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Kadlof M, Banecki K, Chiliński M, Plewczynski D. Chromatin image-driven modelling. Methods 2024; 226:54-60. [PMID: 38636797 DOI: 10.1016/j.ymeth.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/13/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
The challenge of modelling the spatial conformation of chromatin remains an open problem. While multiple data-driven approaches have been proposed, each has limitations. This work introduces two image-driven modelling methods based on the Molecular Dynamics Flexible Fitting (MDFF) approach: the force method and the correlational method. Both methods have already been used successfully in protein modelling. We propose a novel way to employ them for building chromatin models directly from 3D images. This approach is termed image-driven modelling. Additionally, we introduce the initial structure generator, a tool designed to generate optimal starting structures for the proposed algorithms. The methods are versatile and can be applied to various data types, with minor modifications to accommodate new generation imaging techniques.
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Affiliation(s)
- Michał Kadlof
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.
| | - Krzysztof Banecki
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland; Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Mateusz Chiliński
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland; Centre of New Technologies, University of Warsaw, Warsaw, Poland; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dariusz Plewczynski
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland; Centre of New Technologies, University of Warsaw, Warsaw, Poland
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2
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Doležalová A, Beránková D, Koláčková V, Hřibová E. Insight into chromatin compaction and spatial organization in rice interphase nuclei. FRONTIERS IN PLANT SCIENCE 2024; 15:1358760. [PMID: 38863533 PMCID: PMC11165205 DOI: 10.3389/fpls.2024.1358760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Chromatin organization and its interactions are essential for biological processes, such as DNA repair, transcription, and DNA replication. Detailed cytogenetics data on chromatin conformation, and the arrangement and mutual positioning of chromosome territories in interphase nuclei are still widely missing in plants. In this study, level of chromatin condensation in interphase nuclei of rice (Oryza sativa) and the distribution of chromosome territories (CTs) were analyzed. Super-resolution, stimulated emission depletion (STED) microscopy showed different levels of chromatin condensation in leaf and root interphase nuclei. 3D immuno-FISH experiments with painting probes specific to chromosomes 9 and 2 were conducted to investigate their spatial distribution in root and leaf nuclei. Six different configurations of chromosome territories, including their complete association, weak association, and complete separation, were observed in root meristematic nuclei, and four configurations were observed in leaf nuclei. The volume of CTs and frequency of their association varied between the tissue types. The frequency of association of CTs specific to chromosome 9, containing NOR region, is also affected by the activity of the 45S rDNA locus. Our data suggested that the arrangement of chromosomes in the nucleus is connected with the position and the size of the nucleolus.
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Affiliation(s)
| | | | | | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Science, Centre of Plants Structural and Functional Genomics, Olomouc, Czechia
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3
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Field N, Graumann K. Use of Super-Resolution Live Cell Imaging to Distinguish Endoplasmic Reticulum: Nuclear Envelope Subcellular Localization. Methods Mol Biol 2024; 2772:285-290. [PMID: 38411822 DOI: 10.1007/978-1-0716-3710-4_21] [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: 02/28/2024]
Abstract
A distinguishing feature of eukaryotes is the presence of a nuclear envelope (NE) and endomembrane system. The NE is a double-membrane system that surrounds chromatin and is continuous with the endoplasmic reticulum (ER). This interface is crucial in various processes such as calcium signaling and ER-associated degradation. The outer nuclear membrane and ER share a multitude of proteins although some are only functional in one domain, whereas the inner nuclear membrane has its own unique proteome. Until recently, it was not possible to distinguish between the inner and outer nuclear membranes as well as perinuclear ER using light microscopy - only electron microscopy was suitable for this. Now, however, using super-resolution live cell imaging, this can be achieved while still observing protein and membrane dynamics in real time. The protocols described here will allow researchers to determine subcellular localization of potential NE/ER proteins in live plant cells, helping to gain new insights into protein functionality.
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Affiliation(s)
- Nadine Field
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
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4
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Kikuchi S, Sakamoto T, Matsunaga S, Iwamoto A. Novel whole-mount FISH analysis for intact root of Arabidopsis thaliana with spatial reference to 3D visualization. JOURNAL OF PLANT RESEARCH 2023; 136:423-428. [PMID: 36719512 DOI: 10.1007/s10265-023-01438-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Whole-mount fluorescent in situ hybridization (WM-FISH) is an effective tool to observe chromosome behavior in tissues or organs. However, it is difficult to obtain a precise spatial profile of fluorescent signals in roots using conventional WM-FISH mainly because of the severe damage caused during the processing. To address this problem, we established a novel WM-FISH analysis for intact roots of Arabidopsis thaliana and successfully obtained a precise spatial profile of nuclear size and centromere signals. The two main improvements in the novel WM-FISH analysis are: (i) hybridization was performed directly on MAS-coated glass slides covered with silicon wells and (ii) conditions for enzyme treatment were optimized (37 °C, 45 s). After the WM-FISH using a centromere probe, we analyzed the results by 3D data processing to quantify the nuclear volume and number of centromere signals of the obtained cortical cell files and determined the position of each nucleus in intact roots. Then we plotted the nuclear volume and number of centromere signals versus distance from the quiescent center to evaluate the precise spatial profile of each parameter.
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Affiliation(s)
- Suzuka Kikuchi
- Department of Biological Sciences, Graduate School of Science, Kanagawa University, 2946, 259-1293, Tsuchiya, Hiratsuka, Kanagawa, Japan.
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, 278-8510, Noda, Chiba, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, 277-8561, Kashiwa, Chiba, Japan
| | - Akitoshi Iwamoto
- Department of Biological Sciences, Graduate School of Science, Kanagawa University, 2946, 259-1293, Tsuchiya, Hiratsuka, Kanagawa, Japan
- Department of Biological Science, Faculty of Science, Kanagawa University, 2946, 259-1293, Tsuchiya, Hiratsuka, Kanagawa, Japan
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5
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Duncan S, Johansson HE, Ding Y. Reference genes for quantitative Arabidopsis single molecule RNA fluorescence in situ hybridization. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2405-2415. [PMID: 36579724 PMCID: PMC10082928 DOI: 10.1093/jxb/erac521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 06/06/2023]
Abstract
Subcellular mRNA quantities and spatial distributions are fundamental for driving gene regulatory programmes. Single molecule RNA fluorescence in situ hybridization (smFISH) uses fluorescent probes to label individual mRNA molecules, thereby facilitating both localization and quantitative studies. Validated reference mRNAs function as positive controls and are required for calibration. Here we present selection criteria for the first set of Arabidopsis smFISH reference genes. Following sequence and transcript data assessments, four mRNA probe sets were selected for imaging. Transcript counts per cell, correlations with cell size, and corrected fluorescence intensities were all calculated for comparison. In addition to validating reference probe sets, we present sample preparation steps that can retain green fluorescent protein fluorescence, thereby providing a method for simultaneous RNA and protein detection. In summary, our reference gene analyses, modified protocol, and simplified quantification method together provide a firm foundation for future quantitative single molecule RNA studies in Arabidopsis root apical meristem cells.
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Affiliation(s)
| | - Hans E Johansson
- LGC Biosearch Technologies, 2199 S. McDowell Blvd, Petaluma, CA 94954, USA
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich, UK
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6
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Planchette AL, Schmidt C, Burri O, Gomez de Agüero M, Radenovic A, Mylonas A, Extermann J. Optical imaging of the small intestine immune compartment across scales. Commun Biol 2023; 6:352. [PMID: 37002381 PMCID: PMC10066397 DOI: 10.1038/s42003-023-04642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 02/28/2023] [Indexed: 04/03/2023] Open
Abstract
The limitations of 2D microscopy constrain our ability to observe and understand tissue-wide networks that are, by nature, 3-dimensional. Optical projection tomography (OPT) enables the acquisition of large volumes (ranging from micrometres to centimetres) in various tissues. We present a multi-modal workflow for the characterization of both structural and quantitative parameters of the mouse small intestine. As proof of principle, we evidence its applicability for imaging the mouse intestinal immune compartment and surrounding mucosal structures. We quantify the volumetric size and spatial distribution of Isolated Lymphoid Follicles (ILFs) and quantify the density of villi throughout centimetre-long segments of intestine. Furthermore, we exhibit the age and microbiota dependence for ILF development, and leverage a technique that we call reverse-OPT for identifying and homing in on regions of interest. Several quantification capabilities are displayed, including villous density in the autofluorescent channel and the size and spatial distribution of the signal of interest at millimetre-scale volumes. The concatenation of 3D imaging with reverse-OPT and high-resolution 2D imaging allows accurate localisation of ROIs and adds value to interpretations made in 3D. Importantly, OPT may be used to identify sparsely-distributed regions of interest in large volumes whilst retaining compatibility with high-resolution microscopy modalities, including confocal microscopy. We believe this pipeline to be approachable for a wide-range of specialties, and to provide a new method for characterisation of the mouse intestinal immune compartment.
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Affiliation(s)
- Arielle Louise Planchette
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Cédric Schmidt
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
| | - Olivier Burri
- BioImaging & Optics Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Mercedes Gomez de Agüero
- Host-microbial interactions group, Institute of Systems Immunology, Max Planck research group, University of Würzburg, Würzburg, Germany
- Mucosal Immunology Group, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Alessio Mylonas
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Jérôme Extermann
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
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7
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Jiang Y, Ding P. Calcium signaling in plant immunity: a spatiotemporally controlled symphony. TRENDS IN PLANT SCIENCE 2023; 28:74-89. [PMID: 36504136 DOI: 10.1016/j.tplants.2022.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Calcium ions (Ca2+) are prominent intracellular messengers in all eukaryotic cells. Recent studies have emphasized the crucial roles of Ca2+ in plant immunity. Here, we review the latest progress on the spatiotemporal control of Ca2+ function in plant immunity. We discuss discoveries of how Ca2+ influx is triggered upon the activation of immune receptors, how Ca2+-permeable channels are activated, how Ca2+ signals are decoded inside plant cells, and how these signals are switched off. Despite recent advances, many open questions remain and we highlight the existing toolkit and the new technologies to address the outstanding questions of Ca2+ signaling in plant immunity.
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Affiliation(s)
- Yuxiang Jiang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Pingtao Ding
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333, BE, The Netherlands.
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8
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Randall RS, Jourdain C, Nowicka A, Kaduchová K, Kubová M, Ayoub MA, Schubert V, Tatout C, Colas I, Kalyanikrishna, Desset S, Mermet S, Boulaflous-Stevens A, Kubalová I, Mandáková T, Heckmann S, Lysak MA, Panatta M, Santoro R, Schubert D, Pecinka A, Routh D, Baroux C. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus 2022; 13:277-299. [PMID: 36447428 PMCID: PMC9754023 DOI: 10.1080/19491034.2022.2144013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
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Affiliation(s)
- Ricardo S Randall
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | | | - Anna Nowicka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Kateřina Kaduchová
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Michaela Kubová
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Mohammad A. Ayoub
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Christophe Tatout
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Isabelle Colas
- The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, Scotland UK
| | | | - Sophie Desset
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Sarah Mermet
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Aurélia Boulaflous-Stevens
- Institut Génétique, Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, 63001Clermont-Ferrand, France
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC) and Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466Seeland, Germany
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zürich, Zürich, Switzerland
| | | | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany, v. v. i. (IEB), Olomouc, Czech Republic
| | - Devin Routh
- Service and Support for Science IT (S3IT), Universität Zürich, Zürich, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland,CONTACT Célia Baroux Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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Jiang X, Pees T, Reinhold-Hurek B. Deep-learning-based removal of autofluorescence and fluorescence quantification in plant-colonizing bacteria in vivo. THE NEW PHYTOLOGIST 2022; 235:2481-2495. [PMID: 35752974 DOI: 10.1111/nph.18344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Fluorescence microscopy is common in bacteria-plant interaction studies. However, strong autofluorescence from plant tissues impedes in vivo studies on endophytes tagged with fluorescent proteins. To solve this problem, we developed a deep-learning-based approach to eliminate plant autofluorescence from fluorescence microscopy images, tested for the model endophyte Azoarcus olearius BH72 colonizing Oryza sativa roots. Micrographs from three channels (tdTomato for gene expression, green fluorescent protein (GFP) and AutoFluorescence (AF)) were processed by a neural network based approach, generating images that simulate the background autofluorescence in the tdTomato channel. After subtracting the model-generated signals from each pixel in the genuine channel, the autofluorescence in the tdTomato channel was greatly reduced or even removed. The deep-learning-based approach can be applied for fluorescence detection and quantification, exemplified by a weakly expressed, a cell-density modulated and a nitrogen-fixation gene in A. olearius. A transcriptional nifH::tdTomato fusion demonstrated stronger induction of nif genes inside roots than outside, suggesting extension of the rhizosphere effect for diazotrophs into the endorhizosphere. The pre-trained convolutional neural network model is easily applied to process other images of the same plant tissues with the same settings. This study showed the high potential of deep-learning-based approaches in image processing. With proper training data and strategies, autofluorescence in other tissues or materials can be removed for broad applications.
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Affiliation(s)
- Xun Jiang
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
| | - Tobias Pees
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
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10
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Junghans M, John F, Cihankaya H, Schliebs D, Winklhofer KF, Bader V, Matschke J, Theiss C, Matschke V. ROS scavengers decrease γH2ax spots in motor neuronal nuclei of ALS model mice in vitro. Front Cell Neurosci 2022; 16:963169. [PMID: 36119129 PMCID: PMC9470831 DOI: 10.3389/fncel.2022.963169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/08/2022] [Indexed: 12/05/2022] Open
Abstract
Background: Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease characterized by the loss of motor neurons in cerebral cortex, brainstem and spinal cord. Numerous studies have demonstrated signs of oxidative stress in postmortem neuronal tissue, cerebrospinal fluid, plasma and urine of ALS patients, without focusing on the specific processes within motor neurons. Thus, we aimed to investigate the relevance of reactive oxygen species (ROS) detoxification mechanisms and its consequences on the formation of toxic/lethal DNA double strand breaks (DSBs) in the ALS model of the Wobbler mouse. Methods: Live cell imaging in dissociated motor neuronal cultures was used to investigate the production of ROS using Dihydroethidium (DHE). The expression levels of ROS detoxifying molecules were investigated by qPCR as well as Western blots. Furthermore, the expression levels of DNA damage response proteins p53bp1 and H2ax were investigated using qPCR and immunofluorescence staining. Proof-of-principle experiments using ROS scavengers were performed in vitro to decipher the influence of ROS on the formation of DNA double strand breaks quantifying the γH2ax spots formation. Results: Here, we verified an elevated ROS-level in spinal motor neurons of symptomatic Wobbler mice in vitro. As a result, an increased number of DNA damage response proteins p53bp1 and γH2ax in dissociated motor neurons of the spinal cord of Wobbler mice was observed. Furthermore, we found a significantly altered expression of several antioxidant molecules in the spinal cord of Wobbler mice, suggesting a deficit in ROS detoxification mechanisms. This hypothesis could be verified by using ROS scavenger molecules in vitro to reduce the number of γH2ax foci in dissociated motor neurons and thus counteract the harmful effects of ROS. Conclusion: Our data indicate that maintenance of redox homeostasis may play a key role in the therapy of the neurodegenerative disease ALS. Our results underline a necessity for multimodal treatment approaches to prolong the average lifespan of motor neurons and thus slow down the progression of the disease, since a focused intervention in one pathomechanism seems to be insufficient in ALS therapy.
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Affiliation(s)
- Maya Junghans
- Department of Cytology, Institute of Anatomy, Ruhr University Bochum, Bochum, Germany
| | - Felix John
- Department of Cytology, Institute of Anatomy, Ruhr University Bochum, Bochum, Germany
| | - Hilal Cihankaya
- Department of Cytology, Institute of Anatomy, Ruhr University Bochum, Bochum, Germany
| | - Daniel Schliebs
- Department of Cytology, Institute of Anatomy, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F. Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Cluster of Excellence RESOLV, Bochum, Germany
| | - Verian Bader
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Johann Matschke
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Carsten Theiss
- Department of Cytology, Institute of Anatomy, Ruhr University Bochum, Bochum, Germany
| | - Veronika Matschke
- Department of Cytology, Institute of Anatomy, Ruhr University Bochum, Bochum, Germany
- *Correspondence: Veronika Matschke
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Guo Y, Krupa O, Stein J, Wu G, Krishnamurthy A. SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1920-1932. [PMID: 34133284 PMCID: PMC8924707 DOI: 10.1109/tcbb.2021.3089608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Image-based cell counting is a fundamental yet challenging task with wide applications in biological research. In this paper, we propose a novel unified deep network framework designed to solve this problem for various cell types in both 2D and 3D images. Specifically, we first propose SAU-Net for cell counting by extending the segmentation network U-Net with a Self-Attention module. Second, we design an extension of Batch Normalization (BN) to facilitate the training process for small datasets. In addition, a new 3D benchmark dataset based on the existing mouse blastocyst (MBC) dataset is developed and released to the community. Our SAU-Net achieves state-of-the-art results on four benchmark 2D datasets - synthetic fluorescence microscopy (VGG) dataset, Modified Bone Marrow (MBM) dataset, human subcutaneous adipose tissue (ADI) dataset, and Dublin Cell Counting (DCC) dataset, and the new 3D dataset, MBC. The BN extension is validated using extensive experiments on the 2D datasets, since GPU memory constraints preclude use of 3D datasets. The source code is available at https://github.com/mzlr/sau-net.
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12
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Domb K, Wang N, Hummel G, Liu C. Spatial Features and Functional Implications of Plant 3D Genome Organization. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:173-200. [PMID: 35130445 DOI: 10.1146/annurev-arplant-102720-022810] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The advent of high-throughput sequencing-based methods for chromatin conformation, accessibility, and immunoprecipitation assays has been a turning point in 3D genomics. Altogether, these new tools have been pushing upward the interpretation of pioneer cytogenetic evidence for a higher order in chromatin packing. Here, we review the latest development in our understanding of plant spatial genome structures and different levels of organization and discuss their functional implications. Then, we spotlight the complexity of organellar (i.e., mitochondria and plastids) genomes and discuss their 3D packing into nucleoids. Finally, we propose unaddressed research axes to investigate functional links between chromatin-like dynamics and transcriptional regulation within organellar nucleoids.
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Affiliation(s)
- Katherine Domb
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Nan Wang
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Guillaume Hummel
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
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13
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Tatout C, Mougeot G, Parry G, Baroux C, Pradillo M, Evans D. The INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) Academy: a community resource for plant science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1926-1933. [PMID: 35090020 PMCID: PMC8982392 DOI: 10.1093/jxb/erac005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
This Community Resource paper introduces the range of materials developed by the INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) COST Action made available through the INDEPTH Academy. Recent rapid growth in understanding of the significance of epigenetic controls in plant and crop science has led to a need for shared, high-quality resources, standardization of protocols, and repositories for open access data. The INDEPTH Academy provides a range of masterclass tutorials, standardized protocols, and teaching webinars, together with a rapidly developing repository to support imaging and spatial analysis of the nucleus and deep learning for automated analysis. These resources were developed partly as a response to the COVID-19 pandemic, but also driven by needs and opportunities identified by the INDEPTH community of ~200 researchers in 80 laboratories from 32 countries. This community report outlines the resources produced and how they will be extended beyond the INDEPTH project, but also aims to encourage the wider community to engage with epigenetics and nuclear structure by accessing these resources.
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Affiliation(s)
- Christophe Tatout
- Université Clermont Auvergne, CNRS, INSERM, GReD Clermont-Ferrand, France
| | - Guillaume Mougeot
- Université Clermont Auvergne, CNRS, INSERM, GReD Clermont-Ferrand, France
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Geraint Parry
- GARNet, Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Arabidopsis Events UK, 13 Mayhurst Ave, Woking GU22 8DE, UK
| | - Célia Baroux
- Zürich-Basel Plant Science Center, Department for Plant and Microbial Biology, University of Zürich, Switzerland
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - David Evans
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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14
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Melanthota SK, Gopal D, Chakrabarti S, Kashyap AA, Radhakrishnan R, Mazumder N. Deep learning-based image processing in optical microscopy. Biophys Rev 2022; 14:463-481. [PMID: 35528030 PMCID: PMC9043085 DOI: 10.1007/s12551-022-00949-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
Optical microscopy has emerged as a key driver of fundamental research since it provides the ability to probe into imperceptible structures in the biomedical world. For the detailed investigation of samples, a high-resolution image with enhanced contrast and minimal damage is preferred. To achieve this, an automated image analysis method is preferable over manual analysis in terms of both speed of acquisition and reduced error accumulation. In this regard, deep learning (DL)-based image processing can be highly beneficial. The review summarises and critiques the use of DL in image processing for the data collected using various optical microscopic techniques. In tandem with optical microscopy, DL has already found applications in various problems related to image classification and segmentation. It has also performed well in enhancing image resolution in smartphone-based microscopy, which in turn enablse crucial medical assistance in remote places. Graphical abstract
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Affiliation(s)
- Sindhoora Kaniyala Melanthota
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Dharshini Gopal
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Shweta Chakrabarti
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Anirudh Ameya Kashyap
- Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, 576104 India
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
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15
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The Active Segmentation Platform for Microscopic Image Classification and Segmentation. Brain Sci 2021; 11:brainsci11121645. [PMID: 34942947 PMCID: PMC8699732 DOI: 10.3390/brainsci11121645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/04/2022] Open
Abstract
Image segmentation still represents an active area of research since no universal solution can be identified. Traditional image segmentation algorithms are problem-specific and limited in scope. On the other hand, machine learning offers an alternative paradigm where predefined features are combined into different classifiers, providing pixel-level classification and segmentation. However, machine learning only can not address the question as to which features are appropriate for a certain classification problem. The article presents an automated image segmentation and classification platform, called Active Segmentation, which is based on ImageJ. The platform integrates expert domain knowledge, providing partial ground truth, with geometrical feature extraction based on multi-scale signal processing combined with machine learning. The approach in image segmentation is exemplified on the ISBI 2012 image segmentation challenge data set. As a second application we demonstrate whole image classification functionality based on the same principles. The approach is exemplified using the HeLa and HEp-2 data sets. Obtained results indicate that feature space enrichment properly balanced with feature selection functionality can achieve performance comparable to deep learning approaches. In summary, differential geometry can substantially improve the outcome of machine learning since it can enrich the underlying feature space with new geometrical invariant objects.
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16
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Pasternak T, Pérez-Pérez JM. Methods of In Situ Quantitative Root Biology. PLANTS (BASEL, SWITZERLAND) 2021; 10:2399. [PMID: 34834762 PMCID: PMC8625443 DOI: 10.3390/plants10112399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022]
Abstract
When dealing with plant roots, a multiscale description of the functional root structure is needed. Since the beginning of 21st century, new devices such as laser confocal microscopes have been accessible for coarse root structure measurements, including three-dimensional (3D) reconstruction. Most researchers are familiar with using simple 2D geometry visualization that does not allow quantitative determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for 3D analysis of root features at single-cell resolution, including root asymmetry, lateral root analysis, cell size and nuclear organization, cell-cycle kinetics, and chromatin structure analysis. Quantitative maps of the root apical meristem (RAM) are shown for different species, including Arabidopsis thaliana (L.), Heynh, Nicotiana tabacum L., Medicago sativa L., and Setaria italica (L.) P. Beauv. The 3D analysis of the RAM in these species showed divergence in chromatin organization and cell volume distribution that might be used to study root zonation for each root tissue. Detailed protocols and possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.
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Affiliation(s)
- Taras Pasternak
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Institute of Biology II/Molecular Plant Physiology, 79104 Freiburg, Germany
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17
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Maslova A, Krasikova A. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains. Front Cell Dev Biol 2021; 9:753097. [PMID: 34805161 PMCID: PMC8597843 DOI: 10.3389/fcell.2021.753097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
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Affiliation(s)
| | - Alla Krasikova
- Laboratory of Nuclear Structure and Dynamics, Cytology and Histology Department, Saint Petersburg State University, Saint Petersburg, Russia
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18
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Piovesan A, Vancauwenberghe V, Van De Looverbosch T, Verboven P, Nicolaï B. X-ray computed tomography for 3D plant imaging. TRENDS IN PLANT SCIENCE 2021; 26:1171-1185. [PMID: 34404587 DOI: 10.1016/j.tplants.2021.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/05/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
X-ray computed tomography (CT) is a valuable tool for 3D imaging of plant tissues and organs. Applications include the study of plant development and organ morphogenesis, as well as modeling of transport processes in plants. Some challenges remain, however, including attaining higher contrast for easier quantification, increasing the resolution for imaging subcellular features, and decreasing image acquisition and processing time for high-throughput phenotyping. In addition, phase contrast, multispectral, dark-field, soft X-ray, and time-resolved imaging are emerging. At the same time, a large amount of 3D image data are becoming available, posing challenges for data management. We review recent advances in the area of X-ray CT for plant imaging, and describe opportunities for using such images for studying transport processes in plants.
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Affiliation(s)
- Agnese Piovesan
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium
| | - Valérie Vancauwenberghe
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium
| | - Tim Van De Looverbosch
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium
| | - Pieter Verboven
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium.
| | - Bart Nicolaï
- Katholieke Universiteit (KU) Leuven, Division MeBioS (Mechatronics, Biostatistics, and Sensors) - Postharvest Group, Willem de Croylaan 42, BE-3001 Leuven, Belgium; Flanders Centre of Postharvest Technology (VCBT), Willem de Croylaan 42, BE-3001 Leuven, Belgium
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19
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Graumann K. Finding the missing piece of the puzzle: how NMCPs fit into the plant nuclear lamina. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6077-6080. [PMID: 34592756 DOI: 10.1093/jxb/erab242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This article comments on:Masuda K, Hikida R, Fujino K. 2021. The plant nuclear lamina proteins NMCP1 and NMCP2 form a filamentous network with lateral filament associations. Journal of Experimental Botany 72, 6190–6204.
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Affiliation(s)
- Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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20
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Dubos T, Poulet A, Gonthier-Gueret C, Mougeot G, Vanrobays E, Li Y, Tutois S, Pery E, Chausse F, Probst AV, Tatout C, Desset S. Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0. Nucleus 2021; 11:315-329. [PMID: 33153359 PMCID: PMC7714466 DOI: 10.1080/19491034.2020.1845012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
NucleusJ 1.0, an ImageJ plugin, is a useful tool to analyze nuclear morphology and chromatin organization in plant and animal cells. NucleusJ 2.0 is a new release of NucleusJ, in which image processing is achieved more quickly using a command-lineuser interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unstained nucleoli. These two complementary methods are compared for their accuracy by using three types of datasets available to the community at https://www.brookes.ac.uk/indepth/images/ . Finally, NucleusJ 2.0 was evaluated using original plant genetic material by assessing its efficiency on nuclei stained with DNA dyes or after 3D-DNA Fluorescence in situ hybridization. With these improvements, NucleusJ 2.0 permits the generation of large user-curated datasets that will be useful for software benchmarking or to train convolution neural networks.
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Affiliation(s)
- Tristan Dubos
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Axel Poulet
- Department of Molecular, Cellular & Developmental Biology, Yale University , New Haven, CT, USA
| | | | - Guillaume Mougeot
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University , Oxford, UK
| | - Emmanuel Vanrobays
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Yanru Li
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich , Zürich, Switzerland
| | - Sylvie Tutois
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Emilie Pery
- Institut Pascal, Université Clermont Auvergne , Clermont-Ferrand, France
| | - Frédéric Chausse
- Institut Pascal, Université Clermont Auvergne , Clermont-Ferrand, France
| | - Aline V Probst
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Christophe Tatout
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
| | - Sophie Desset
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France58
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21
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Meschichi A, Ingouff M, Picart C, Mirouze M, Desset S, Gallardo F, Bystricky K, Picault N, Rosa S, Pontvianne F. ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta. FRONTIERS IN PLANT SCIENCE 2021; 12:677849. [PMID: 34295343 PMCID: PMC8290188 DOI: 10.3389/fpls.2021.677849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/09/2021] [Indexed: 05/05/2023]
Abstract
Together with local chromatin structure, gene accessibility, and the presence of transcription factors, gene positioning is implicated in gene expression regulation. Although the basic mechanisms are expected to be conserved in eukaryotes, less is known about the role of gene positioning in plant cells, mainly due to the lack of a highly resolutive approach. In this study, we adapted the use of the ANCHOR system to perform real-time single locus detection in planta. ANCHOR is a DNA-labeling tool derived from the chromosome partitioning system found in many bacterial species. We demonstrated its suitability to monitor a single locus in planta and used this approach to track chromatin mobility during cell differentiation in Arabidopsis thaliana root epidermal cells. Finally, we discussed the potential of this approach to investigate the role of gene positioning during transcription and DNA repair in plants.
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Affiliation(s)
- Anis Meschichi
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Claire Picart
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Marie Mirouze
- Université de Montpellier, DIADE, Montpellier, France
- Institut de Recherche pour le Développement, DIADE, Montpellier, France
| | - Sophie Desset
- iGReD, CNRS UMR 6293, Université Clermont Auvergne, INSERM U1103, Clermont–Ferrand, France
| | | | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Nathalie Picault
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
- *Correspondence: Frédéric Pontvianne
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22
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Maß L, Holtmannspötter M, Zachgo S. Dual-color 3D-dSTORM colocalization and quantification of ROXY1 and RNAPII variants throughout the transcription cycle in root meristem nuclei. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1423-1436. [PMID: 32896918 DOI: 10.1111/tpj.14986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/04/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
To unravel the function of a protein of interest, it is crucial to asses to what extent it associates via direct interactions or by overlapping expression with other proteins. ROXY1, a land plant-specific glutaredoxin, exerts a function in Arabidopsis flower development and interacts with TGA transcription factors in the nucleus. We detected a novel ROXY1 function in the root meristem. Root cells that lack chlorophyll reducing plant-specific background problems that can hamper colocalization 3D microscopy. Thus far, a super-resolution three-dimensional stochastic optical reconstruction microscopy (3D-dSTORM) approach has mainly been applied in animal studies. We established 3D-dSTORM using the roxy1 mutant complemented with green fluorescence protein-ROXY1 and investigated its colocalization with three distinct RNAPII isoforms. To quantify the colocalization results, 3D-dSTORM was coupled with the coordinate-based colocalization method. Interestingly, ROXY1 proteins colocalize with different RNA polymerase II (RNAPII) isoforms that are active at distinct transcription cycle steps. Our colocalization data provide new insights on nuclear glutaredoxin activities suggesting that ROXY1 is not only required in early transcription initiation events via interaction with transcription factors but likely also participates throughout further transcription processes until late termination steps. Furthermore, we showed the applicability of the combined approaches to detect and quantify responses to altered growth conditions, exemplified by analysis of H2 O2 treatment, causing a dissociation of ROXY1 and RNAPII isoforms. We envisage that the powerful dual-color 3D-dSTORM/coordinate-based colocalization combination offers plant cell biologists the opportunity to colocalize and quantify root meristem proteins at an increased, unprecedented resolution level <50 nm, which will enable the detection of novel subcellular protein associations and functions.
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Affiliation(s)
- Lucia Maß
- Botany Department, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
| | - Michael Holtmannspötter
- Integrated Bioimaging Facility iBiOs, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
- Center of Cellular Nanoanalytics Osnabrück, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
| | - Sabine Zachgo
- Botany Department, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
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23
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Němečková A, Koláčková V, Vrána J, Doležel J, Hřibová E. DNA replication and chromosome positioning throughout the interphase in three-dimensional space of plant nuclei. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6262-6272. [PMID: 32805034 DOI: 10.1093/jxb/eraa370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/31/2020] [Indexed: 05/23/2023]
Abstract
Despite much recent progress, our understanding of the principles of plant genome organization and its dynamics in three-dimensional space of interphase nuclei remains surprisingly limited. Notably, it is not clear how these processes could be affected by the size of a plant's nuclear genome. In this study, DNA replication timing and interphase chromosome positioning were analyzed in seven Poaceae species that differ in their genome size. To provide a comprehensive picture, a suite of advanced, complementary methods was used: labeling of newly replicated DNA by ethynyl-2'-deoxyuridine, isolation of nuclei at particular cell cycle phases by flow cytometric sorting, three-dimensional immunofluorescence in situ hybridization, and confocal microscopy. Our results revealed conserved dynamics of DNA replication in all species, and a similar replication timing order for telomeres and centromeres, as well as for euchromatin and heterochromatin regions, irrespective of genome size. Moreover, stable chromosome positioning was observed while transitioning through different stages of interphase. These findings expand upon earlier studies in suggesting that a more complex interplay exists between genome size, organization of repetitive DNA sequences along chromosomes, and higher order chromatin structure and its maintenance in interphase, albeit controlled by currently unknown factors.
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Affiliation(s)
- Alžběta Němečková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Veronika Koláčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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24
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3-D Nucleus Architecture in Oat × Maize Addition Lines. Int J Mol Sci 2020; 21:ijms21124280. [PMID: 32560105 PMCID: PMC7352526 DOI: 10.3390/ijms21124280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
The nucleus architecture of hybrid crop plants is not a well-researched topic, yet it can have important implications for their genetic stability and usefulness in the successful expression of agronomically desired traits. In this work we studied the spatial distribution of introgressed maize chromatin in oat × maize addition lines with the number of added maize chromosomes varying from one to four. The number of chromosome additions was confirmed by genomic in situ hybridization (GISH). Maize chromosome-specific simple sequence repeat (SSR) markers were used to identify the added chromosomes. GISH on 3-D root and leaf nuclei was performed to assess the number, volume, and position of the maize-chromatin occupied regions. We revealed that the maize chromosome territory (CT) associations of varying degree prevailed in the double disomic lines, while CT separation was the most common distribution pattern in the double monosomic line. In all analyzed lines, the regions occupied by maize CTs were located preferentially at the nuclear periphery. A comparison between the tissues showed that the maize CTs in the leaf nuclei are positioned closer to the center of the nucleus than in the root nuclei. These findings shed more light on the processes that shape the nucleus architecture in hybrids.
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25
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Abstract
Plants contain abundant autofluorescent molecules that can be used for biochemical, physiological, or imaging studies. The two most studied molecules are chlorophyll (orange/red fluorescence) and lignin (blue/green fluorescence). Chlorophyll fluorescence is used to measure the physiological state of plants using handheld devices that can measure photosynthesis, linear electron flux, and CO2 assimilation by directly scanning leaves, or by using reconnaissance imaging from a drone, an aircraft or a satellite. Lignin fluorescence can be used in imaging studies of wood for phenotyping of genetic variants in order to evaluate reaction wood formation, assess chemical modification of wood, and study fundamental cell wall properties using Förster Resonant Energy Transfer (FRET) and other methods. Many other fluorescent molecules have been characterized both within the protoplast and as components of cell walls. Such molecules have fluorescence emissions across the visible spectrum and can potentially be differentiated by spectral imaging or by evaluating their response to change in pH (ferulates) or chemicals such as Naturstoff reagent (flavonoids). Induced autofluorescence using glutaraldehyde fixation has been used to enable imaging of proteins/organelles in the cell protoplast and to allow fluorescence imaging of fungal mycelium.
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26
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Evans DE, Graumann K, Foisner R. Editorial for the SEB florence special issue: functional organisation of the nuclear periphery. Nucleus 2020; 10:167-168. [PMID: 31345104 PMCID: PMC8871612 DOI: 10.1080/19491034.2019.1643140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- David E Evans
- a Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University , Oxford UK
| | - Katja Graumann
- a Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University , Oxford UK
| | - Roland Foisner
- a Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University , Oxford UK.,b Max Perutz Laboratories, Medical University of Vienna , Vienna , Austria
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27
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Pontvianne F, Liu C. Chromatin domains in space and their functional implications. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:1-10. [PMID: 31881292 DOI: 10.1016/j.pbi.2019.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/12/2019] [Accepted: 11/26/2019] [Indexed: 05/19/2023]
Abstract
Genome organization displays functional compartmentalization. Many factors, including epigenetic modifications, transcription factors, chromatin remodelers, and RNAs, shape chromatin domains and the three-dimensional genome organization. Various types of chromatin domains with distinct epigenetic and spatial features exhibit different transcriptional activities. As part of the efforts to better understand plant functional genomics, over the past a few years, spatial distribution patterns of plant chromatin domains have been brought to light. In this review, we discuss chromatin domains associated with the nuclear periphery and the nucleolus, as well as chromatin domains staying in proximity and showing physical interactions. The functional implication of these domains is discussed, with a particular focus on the transcriptional regulation and replication timing. Finally, from a biophysical point of view, we discuss potential roles of liquid-liquid phase separation in plant nuclei in the genesis and maintenance of spatial chromatin domains.
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Affiliation(s)
- Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan 66860, France; UPVD, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan 66860, France.
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany.
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Kang H, Wu D, Fan T, Zhu Y. Activities of Chromatin Remodeling Factors and Histone Chaperones and Their Effects in Root Apical Meristem Development. Int J Mol Sci 2020; 21:ijms21030771. [PMID: 31991579 PMCID: PMC7038114 DOI: 10.3390/ijms21030771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic genes are packaged into dynamic but stable chromatin structures to deal with transcriptional reprogramming and inheritance during development. Chromatin remodeling factors and histone chaperones are epigenetic factors that target nucleosomes and/or histones to establish and maintain proper chromatin structures during critical physiological processes such as DNA replication and transcriptional modulation. Root apical meristems are vital for plant root development. Regarding the well-characterized transcription factors involved in stem cell proliferation and differentiation, there is increasing evidence of the functional implications of epigenetic regulation in root apical meristem development. In this review, we focus on the activities of chromatin remodeling factors and histone chaperones in the root apical meristems of the model plant species Arabidopsis and rice.
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