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Garner RM, Molines AT, Theriot JA, Chang F. Vast heterogeneity in cytoplasmic diffusion rates revealed by nanorheology and Doppelgänger simulations. Biophys J 2023; 122:767-783. [PMID: 36739478 PMCID: PMC10027447 DOI: 10.1016/j.bpj.2023.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The cytoplasm is a complex, crowded, actively driven environment whose biophysical characteristics modulate critical cellular processes such as cytoskeletal dynamics, phase separation, and stem cell fate. Little is known about the variance in these cytoplasmic properties. Here, we employed particle-tracking nanorheology on genetically encoded multimeric 40 nm nanoparticles (GEMs) to measure diffusion within the cytoplasm of individual fission yeast (Schizosaccharomyces pombe) cellscells. We found that the apparent diffusion coefficients of individual GEM particles varied over a 400-fold range, while the differences in average particle diffusivity among individual cells spanned a 10-fold range. To determine the origin of this heterogeneity, we developed a Doppelgänger simulation approach that uses stochastic simulations of GEM diffusion that replicate the experimental statistics on a particle-by-particle basis, such that each experimental track and cell had a one-to-one correspondence with their simulated counterpart. These simulations showed that the large intra- and inter-cellular variations in diffusivity could not be explained by experimental variability but could only be reproduced with stochastic models that assume a wide intra- and inter-cellular variation in cytoplasmic viscosity. The simulation combining intra- and inter-cellular variation in viscosity also predicted weak nonergodicity in GEM diffusion, consistent with the experimental data. To probe the origin of this variation, we found that the variance in GEM diffusivity was largely independent of factors such as temperature, the actin and microtubule cytoskeletons, cell-cyle stage, and spatial locations, but was magnified by hyperosmotic shocks. Taken together, our results provide a striking demonstration that the cytoplasm is not "well-mixed" but represents a highly heterogeneous environment in which subcellular components at the 40 nm size scale experience dramatically different effective viscosities within an individual cell, as well as in different cells in a genetically identical population. These findings carry significant implications for the origins and regulation of biological noise at cellular and subcellular levels.
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Affiliation(s)
- Rikki M Garner
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Arthur T Molines
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Julie A Theriot
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts
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2
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Weinhardt V, Chen JH, Ekman A, McDermott G, Le Gros MA, Larabell C. Imaging cell morphology and physiology using X-rays. Biochem Soc Trans 2019; 47:489-508. [PMID: 30952801 PMCID: PMC6716605 DOI: 10.1042/bst20180036] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/02/2019] [Accepted: 01/09/2019] [Indexed: 02/07/2023]
Abstract
Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.
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Affiliation(s)
- Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Axel Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Gerry McDermott
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Mark A Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
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3
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Ma L, Zhang X, Xu Z, Späth A, Xing Z, Sun T, Tai R. Three-dimensional focal stack imaging in scanning transmission X-ray microscopy with an improved reconstruction algorithm. OPTICS EXPRESS 2019; 27:7787-7802. [PMID: 30876336 DOI: 10.1364/oe.27.007787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/25/2019] [Indexed: 06/09/2023]
Abstract
Focal stack (FS) is an effective technique for fast 3D imaging in high-resolution scanning transmission X-ray microscopy. Its crucial issue is to assign each object within the sample to the correct position along the optical axis according to a proper focus measure. There is probably information loss with previous algorithms for FS reconstruction because the old algorithms can only detect one focused object along each optical-axial pixel line (OAPL). In this study, we present an improved FS algorithm, which utilizes an elaborately calculated threshold for normalized local variances to extract multiple focused objects in each OAPL. Simulation and experimental results show its feasibility and high efficiency for 3D imaging of high contrast, sparse samples. It is expected that our advanced approach has potential applications in 3D X-ray microscopy for more complex samples.
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4
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Niclis JC, Murphy SV, Parkinson DY, Zedan A, Sathananthan AH, Cram DS, Heraud P. Three-dimensional imaging of human stem cells using soft X-ray tomography. J R Soc Interface 2016; 12:20150252. [PMID: 26063819 DOI: 10.1098/rsif.2015.0252] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Three-dimensional imaging of human stem cells using transmission soft X-ray tomography (SXT) is presented for the first time. Major organelle types--nuclei, nucleoli, mitochondria, lysosomes and vesicles--were discriminated at approximately 50 nm spatial resolution without the use of contrast agents, on the basis of measured linear X-ray absorption coefficients and comparison of the size and shape of structures to transmission electron microscopy (TEM) images. In addition, SXT was used to visualize the distribution of a cell surface protein using gold-labelled antibody staining. We present the strengths of SXT, which include excellent spatial resolution (intermediate between that of TEM and light microscopy), the lack of the requirement for fixative or contrast agent that might perturb cellular morphology or produce imaging artefacts, and the ability to produce three-dimensional images of cells without microtome sectioning. Possible applications to studying the differentiation of human stem cells are discussed.
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Affiliation(s)
- J C Niclis
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia The Florey Institute of Neuroscience and Mental Health, Melbourne University, Parkville, Victoria 3052, Australia
| | - S V Murphy
- The Ritchie Centre, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3800, Australia Wake Forest Baptist Medical Center, Wake Forest Institute for Regenerative Medicine, Winston-Salem, NC, USA
| | - D Y Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, US Department of Energy, Berkeley, CA, USA
| | - A Zedan
- Advanced Light Source, Lawrence Berkeley National Laboratory, US Department of Energy, Berkeley, CA, USA
| | - A H Sathananthan
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - D S Cram
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - P Heraud
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia Centre for Biospectroscopy, School of Chemistry, Monash University, Melbourne, Victoria, Australia
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5
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Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells. Viruses 2015; 7:6316-45. [PMID: 26633469 PMCID: PMC4690864 DOI: 10.3390/v7122940] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/16/2015] [Accepted: 11/16/2015] [Indexed: 02/06/2023] Open
Abstract
As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications.
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Duke EMH, Razi M, Weston A, Guttmann P, Werner S, Henzler K, Schneider G, Tooze SA, Collinson LM. Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM). Ultramicroscopy 2014; 143:77-87. [PMID: 24238600 PMCID: PMC4045213 DOI: 10.1016/j.ultramic.2013.10.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 10/01/2013] [Accepted: 10/07/2013] [Indexed: 12/20/2022]
Abstract
Cryo-soft X-ray tomography (cryo-SXT) is a powerful imaging technique that can extract ultrastructural information from whole, unstained mammalian cells as close to the living state as possible. Subcellular organelles including the nucleus, the Golgi apparatus and mitochondria have been identified by morphology alone, due to the similarity in contrast to transmission electron micrographs. In this study, we used cryo-SXT to image endosomes and autophagosomes, organelles that are particularly susceptible to chemical fixation artefacts during sample preparation for electron microscopy. We used two approaches to identify these compartments. For early and recycling endosomes, which are accessible to externally-loaded markers, we used an anti-transferrin receptor antibody conjugated to 10nm gold particles. For autophagosomes, which are not accessible to externally-applied markers, we developed a correlative cryo-fluorescence and cryo-SXT workflow (cryo-CLXM) to localise GFP-LC3 and RFP-Atg9. We used a stand-alone cryo-fluorescence stage in the home laboratory to localise the cloned fluorophores, followed by cryo-soft X-ray tomography at the synchrotron to analyse cellular ultrastructure. We mapped the 3D ultrastructure of the endocytic and autophagic structures, and discovered clusters of omegasomes arising from 'hotspots' on the ER. Thus, immunogold markers and cryo-CLXM can be used to analyse cellular processes that are inaccessible using other imaging modalities.
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Affiliation(s)
- Elizabeth M H Duke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Minoo Razi
- Secretory Pathways Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Anne Weston
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Peter Guttmann
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Soft Matter and Functional Materials, 12489 Berlin, Germany
| | - Stephan Werner
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Soft Matter and Functional Materials, 12489 Berlin, Germany
| | - Katja Henzler
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Soft Matter and Functional Materials, 12489 Berlin, Germany
| | - Gerd Schneider
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Soft Matter and Functional Materials, 12489 Berlin, Germany
| | - Sharon A Tooze
- Secretory Pathways Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Lucy M Collinson
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK.
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7
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Carzaniga R, Domart MC, Collinson LM, Duke E. Cryo-soft X-ray tomography: a journey into the world of the native-state cell. PROTOPLASMA 2014; 251:449-58. [PMID: 24264466 PMCID: PMC3927064 DOI: 10.1007/s00709-013-0583-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 05/21/2023]
Abstract
One of the ultimate aims of imaging in biology is to achieve molecular localisation in the context of the structure of cells in their native state. Here, we review the current state of the art in cryo-soft X-ray tomography (cryo-SXT), which is the only imaging modality that can provide nanoscale 3D information from cryo-preserved, unstained, whole cells thicker than 1 μm. Correlative cryo-fluorescence and cryo-SXT adds functional information to structure, enabling studies of cellular events that cannot be captured using light, electron or X-ray microscopes alone.
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Affiliation(s)
- Raffaella Carzaniga
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London, WC2A 3LY UK
| | - Marie-Charlotte Domart
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London, WC2A 3LY UK
| | - Lucy M. Collinson
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London, WC2A 3LY UK
| | - Elizabeth Duke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE UK
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8
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Obst M, Schmid G. 3D chemical mapping: application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences. Methods Mol Biol 2014; 1117:757-781. [PMID: 24357389 DOI: 10.1007/978-1-62703-776-1_34] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The identification of environmental processes and mechanisms often requires information on the organochemical and inorganic composition of specimens at high spatial resolution. X-ray spectroscopy (XAS) performed in the soft X-ray range (100-2,200 eV) provides chemical speciation information for elements that are of high biogeochemical relevance such as carbon, nitrogen, and oxygen but also includes transition metals such as iron, manganese, or nickel. Synchrotron-based scanning transmission X-ray microscopy (STXM) combines XAS with high resolution mapping on the 20-nm scale. This provides two-dimensional (2D) quantitative information about the distribution of chemical species such as organic macromolecules, metals, or mineral phases within environmental samples. Furthermore, the combination of STXM with angle-scan tomography allows for three-dimensional (3D) spectromicroscopic analysis of bio-, geo-, or environmental samples. For the acquisition of STXM tomography data, the sample is rotated around an axis perpendicular to the X-ray beam. Various sample preparation approaches such as stripes cut from TEM grids or the preparation of wet cells allow for preparing environmentally relevant specimens in a dry or in a fully hydrated state for 2D and 3D STXM measurements. In this chapter we give a short overview about the principles of STXM, its application to environmental sciences, different preparation techniques, and the analysis and 3D reconstruction of STXM tomography data.
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Affiliation(s)
- Martin Obst
- Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany
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9
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Carzaniga R, Domart MC, Duke E, Collinson LM. Correlative cryo-fluorescence and cryo-soft X-ray tomography of adherent cells at European synchrotrons. Methods Cell Biol 2014; 124:151-78. [PMID: 25287841 DOI: 10.1016/b978-0-12-801075-4.00008-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cryo-soft X-ray tomography (cryo-SXT) is a synchrotron-hosted imaging technique used to analyze the ultrastructure of intact, cryo-prepared cells. Correlation of cryo-fluorescence microscopy and cryo-SXT can be used to localize fluorescent proteins to organelles preserved close to native state. Cryo-correlative light and X-ray microscopy (cryo-CLXM) is particularly useful for the study of organelles that are susceptible to chemical fixation artifacts during sample preparation for electron microscopy. In our recent work, we used cryo-CLXM to characterize GFP-LC3-positive early autophagosomes in nutrient-starved HEK293A cells (Duke et al., 2013). Cup-shaped omegasomes were found to form at "hot-spots" on the endoplasmic reticulum. Furthermore, cryo-SXT image stacks revealed the presence of large complex networks of tubulated mitochondria in the starved cells, which would be challenging to model at this scale and resolution using light or electron microscopy. In this chapter, we detail the cryo-CLXM workflow that we developed and optimized for studying adherent mammalian cells. We show examples of data collected at the three European synchrotrons that currently host cryo-SXT microscopes, and describe how raw cryo-SXT datasets are processed into tomoX stacks, modeled, and correlated with cryo-fluorescence data to identify structures of interest.
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Affiliation(s)
- Raffaella Carzaniga
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London, United Kingdom
| | - Marie-Charlotte Domart
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London, United Kingdom
| | - Elizabeth Duke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Lucy M Collinson
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London, United Kingdom
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10
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Wang Z, Gao K, Chen J, Hong Y, Ge X, Wang D, Pan Z, Zhu P, Yun W, Jacobsen C, Wu Z. Advantages of intermediate X-ray energies in Zernike phase contrast X-ray microscopy. Biotechnol Adv 2013; 31:387-92. [DOI: 10.1016/j.biotechadv.2012.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/06/2012] [Indexed: 01/22/2023]
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11
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McAughtrie S, Lau K, Faulds K, Graham D. 3D optical imaging of multiple SERS nanotags in cells. Chem Sci 2013. [DOI: 10.1039/c3sc51437d] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Oton J, Sorzano COS, Pereiro E, Cuenca-Alba J, Navarro R, Carazo JM, Marabini R. Image formation in cellular X-ray microscopy. J Struct Biol 2012; 178:29-37. [PMID: 22343468 DOI: 10.1016/j.jsb.2012.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 01/15/2023]
Abstract
Soft X-ray Tomographic (TomoX) microscopy has become a reality in the last years. The resolution range of this technique nicely fits between confocal and electron microscopies and will play a key role in the elucidation of the organization between the molecular and the organelle levels. In fact, it offers the possibility of imaging three-dimensional structures of hydrated biological specimens near their native state without chemical pre-treatment. Ideally, TomoX reconstructs the specimen absorption coefficients from projections of this specimen, but, unfortunately, X-ray micrographs are only an approximation to projections of the specimen, resulting in inaccuracies if a tomographic reconstruction is performed without explicitly incorporating these approximations. In an attempt to mitigate some of these inaccuracies, we develop in this work an image formation model within the approximation of assuming incoherent illumination.
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Affiliation(s)
- Joaquin Oton
- Centro Nacional de Biotecnología, Ciudad Universitaria de Cantoblanco, Calle Darwin, 3, 28049 Madrid, Spain
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Hanssen E, Knoechel C, Dearnley M, Dixon MW, Le Gros M, Larabell C, Tilley L. Soft X-ray microscopy analysis of cell volume and hemoglobin content in erythrocytes infected with asexual and sexual stages of Plasmodium falciparum. J Struct Biol 2012; 177:224-32. [DOI: 10.1016/j.jsb.2011.09.003] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/05/2011] [Accepted: 09/09/2011] [Indexed: 12/13/2022]
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Crank M, Harilal SS, Hassan SM, Hassanein A. Excitation wavelength dependence of water-window line emissions from boron-nitride laser-produced plasmas. JOURNAL OF APPLIED PHYSICS 2012; 111:33301-333016. [PMID: 22396624 PMCID: PMC3293343 DOI: 10.1063/1.3682087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/03/2012] [Indexed: 05/26/2023]
Abstract
We investigated the effects of laser excitation wavelength on water-window emission lines of laser-produced boron-nitride plasmas. Plasmas are produced by focusing 1064 nm and harmonically generated 532 and 266 nm radiation from a Nd:YAG laser on BN target in vacuum. Soft x-ray emission lines in the water-window region are recorded using a grazing-incidence spectrograph. Filtered photodiodes are used to obtain complementary data for water-window emission intensity and angular dependence. Spectral emission intensity changes in nitrogen Ly-α and He-α are used to show how laser wavelength affects emission. Our results show that the relative intensity of spectral lines is laser wavelength dependent, with the ratio of Ly-α to He-α emission intensity decreasing as laser wavelength is shortened. Filtered photodiode measurements of angular dependence showed that 266 and 532 nm laser wavelengths produce uniform emission.
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15
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McDermott G, Fox DM, Epperly L, Wetzler M, Barron AE, Le Gros MA, Larabell CA. Visualizing and quantifying cell phenotype using soft X-ray tomography. Bioessays 2012; 34:320-7. [PMID: 22290620 DOI: 10.1002/bies.201100125] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Soft X-ray tomography (SXT) is an imaging technique capable of characterizing and quantifying the structural phenotype of cells. In particular, SXT is used to visualize the internal architecture of fully hydrated, intact eukaryotic and prokaryotic cells at high spatial resolution (50 nm or better). Image contrast in SXT is derived from the biochemical composition of the cell, and obtained without the need to use potentially damaging contrast-enhancing agents, such as heavy metals. The cells are simply cryopreserved prior to imaging, and are therefore imaged in a near-native state. As a complement to structural imaging by SXT, the same specimen can now be imaged by correlated cryo-light microscopy. By combining data from these two modalities specific molecules can be localized directly within the framework of a high-resolution, three-dimensional reconstruction of the cell. This combination of data types allows sophisticated analyses to be carried out on the impact of environmental and/or genetic factors on cell phenotypes.
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Affiliation(s)
- Gerry McDermott
- Department of Anatomy, University of California, San Francisco, CA, USA
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16
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Zheng T, Li W, Guan Y, Song X, Xiong Y, Liu G, Tian Y. Quantitative 3D imaging of yeast by hard X-ray tomography. Microsc Res Tech 2011; 75:662-6. [PMID: 22505187 DOI: 10.1002/jemt.21108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 09/16/2011] [Indexed: 11/07/2022]
Abstract
Full-field hard X-ray tomography could be used to obtain three-dimensional (3D) nanoscale structures of biological samples. The image of the fission yeast, Schizosaccharomyces pombe, was clearly visualized based on Zernike phase contrast imaging technique and heavy metal staining method at a spatial resolution better than 50 nm at the energy of 8 keV. The distributions and shapes of the organelles during the cell cycle were clearly visualized and two types of organelle were distinguished. The results for cells during various phases were compared and the ratios of organelle volume to cell volume can be analyzed quantitatively. It showed that the ratios remained constant between growth and division phase and increased strongly in stationary phase, following the shape and size of two types of organelles changes. Our results demonstrated that hard X-ray microscopy was a complementary method for imaging and revealing structural information for biological samples.
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Affiliation(s)
- Ting Zheng
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, China
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Yang Y, Li W, Liu G, Zhang X, Chen J, Wu W, Guan Y, Xiong Y, Tian Y, Wu Z. 3D visualization of subcellular structures of Schizosaccharomyces pombe by hard X-ray tomography. J Microsc 2011; 240:14-20. [PMID: 21050209 DOI: 10.1111/j.1365-2818.2010.03379.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cellular structures of the fission yeast, Schizosaccharomyces pombe, were examined by using hard X-ray tomography. Since cells are nearly transparent to hard X-rays, Zernike phase contrast and heavy metal staining were introduced to improve image contrast. Through using such methods, images taken at 8 keV displayed sufficient contrast for observing cellular structures. The cell wall, the intracellular organelles and the entire structural organization of the whole cells were visualized in three-dimensional at a resolution better than 100 nm. Comparison between phase contrast and absorption contrast was also made, indicating the obvious advantage of phase contrast for cellular imaging at this energy. Our results demonstrate that hard X-ray tomography with Zernike phase contrast is suitable for cellular imaging. Its unique abilities make it have potential to become a useful tool for revealing structural information from cells, especially thick eukaryotic cells.
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Affiliation(s)
- Y Yang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
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18
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Uchida M, Sun Y, McDermott G, Knoechel C, Le Gros MA, Parkinson D, Drubin DG, Larabell CA. Quantitative analysis of yeast internal architecture using soft X-ray tomography. Yeast 2010; 28:227-36. [PMID: 21360734 DOI: 10.1002/yea.1834] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 11/09/2010] [Indexed: 01/18/2023] Open
Abstract
We used soft X-ray tomography (SXT)--a high-resolution, quantitative imaging technique--to measure cell size and organelle volumes in yeasts. Cell size is a key factor in initiating cell division in yeasts, whereas the number and volume of the organelles have a profound impact on the function and viability of a cell. Consequently, determining these cell parameters is fundamentally important in understanding yeast biology. SXT is well suited to this type of analysis. Specimens are imaged in a near-native state, and relatively large numbers of cells can be readily analysed. In this study, we characterized haploid and diploid strains of Saccharomyces cerevisiae at each of the key stages in the cell cycle and determined the relationships that exist cellular and organelle volumes. We then compared these results with SXT data obtained from Schizosaccharomyces pombe, the three main phenotypes displayed by the opportunistic yeast pathogen Candida albicans and from a coff1-22 mutant strain of S. cerevisiae. This comparison revealed that volumetric ratios were invariant, irrespective of yeast strain, ploidy or morphology, leading to the conclusion these volumetric ratios are common in all yeasts.
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Affiliation(s)
- Maho Uchida
- Department of Anatomy, University of California at San Francisco, CA 94143-2722, USA
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19
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Larabell CA, Nugent KA. Imaging cellular architecture with X-rays. Curr Opin Struct Biol 2010; 20:623-31. [PMID: 20869868 PMCID: PMC3268817 DOI: 10.1016/j.sbi.2010.08.008] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 08/10/2010] [Accepted: 08/26/2010] [Indexed: 01/26/2023]
Abstract
X-ray imaging of biological samples is progressing rapidly. In this paper we review the progress to date in high-resolution imaging of cellular architecture. In particular we survey the progress in soft X-ray tomography and argue that the field is coming of age and that important biological insights are starting to emerge. We then review the new ideas based on coherent diffraction. These methods are at a much earlier stage of development but, as they eliminate the need for X-ray optics, have the capacity to provide substantially better spatial resolution than zone plate-based methods.
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Affiliation(s)
- Carolyn A Larabell
- Department of Anatomy, University of California at San Francisco, 1550 4th Street, San Francisco, CA 94158, USA.
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20
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Hanssen E, Knoechel C, Klonis N, Abu-Bakar N, Deed S, LeGros M, Larabell C, Tilley L. Cryo transmission X-ray imaging of the malaria parasite, P. falciparum. J Struct Biol 2010; 173:161-8. [PMID: 20826218 DOI: 10.1016/j.jsb.2010.08.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/13/2010] [Accepted: 08/25/2010] [Indexed: 11/19/2022]
Abstract
Cryo transmission X-ray microscopy in the "water window" of photon energies has recently been introduced as a method that exploits the natural contrast of biological samples. We have used cryo tomographic X-ray imaging of the intra-erythrocytic malaria parasite, Plasmodium falciparum, to undertake a survey of the cellular features of this important human pathogen. We examined whole hydrated cells at different stages of growth and defined some of the structures with different X-ray density, including the parasite nucleus, cytoplasm, digestive vacuole and the hemoglobin degradation product, hemozoin. As the parasite develops from an early cup-shaped morphology to a more rounded shape, puncta of hemozoin are formed; these coalesce in the mature trophozoite into a central compartment. In some trophozoite stage parasites we observed invaginations of the parasite surface and, using a selective permeabilization process, showed that these remain connected to the RBC cytoplasm. Some of these invaginations have large openings consistent with phagocytic structures and we observed independent endocytic vesicles in the parasite cytoplasm which appear to play a role in hemoglobin uptake. In schizont stage parasites staggered mitosis was observed and X-ray-dense lipid-rich structures were evident at their apical ends of the developing daughter cells. Treatment of parasites with the antimalarial drug artemisinin appears to affect parasite development and their ability to produce the hemoglobin breakdown product, hemozoin.
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Affiliation(s)
- Eric Hanssen
- Electron Microscopy Unit Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.
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21
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Chen J, Yang Y, Zhang X, Andrews JC, Pianetta P, Guan Y, Liu G, Xiong Y, Wu Z, Tian Y. 3D nanoscale imaging of the yeast, Schizosaccharomyces pombe, by full-field transmission X-ray microscopy at 5.4 keV. Anal Bioanal Chem 2010; 397:2117-21. [PMID: 20349228 PMCID: PMC2896439 DOI: 10.1007/s00216-010-3617-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 11/30/2022]
Abstract
Three-dimensional (3D) nanoscale structures of the fission yeast, Schizosaccharomyces pombe, can be obtained by full-field transmission hard X-ray microscopy with 30 nm resolution using synchrotron radiation sources. Sample preparation is relatively simple and the samples are portable across various imaging environments, allowing for high-throughput sample screening. The yeast cells were fixed and double-stained with Reynold's lead citrate and uranyl acetate. We performed both absorption contrast and Zernike phase contrast imaging on these cells in order to test this method. The membranes, nucleus, and subcellular organelles of the cells were clearly visualized using absorption contrast mode. The X-ray images of the cells could be used to study the spatial distributions of the organelles in the cells. These results show unique structural information, demonstrating that hard X-ray microscopy is a complementary method for imaging and analyzing biological samples.
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Affiliation(s)
- Jie Chen
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
| | - Yunhao Yang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
| | - Xiaobo Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
| | - Joy C. Andrews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Piero Pianetta
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
| | - Gang Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
| | - Ying Xiong
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
| | - Ziyu Wu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
| | - Yangchao Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei Anhui 230029, People’s Republic of China
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22
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McDermott G, Le Gros MA, Knoechel CG, Uchida M, Larabell CA. Soft X-ray tomography and cryogenic light microscopy: the cool combination in cellular imaging. Trends Cell Biol 2009; 19:587-95. [PMID: 19818625 PMCID: PMC3276488 DOI: 10.1016/j.tcb.2009.08.005] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 08/18/2009] [Accepted: 08/19/2009] [Indexed: 11/19/2022]
Abstract
Soft X-ray tomography (SXT) is ideally suited to imaging sub-cellular architecture and organization, particularly in eukaryotic cells. SXT is similar in concept to the well-established medical diagnostic technique computed axial tomography (CAT), except SXT is capable of imaging with a spatial resolution of 50nm, or better. In SXT, cells are imaged using photons from a region of the spectrum known as the 'water window'. This results in quantitative, high-contrast images of intact, fully hydrated cells without the need to use contrast-enhancing agents. The cells that are visualized are in close-to-native, fully functional state. The utility of SXT has recently been enhanced by the development of high numerical aperture cryogenic light microscopy for correlated imaging. This multi-modal approach allows labelled molecules to be localized in the context of a high-resolution 3-D tomographic reconstruction of the cell.
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Affiliation(s)
- Gerry McDermott
- Department of Anatomy, University of California San Francisco, CA 94143, USA
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23
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Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans. Proc Natl Acad Sci U S A 2009; 106:19375-80. [PMID: 19880740 DOI: 10.1073/pnas.0906145106] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The opportunistic pathogen Candida albicans can undergo phenotypic switching between a benign, unicellular phenotype and an invasive, multicellular form that causes candidiasis. Increasingly, strains of Candida are becoming resistant to antifungal drugs, making the treatment of candidiasis difficult, especially in immunocompromised or critically ill patients. Consequently, there is a pressing need to develop new drugs that circumvent fungal drug-resistance mechanisms. In this work we used soft X-ray tomography to image the subcellular changes that occur as a consequence of both phenotypic switching and of treating C. albicans with antifungal peptoids, a class of candidate therapeutics unaffected by drug resistance mechanisms. Peptoid treatment suppressed formation of the pathogenic hyphal phenotype and resulted in striking changes in cell and organelle morphology, most dramatically in the nucleus and nucleolus, and in the number, size, and location of lipidic bodies. In particular, peptoid treatment was seen to cause the inclusion of lipidic bodies into the nucleus.
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24
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Cryo-X-ray tomography of vaccinia virus membranes and inner compartments. J Struct Biol 2009; 168:234-9. [PMID: 19616103 DOI: 10.1016/j.jsb.2009.07.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 07/06/2009] [Accepted: 07/10/2009] [Indexed: 11/23/2022]
Abstract
Vitrified unstained purified vaccinia virus particles have been used as a test sample to evaluate the capabilities of cryo-X-ray tomography. Embedded in a thick layer of vitreous ice, the viral particles representing the mature form of the virus (MV) were visualized using full-field transmission X-ray tomography. The tomographic reconstructions reveal the viral brick-shaped characteristic structures with a size of 250x270x360nm(3). The X-ray tomograms show the presence of a clearly defined external envelope, together with an inner core surrounded by an internal envelope, including areas with clear differential density, which correlate well with those features previously described for these viral particles using electron microscopy analyses. A quantitative assessment of the resolution attained in X-ray and electron tomograms of the viral particles prepared under the same conditions yields values of 25.7 and 6.7nm half-pitch, respectively. Although the resolution of the X-ray microscope is well above the dimensions of the membranous compartments, the strong differential contrast exhibited makes it possible to precisely reveal them without any contrasting reagent within this small and complex biological sample.
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25
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Williams GJ, Hanssen E, Peele AG, Pfeifer MA, Clark J, Abbey B, Cadenazzi G, de Jonge MD, Vogt S, Tilley L, Nugent KA. High-resolution X-ray imaging of Plasmodium falciparum-infected red blood cells. Cytometry A 2008; 73:949-57. [PMID: 18671251 DOI: 10.1002/cyto.a.20616] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methods for imaging cellular architecture and ultimately macromolecular complexes and individual proteins, within a cellular environment, are an important goal for cell and molecular biology. Coherent diffractive imaging (CDI) is a method of lensless imaging that can be applied to any individual finite object. A diffraction pattern from a single biological structure is recorded and an iterative Fourier transform between real space and reciprocal space is used to reconstruct information about the architecture of the sample to high resolution. As a test system for cellular imaging, we have applied CDI to an important human pathogen, the malaria parasite, Plasmodium falciparum. We have employed a novel CDI approach, known as Fresnel CDI, which uses illumination with a curved incident wavefront, to image red blood cells infected with malaria parasites. We have examined the intrinsic X-ray absorption contrast of these cells and compared them with cells contrasted with heavy metal stains or immunogold labeling. We compare CDI images with data obtained from the same cells using scanning electron microscopy, light microscopy, and scanning X-ray fluorescence microscopy. We show that CDI can offer new information both within and at the surface of complex biological specimens at a spatial resolution of better than 40 nm. and we demonstrate an imaging modality that conveniently combines scanning X-ray fluorescence microscopy with CDI. The data provide independent confirmation of the validity of the coherent diffractive image and demonstrate that CDI offers the potential to become an important and reliable new high-resolution imaging modality for cell biology. CDI can detect features at high resolution within unsectioned cells.
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Affiliation(s)
- Garth J Williams
- ARC Centre of Excellence for Coherent X-Ray Science & School of Physics, The University of Melbourne, Vic., 3010 Australia
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26
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Heymann JAW, Shi D, Kim S, Bliss D, Milne JLS, Subramaniam S. 3D imaging of mammalian cells with ion-abrasion scanning electron microscopy. J Struct Biol 2008; 166:1-7. [PMID: 19116171 DOI: 10.1016/j.jsb.2008.11.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Revised: 10/18/2008] [Accepted: 11/17/2008] [Indexed: 12/20/2022]
Abstract
Understanding the hierarchical organization of molecules and organelles within the interior of large eukaryotic cells is a challenge of fundamental interest in cell biology. We are using ion-abrasion scanning electron microscopy (IA-SEM) to visualize this hierarchical organization in an approach that combines focused ion-beam milling with scanning electron microscopy. Here, we extend our previous studies on imaging yeast cells to image subcellular architecture in human melanoma cells and melanocytes at resolutions as high as approximately 6 and approximately 20 nm in the directions parallel and perpendicular, respectively, to the direction of ion-beam milling. The 3D images demonstrate the striking spatial relationships between specific organelles such as mitochondria and membranes of the endoplasmic reticulum, and the distribution of unique cellular components such as melanosomes. We also show that 10nm-sized gold particles and quantum dot particles with 7 nm-sized cores can be detected in single cross-sectional images. IA-SEM is thus a useful tool for imaging large mammalian cells in their entirety at resolutions in the nanometer range.
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Affiliation(s)
- Jurgen A W Heymann
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Building 50, Room 4306, Bethesda, MD 20892, USA
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27
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Parkinson DY, McDermott G, Etkin LD, Le Gros MA, Larabell CA. Quantitative 3-D imaging of eukaryotic cells using soft X-ray tomography. J Struct Biol 2008; 162:380-6. [PMID: 18387313 PMCID: PMC2505111 DOI: 10.1016/j.jsb.2008.02.003] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/31/2008] [Accepted: 02/01/2008] [Indexed: 11/20/2022]
Abstract
Imaging has long been one of the principal techniques used in biological and biomedical research. Indeed, the field of cell biology grew out of the first electron microscopy images of organelles in a cell. Since this landmark event, much work has been carried out to image and classify the organelles in eukaryotic cells using electron microscopy. Fluorescently labeled organelles can now be tracked in live cells, and recently, powerful light microscope techniques have pushed the limit of optical resolution to image single molecules. In this paper, we describe the use of soft X-ray tomography, a new tool for quantitative imaging of organelle structure and distribution in whole, fully hydrated eukaryotic Schizosaccharomyces pombe cells. In addition to imaging intact cells, soft X-ray tomography has the advantage of not requiring the use of any staining or fixation protocols--cells are simply transferred from their growth environment to a sample holder and immediately cryofixed. In this way the cells can be imaged in a near native state. Soft X-ray tomography is also capable of imaging relatively large numbers of cells in a short period of time, and is therefore a technique that has the potential to produce information on organelle morphology from statistically significant numbers of cells.
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Affiliation(s)
- Dilworth Y Parkinson
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 6-2100, Berkeley, CA 94720, USA
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28
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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