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García-Armenta E, Gutiérrez-López GF. Fractal Microstructure of Foods. FOOD ENGINEERING REVIEWS 2022. [DOI: 10.1007/s12393-021-09302-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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2
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Shaw SL, Siebe M, Cioffi T. Imaging Chambers for Arabidopsis Seedlings for Mitotic Studies. Methods Mol Biol 2022; 2415:47-59. [PMID: 34972945 DOI: 10.1007/978-1-0716-1904-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Flowering plants evolved away from creating centrosomes or conventional microtubule organizing centers. Therein, plants have posed a long-standing challenge to many of the conventional ideas for mitotic spindle construction and the process of chromosome segregation. The Arabidopsis seedling has emerged as a leading model for plant cell biological studies of the cytoskeleton and vesicle trafficking. Here we describe methods for creating a reusable chamber for mitotic studies in both seedling root and shoot cells with instruction for best practices with conventional microscopic techniques.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, IN, USA.
| | - Mathew Siebe
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Timothy Cioffi
- Department of Biology, Indiana University, Bloomington, IN, USA
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3
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Control of vein-forming, striped gene expression by auxin signaling. BMC Biol 2021; 19:213. [PMID: 34556094 PMCID: PMC8461865 DOI: 10.1186/s12915-021-01143-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals, gene expression is activated in striped domains by the differential affinity of broadly expressed transcription factors for their target genes and the combinatorial interaction between such target genes. In plants, how gene expression is activated in striped domains is instead unknown. We address this question for the broadly expressed MONOPTEROS (MP) transcription factor and its target gene ARABIDOPSIS THALIANA HOMEOBOX FACTOR8 (ATHB8). Results We find that ATHB8 promotes vein formation and that such vein-forming function depends on both levels of ATHB8 expression and width of ATHB8 expression domains. We further find that ATHB8 expression is activated in striped domains by a combination of (1) activation of ATHB8 expression through binding of peak levels of MP to a low-affinity MP-binding site in the ATHB8 promoter and (2) repression of ATHB8 expression by MP target genes of the AUXIN/INDOLE-3-ACETIC-ACID-INDUCIBLE family. Conclusions Our findings suggest that a common regulatory logic controls activation of gene expression in striped domains in both plants and animals despite the independent evolution of their multicellularity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01143-9.
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4
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Ge S, Dupuy LX, MacDonald MP. In situ laser manipulation of root tissues in transparent soil. PLANT AND SOIL 2021; 468:475-489. [PMID: 34789948 PMCID: PMC8580905 DOI: 10.1007/s11104-021-05133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
AIMS Laser micromanipulation such as dissection or optical trapping enables remote physical modification of the activity of tissues, cells and organelles. To date, applications of laser manipulation to plant roots grown in soil have been limited. Here, we show laser manipulation can be applied in situ when plant roots are grown in transparent soil. METHODS We have developed a Q-switched laser manipulation and imaging instrument to perform controlled dissection of roots and to study light-induced root growth responses. We performed a detailed characterisation of the properties of the cutting beams through the soil, studying dissection and optical ablation. Furthermore, we also studied the use of low light doses to control the root elongation rate of lettuce seedlings (Lactuca sativa) in air, agar, gel and transparent soil. RESULTS We show that whilst soil inhomogeneities affect the thickness and circularity of the beam, those distortions are not inherently limiting. The ability to induce changes in root elongation or complete dissection of microscopic regions of the root is robust to substrate heterogeneity and microscopy set up and is maintained following the limited distortions induced by the transparent soil environment. CONCLUSIONS Our findings show that controlled in situ laser dissection of root tissues is possible with a simple and low-cost optical set-up. We also show that, in the absence of dissection, a reduced laser light power density can provide reversible control of root growth, achieving a precise "point and shoot" method for root manipulation.
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Affiliation(s)
- Sisi Ge
- School of Science and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN UK
| | - Lionel X. Dupuy
- Neiker, Department of Conservation of Natural Resources, Berreaga 1, 48.160, Derio, Spain
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Michael P. MacDonald
- School of Science and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN UK
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Sánchez Pina MA, Gómez-Aix C, Méndez-López E, Gosalvez Bernal B, Aranda MA. Imaging Techniques to Study Plant Virus Replication and Vertical Transmission. Viruses 2021; 13:358. [PMID: 33668729 PMCID: PMC7996213 DOI: 10.3390/v13030358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
Plant viruses are obligate parasites that need to usurp plant cell metabolism in order to infect their hosts. Imaging techniques have been used for quite a long time to study plant virus-host interactions, making it possible to have major advances in the knowledge of plant virus infection cycles. The imaging techniques used to study plant-virus interactions have included light microscopy, confocal laser scanning microscopy, and scanning and transmission electron microscopies. Here, we review the use of these techniques in plant virology, illustrating recent advances in the area with examples from plant virus replication and virus plant-to-plant vertical transmission processes.
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Affiliation(s)
- María Amelia Sánchez Pina
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
| | - Cristina Gómez-Aix
- Abiopep S.L., R&D Department, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2º, 30100 Murcia, Spain;
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
| | - Blanca Gosalvez Bernal
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
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6
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Advanced microscopy techniques for revealing molecular structure of starch granules. Biophys Rev 2020; 12:105-122. [PMID: 31950343 DOI: 10.1007/s12551-020-00614-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/07/2020] [Indexed: 01/04/2023] Open
Abstract
Starch is a major source of our daily diet and it is important to understand the molecular structure that plays a significant role in its wide number of applications. In this review article, microscopic structures of starch granules from potato, corn, rice canna, tania, wheat, sweet potato, and cassava are revealed using advanced microscopic techniques. Optical microscopy depicts the size and shape, polarization microscopy shows the anisotropy properties of starch granules, scanning electron microscopy (SEM) displays surface topography, and confocal microscopy is used to observe the three-dimensional internal structure of starch granules. The crystallinity of starch granules is revealed by second harmonic generation (SHG) microscopy and atomic force microscopy (AFM) provides mechanical properties including strength, texture, and elasticity. These properties play an important role in understanding the stability of starch granules under various processing conditions like heating, enzyme degradation, and hydration and determining its applications in various industries such as food packaging and textile industries.
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Dumur T, Duncan S, Graumann K, Desset S, Randall RS, Scheid OM, Prodanov D, Tatout C, Baroux C. Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions. Nucleus 2019; 10:181-212. [PMID: 31362571 PMCID: PMC6682351 DOI: 10.1080/19491034.2019.1644592] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel.
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Affiliation(s)
- Tao Dumur
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Susan Duncan
- Norwich Research Park, Earlham Institute, Norwich, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Dimiter Prodanov
- Environment, Health and Safety, Neuroscience Research Flanders, Leuven, Belgium
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont–Ferrand, France
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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8
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Zou J, Chen G, Du F, Yuan Y, Huang X, Dong J, Xie K, Cui X, Tang Z. A general fluorescent light-up probe for staining and quantifying protein. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190580. [PMID: 31598246 PMCID: PMC6731743 DOI: 10.1098/rsos.190580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Proteins are the primary functional agents in all cellular processes, facilitating various functions such as enzymes and structure-forming or signal-transducing molecules. In this work, we report a fluorescent dye, PyMDI-Zn, which could specifically bind with proteins and provide a red-shifted fluorescent emission. The visual analysis of protein in sodium dodecyl sulfate-polyacrylamide gel electrophoresis could be realized in 5 min by using PyMDI-Zn as a light-up dye. Based on its cell penetration and low toxicity, PyMDI-Zn could also be applied to locate protein-rich regions and organelles in live cell imaging. Moreover, the direct protein quantitation can be realized based on PyMDI-Zn, providing a method of screening for food adulteration by nitrogen-rich compounds.
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Affiliation(s)
- Jiawei Zou
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Kexin Xie
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
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Baroux C, Schubert V. Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations. Methods Mol Biol 2018; 1675:537-589. [PMID: 29052212 DOI: 10.1007/978-1-4939-7318-7_31] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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10
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Visualization of BRI1 and SERK3/BAK1 Nanoclusters in Arabidopsis Roots. PLoS One 2017; 12:e0169905. [PMID: 28114413 PMCID: PMC5256950 DOI: 10.1371/journal.pone.0169905] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/23/2016] [Indexed: 01/06/2023] Open
Abstract
Brassinosteroids (BRs) are plant hormones that are perceived at the plasma membrane (PM) by the ligand binding receptor BRASSINOSTEROID-INSENSITIVE1 (BRI1) and the co-receptor SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASE 3/BRI1 ASSOCIATED KINASE 1 (SERK3/BAK1). To visualize BRI1-GFP and SERK3/BAK1-mCherry in the plane of the PM, variable-angle epifluorescence microscopy (VAEM) was employed, which allows selective illumination of a thin surface layer. VAEM revealed an inhomogeneous distribution of BRI1-GFP and SERK3/BAK1-mCherry at the PM, which we attribute to the presence of distinct nanoclusters. Neither the BRI1 nor the SERK3/BAK1 nanocluster density is affected by depletion of endogenous ligands or application of exogenous ligands. To reveal interacting populations of receptor complexes, we utilized selective-surface observation—fluorescence lifetime imaging microscopy (SSO-FLIM) for the detection of Förster resonance energy transfer (FRET). Using this approach, we observed hetero-oligomerisation of BRI1 and SERK3 in the nanoclusters, which did not change upon depletion of endogenous ligand or signal activation. Upon ligand application, however, the number of BRI1-SERK3 /BAK1 hetero-oligomers was reduced, possibly due to endocytosis of active signalling units of BRI1-SERK3/BAK1 residing in the PM. We propose that formation of nanoclusters in the plant PM is subjected to biophysical restraints, while the stoichiometry of receptors inside these nanoclusters is variable and important for signal transduction.
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11
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Celler K, Fujita M, Kawamura E, Ambrose C, Herburger K, Holzinger A, Wasteneys GO. Microtubules in Plant Cells: Strategies and Methods for Immunofluorescence, Transmission Electron Microscopy, and Live Cell Imaging. Methods Mol Biol 2016; 1365:155-84. [PMID: 26498784 DOI: 10.1007/978-1-4939-3124-8_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microtubules (MTs) are required throughout plant development for a wide variety of processes, and different strategies have evolved to visualize and analyze them. This chapter provides specific methods that can be used to analyze microtubule organization and dynamic properties in plant systems and summarizes the advantages and limitations for each technique. We outline basic methods for preparing samples for immunofluorescence labeling, including an enzyme-based permeabilization method, and a freeze-shattering method, which generates microfractures in the cell wall to provide antibodies access to cells in cuticle-laden aerial organs such as leaves. We discuss current options for live cell imaging of MTs with fluorescently tagged proteins (FPs), and provide chemical fixation, high-pressure freezing/freeze substitution, and post-fixation staining protocols for preserving MTs for transmission electron microscopy and tomography.
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Affiliation(s)
- Katherine Celler
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Miki Fujita
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Eiko Kawamura
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chris Ambrose
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Klaus Herburger
- Functional Plant Biology, Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria
| | - Andreas Holzinger
- Functional Plant Biology, Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020, Innsbruck, Austria.
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12
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Yokoo R, Hood RD, Savage DF. Live-cell imaging of cyanobacteria. PHOTOSYNTHESIS RESEARCH 2015; 126:33-46. [PMID: 25366827 DOI: 10.1007/s11120-014-0049-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Cyanobacteria are a diverse bacterial phylum whose members possess a high degree of ultrastructural organization and unique gene regulatory mechanisms. Unraveling this complexity will require the use of live-cell fluorescence microscopy, but is impeded by the inherent fluorescent background associated with light-harvesting pigments and the need to feed photosynthetic cells light. Here, we outline a roadmap for overcoming these challenges. Specifically, we show that although basic cyanobacterial biology creates challenging experimental constraints, these restrictions can be mitigated by the careful choice of fluorophores and microscope instrumentation. Many of these choices are motivated by recent successful live-cell studies. We therefore also highlight how live-cell imaging has advanced our understanding of bacterial microcompartments, circadian rhythm, and the organization and segregation of the bacterial nucleoid.
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Affiliation(s)
- Rayka Yokoo
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Rachel D Hood
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - David F Savage
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA, 94720, USA.
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13
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Calder G, Hindle C, Chan J, Shaw P. An optical imaging chamber for viewing living plant cells and tissues at high resolution for extended periods. PLANT METHODS 2015; 11:22. [PMID: 25806083 PMCID: PMC4371620 DOI: 10.1186/s13007-015-0065-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/12/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Recent developments in both microscopy and fluorescent protein technologies have made live imaging a powerful tool for the study of plant cells. However, the complications of keeping plant material alive during a long duration experiment while maintaining maximum resolution has limited the use of these methods. RESULTS Here, we describe an imaging chamber designed to overcome these limitations, which is flexible enough to support a range of sizes of plant materials. We were able use confocal microscopy to follow growth and development of plant cells and tissues over several days. The chamber design is based on a perfusion system, so that the addition of drugs and other experimental treatments are also possible. CONCLUSIONS In this article we present a design of imaging chamber that makes it possible to image plant material with high resolution for extended periods of time.
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Affiliation(s)
- Grant Calder
- Department of Cell & Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Chris Hindle
- Department of Cell & Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jordi Chan
- Department of Cell & Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Peter Shaw
- Department of Cell & Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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14
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Xia Y, Petti C, Williams MA, DeBolt S. Experimental approaches to study plant cell walls during plant-microbe interactions. FRONTIERS IN PLANT SCIENCE 2014; 5:540. [PMID: 25352855 PMCID: PMC4196508 DOI: 10.3389/fpls.2014.00540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/23/2014] [Indexed: 05/27/2023]
Abstract
Plant cell walls provide physical strength, regulate the passage of bio-molecules, and act as the first barrier of defense against biotic and abiotic stress. In addition to providing structural integrity, plant cell walls serve an important function in connecting cells to their extracellular environment by sensing and transducing signals to activate cellular responses, such as those that occur during pathogen infection. This mini review will summarize current experimental approaches used to study cell wall functions during plant-pathogen interactions. Focus will be paid to cell imaging, spectroscopic analyses, and metabolic profiling techniques.
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Affiliation(s)
| | | | | | - Seth DeBolt
- Department of Horticulture, University of KentuckyLexington, KY, USA
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15
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Model M. Intensity calibration and flat-field correction for fluorescence microscopes. CURRENT PROTOCOLS IN CYTOMETRY 2014; 68:10.14.1-10.14.10. [PMID: 24692055 DOI: 10.1002/0471142956.cy1014s68] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Standardization in fluorescence microscopy involves calibration of intensity in reproducible units and correction for spatial nonuniformity of illumination (flat-field or shading correction). Both goals can be achieved using concentrated solutions of fluorescent dyes. When a drop of a highly concentrated fluorescent dye is placed between a slide and a coverslip it produces a spatially uniform field, resistant to photobleaching and with reproducible quantum yield; it can be used as a brightness standard for wide-field and confocal microscopes. For wide-field microscopes, calibration can be further extended to absolute molecular units. This can be done by imaging a solution of known concentration and known depth; the latter can be prepared by placing a small spherical lens in a diluted solution of the same fluorophore that is used in the biological specimen.
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Affiliation(s)
- Michael Model
- Department of Biological Sciences, Kent State University, Kent, Ohio
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16
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Thomas P, Sekhar AC. Live cell imaging reveals extensive intracellular cytoplasmic colonization of banana by normally non-cultivable endophytic bacteria. AOB PLANTS 2014; 6:plu002. [PMID: 24790123 PMCID: PMC4038436 DOI: 10.1093/aobpla/plu002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/09/2013] [Indexed: 05/04/2023]
Abstract
It is generally believed that endophytic microorganisms are intercellular inhabitants present in either cultivable or non-cultivable form primarily as root colonizers. The objective of this study was to determine whether the actively mobile micro-particles observed in the intracellular matrix of fresh tissue sections of banana included endophytic bacteria. Tissue sections (50-100 µm) from apical leaf sheaths of surface-disinfected suckers (cv. Grand Naine) displayed 'Brownian motion'-reminiscent abundant motile micro-particles under bright-field and phase-contrast (×1000), which appeared similar in size and motility to the pure cultures of endophytes previously isolated from banana. Observations on callus, embryonic cells and protoplasts with intact cell wall/plasma membrane confirmed their cytoplasmic nature. The motility of these entities reduced or ceased upon tissue fixation or staining with safranin/crystal violet (0.5 % w/v), but continued uninterrupted following treatment with actin-disrupting drugs, ruling out the possibility of micro-organelles like peroxisomes. Staining with 2,3,5-triphenyl tetrazolium chloride (TTC) confirmed them to be live bacteria with similar observations after dilute safranin (0.005 %) treatment. Tissue staining with SYTO-9 coupled with epi-fluorescence or confocal laser scanning microscopy showed bacterial colonization along the peri-space between cell wall and plasma membrane initially. SYTO-9 counterstaining on TTC- or safranin-treated tissue and those subjected to enzymatic permeabilization revealed the cytoplasmic bacteria. These included organisms moving freely in the cytoplasm and those adhering to the nuclear envelope or vacuoles and the intravacuolar colonizers. The observations appeared ubiquitous to different genomes and genotypes of banana. Plating the tissue homogenate on nutrient media seldom yielded colony growth. This study, supported largely by live cell video-imaging, demonstrates enormous intracellular colonization in bananas by normally non-cultivable endophytic bacteria in two niches, namely cytoplasmic and periplasmic, designated as 'Cytobacts' and 'Peribacts', respectively. The integral intracellular association with their clonal perpetuation suggests a mutualistic relationship between endophytes and the host.
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Affiliation(s)
- Pious Thomas
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessarghatta Lake, Bangalore 560 089, India
| | - Aparna Chandra Sekhar
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessarghatta Lake, Bangalore 560 089, India
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65,000 shades of grey: use of digital image files in light microscopy. Methods Cell Biol 2014; 114:317-36. [PMID: 23931512 DOI: 10.1016/b978-0-12-407761-4.00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
Computers dominate image capture and analysis in modern light microscopy. The output of an imaging experiment is a binary coded file, called an image file, which contains the spatial, temporal and intensity information present in the sample. Understanding what comprises an image file, and how these files are generated is necessary in order to optimize the use of the digital light microscope. In this chapter, we discuss image file formats, and the various components of these files, such as bit-depth, sampling rate, color theory, and compression, from the perspective of the non-computer scientist. We also discuss the problem of proprietary file formats, and how these often are incompatible with certain types of imaging software. We present several solutions to this issue. Finally, we present the use of digital movie formats, compression routines, and provide some real world examples for optimizing the generation of digital movies.
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Palmer AJ, Ford SH, Butler SJ, Hawkins TJ, Hussey PJ, Pal R, Walton JW, Parker D. Emissive europium complexes that stain the cell walls of healthy plant cells, pollen tubes and roots. RSC Adv 2014. [DOI: 10.1039/c3ra45426f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Hornick JE, Hinchcliffe EH. It's all about the pentiums: The use, manipulation, and storage of digital microscopy imaging data for the biological sciences. Mol Reprod Dev 2014; 82:508-17. [PMID: 24375801 DOI: 10.1002/mrd.22294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/16/2013] [Indexed: 11/09/2022]
Abstract
Digital microscopy has revolutionized quantitative imaging, with binary-encoded computer files serving to capture and store imaging data sets for analysis. With the ever-present use of computers to generate and store imaging data, it becomes increasingly important to understand how these files are created, and how they can be both used and mis-used. This is a particularly important task for the biologist who may have limited background in computer science. Here we discuss some of the basic aspects of digital data storage and use, including file types, storage media, and the choice between commercial and open-source software. Often, open-source software is written by a user or group of users, and then distributed to the scientific community at large. These can be important tools, but there are some hidden costs to this freeware that we will discuss. We will also compare open-source software to commercial imaging software, which is often written for use by non-computer scientists.
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Affiliation(s)
- Jessica E Hornick
- Department of Obstetrics and Gynecology, Robert H. Lurie Cancer Center, Northwestern University School of Medicine, Chicago, Illinois
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20
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Thomas P, Reddy KM. Microscopic elucidation of abundant endophytic bacteria colonizing the cell wall–plasma membrane peri-space in the shoot-tip tissue of banana. AOB PLANTS 2013; 5:plt011. [PMCID: PMC4455319 DOI: 10.1093/aobpla/plt011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 02/05/2013] [Indexed: 05/21/2023]
Abstract
Plants are known to harbor endophytic bacteria, the organisms residing internally without imparting any apparent adverse effects on the host. Endophytes are generally known to be present in few numbers colonizing the intercellular spaces, primarily in roots. This study adopting SYTO 9 staining and live confocal imaging of fresh tissue sections from the shoot-tip region of banana, supported by transmission electron microscopy, brings out, possibly for the first time, extensive bacterial colonization in the confined cell wall – plasma membrane peri-space. The integral host-association and their abundance suggest a prominent role of endophytes in the biology of the host. This study was aimed at generating microscopic evidence of intra-tissue colonization in banana in support of the previous findings on widespread association of endophytic bacteria with the shoot tips of field-grown plants and micropropagated cultures, and to understand the extent of tissue colonization. Leaf-sheath tissue sections (∼50–100 µm) from aseptically gathered shoot tips of cv. Grand Naine were treated with Live/Dead bacterial viability kit components SYTO 9 (S9) and propidium iodide (PI) followed by epifluorescence or confocal laser scanning microscopy (CLSM). The S9, which targets live bacteria, showed abundant green-fluorescing particles along the host cell periphery in CLSM, apparently in between the plasma membrane and the cell wall. These included non-motile and occasional actively motile single bacterial cells seen in different x–y planes and z-stacks over several cell layers, with the fluorescence signal similar to that of pure cultures of banana endophytes. Propidium iodide, which stains dead bacteria, did not detect any, but post-ethanol treatment, both PI and 4′,6-diamidino-2-phenylindole detected abundant bacteria. Propidium iodide showed clear nuclear staining, as did S9 to some extent, and the fluorophores appeared to detect bacteria at the exclusion of DNA-containing plant organelles as gathered from bright-field and phase-contrast microscopy. The S9–PI staining did not work satisfactorily with formalin- or paraformaldehyde-fixed tissue. The extensive bacterial colonization in fresh tissue was further confirmed with the suckers of different cultivars, and was supported by transmission electron microscopy. This study thus provides clear microscopic evidence of the extensive endophytic bacterial inhabitation in the confined cell wall–plasma membrane peri-space in shoot tissue of banana with the organisms sharing an integral association with the host. The abundant tissue colonization suggests a possible involvement of endophytes in the biology of the host besides recognizing cell wall–plasma membrane peri-space as a major niche for plant-associated bacteria.
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Affiliation(s)
- Pious Thomas
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessarghatta Lake, Bangalore 560089, India
- Corresponding author's e-mail addresses: ,
| | - Krishna M. Reddy
- Division of Plant Pathology, Indian Institute of Horticultural Research, Hessarghatta Lake, Bangalore 560089, India
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21
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Live-Cell Imaging of Microtubules and Microtubule-Associated Proteins in Arabidopsis thaliana. Methods Cell Biol 2013. [DOI: 10.1016/b978-0-12-407757-7.00015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Domozych DS. The quest for four-dimensional imaging in plant cell biology: it's just a matter of time. ANNALS OF BOTANY 2012; 110:461-74. [PMID: 22628381 PMCID: PMC3394652 DOI: 10.1093/aob/mcs107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/04/2012] [Indexed: 05/22/2023]
Abstract
BACKGROUND Analysis of plant cell dynamics over time, or four-dimensional imaging (4-DI), represents a major goal of plant science. The ability to resolve structures in the third dimension within the cell or tissue during developmental events or in response to environmental or experimental stresses (i.e. 4-DI) is critical to our understanding of gene expression, post-expression modulations of macromolecules and sub-cellular system interactions. SCOPE Microscopy-based technologies have been profoundly integral to this type of investigation, and new and refined microscopy technologies now allow for the visualization of cell dynamics with unprecedented resolution, contrast and experimental versatility. However, certain realities of light and electron microscopy, choice of specimen and specimen preparation techniques limit the scope of readily attaining 4-DI. Today, the plant microscopist must use a combinatorial strategy whereby multiple microscopy-based investigations are used. Modern fluorescence, confocal laser scanning, transmission electron and scanning electron microscopy provide effective conduits for synthesizing data detailing live cell dynamics and highly resolved snapshots of specific cell structures that will ultimately lead to 4-DI. This review provides a synopsis of such technologies available.
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Affiliation(s)
- David S Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, NY 12866, USA.
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Howe ES, Clemente TE, Bass HW. Maize histone H2B-mCherry: a new fluorescent chromatin marker for somatic and meiotic chromosome research. DNA Cell Biol 2012; 31:925-38. [PMID: 22662764 PMCID: PMC3378959 DOI: 10.1089/dna.2011.1514] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/26/2012] [Accepted: 01/26/2012] [Indexed: 11/12/2022] Open
Abstract
Cytological studies of fluorescent proteins are rapidly yielding insights into chromatin structure and dynamics. Here we describe the production and cytological characterization of new transgenic maize lines expressing a fluorescent histone fusion protein, H2B-mCherry. The transgene is expressed under the control of the maize ubiquitin1 promoter, including its first exon and intron. Polymerase chain reaction-based genotyping and root-tip microscopy showed that most of the lines carrying the transgene also expressed it, producing bright uniform staining of nuclei. Further, plants showing expression in root tips at the seedling stage also showed expression during meiosis, late in the life cycle. Detailed high-resolution three-dimensional imaging of cells and nuclei from various somatic and meiotic cell types showed that H2B-mCherry produced remarkably clear images of chromatin and chromosome fiber morphology, as seen in somatic, male meiotic prophase, and early microgametophyte cells. H2B-mCherry also yielded distinct nucleolus staining and was shown to be compatible with fluorescence in situ hybridization. We found several instances where H2B-mCherry was superior to DAPI as a generalized chromatin stain. Our study establishes these histone H2B-mCherry lines as new biological reagents for visualizing chromatin structure, chromosome morphology, and nuclear dynamics in fixed and living cells in a model plant genetic system.
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Affiliation(s)
- Elizabeth S. Howe
- Department of Biological Science, Florida State University, Tallahassee, Florida
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida
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24
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Vizcay-Barrena G, Webb SED, Martin-Fernandez ML, Wilson ZA. Subcellular and single-molecule imaging of plant fluorescent proteins using total internal reflection fluorescence microscopy (TIRFM). JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5419-28. [PMID: 21865179 PMCID: PMC3223039 DOI: 10.1093/jxb/err212] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 05/18/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) has been proven to be an extremely powerful technique in animal cell research for generating high contrast images and dynamic protein conformation information. However, there has long been a perception that TIRFM is not feasible in plant cells because the cell wall would restrict the penetration of the evanescent field and lead to scattering of illumination. By comparative analysis of epifluorescence and TIRF in root cells, it is demonstrated that TIRFM can generate high contrast images, superior to other approaches, from intact plant cells. It is also shown that TIRF imaging is possible not only at the plasma membrane level, but also in organelles, for example the nucleus, due to the presence of the central vacuole. Importantly, it is demonstrated for the first time that this is TIRF excitation, and not TIRF-like excitation described as variable-angle epifluorescence microscopy (VAEM), and it is shown how to distinguish the two techniques in practical microscopy. These TIRF images show the highest signal-to-background ratio, and it is demonstrated that they can be used for single-molecule microscopy. Rare protein events, which would otherwise be masked by the average molecular behaviour, can therefore be detected, including the conformations and oligomerization states of interacting proteins and signalling networks in vivo. The demonstration of the application of TIRFM and single-molecule analysis to plant cells therefore opens up a new range of possibilities for plant cell imaging.
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Affiliation(s)
- Gema Vizcay-Barrena
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Stephen E. D. Webb
- Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire OX11 0QX, UK
| | - Marisa L. Martin-Fernandez
- Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire OX11 0QX, UK
| | - Zoe A. Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
- To whom correspondence should be addressed. E-mail:
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25
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Shaw SL, Lucas J. Intrabundle microtubule dynamics in the Arabidopsis cortical array. Cytoskeleton (Hoboken) 2010; 68:56-67. [PMID: 20960529 DOI: 10.1002/cm.20495] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 09/09/2010] [Accepted: 10/07/2010] [Indexed: 11/06/2022]
Abstract
We tested the general hypothesis that bundling stabilizes the dynamic properties of the constituent microtubules (MTs) in vivo. We quantified the assembly dynamics of bundled and unbundled MTs in the interphase cortical array of Arabidopsis hypocotyl cells using high dynamic range spinning disk confocal microscopy. We find no evidence that bundled MTs are stabilized against depolymerization through changes to their dynamic properties. Our observations of MT plus and minus ends indicate that both bundled and unbundled polymers undergo persistent treadmilling in this system. We conclude that the temporal persistence of MT subassemblies in the Arabidopsis cortical array is largely dependent upon recruitment or nucleation of new treadmilling MTs and not on polymer stabilization. Monte Carlo simulations suggest that small differences discovered in the dynamic properties between bundled and unbundled polymers would produce relatively small macroscopic effects on the larger MT array.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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26
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Abstract
Microtubules are required throughout plant development for a wide variety of processes, and different strategies have been evolved to visualize them. This chapter summarizes the most effective of these methods and points out potential problems and pitfalls. We outline the freeze-shattering method for immunolabeling microtubules in aerial organs such as leaves that require mechanical permeabilization, discuss current options for live cell imaging of MTs with fluorescently tagged proteins (FPs), and provide different fixation protocols for preserving MTs for transmission electron microscopy including chemical fixation, high pressure freezing/freeze substitution, and post-fixation staining procedures for transmission electron microscopy.
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Affiliation(s)
- Andreas Holzinger
- Institute of Botany, Department of Physiology and Cell Physiology, University of Innsbruck, Innsbruck, Austria
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27
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Skommer J, McGuinness D, Wlodkowic D. Self-adhesive microculture system for extended live cell imaging. Biotech Histochem 2010; 86:174-80. [DOI: 10.3109/10520290903547075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Matzke AJM, Watanabe K, van der Winden J, Naumann U, Matzke M. High frequency, cell type-specific visualization of fluorescent-tagged genomic sites in interphase and mitotic cells of living Arabidopsis plants. PLANT METHODS 2010; 6:2. [PMID: 20148117 PMCID: PMC2820019 DOI: 10.1186/1746-4811-6-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 01/19/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND Interphase chromosome organization and dynamics can be studied in living cells using fluorescent tagging techniques that exploit bacterial operator/repressor systems and auto-fluorescent proteins. A nuclear-localized Repressor Protein-Fluorescent Protein (RP-FP) fusion protein binds to operator repeats integrated as transgene arrays at defined locations in the genome. Under a fluorescence microscope, the tagged sites appear as bright fluorescent dots in living cells. This technique has been used successfully in plants, but is often hampered by low expression of genes encoding RP-FP fusion proteins, perhaps owing to one or more gene silencing mechanisms that are prevalent in plant cells. RESULTS We used two approaches to overcome this problem. First, we tested mutations in four factors involved in different types of gene silencing and/or epigenetic modifications for their effects on nuclear fluorescence. Only mutations in DDM1, a chromatin remodelling ATPase involved in repeat-induced heterochromatin formation and DNA methylation, released silencing of the RP-FP fusion protein. This result suggested that the operator repeats can trigger silencing of the adjacent gene encoding the RP-FP fusion protein. In the second approach, we transformed the tagged lines with a second T-DNA encoding the RP-FP fusion protein but lacking operator repeats. This strategy avoided operator repeat-induced gene silencing and increased the number of interphase nuclei displaying fluorescent dots. In a further extension of the technique, we show that green fluorescent-tagged sites can be visualized on moving mitotic chromosomes stained with red fluorescent-labelled histone H2B. CONCLUSIONS The results illustrate the propensity of operator repeat arrays to form heterochromatin that can silence the neighbouring gene encoding the RP-FP fusion protein. Supplying the RP-FP fusion protein in trans from a second T-DNA largely alleviates this problem. Depending on the promoter used to drive expression of the RP-FP fusion protein gene, the fluorescent tagged sites can be visualized at high frequency in different cell types. The ability to observe fluorescent dots on both interphase and mitotic chromosomes allows tagged sites to be tracked throughout the cell cycle. These improvements enhance the versatility of the fluorescent tagging technique for future studies of chromosome arrangement and dynamics in living plants.
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Affiliation(s)
- Antonius JM Matzke
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Koichi Watanabe
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Correnstrasse 3, D-O6466 Gatersleben, Germany
| | - Johannes van der Winden
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Ulf Naumann
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Marjori Matzke
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
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Guo YH, Yu YP, Wang D, Wu CA, Yang GD, Huang JG, Zheng CC. GhZFP1, a novel CCCH-type zinc finger protein from cotton, enhances salt stress tolerance and fungal disease resistance in transgenic tobacco by interacting with GZIRD21A and GZIPR5. THE NEW PHYTOLOGIST 2009; 183:62-75. [PMID: 19402879 DOI: 10.1111/j.1469-8137.2009.02838.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
* Zinc finger proteins are a superfamily involved in many aspects of plant growth and development. However, CCCH-type zinc finger proteins involved in plant stress tolerance are poorly understood. * A cDNA clone designated Gossypium hirsutum zinc finger protein 1 (GhZFP1), which encodes a novel CCCH-type zinc finger protein, was isolated from a salt-induced cotton (G. hirsutum) cDNA library using differential hybridization screening and further studied in transgenic tobacco Nicotiana tabacum cv. NC89. Using yeast two-hybrid screening (Y2H), proteins GZIRD21A (GhZFP1 interacting and responsive to dehydration protein 21A) and GZIPR5 (GhZFP1 interacting and pathogenesis-related protein 5), which interacted with GhZFP1, were isolated. * GhZFP1 contains two typical zinc finger motifs (Cx8Cx5Cx3H and Cx5Cx4Cx3H), a putative nuclear export sequence (NES) and a potential nuclear localization signal (NLS). Transient expression analysis using a GhZFP1::GFP fusion gene in onion epidermal cells indicated a nuclear localization for GhZFP1. RNA blot analysis showed that the GhZFP1 transcript was induced by salt (NaCl), drought and salicylic acid (SA). The regions in GhZFP1 that interact with GZIRD21A and GZIPR5 were identified using truncation mutations. * Overexpression of GhZFP1 in transgenic tobacco enhanced tolerance to salt stress and resistance to Rhizoctonia solani. Therefore, it appears that GhZFP1 might be involved as an important regulator in plant responses to abiotic and biotic stresses.
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Affiliation(s)
- Ying-Hui Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yue-Ping Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Dong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Chang-Ai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Guo-Dong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Jin-Guang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Cheng-Chao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
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30
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Silicone-urethane adhesive for improved coverslip mounting and leak-free preparation of living cell observation chambers. Biotechniques 2009; 46:225-7. [DOI: 10.2144/000113071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Using a combination of silicone and urethane resin, we established a rapid technique for preparing living specimens for microscopy. One major advantage of this technique is that the coverslip is rigidly attached and does not detach during handling. As a result, it is possible to continuously observe living cells at high magnification and resolution using an oil immersion objective. Another advantage is that living cells are quickly confined to the space between the glass slide and coverslip, protecting them from environmental changes, which can cause serious effects on cell function and morphology. Moreover, high-resolution observations of real-time responses of cells are possible, using the combination of the mounting technique and a simple flow chamber.
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Abstract
Reporter genes have been widely used in plant molecular biology, typically to discern patterns of gene expression, but also as markers of transformed cells during stable transformation procedures.The ideal marker gene would be expected to display characteristics such as ease and cheapness of use, lack of toxicity, and robustness; and the most commonly used ones--GUS, GFP, LUC, and C1+R/B (anthocyanin accumulation) exhibit most if not all of these properties. Each, however, differs in potentially important ways, and before deciding which to use it is important to consider carefully your particular set of experiments and the plant tissue you will be using. In this chapter, I will introduce each marker, outline protocols for their use, and discuss their strengths and weaknesses.
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Affiliation(s)
- Alison Huttly
- Department of Plant Sciences, Rothamsted Research, Centre for Crop Genetic Improvement, Harpenden, Hertfordshire, UK
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32
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Lalonde S, Ehrhardt DW, Loqué D, Chen J, Rhee SY, Frommer WB. Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 53:610-635. [PMID: 18269572 DOI: 10.1111/j.1365-313x.2007.03332.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Homotypic and heterotypic protein interactions are crucial for all levels of cellular function, including architecture, regulation, metabolism, and signaling. Therefore, protein interaction maps represent essential components of post-genomic toolkits needed for understanding biological processes at a systems level. Over the past decade, a wide variety of methods have been developed to detect, analyze, and quantify protein interactions, including surface plasmon resonance spectroscopy, NMR, yeast two-hybrid screens, peptide tagging combined with mass spectrometry and fluorescence-based technologies. Fluorescence techniques range from co-localization of tags, which may be limited by the optical resolution of the microscope, to fluorescence resonance energy transfer-based methods that have molecular resolution and can also report on the dynamics and localization of the interactions within a cell. Proteins interact via highly evolved complementary surfaces with affinities that can vary over many orders of magnitude. Some of the techniques described in this review, such as surface plasmon resonance, provide detailed information on physical properties of these interactions, while others, such as two-hybrid techniques and mass spectrometry, are amenable to high-throughput analysis using robotics. In addition to providing an overview of these methods, this review emphasizes techniques that can be applied to determine interactions involving membrane proteins, including the split ubiquitin system and fluorescence-based technologies for characterizing hits obtained with high-throughput approaches. Mass spectrometry-based methods are covered by a review by Miernyk and Thelen (2008; this issue, pp. 597-609). In addition, we discuss the use of interaction data to construct interaction networks and as the basis for the exciting possibility of using to predict interaction surfaces.
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Affiliation(s)
- Sylvie Lalonde
- Carnegie Institution, 260 Panama Street, Stanford, CA 94305, USA.
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33
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Nelson BK, Cai X, Nebenführ A. A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:1126-36. [PMID: 17666025 DOI: 10.1111/j.1365-313x.2007.03212.x] [Citation(s) in RCA: 1457] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Genome sequencing has resulted in the identification of a large number of uncharacterized genes with unknown functions. It is widely recognized that determination of the intracellular localization of the encoded proteins may aid in identifying their functions. To facilitate these localization experiments, we have generated a series of fluorescent organelle markers based on well-established targeting sequences that can be used for co-localization studies. In particular, this organelle marker set contains indicators for the endoplasmic reticulum, the Golgi apparatus, the tonoplast, peroxisomes, mitochondria, plastids and the plasma membrane. All markers were generated with four different fluorescent proteins (FP) (green, cyan, yellow or red FPs) in two different binary plasmids for kanamycin or glufosinate selection, respectively, to allow for flexible combinations. The labeled organelles displayed characteristic morphologies consistent with previous descriptions that could be used for their positive identification. Determination of the intracellular distribution of three previously uncharacterized proteins demonstrated the usefulness of the markers in testing predicted subcellular localizations. This organelle marker set should be a valuable resource for the plant community for such co-localization studies. In addition, the Arabidopsis organelle marker lines can also be employed in plant cell biology teaching labs to demonstrate the distribution and dynamics of these organelles.
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Affiliation(s)
- Brook K Nelson
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996-0840, USA
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Stark M, Manz B, Ehlers A, Küppers M, Riemann I, Volke F, Siebert U, Weschke W, König K. Multiparametric high-resolution imaging of barley embryos by multiphoton microscopy and magnetic resonance micro-imaging. Microsc Res Tech 2007; 70:426-32. [PMID: 17380495 DOI: 10.1002/jemt.20426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nonlinear optical microscopy and magnetic resonance imaging (MRI) address different properties of the sample and operate on different geometrical scales. MRI maps density and mobility of molecules tracking specific molecular signatures. Multiphoton imaging profits from the nonlinear absorption of light in the focus of a femtosecond laser source stimulating the autofluorescence of biomolecules. As this effect relies on a high light intensity, the accessible field of view is limited, but the resolution is very high (a few hundred nanometers). Here, we aim to link the different accessible scales and properties addressed in the different techniques to obtain a synoptic view. As model specimen we studied embryos of barley. Multiphoton stimulated autofluorescence images and images of second harmonic generation are achieved even down to low magnification (10x), low numerical aperture (N.A. 0.25) conditions. The overview images allowed morphological assignments and fluorescence lifetime imaging provides further information to identify accumulation of endogenous fluorophores. The second, complementary contribution from high-resolution MR images provides a 3D model and shows the embedding of the embryo in the grain. Images of the proton density were acquired using a standard 3D spin-echo imaging pulse sequence. Details directly comparable to the low magnification optical data are visible. Eventually, passing from the MR images of the whole grain via low magnification to high resolution autofluorescence data bridges the scale barrier, and might provide the possibility to trace transport and accumulation of, e.g., nutrients from large structure of the plant to the (sub-) cellular level.
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Affiliation(s)
- Martin Stark
- Fraunhofer Institute of Biomedical Technology, IBMT, Ensheimerstrasse 48, 66386 St. Ingbert, Germany.
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Buchner O, Lütz C, Holzinger A. Design and construction of a new temperature-controlled chamber for light and confocal microscopy under monitored conditions: biological application for plant samples. J Microsc 2007; 225:183-91. [PMID: 17359253 DOI: 10.1111/j.1365-2818.2007.01730.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new light microscope-temperature-controlled chamber (LM-TCC) has been constructed. The special feature of the light microscope-temperature-controlled chamber is the Peltier-element temperature control of a specimen holder for biological samples, with a volume capacity of 1 mL. This system has marked advantages when compared to other approaches for temperature-controlled microscopy. It works in a temperature range of -10 degrees C to +95 degrees C with an accuracy of +/-0.1 degrees C in the stationary phase. The light microscope-temperature-controlled chamber allows rapid temperature shift rates. A maximum heating rate of 12.9 degrees C min(-1) and a maximum cooling rate of 6.0 degrees C min(-1) are achieved with minimized overshoots (<or=1.9 degrees C). This machinery operates at low cost and external coolants are not required. Especially with samples absorbing irradiation strongly, temperature control during microscopy is necessary to avoid overheating of samples. For example, leaf segments of Ficaria verna exposed to 4500 micromol photons m(-2) s(-1) in a standard microscopic preparation show a temperature increase (deltaT) of 18.0 degrees C, whereas in the light microscope-temperature-controlled chamber this is reduced to 4 degrees C. The kinetics of microscope-light induced deltaT are described and infrared thermography demonstrates the dissipation of the temperature. Chloroplasts of the cold adapted plant Ranunculus glacialis show the tendency to form stroma-filled protrusions in relation to the exposure temperature. The relative number of chloroplasts with protrusions is reduced at 5 degrees C when compared to 25 degrees C. This effect is reversible. The new light microscope-temperature-controlled chamber will be useful in a wide range of biological applications where a rapid change of temperature during microscopic observations is necessary or has to be avoided allowing a simulation of ecologically relevant temperature scenarios.
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Affiliation(s)
- O Buchner
- University of Innsbruck, Institute of Botany, Sternwartestrasse 15, A-6020 Innsbruck, Austria
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Sawchuk MG, Head P, Donner TJ, Scarpella E. Time-lapse imaging of Arabidopsis leaf development shows dynamic patterns of procambium formation. THE NEW PHYTOLOGIST 2007; 176:560-571. [PMID: 17953541 DOI: 10.1111/j.1469-8137.2007.02193.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The principles underlying the formation of leaf veins have long intrigued developmental biologists. In leaves, networks of vascular precursor procambial cells emerge from seemingly homogeneous subepidermal tissue through the selection of anatomically inconspicuous preprocambial cells. Understanding dynamics of procambium formation has been hampered by the difficulty of observing the process in vivo. Here we present a live-imaging technique that allows visual access to complex events occurring in developing leaves. We combined this method with stage-specific fluorescent markers in Arabidopsis (Arabidopsis thaliana) to visualize preprocambial strand formation and procambium differentiation during the undisturbed course of development and upon defined perturbations of vein ontogeny. Under all experimental conditions, we observed extension, termination and fusion of preprocambial strands and simultaneous initiation of procambium differentiation along entire individual veins. Our findings strongly suggest that progressiveness of preprocambial strand formation and simultaneity of procambium differentiation represent inherent properties of the mechanism underlying vein formation.
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Affiliation(s)
| | | | - Tyler J Donner
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB, T6G 2E9 Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB, T6G 2E9 Canada
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Koh S, Somerville S. Show and tell: cell biology of pathogen invasion. CURRENT OPINION IN PLANT BIOLOGY 2006; 9:406-13. [PMID: 16714141 DOI: 10.1016/j.pbi.2006.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 05/03/2006] [Indexed: 05/09/2023]
Abstract
Because the initial stages of pathogen invasion are often confined to a limited number of host cells, measures of host responses that are averaged over attacked and non-attacked cells provide an unsatisfactory view of these events. To identify the earliest and often transient responses to pathogen attack, there is considerable interest in monitoring the subcellular events that occur specifically in living host cells. Recent improvements in live-cell imaging using fluorescent-tagged markers have expanded the scope of the experiments that can be performed. Changes in the subcellular distribution of organelles and of fluorescently tagged proteins can be monitored in real time in living tissues during pathogen attack, and the dynamic nature of such changes across space and over time can be determined. The application of these sensitive imaging methods has extended earlier observations, made with Nomarski microscopy or inferred from static transmission electron micrographs, about the focal accumulation of subcellular organelles at sites of pathogen attack. In addition, recent experiments have demonstrated the focused accumulation and interaction of specific plant proteins at penetration sites, opening a new window on early host responses and raising questions about the underlying plant processes that sense and direct this marshalling of host resources to block pathogen entry.
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Affiliation(s)
- Serry Koh
- Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, California 94305, USA
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