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Groysbeck N, Hanss V, Donzeau M, Strub JM, Cianférani S, Spehner D, Bahri M, Ersen O, Eltsov M, Schultz P, Zuber G. Bioactivated and PEG-Protected Circa 2 nm Gold Nanoparticles for in Cell Labelling and Cryo-Electron Microscopy. SMALL METHODS 2023; 7:e2300098. [PMID: 37035956 DOI: 10.1002/smtd.202300098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/09/2023] [Indexed: 06/09/2023]
Abstract
Advances in cryo-electron microscopy (EM) enable imaging of protein assemblies within mammalian cells in a near native state when samples are preserved by cryogenic vitrification. To accompany this progress, specialized EM labelling protocols must be developed. Gold nanoparticles (AuNPs) of 2 nm are synthesized and functionalized to bind selected intracellular targets inside living human cells and to be detected in vitreous sections. As a proof of concept, thioaminobenzoate-, thionitrobenzoate-coordinated gold nanoparticles are functionalized on their surface with SV40 Nuclear Localization Signal (NLS)-containing peptides and 2 kDa polyethyleneglycols (PEG) by thiolate exchange to target the importin-mediated nuclear machinery and facilitate cytosolic diffusion by shielding the AuNP surface from non-specific binding to cell components, respectively. After delivery by electroporation into the cytoplasm of living human cells, the PEG-coated AuNPs diffuse freely in the cytoplasm but do not enter the nucleus. Incorporation of NLS within the PEG coverage promotes a quick nuclear import of the nanoparticles in relation to the density of NLS onto the AuNPs. Cryo-EM of vitreous cell sections demonstrate the presence of 2 nm AuNPs as single entities in the nucleus. Biofunctionalized AuNPs combined with live-cell electroporation procedures are thus potent labeling tools for the identification of macromolecules in cellular cryo-EM.
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Affiliation(s)
- Nadja Groysbeck
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
| | - Victor Hanss
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Mariel Donzeau
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, F-67000, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, F-67000, France
| | - Danièle Spehner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Mounib Bahri
- Albert Crewe Centre, University of Liverpool, 4. Waterhouse Building, Block C, 1-3 Brownlow Street, London, L69 3GL, UK
| | - Ovidiu Ersen
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), 23 rue de Loess, Strasbourg, 67034, France
| | - Mikhael Eltsov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Patrick Schultz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Guy Zuber
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
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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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Segmentation and Pore Structure Estimation in SEM Images of Tissue Engineering Scaffolds Using Genetic Algorithm. Ann Biomed Eng 2020; 49:1033-1045. [PMID: 33057890 DOI: 10.1007/s10439-020-02638-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/24/2020] [Indexed: 12/16/2022]
Abstract
A python computer package is developed to segment and analyze scanning electron microscope (SEM) images of scaffolds for bone tissue engineering. The method requires only a portion of an SEM image to be labeled and used for training. The algorithm is then able to detect the pore characteristics for other SEM images acquired at different ambient conditions from different scaffolds with the same material as the labeled image. The quality of SEM images is first enhanced using histogram equalization. Then, a global thresholding method is used to perform the image analysis. The thresholding values for the SEM images are obtained using genetic algorithm (GA). The image analysis results include pore distributions of pore size, pore elongation and pore orientation. The results agree satisfactorily with the experimental data for the chitosan-alginate porous scaffolds considered. Applications of the method developed for image segmentation is not limited to scaffold pore structure analysis. The method can also be used for any SEM image containing multiple objects such as different types of cells and subcellular components.
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Cremer T, Cremer M, Hübner B, Silahtaroglu A, Hendzel M, Lanctôt C, Strickfaden H, Cremer C. The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus. Bioessays 2020; 42:e1900132. [PMID: 31994771 DOI: 10.1002/bies.201900132] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Indexed: 12/11/2022]
Abstract
This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.
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Affiliation(s)
- Thomas Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Marion Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Barbara Hübner
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Byg.18.03, 2200, Copenhagen N, Denmark
| | - Michael Hendzel
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christian Lanctôt
- Integration Santé, 1250 Avenue de la Station local 2-304, Shawinigan, Québec, G9N 8K9, Canada
| | - Hilmar Strickfaden
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christoph Cremer
- Institute of Molecular Biology (IMB) Ackermannweg 4, 55128 Mainz, Germany, and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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5
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Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Śliwińska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczyński D, Ruan Y, Wilczyński GM. Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization. Nat Commun 2020; 11:2120. [PMID: 32358536 PMCID: PMC7195386 DOI: 10.1038/s41467-020-15987-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 × 5 × 30 nm in xyz dimensions) that is superior to the current super-resolution by fluorescence light microscopy. We apply 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualize a large number of distinctive 3D chromatin folding structures in ultra-resolution. We further quantitatively characterize the reconstituted chromatin folding structures by identifying sub-domains, and uncover a high level heterogeneity of chromatin folding ultrastructures in individual nuclei, suggestive of extensive dynamic fluidity in 3D chromatin states.
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Affiliation(s)
- Paweł Trzaskoma
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Błażej Ruszczycki
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT, 06032, USA
| | - Katarzyna K Pels
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Katarzyna Krawczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Grzegorz Bokota
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Andrzej A Szczepankiewicz
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Jesse Aaron
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA, 20147, USA
| | - Agnieszka Walczak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 6 Uniwersytetu Poznanskiego St, 61-614, Poznan, Poland
| | - Małgorzata A Śliwińska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Adriana Magalska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Michal Kadlof
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Artur Wolny
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Zofia Parteka
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Sebastian Arabasz
- Łukasiewicz Research NETWORK - PORT Polish Center for Technology Development, 147 Stablowicka St, 54-066, Wroclaw, Poland
| | - Magdalena Kiss-Arabasz
- Łukasiewicz Research NETWORK - PORT Polish Center for Technology Development, 147 Stablowicka St, 54-066, Wroclaw, Poland
| | - Dariusz Plewczyński
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
- Mathematics and Information Science, Warsaw Technical University, 75 Koszykowa St, 00-662, Warsaw, Poland
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT, 06032, USA.
| | - Grzegorz M Wilczyński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland.
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Porrati F, Grewe D, Seybert A, Frangakis AS, Eltsov M. FIB-SEM imaging properties of Drosophila melanogaster tissues embedded in Lowicryl HM20. J Microsc 2018; 273:91-104. [PMID: 30417390 DOI: 10.1111/jmi.12764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 09/17/2018] [Accepted: 10/12/2018] [Indexed: 11/27/2022]
Abstract
Lowicryl resins enable processing of biological material for electron microscopy at the lowest temperatures compatible with resin embedding. When combined with high-pressure freezing and freeze-substitution, Lowicryl embedding supports preservation of fine structural details and fluorescent markers. Here, we analysed the applicability of Lowicryl HM20 embedding for focused ion beam (FIB) scanning electron microscopy (SEM) tomography of Drosophila melanogaster embryonic and larval model systems. We show that the freeze-substitution with per-mill concentrations of uranyl acetate provided sufficient contrast and an image quality of SEM imaging in the range of similar samples analysed by transmission electron microscopy (TEM). Preservation of genetically encoded fluorescent proteins allowed correlative localization of regions of interest (ROI) within the embedded tissue block. TEM on sections cut from the block face enabled evaluation of structural preservation to allow ROI ranking and thus targeted, time-efficient FIB-SEM tomography data collection. The versatility of Lowicryl embedding opens new perspectives for designing hybrid SEM-TEM workflows to comprehensively analyse biological structures. LAY DESCRIPTION: Focused ion beam scanning electron microscopy is becoming a widely used technique for the three-dimensional analysis of biological samples at fine structural details beyond levels feasible for light microscopy. To withstand the abrasion of material by the ion beam and the imaging by the scanning electron beam, biological samples have to be embedded into resins, most commonly these are very dense epoxy-based plastics. However, dense resins generate electron scattering which interferes with the signal from the biological specimen. Furthermore, to improve the imaging contrast, epoxy embedding requires chemical treatments with e.g. heavy metals, which deteriorate the ultrastructure of the biological specimen. In this study we explored the applicability of an electron lucent resin, Lowicryl HM 20, for focused ion beam scanning electron microscopy. The Lowicryl embedding workflow operates at milder chemical treatments and lower temperatures, thus preserving the sub-cellular and sub-organellar organization, as well as fluorescent markers visible by light microscopy. Here we show that focus ion beam scanning electron microscopy of Lowicryl-embedded fruit flies tissues provides reliable imaging revealing fine structural details. Our workflow benefited from use of transmission electron microscopy for the quality control of the ultrastructural preservation and fluorescent light microscopy for localization of regions of interest. The versatility of Lowicryl embedding opens up new perspectives for designing hybrid workflows combining fluorescent light, scanning, and transmission electron microscopy techniques to comprehensively analyze biological structures.
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Affiliation(s)
- F Porrati
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - D Grewe
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - A Seybert
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - A S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - M Eltsov
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
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Mai KKK, Kang BH. Semiautomatic Segmentation of Plant Golgi Stacks in Electron Tomograms Using 3dmod. Methods Mol Biol 2017; 1662:97-104. [PMID: 28861820 DOI: 10.1007/978-1-4939-7262-3_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Electron tomography is a powerful tool for visualizing subcellular organelles. With the advances in cryo-fixation techniques, it is now possible to reconstruct complex structures in cells preserved close to their native states in three-dimension (3D) using electron tomography. In order to better visualize these objects, 3D models are made from outlines of organelles in individual tomographic slices, which can be used to display morphological features and quantify structural parameters. While outlines of simple organelles can be drawn by hand fairly quickly, it is possible to accelerate 3D modeling of more complex organelles by means of semiautomatic segmentation. In this chapter, we use the example of reconstructing Golgi cisternae of a plant cell into 3D models using the semiautomatic protocol.
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Affiliation(s)
- Keith Ka Ki Mai
- State Key Laboratory of Agrobiotechnology, Centre for Cell and Developmental Biology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Byung-Ho Kang
- State Key Laboratory of Agrobiotechnology, Centre for Cell and Developmental Biology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China.
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