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Trépout S, Sgarra ML, Marco S, Ramm G. An introduction to scanning transmission electron microscopy for the study of protozoans. Mol Microbiol 2024; 121:659-670. [PMID: 38140856 DOI: 10.1111/mmi.15213] [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] [Received: 08/01/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
Since its inception in the 1930s, transmission electron microscopy (TEM) has been a powerful method to explore the cellular structure of parasites. TEM usually requires samples of <100 nm thick and with protozoans being larger than 1 μm, their study requires resin embedding and ultrathin sectioning. During the past decade, several new methods have been developed to improve, facilitate, and speed up the structural characterisation of biological samples, offering new imaging modalities for the study of protozoans. In particular, scanning transmission electron microscopy (STEM) can be used to observe sample sections as thick as 1 μm thus becoming an alternative to conventional TEM. STEM can also be performed under cryogenic conditions in combination with cryo-electron tomography providing access to the study of thicker samples in their native hydrated states in 3D. This method, called cryo-scanning transmission electron tomography (cryo-STET), was first developed in 2014. This review presents the basic concepts and benefits of STEM methods and provides examples to illustrate the potential for new insights into the structure and ultrastructure of protozoans.
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Affiliation(s)
- Sylvain Trépout
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia
| | | | - Sergio Marco
- Vaccine CMC Development & Supply, Sanofi, Neuville sur Saône, France
| | - Georg Ramm
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia
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Imaging biological samples by integrated differential phase contrast (iDPC) STEM technique. J Struct Biol 2022; 214:107837. [DOI: 10.1016/j.jsb.2022.107837] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/19/2022]
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Trépout S. In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100033. [PMID: 32775999 PMCID: PMC7394968 DOI: 10.1016/j.yjsbx.2020.100033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 11/26/2022]
Abstract
Flagellar and cellular membranes are in close contact next to the FAZ filament. Sticks are heterogeneously distributed along the FAZ filament length. Thin appendages are present between the sticks and the neighbouring microtubules. The FAZ could elongate thanks to the action of dynein on subpellicular microtubules.
The flagellum of Trypanosoma brucei is a 20 µm-long organelle responsible for locomotion and cell morphogenesis. The flagellum attachment zone (FAZ) is a multi-protein complex whose function is to attach the flagellum to the cell body but also to guide cytokinesis. Cryo-transmission electron microscopy is a tool of choice to access the structure of the FAZ in a close-to-native state. However, because of the large dimension of the cell body, the whole FAZ cannot be structurally studied in situ at the nanometre scale in 3D using classical transmission electron microscopy approaches. In the present work, cryo-scanning transmission electron tomography, a new method capable of investigating cryo-fixed thick biological samples, has been used to study whole T. brucei cells at the bloodstream stage. The method has been used to visualise and characterise the structure and organisation of the FAZ filament. It is composed of an array of cytoplasmic stick-like structures. These sticks are heterogeneously distributed between the posterior part and the anterior tip of the cell. This cryo-STET investigation provides new insights into the structure of the FAZ filament. In combination with protein structure predictions, this work proposes a new model for the elongation of the FAZ.
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Trépout S, Tassin AM, Marco S, Bastin P. STEM tomography analysis of the trypanosome transition zone. J Struct Biol 2017; 202:51-60. [PMID: 29248600 DOI: 10.1016/j.jsb.2017.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/20/2017] [Accepted: 12/10/2017] [Indexed: 02/06/2023]
Abstract
The protist Trypanosoma brucei is an emerging model for the study of cilia and flagella. Here, we used scanning transmission electron microscopy (STEM) tomography to describe the structure of the trypanosome transition zone (TZ). At the base of the TZ, nine transition fibres irradiate from the B microtubule of each doublet towards the membrane. The TZ adopts a 9 + 0 structure throughout its length of ∼300 nm and its lumen contains an electron-dense structure. The proximal portion of the TZ has an invariant length of 150 nm and is characterised by a collarette surrounding the membrane and the presence of electron-dense material between the membrane and the doublets. The distal portion exhibits more length variation (from 55 to 235 nm) and contains typical Y-links. STEM analysis revealed a more complex organisation of the Y-links compared to what was reported by conventional transmission electron microscopy. Observation of the very early phase of flagellum assembly demonstrated that the proximal portion and the collarette are assembled early during construction. The presence of the flagella connector that maintains the tip of the new flagellum to the side of the old was confirmed and additional filamentous structures making contact with the membrane of the flagellar pocket were also detected. The structure and potential functions of the TZ in trypanosomes are discussed, as well as its mode of assembly.
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Affiliation(s)
- Sylvain Trépout
- Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, F-91405 Orsay, France; INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
| | - Anne-Marie Tassin
- Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, F-91405 Orsay, France; INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Sergio Marco
- Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, F-91405 Orsay, France; INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
| | - Philippe Bastin
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, 25 Rue du Docteur Roux, 75015 Paris, France.
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Donati L, Nilchian M, Trépout S, Messaoudi C, Marco S, Unser M. Compressed sensing for STEM tomography. Ultramicroscopy 2017; 179:47-56. [PMID: 28411510 DOI: 10.1016/j.ultramic.2017.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 03/28/2017] [Accepted: 04/04/2017] [Indexed: 11/17/2022]
Abstract
A central challenge in scanning transmission electron microscopy (STEM) is to reduce the electron radiation dosage required for accurate imaging of 3D biological nano-structures. Methods that permit tomographic reconstruction from a reduced number of STEM acquisitions without introducing significant degradation in the final volume are thus of particular importance. In random-beam STEM (RB-STEM), the projection measurements are acquired by randomly scanning a subset of pixels at every tilt view. In this work, we present a tailored RB-STEM acquisition-reconstruction framework that fully exploits the compressed sensing principles. We first demonstrate that RB-STEM acquisition fulfills the "incoherence" condition when the image is expressed in terms of wavelets. We then propose a regularized tomographic reconstruction framework to recover volumes from RB-STEM measurements. We demonstrate through simulations on synthetic and real projection measurements that the proposed framework reconstructs high-quality volumes from strongly downsampled RB-STEM data and outperforms existing techniques at doing so. This application of compressed sensing principles to STEM paves the way for a practical implementation of RB-STEM and opens new perspectives for high-quality reconstructions in STEM tomography.
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Affiliation(s)
- Laurène Donati
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Masih Nilchian
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Sylvain Trépout
- INSERM, U1196, Orsay F-91405, France; Institut Curie, Centre de Recherche, Orsay F-91405, France; CNRS, UMR9187, Orsay F-91405, France; Université Paris-Sud, Orsay F-91405, France
| | - Cédric Messaoudi
- INSERM, U1196, Orsay F-91405, France; Institut Curie, Centre de Recherche, Orsay F-91405, France; CNRS, UMR9187, Orsay F-91405, France; Université Paris-Sud, Orsay F-91405, France
| | - Sergio Marco
- INSERM, U1196, Orsay F-91405, France; Institut Curie, Centre de Recherche, Orsay F-91405, France; CNRS, UMR9187, Orsay F-91405, France; Université Paris-Sud, Orsay F-91405, France
| | - Michael Unser
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Trépout S, Bastin P, Marco S. Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography. J Vis Exp 2017. [PMID: 28362414 DOI: 10.3791/55215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
This report describes a protocol for preparing thick biological specimens for further observation using a scanning transmission electron microscope. It also describes an imaging method for studying the 3D structure of thick biological specimens by scanning transmission electron tomography. The sample preparation protocol is based on conventional methods in which the sample is fixed using chemical agents, treated with a heavy atom salt contrasting agent, dehydrated in a series of ethanol baths, and embedded in resin. The specific imaging conditions for observing thick samples by scanning transmission electron microscopy are then described. Sections of the sample are observed using a through-focus method involving the collection of several images at various focal planes. This enables the recovery of in-focus information at various heights throughout the sample. This particular collection pattern is performed at each tilt angle during tomography data collection. A single image is then generated, merging the in-focus information from all the different focal planes. A classic tilt-series dataset is then generated. The advantage of the method is that the tilt-series alignment and reconstruction can be performed using standard tools. The collection of through-focal images allows the reconstruction of a 3D volume that contains all of the structural details of the sample in focus.
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Affiliation(s)
| | - Philippe Bastin
- Institut Pasteur, Trypanosome Cell Biology Unit, Department of Parasites & Insect Vectors, INSERM U1201
| | - Sergio Marco
- Institut Curie, INSERM U1196, Campus Universitaire d'Orsay
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Ekman AA, Chen JH, Guo J, McDermott G, Le Gros MA, Larabell CA. Mesoscale imaging with cryo-light and X-rays: Larger than molecular machines, smaller than a cell. Biol Cell 2017; 109:24-38. [PMID: 27690365 PMCID: PMC5261833 DOI: 10.1111/boc.201600044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
In the context of cell biology, the term mesoscale describes length scales ranging from that of an individual cell, down to the size of the molecular machines. In this spatial regime, small building blocks self-organise to form large, functional structures. A comprehensive set of rules governing mesoscale self-organisation has not been established, making the prediction of many cell behaviours difficult, if not impossible. Our knowledge of mesoscale biology comes from experimental data, in particular, imaging. Here, we explore the application of soft X-ray tomography (SXT) to imaging the mesoscale, and describe the structural insights this technology can generate. We also discuss how SXT imaging is complemented by the addition of correlative fluorescence data measured from the same cell. This combination of two discrete imaging modalities produces a 3D view of the cell that blends high-resolution structural information with precise molecular localisation data.
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Affiliation(s)
- Axel A. Ekman
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jessica Guo
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Gerry McDermott
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mark A. Le Gros
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn A. Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Rez P, Larsen T, Elbaum M. Exploring the theoretical basis and limitations of cryo-STEM tomography for thick biological specimens. J Struct Biol 2016; 196:466-478. [DOI: 10.1016/j.jsb.2016.09.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/15/2016] [Accepted: 09/22/2016] [Indexed: 11/30/2022]
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Overview of chemical imaging methods to address biological questions. Micron 2016; 84:23-36. [DOI: 10.1016/j.micron.2016.02.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 01/24/2016] [Accepted: 02/08/2016] [Indexed: 11/23/2022]
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