their Cd-sensitivity (Cd-sensitive VIR4788 and Cd-tolerant VIR7128). In pea seedlings grown under hydropony, 25 and 250 microM Cd concentrations lead to an increase in 4 C together with a decrease in 2 C nuclei. The same genotypes, grown in soil/sand substrate, were inoculated or not with the AM fungus Glomus mosseae BEG12 and treated or not with Cd at transplanting (Cd1) or 2 weeks after (Cd2). The Cd2 increased the proportion of 6 and 8 C nuclei in the mycorrhizal VIR4788 and in the non-mycorrhizal VIR7128 genotypes. Thus, changes in ploidy levels reflect pea responses towards Cd, which are modulated by the symbiotic interaction. The Cd-induced increase in ploidy may account for changes in DNA transcription and/or translation.
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Affiliation(s)
- Ombretta Repetto
- Department of Environmental and Life Science, University of Piemonte Orientale 'Amedeo Avogadro', Via Bellini 25G, 15100, Alessandria, Italy
- UMR 1088 INRA/CNRS5484/UB, PME (Plante-Microbe-Environnement) INRA-CMSE, Domaine d'Epoisses, BP 86510, 21065, Dijon Cedex, France
| | - Nadia Massa
- Department of Environmental and Life Science, University of Piemonte Orientale 'Amedeo Avogadro', Via Bellini 25G, 15100, Alessandria, Italy
| | - Vivienne Gianinazzi-Pearson
- UMR 1088 INRA/CNRS5484/UB, PME (Plante-Microbe-Environnement) INRA-CMSE, Domaine d'Epoisses, BP 86510, 21065, Dijon Cedex, France
| | - Eliane Dumas-Gaudot
- UMR 1088 INRA/CNRS5484/UB, PME (Plante-Microbe-Environnement) INRA-CMSE, Domaine d'Epoisses, BP 86510, 21065, Dijon Cedex, France.
| | - Graziella Berta
- Department of Environmental and Life Science, University of Piemonte Orientale 'Amedeo Avogadro', Via Bellini 25G, 15100, Alessandria, Italy
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