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Zheng T, Cai S. Recent technical advances in cellular cryo-electron tomography. Int J Biochem Cell Biol 2024; 175:106648. [PMID: 39181502 DOI: 10.1016/j.biocel.2024.106648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Understanding the in situ structure, organization, and interactions of macromolecules is essential for elucidating their functions and mechanisms of action. Cellular cryo-electron tomography (cryo-ET) is a cutting-edge technique that reveals in situ molecular-resolution architectures of macromolecules in their lifelike states. It also provides insights into the three-dimensional distribution of macromolecules and their spatial relationships with various subcellular structures. Thus, cellular cryo-ET bridges the gap between structural biology and cell biology. With rapid advancements, this technique achieved substantial improvements in throughput, automation, and resolution. This review presents the fundamental principles and methodologies of cellular cryo-ET, highlighting recent developments in sample preparation, data collection, and image processing. We also discuss emerging trends and potential future directions. As cellular cryo-ET continues to develop, it is set to play an increasingly vital role in structural cell biology.
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Affiliation(s)
- Tianyu Zheng
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shujun Cai
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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2
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Shao B, Killion M, Oliver A, Vang C, Zeleke F, Neikirk K, Vue Z, Garza-Lopez E, Shao JQ, Mungai M, Lam J, Williams Q, Altamura CT, Whiteside A, Kabugi K, McKenzie J, Ezedimma M, Le H, Koh A, Scudese E, Vang L, Marshall AG, Crabtree A, Tanghal JI, Stephens D, Koh HJ, Jenkins BC, Murray SA, Cooper AT, Williams C, Damo SM, McReynolds MR, Gaddy JA, Wanjalla CN, Beasley HK, Hinton A. Ablation of Sam50 is associated with fragmentation and alterations in metabolism in murine and human myotubes. J Cell Physiol 2024; 239:e31293. [PMID: 38770789 PMCID: PMC11324413 DOI: 10.1002/jcp.31293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 03/30/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024]
Abstract
The sorting and assembly machinery (SAM) Complex is responsible for assembling β-barrel proteins in the mitochondrial membrane. Comprising three subunits, Sam35, Sam37, and Sam50, the SAM complex connects the inner and outer mitochondrial membranes by interacting with the mitochondrial contact site and cristae organizing system complex. Sam50, in particular, stabilizes the mitochondrial intermembrane space bridging (MIB) complex, which is crucial for protein transport, respiratory chain complex assembly, and regulation of cristae integrity. While the role of Sam50 in mitochondrial structure and metabolism in skeletal muscle remains unclear, this study aims to investigate its impact. Serial block-face-scanning electron microscopy and computer-assisted 3D renderings were employed to compare mitochondrial structure and networking in Sam50-deficient myotubes from mice and humans with wild-type (WT) myotubes. Furthermore, autophagosome 3D structure was assessed in human myotubes. Mitochondrial metabolic phenotypes were assessed using Gas Chromatography-Mass Spectrometry-based metabolomics to explore differential changes in WT and Sam50-deficient myotubes. The results revealed increased mitochondrial fragmentation and autophagosome formation in Sam50-deficient myotubes compared to controls. Metabolomic analysis indicated elevated metabolism of propanoate and several amino acids, including ß-Alanine, phenylalanine, and tyrosine, along with increased amino acid and fatty acid metabolism in Sam50-deficient myotubes. Furthermore, impairment of oxidative capacity was observed upon Sam50 ablation in both murine and human myotubes, as measured with the XF24 Seahorse Analyzer. Collectively, these findings support the critical role of Sam50 in establishing and maintaining mitochondrial integrity, cristae structure, and mitochondrial metabolism. By elucidating the impact of Sam50-deficiency, this study enhances our understanding of mitochondrial function in skeletal muscle.
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Affiliation(s)
- Bryanna Shao
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Mason Killion
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Ashton Oliver
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Chia Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Faben Zeleke
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Edgar Garza-Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Jian-Qiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, Iowa, USA
| | - Margaret Mungai
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Jacob Lam
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Qiana Williams
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Christopher T Altamura
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Aaron Whiteside
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, Ohio, USA
| | - Kinuthia Kabugi
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Jessica McKenzie
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Maria Ezedimma
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Han Le
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Alice Koh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Estevão Scudese
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Larry Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Amber Crabtree
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Dominique Stephens
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Ho-Jin Koh
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - Brenita C Jenkins
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sandra A Murray
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anthonya T Cooper
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Clintoria Williams
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, Ohio, USA
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, Tennessee, USA
| | - Melanie R McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jennifer A Gaddy
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- US Department of Veterans Affairs, Tennessee Valley Healthcare Systems, Nashville, Tennessee, USA
| | - Celestine N Wanjalla
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Heather K Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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3
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [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] [Received: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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4
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Neikirk K, Lopez EG, Marshall AG, Alghanem A, Krystofiak E, Kula B, Smith N, Shao J, Katti P, Hinton A. Call to action to properly utilize electron microscopy to measure organelles to monitor disease. Eur J Cell Biol 2023; 102:151365. [PMID: 37864884 DOI: 10.1016/j.ejcb.2023.151365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/23/2023] Open
Abstract
This review provides an overview of the current methods for quantifying mitochondrial ultrastructure, including cristae morphology, mitochondrial contact sites, and recycling machinery and a guide to utilizing electron microscopy to effectively measure these organelles. Quantitative analysis of mitochondrial ultrastructure is essential for understanding mitochondrial biology and developing therapeutic strategies for mitochondrial-related diseases. Techniques such as transmission electron microscopy (TEM) and serial block face-scanning electron microscopy, as well as how they can be combined with other techniques including confocal microscopy, super-resolution microscopy, and correlative light and electron microscopy are discussed. Beyond their limitations and challenges, we also offer specific magnifications that may be best suited for TEM analysis of mitochondrial, endoplasmic reticulum, and recycling machinery. Finally, perspectives on future quantification methods are offered.
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Affiliation(s)
- Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Edgar-Garza Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Ahmad Alghanem
- King Abdullah International Medical Research Center (KAIMRC), Ali Al Arini, Ar Rimayah, Riyadh 11481, Saudi Arabia
| | - Evan Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Bartosz Kula
- Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester, School of Medicine and Dentistry, Rochester 14642, USA
| | - Nathan Smith
- Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester, School of Medicine and Dentistry, Rochester 14642, USA
| | - Jianqiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA, USA
| | - Prasanna Katti
- National Heart, Lung and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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5
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Shao B, Killion M, Oliver A, Vang C, Zeleke F, Neikirk K, Vue Z, Garza-Lopez E, Shao JQ, Mungai M, Lam J, Williams Q, Altamura CT, Whiteside A, Kabugi K, McKenzie J, Koh A, Scudese E, Vang L, Marshall AG, Crabtree A, Tanghal JI, Stephens D, Koh HJ, Jenkins BC, Murray SA, Cooper AT, Williams C, Damo SM, McReynolds MR, Gaddy JA, Wanjalla CN, Beasley HK, Hinton A. Ablation of Sam50 is associated with fragmentation and alterations in metabolism in murine and human myotubes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541602. [PMID: 37292887 PMCID: PMC10245823 DOI: 10.1101/2023.05.20.541602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Sorting and Assembly Machinery (SAM) Complex is responsible for assembling β-barrel proteins in the mitochondrial membrane. Comprising three subunits, Sam35, Sam37, and Sam50, the SAM complex connects the inner and outer mitochondrial membranes by interacting with the mitochondrial contact site and cristae organizing system (MICOS) complex. Sam50, in particular, stabilizes the mitochondrial intermembrane space bridging (MIB) complex, which is crucial for protein transport, respiratory chain complex assembly, and regulation of cristae integrity. While the role of Sam50 in mitochondrial structure and metabolism in skeletal muscle remains unclear, this study aims to investigate its impact. Serial block-face-scanning electron microscopy (SBF-SEM) and computer-assisted 3D renderings were employed to compare mitochondrial structure and networking in Sam50-deficient myotubes from mice and humans with wild-type (WT) myotubes. Furthermore, autophagosome 3D structure was assessed in human myotubes. Mitochondrial metabolic phenotypes were assessed using Gas Chromatography-Mass Spectrometry-based metabolomics to explore differential changes in WT and Sam50-deficient myotubes. The results revealed increased mitochondrial fragmentation and autophagosome formation in Sam50-deficient myotubes compared to controls. Metabolomic analysis indicated elevated metabolism of propanoate and several amino acids, including ß-Alanine, phenylalanine, and tyrosine, along with increased amino acid and fatty acid metabolism in Sam50-deficient myotubes. Furthermore, impairment of oxidative capacity was observed upon Sam50 ablation in both murine and human myotubes, as measured with the XF24 Seahorse Analyzer. Collectively, these findings support the critical role of Sam50 in establishing and maintaining mitochondrial integrity, cristae structure, and mitochondrial metabolism. By elucidating the impact of Sam50-deficiency, this study enhances our understanding of mitochondrial function in skeletal muscle.
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Affiliation(s)
- Bryanna Shao
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Mason Killion
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ashton Oliver
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Chia Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Faben Zeleke
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Edgar Garza-Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Jian-Qiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA, 52242, USA
| | - Margaret Mungai
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Jacob Lam
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Qiana Williams
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Christopher T Altamura
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Aaron Whiteside
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, OH 45435 USA
| | - Kinuthia Kabugi
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jessica McKenzie
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Alice Koh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Estevão Scudese
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Larry Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Amber Crabtree
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | | | - Dominique Stephens
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ho-Jin Koh
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209
| | - Brenita C Jenkins
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
| | - Sandra A Murray
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Anthonya T Cooper
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Clintoria Williams
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, OH 45435 USA
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, TN, 37208, USA
| | - Melanie R McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
| | - Jennifer A Gaddy
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Tennessee Valley Healthcare Systems, U.S. Department of Veterans Affairs, Nashville, TN, 37212, USA
| | - Celestine N Wanjalla
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Heather K Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
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6
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Lin C, Zhang L, Zhang Z, Jiang Y, Li X. Locating cellular contents during cryoFIB milling using cellular secondary-electron imaging. J Struct Biol 2023; 215:108005. [PMID: 37495195 DOI: 10.1016/j.jsb.2023.108005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Cryo-electron tomography (cryoET) is a powerful technology that allows in-situ observation of the molecular structure of tissues and cells. Cryo-focused ion beam (cryoFIB) milling plays an important role in the preparation of high-quality thin lamellar samples for cryoET studies, thus, promoting the rapid development of cryoET in recent years. However, locating the regions of interest in a large cell or tissue during cryoFIB milling remains a major challenge limiting cryoET applications on arbitrary biological samples. Here, we report an on-the-fly localization method based on cellular secondary electron imaging (CSEI), which is derived from a basic imaging function of the cryoFIB instruments and enables high-contrast imaging of the cellular contents of frozen-hydrated biological samples. Moreover, CSEI does not require fluorescent labels and additional devices. The present study discusses the imaging principles and settings for optimizing CSEI. Tests on several commercially available cryoFIB instruments demonstrated that CSEI was feasible on mainstream instruments to observe all types of cellular contents and reliable under different milling conditions. We established a simple milling-localization workflow and tested it using the basal body of Chlamydomonas reinhardtii.
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Affiliation(s)
- Chao Lin
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China
| | - Li Zhang
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China
| | - Ziying Zhang
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China
| | - Yifeng Jiang
- ZEISS Microscopy Customer Center, Beijing laboratory, Beijing 100088, China
| | - Xueming Li
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China.
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7
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Marshall AG, Damo SM, Hinton A. Revisiting focused ion beam scanning electron microscopy. Trends Biochem Sci 2023; 48:585-586. [PMID: 36990957 DOI: 10.1016/j.tibs.2023.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 02/23/2023] [Indexed: 03/29/2023]
Affiliation(s)
- Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, TN, 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA.
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8
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Collinson LM, Bosch C, Bullen A, Burden JJ, Carzaniga R, Cheng C, Darrow MC, Fletcher G, Johnson E, Narayan K, Peddie CJ, Winn M, Wood C, Patwardhan A, Kleywegt GJ, Verkade P. Volume EM: a quiet revolution takes shape. Nat Methods 2023; 20:777-782. [PMID: 37076630 PMCID: PMC7614633 DOI: 10.1038/s41592-023-01861-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Volume Electron Microscopy is a group of techniques that reveal the 3D ultrastructure of cells and tissues through volumes greater than 1 cubic micron. A burgeoning grass roots community effort is fast building the profile, and revealing the impact, of vEM technology in the life sciences and clinical research.
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Affiliation(s)
- Lucy M Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, UK.
| | - Carles Bosch
- Sensory Circuits and Neurotechnology Laboratory, Francis Crick Institute, London, UK
| | - Anwen Bullen
- UCL Ear Institute, University College London, London, UK
| | - Jemima J Burden
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Raffaella Carzaniga
- Zeiss Research Microscopy Solutions, Carl Zeiss Ltd, Zeiss Group, Cambourne, UK
| | | | - Michele C Darrow
- Artificial Intelligence & Informatics, The Rosalind Franklin Institute, Didcot, UK
- SPT Labtech Ltd., Melbourn, UK
| | | | - Errin Johnson
- Dunn School Bioimaging Facility, Sir William Dunn School of Pathology, Oxford University, Oxford, UK
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, UK
| | - Martyn Winn
- UKRI-STFC, Rutherford Appleton Laboratory, Didcot, UK
| | - Charles Wood
- Future Technology Centre, School of Mechanical and Design Engineering, University of Portsmouth, Portsmouth, UK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK.
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9
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de Beer M, Daviran D, Roverts R, Rutten L, Macías-Sánchez E, Metz JR, Sommerdijk N, Akiva A. Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP. Commun Biol 2023; 6:510. [PMID: 37169904 PMCID: PMC10175257 DOI: 10.1038/s42003-023-04887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/28/2023] [Indexed: 05/13/2023] Open
Abstract
Cryo-correlative light and electron microscopy (cryoCLEM) is a powerful strategy to high resolution imaging in the unperturbed hydrated state. In this approach fluorescence microscopy aids localizing the area of interest, and cryogenic focused ion beam/scanning electron microscopy (cryoFIB/SEM) allows preparation of thin cryo-lamellae for cryoET. However, the current method cannot be accurately applied on bulky (3D) samples such as tissues and organoids. 3D cryo-correlative imaging of large volumes is needed to close the resolution gap between cryo-light microscopy and cryoET, placing sub-nanometer observations in a larger biological context. Currently technological hurdles render 3D cryoCLEM an unexplored approach. Here we demonstrate a cryoCLEM workflow for tissues, correlating cryo-Airyscan confocal microscopy with 3D cryoFIB/SEM volume imaging. Accurate correlation is achieved by imprinting a FinderTOP pattern in the sample surface during high pressure freezing, and allows precise targeting for cryoFIB/SEM volume imaging.
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Affiliation(s)
- Marit de Beer
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Deniz Daviran
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rona Roverts
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luco Rutten
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elena Macías-Sánchez
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Stratigraphy and Paleontology, University of Granada, Granada, Spain
| | - Juriaan R Metz
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Anat Akiva
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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10
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Pham TLB, Nguyen DPH, Luu TTT, Nguyen LS, Binh NT, Nguyen QD, Tran PA. Encapsulation of Human Umbilical Cord Mesenchymal Stem Cells in LunaGel Photocrosslinkable Extracellular Matrix and Subcutaneous Transplantation in Mice. Biomedicines 2023; 11:biomedicines11041158. [PMID: 37189776 DOI: 10.3390/biomedicines11041158] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Stem cells have significant potential in regenerative medicines. However, a major issue with implanting stem cells in the regeneration of new tissue is the methods to implant them and cell viability and functions before and after implantation. Here we developed a simple yet effective method that used photo-crosslinkable gelatin-based hydrogel (LunaGelTM) as a scaffold for the encapsulation, expansion, and eventually, transplantation of human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) into mice subcutaneously. We demonstrated the proliferation and maintenance of the original expression of mesenchymal stem cell markers as well as the ability to differentiate into mesoderm-derived cells. The hydrogel was highly stable with no signs of degradation after 20 days in PBS. The hUC-MSCs remained viable after transplantation into mice's subcutaneous pockets and migrated to integrate with the surrounding tissues. We showed a collagen-rich layer surrounding the transplanted cell-laden scaffold indicating the effects of growth factors secreted by the hUC-MSCs. A connective tissue layer was found between the implanted cell-laden scaffold and the collagen layer, and immunohistochemical staining results suggested that this tissue was derived from the MSCs which migrated from within the scaffold. The results, thus, also suggested a protective effect the scaffold has on the encapsulated cells from the antibodies and cytotoxic cells of the host immune system.
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Affiliation(s)
- Truc Le-Buu Pham
- Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | | | - Thao Thi-Thu Luu
- Histology-Embryology-Pathology Department, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Luong Si Nguyen
- Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Trong Binh
- Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Quan Dang Nguyen
- Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Phong Anh Tran
- Interface Science and Materials Engineering Group, School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane City, QLD 4000, Australia
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11
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Wang S, Zhou H, Chen W, Jiang Y, Yan X, You H, Li X. CryoFIB milling large tissue samples for cryo-electron tomography. Sci Rep 2023; 13:5879. [PMID: 37041258 PMCID: PMC10090186 DOI: 10.1038/s41598-023-32716-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/31/2023] [Indexed: 04/13/2023] Open
Abstract
Cryo-electron tomography (cryoET) is a powerful tool for exploring the molecular structure of large organisms. However, technical challenges still limit cryoET applications on large samples. In particular, localization and cutting out objects of interest from a large tissue sample are still difficult steps. In this study, we report a sample thinning strategy and workflow for tissue samples based on cryo-focused ion beam (cryoFIB) milling. This workflow provides a full solution for isolating objects of interest by starting from a millimeter-sized tissue sample and ending with hundred-nanometer-thin lamellae. The workflow involves sample fixation, pre-sectioning, a two-step milling strategy, and localization of the object of interest using cellular secondary electron imaging (CSEI). The milling strategy consists of two steps, a coarse milling step to improve the milling efficiency, followed by a fine milling step. The two-step milling creates a furrow-ridge structure with an additional conductive Pt layer to reduce the beam-induced charging issue. CSEI is highlighted in the workflow, which provides on-the-fly localization during cryoFIB milling. Tests of the complete workflow were conducted to demonstrate the high efficiency and high feasibility of the proposed method.
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Affiliation(s)
- Sihan Wang
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing, 100084, China
- Advanced Innovation Center for Structural Biology, Beijing, 100084, China
| | - Heng Zhou
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing, 100084, China
- Advanced Innovation Center for Structural Biology, Beijing, 100084, China
| | - Wei Chen
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Yifeng Jiang
- ZEISS Microscopy Customer Center, Beijing Laboratory, Beijing, 100088, China
| | - Xuzhen Yan
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, 100050, China
| | - Hong You
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, 100050, China.
| | - Xueming Li
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Beijing, 100084, China.
- Advanced Innovation Center for Structural Biology, Beijing, 100084, China.
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12
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Czymmek KJ, Duncan KE, Berg H. Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:245-255. [PMID: 36947723 DOI: 10.1094/mpmi-10-22-0208-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Keith E Duncan
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Howard Berg
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
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13
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Perdigão LMA, Ho EML, Cheng ZC, Yee NBY, Glen T, Wu L, Grange M, Dumoux M, Basham M, Darrow MC. Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy images. BIOLOGICAL IMAGING 2023; 3:e9. [PMID: 38487692 PMCID: PMC10936406 DOI: 10.1017/s2633903x23000119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2024]
Abstract
An emergent volume electron microscopy technique called cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological structures by building a three-dimensional picture of biological samples at mesoscale resolution. This is achieved by collecting consecutive SEM images after successive rounds of FIB milling that expose a new surface after each milling step. Due to instrumental limitations, some image processing is necessary before 3D visualization and analysis of the data is possible. SEM images are affected by noise, drift, and charging effects, that can make precise 3D reconstruction of biological features difficult. This article presents Okapi-EM, an open-source napari plugin developed to process and analyze cryogenic serial pFIB/SEM images. Okapi-EM enables automated image registration of slices, evaluation of image quality metrics specific to pFIB-SEM imaging, and mitigation of charging artifacts. Implementation of Okapi-EM within the napari framework ensures that the tools are both user- and developer-friendly, through provision of a graphical user interface and access to Python programming.
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Affiliation(s)
- Luís M. A. Perdigão
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
| | - Elaine M. L. Ho
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
| | - Zhiyuan C. Cheng
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
- School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Neville B.-Y. Yee
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
| | - Thomas Glen
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Liang Wu
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michael Grange
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Mark Basham
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
- Diamond Light Source, Didcot, UK
| | - Michele C. Darrow
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
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14
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [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: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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15
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Kahil K, Kaplan-Ashiri I, Wolf SG, Rechav K, Weiner S, Addadi L. Elemental compositions of sea urchin larval cell vesicles evaluated by cryo-STEM-EDS and cryo-SEM-EDS. Acta Biomater 2023; 155:482-490. [PMID: 36375785 DOI: 10.1016/j.actbio.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/15/2022]
Abstract
During spicule formation in sea urchin larvae, calcium ions translocate within the primary mesenchymal cells (PMCs) from endocytosed seawater vacuoles to various organelles and vesicles where they accumulate, and subsequently precipitate. During this process, calcium ions are concentrated by more than three orders of magnitude, while other abundant ions (Na, Mg) must be removed. To obtain information about the overall ion composition in the vesicles, we used quantitative cryo-SEM-EDS and cryo-STEM-EDS analyzes. For cryo-STEM-EDS, thin (500 nm) frozen hydrated lamellae of PMCs were fabricated using cryo-focused ion beam-SEM. The lamellae were then loaded into a cryo-TEM, imaged and the ion composition of electron dense bodies was measured. Analyzes performed on 18 Ca-rich particles/particle clusters from 6 cells contained Ca, Na, Mg, S and P in different ratios. Surprisingly, all the Ca-rich particles contained P in amounts up to almost 1:1 of Ca. These cryo-STEM-EDS results were qualitatively confirmed by cryo-SEM-EDS analyzes of 310 vesicles, performed on high pressure frozen and cryo-planed samples. We discuss the advantages and limitations of the two techniques, and their potential applicability, especially to study ion transport pathways and ion trafficking in cells involved in mineralization. STATEMENT OF SIGNIFICANCE: The 'inorganic side of life', encompassing ion trafficking and ion storage in soft tissues of organisms, is a generally overlooked problem. Addressing such a problem becomes possible through the application of innovative techniques, performed in cryogenic conditions, which preserve the tissues in quasi-physiological state. We developed here a set of analytical tools, cryo-SEM-EDS, and cryo-STEM-EDS, which allow reconstructing the ion composition inside vesicles in sea urchin larval cells, on their way to deposit mineral in the skeletons. The techniques are complex, and we evaluate here the advantages and disadvantages of each technique. The methodologies that we are developing here can be applied to other cells and other pathways as well, eventually leading to quantitative elemental analyzes of tissues under cryogenic conditions.
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Affiliation(s)
- Keren Kahil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ifat Kaplan-Ashiri
- Department of Chemical Research Support, Weizmann Institute, Rehovot 7610001, Israel
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute, Rehovot 7610001, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute, Rehovot 7610001, Israel
| | - Steve Weiner
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Lia Addadi
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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16
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Kapteijn R, Shitut S, Aschmann D, Zhang L, de Beer M, Daviran D, Roverts R, Akiva A, van Wezel GP, Kros A, Claessen D. Endocytosis-like DNA uptake by cell wall-deficient bacteria. Nat Commun 2022; 13:5524. [PMID: 36138004 PMCID: PMC9500057 DOI: 10.1038/s41467-022-33054-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022] Open
Abstract
Horizontal gene transfer in bacteria is widely believed to occur via conjugation, transduction and transformation. These mechanisms facilitate the passage of DNA across the protective cell wall using sophisticated machinery. Here, we report that cell wall-deficient bacteria can engulf DNA and other extracellular material via an endocytosis-like process. Specifically, we show that L-forms of the filamentous actinomycete Kitasatospora viridifaciens can take up plasmid DNA, polysaccharides (dextran) and 150-nm lipid nanoparticles. The process involves invagination of the cytoplasmic membrane, leading to formation of intracellular vesicles that encapsulate extracellular material. DNA uptake is not affected by deletion of genes homologous to comEC and comEA, which are required for natural transformation in other species. However, uptake is inhibited by sodium azide or incubation at 4 °C, suggesting the process is energy-dependent. The encapsulated materials are released into the cytoplasm upon degradation of the vesicle membrane. Given that cell wall-deficient bacteria are considered a model for early life forms, our work reveals a possible mechanism for primordial cells to acquire food or genetic material before invention of the bacterial cell wall. Horizontal gene transfer in bacteria can occur through mechanisms such as conjugation, transduction and transformation, which facilitate the passage of DNA across the cell wall. Here, Kapteijn et al. show that cell wall-deficient bacteria can take up DNA and other extracellular materials via an endocytosis-like process.
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Affiliation(s)
- Renée Kapteijn
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands
| | - Shraddha Shitut
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands
| | - Dennis Aschmann
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, Leiden, The Netherlands
| | - Le Zhang
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands
| | - Marit de Beer
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Deniz Daviran
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Rona Roverts
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Anat Akiva
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Nijmegen, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands.
| | - Alexander Kros
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, Leiden, The Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, Leiden, The Netherlands.
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17
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Varsano N, Wolf SG. Electron microscopy of cellular ultrastructure in three dimensions. Curr Opin Struct Biol 2022; 76:102444. [PMID: 36041268 DOI: 10.1016/j.sbi.2022.102444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 11/03/2022]
Abstract
Electron microscopy in three dimensions (3D) of cells and tissues can be essential for understanding the ultrastructural aspects of biological processes. The quest for 3D information reveals challenges at many stages of the workflow, from sample preparation, to imaging, data analysis and segmentation. Here, we outline several available methods, including volume SEM imaging, cryo-TEM and cryo-STEM tomography, each one occupying a different domain in the basic tradeoff between field-of-view and resolution. We discuss the considerations for choosing a suitable method depending on research needs and highlight recent developments that are essential for making 3D volume imaging of cells and tissues a standard tool for cellular and structural biologists.
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Affiliation(s)
- Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl St., Rehovot 76100, Israel
| | - Sharon Grayer Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl St., Rehovot 76100, Israel.
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18
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Examining atherosclerotic lesions in three dimensions at the nanometer scale with cryo-FIB-SEM. Proc Natl Acad Sci U S A 2022; 119:e2205475119. [PMID: 35939716 PMCID: PMC9407640 DOI: 10.1073/pnas.2205475119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We employed in a correlative manner an unconventional combination of methods, comprising cathodoluminescence, cryo-scanning electron microscopy (SEM), and cryo-focused ion beam (FIB)-SEM, to examine the volumes of thousands of cubed micrometers from rabbit atherosclerotic tissues, maintained in close-to-native conditions, with a resolution of tens of nanometers. Data from three different intralesional regions, at the media-lesion interface, in the core, and toward the lumen, were analyzed following segmentation and volume or surface representation. The media-lesion interface region is rich in cells and lipid droplets, whereas the core region is markedly richer in crystals and has lower cell density. In the three regions, thin crystals appear to be associated with intracellular or extracellular lipid droplets and multilamellar bodies. Large crystals are independently positioned in the tissue, not associated with specific cellular components. This extensive evidence strongly supports the idea that the lipid droplet surfaces and the outer membranes of multilamellar bodies play a role in cholesterol crystal nucleation and growth and that crystal formation occurs, in part, inside cells. The correlative combination of methods that allowed the direct examination of cholesterol crystals and lipid deposits in the atherosclerotic lesions may be similarly used for high-resolution examination of other tissues containing pathological or physiological cholesterol deposits.
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19
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Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals. CHEMISTRY 2022. [DOI: 10.3390/chemistry4030059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.
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20
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Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM. Volume electron microscopy. NATURE REVIEWS. METHODS PRIMERS 2022; 2:51. [PMID: 37409324 PMCID: PMC7614724 DOI: 10.1038/s43586-022-00131-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 07/07/2023]
Abstract
Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.
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Affiliation(s)
- Christopher J. Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kimberly Meechan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Present address: Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristina D. Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Constantin Pape
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert G. Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Yannick Schwab
- Cell Biology and Biophysics Unit/ Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Aubrey Aubrey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Lucy M. Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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21
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Scher N, Rechav K, Paul-Gilloteaux P, Avinoam O. Sample preparation and image registration for correlative cryo-FM and cryo-FIB-SEM of plunge-frozen mammalian cells. STAR Protoc 2022; 3:101142. [PMID: 35199027 PMCID: PMC8844706 DOI: 10.1016/j.xpro.2022.101142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
We recently demonstrated how lipid droplets can serve as in situ fiducials for correlating cryo-fluorescence microscopy (cryo-FM) and cryo-focused ion beam scanning electron microscopy (cryo-FIB-SEM) datasets of mammalian cells grown on grids. Here we describe a step-by-step protocol for correlative cryo-FM and cryo-FIB-SEM, starting from sample preparation of C2C12 cell line, followed by imaging with cryo-FM and cryo-FIB-SEM. Finally, we detail how to perform the 3D-correlation with sub-micron accuracy. For complete details on the use and execution of this profile, please refer to Scher et al. (2021).
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Affiliation(s)
- Nadav Scher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Perrine Paul-Gilloteaux
- Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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22
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Sexton DL, Burgold S, Schertel A, Tocheva EI. Super-resolution confocal cryo-CLEM with cryo-FIB milling for in situ imaging of Deinococcus radiodurans. Curr Res Struct Biol 2022; 4:1-9. [PMID: 34977598 PMCID: PMC8688812 DOI: 10.1016/j.crstbi.2021.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022] Open
Abstract
Studying bacterial cell envelope architecture with electron microscopy is challenging due to the poor preservation of microbial ultrastructure with traditional methods. Here, we established and validated a super-resolution cryo-correlative light and electron microscopy (cryo-CLEM) method, and combined it with cryo-focused ion beam (cryo-FIB) milling and scanning electron microscopy (SEM) volume imaging to structurally characterize the bacterium Deinococcus radiodurans. Subsequent cryo-electron tomography (cryo-ET) revealed an unusual diderm cell envelope architecture with a thick layer of peptidoglycan (PG) between the inner and outer membranes, an additional periplasmic layer, and a proteinaceous surface S-layer. Cells grew in tetrads, and division septa were formed by invagination of the inner membrane (IM), followed by a thick layer of PG. Cytoskeletal filaments, FtsA and FtsZ, were observed at the leading edges of constricting septa. Numerous macromolecular complexes were found associated with the cytoplasmic side of the IM. Altogether, our study revealed several unique ultrastructural features of D. radiodurans cells, opening new lines of investigation into the physiology and evolution of the bacterium. User-friendly, commercially available method for correlative cryo-super resolution light microscopy (LM) and cryo-FIB-milling. Cryo-super resolution LM, cryo-FIB milling, cryo-SEM volume imaging, and cryo-electron tomography (cryo-ET) to study Deinococcus radiodurans. Unique D. radiodurans cell envelope is composed of two membranes, thick peptidoglycan, an additional layer, and an S-layer. Cytoskeletal filaments FtsA and FtsZ were observed at the leading edges of division septa.
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Affiliation(s)
- Danielle L Sexton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | | | | | - Elitza I Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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23
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Friedman O, Böhm A, Rechav K, Pinkas I, Brumfeld V, Pass G, Weiner S, Addadi L. Structural Organization of Xanthine Crystals in the Median Ocellus of a Member of the Ancestral Insect Group Archaeognatha. J Struct Biol 2022; 214:107834. [DOI: 10.1016/j.jsb.2022.107834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
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24
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Kahil K, Weiner S, Addadi L, Gal A. Ion Pathways in Biomineralization: Perspectives on Uptake, Transport, and Deposition of Calcium, Carbonate, and Phosphate. J Am Chem Soc 2021; 143:21100-21112. [PMID: 34881565 PMCID: PMC8704196 DOI: 10.1021/jacs.1c09174] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 12/19/2022]
Abstract
Minerals are formed by organisms in all of the kingdoms of life. Mineral formation pathways all involve uptake of ions from the environment, transport of ions by cells, sometimes temporary storage, and ultimately deposition in or outside of the cells. Even though the details of how all this is achieved vary enormously, all pathways need to respect both the chemical limitations of ion manipulation, as well as the many "housekeeping" roles of ions in cell functioning. Here we provide a chemical perspective on the biological pathways of biomineralization. Our approach is to compare and contrast the ion pathways involving calcium, phosphate, and carbonate in three very different organisms: the enormously abundant unicellular marine coccolithophores, the well investigated sea urchin larval model for single crystal formation, and the complex pathways used by vertebrates to form their bones. The comparison highlights both common and unique processes. Significantly, phosphate is involved in regulating calcium carbonate deposition and carbonate is involved in regulating calcium phosphate deposition. One often overlooked commonality is that, from uptake to deposition, the solutions involved are usually supersaturated. This therefore requires not only avoiding mineral deposition where it is not needed but also exploiting this saturated state to produce unstable mineral precursors that can be conveniently stored, redissolved, and manipulated into diverse shapes and upon deposition transformed into more ordered and hence often functional final deposits.
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Affiliation(s)
- Keren Kahil
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Steve Weiner
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Lia Addadi
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Assaf Gal
- Department
of Chemical and Structural Biology and Department of Plant and Environmental
Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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25
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Varsano N, Kahil K, Haimov H, Rechav K, Addadi L, Weiner S. Characterization of the growth plate-bone interphase region using cryo-FIB SEM 3D volume imaging. J Struct Biol 2021; 213:107781. [PMID: 34411695 DOI: 10.1016/j.jsb.2021.107781] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/27/2022]
Abstract
The interphase region at the base of the growth plate includes blood vessels, cells and mineralized tissues. In this region, cartilage is mineralized and replaced with bone. Blood vessel extremities permeate this space providing nutrients, oxygen and signaling factors. All these different components form a complex intertwined 3D structure. Here we use cryo-FIB SEM to elaborate this 3D structure without removing the water. As it is challenging to image mineralized and unmineralized tissues in a hydrated state, we provide technical details of the parameters used. We obtained two FIB SEM image stacks that show that the blood vessels are in intimate contact not only with cells, but in some locations also with mineralized tissues. There are abundant red blood cells at the extremities of the vessels. We also documented large multinucleated cells in contact with mineralized cartilage and possibly also with bone. We observed membrane bound mineralized particles in these cells, as well as in blood serum, but not in the hypertrophic chondrocytes. We confirm that there is an open pathway from the blood vessel extremities to the mineralizing cartilage. Based on the sparsity of the mineralized particles, we conclude that mainly ions in solution are used for mineralizing cartilage and bone, but these are augmented by the supply of mineralized particles.
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Affiliation(s)
- Neta Varsano
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Keren Kahil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Heden Haimov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lia Addadi
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Steve Weiner
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
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26
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Scher N, Rechav K, Paul-Gilloteaux P, Avinoam O. In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging. iScience 2021; 24:102714. [PMID: 34258551 PMCID: PMC8253967 DOI: 10.1016/j.isci.2021.102714] [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] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 11/26/2022] Open
Abstract
Imaging of cells and tissues has improved significantly over the last decade. Dual-beam instruments with a focused ion beam mounted on a scanning electron microscope (FIB-SEM), offering high-resolution 3D imaging of large volumes and fields-of-view are becoming widely used in the life sciences. FIB-SEM has most recently been implemented on fully hydrated, cryo-immobilized, biological samples. Correlative light and electron microscopy workflows combining fluorescence microscopy (FM) with FIB-SEM imaging exist, whereas workflows combining cryo-FM and cryo-FIB-SEM imaging are not yet commonly available. Here, we demonstrate that fluorescently labeled lipid droplets can serve as in situ fiducial markers for correlating cryo-FM and FIB-SEM datasets and that this approach can be used to target the acquisition of large FIB-SEM stacks spanning tens of microns under cryogenic conditions. We also show that cryo-FIB-SEM imaging is particularly informative for questions related to organelle structure and inter-organellar contacts, nuclear organization, and mineral deposits in cells.
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Affiliation(s)
- Nadav Scher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Perrine Paul-Gilloteaux
- Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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27
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Weiner S, Raguin E, Shahar R. High resolution 3D structures of mineralized tissues in health and disease. Nat Rev Endocrinol 2021; 17:307-316. [PMID: 33758360 DOI: 10.1038/s41574-021-00479-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 02/06/2023]
Abstract
A thorough knowledge of the structures of healthy mineralized tissues, such as bone or cartilage, is key to understanding the pathological changes occurring during disease. Such knowledge enables the underlying mechanisms that are responsible for pathology to be pinpointed. One high-resolution 3D method in particular - focused ion beam-scanning electron microscopy (FIB-SEM) - has fundamentally changed our understanding of healthy vertebrate mineralized tissues. FIB-SEM can be used to study demineralized matrix, the hydrated components of tissue (including cells) using cryo-fixation and even untreated mineralized tissue. The latter requires minimal sample preparation, making it possible to study enough samples to carry out studies capable of detecting statistically significant differences - a pre-requisite for the study of pathological tissues. Here, we present an imaging and characterization strategy for tissue structures at different length scales, describe new insights obtained on healthy mineralized tissues using FIB-SEM, and suggest future research directions for both healthy and diseased mineralized tissues.
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Affiliation(s)
- Steve Weiner
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Emeline Raguin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Shahar
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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28
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Chiou AE, Hinckley JA, Khaitan R, Varsano N, Wang J, Malarkey HF, Hernandez CJ, Williams RM, Estroff LA, Weiner S, Addadi L, Wiesner UB, Fischbach C. Fluorescent Silica Nanoparticles to Label Metastatic Tumor Cells in Mineralized Bone Microenvironments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2001432. [PMID: 32462807 PMCID: PMC7704907 DOI: 10.1002/smll.202001432] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 05/05/2023]
Abstract
During breast cancer bone metastasis, tumor cells interact with bone microenvironment components including inorganic minerals. Bone mineralization is a dynamic process and varies spatiotemporally as a function of cancer-promoting conditions such as age and diet. The functional relationship between skeletal dissemination of tumor cells and bone mineralization, however, is unclear. Standard histological analysis of bone metastasis frequently relies on prior demineralization of bone, while methods that maintain mineral are often harsh and damage fluorophores commonly used to label tumor cells. Here, fluorescent silica nanoparticles (SNPs) are introduced as a robust and versatile labeling strategy to analyze tumor cells within mineralized bone. SNP uptake and labeling efficiency of MDA-MB-231 breast cancer cells is characterized with cryo-scanning electron microscopy and different tissue processing methods. Using a 3D in vitro model of marrow-containing, mineralized bone as well as an in vivo model of bone metastasis, SNPs are demonstrated to allow visualization of labeled tumor cells in mineralized bone using various imaging modalities including widefield, confocal, and light sheet microscopy. This work suggests that SNPs are valuable tools to analyze tumor cells within mineralized bone using a broad range of bone processing and imaging techniques with the potential to increase the understanding of bone metastasis.
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Affiliation(s)
- Aaron E Chiou
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Joshua A Hinckley
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Rupal Khaitan
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Neta Varsano
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Jonathan Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Henry F Malarkey
- Department of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher J Hernandez
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Rebecca M Williams
- Biotechnology Resource Center Imaging Facility, Cornell University, Ithaca, NY, 14853, USA
| | - Lara A Estroff
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
| | - Steve Weiner
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lia Addadi
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ulrich B Wiesner
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Claudia Fischbach
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
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29
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Elad N, Wolf SG. Maintaining Context in Ice: Cryo-EM/ET Workflow Optimizations. Structure 2021; 28:1179-1181. [PMID: 33147474 DOI: 10.1016/j.str.2020.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue of Structure, breakthroughs in cryo-EM/ET research are presented. Klebl et al. (2020) demonstrate how speed in sample vitrification impacts the quality of macromolecular particles in resultant cryo-EM grids. Wu et al. (2020) combine fluorescence, ion beam milling, and tomography to unravel unique features in vitrified yeast cells.
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Affiliation(s)
- Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.
| | - Sharon Grayer Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.
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30
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Multiscale Electron Microscopy for the Study of Viral Replication Organelles. Viruses 2021; 13:v13020197. [PMID: 33525547 PMCID: PMC7912242 DOI: 10.3390/v13020197] [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] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022] Open
Abstract
During infection with positive-strand RNA viruses, viral RNA synthesis associates with modified intracellular membranes that form unique and captivating structures in the cytoplasm of the infected cell. These viral replication organelles (ROs) play a key role in the replicative cycle of important human pathogens like coronaviruses, enteroviruses, or flaviviruses. From their discovery to date, progress in our understanding of viral ROs has closely followed new developments in electron microscopy (EM). This review gives a chronological account of this progress and an introduction to the different EM techniques that enabled it. With an ample repertoire of imaging modalities, EM is nowadays a versatile technique that provides structural and functional information at a wide range of scales. Together with well-established approaches like electron tomography or labeling methods, we examine more recent developments, such as volume scanning electron microscopy (SEM) and in situ cryotomography, which are only beginning to be applied to the study of viral ROs. We also highlight the first cryotomography analyses of viral ROs, which have led to the discovery of macromolecular complexes that may serve as RO channels that control the export of newly-made viral RNA. These studies are key first steps towards elucidating the macromolecular complexity of viral ROs.
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31
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Bayguinov PO, Fisher MR, Fitzpatrick JAJ. Assaying three-dimensional cellular architecture using X-ray tomographic and correlated imaging approaches. J Biol Chem 2020; 295:15782-15793. [PMID: 32938716 PMCID: PMC7667966 DOI: 10.1074/jbc.rev120.009633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Much of our understanding of the spatial organization of and interactions between cellular organelles and macromolecular complexes has been the result of imaging studies utilizing either light- or electron-based microscopic analyses. These classical approaches, while insightful, are nonetheless limited either by restrictions in resolution or by the sheer complexity of generating multidimensional data. Recent advances in the use and application of X-rays to acquire micro- and nanotomographic data sets offer an alternative methodology to visualize cellular architecture at the nanoscale. These new approaches allow for the subcellular analyses of unstained vitrified cells and three-dimensional localization of specific protein targets and have served as an essential tool in bridging light and electron correlative microscopy experiments. Here, we review the theory, instrumentation details, acquisition principles, and applications of both soft X-ray tomography and X-ray microscopy and how the use of these techniques offers a succinct means of analyzing three-dimensional cellular architecture. We discuss some of the recent work that has taken advantage of these approaches and detail how they have become integral in correlative microscopy workflows.
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Affiliation(s)
- Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Max R Fisher
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA; Departments of Cell Biology and Physiology and Neuroscience, Washington University School of Medicine, Saint Louis, Missouri, USA; Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA.
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32
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Chang IY, Rahman M, Harned A, Cohen-Fix O, Narayan K. Cryo-fluorescence microscopy of high-pressure frozen C. elegans enables correlative FIB-SEM imaging of targeted embryonic stages in the intact worm. Methods Cell Biol 2020; 162:223-252. [PMID: 33707014 PMCID: PMC9472676 DOI: 10.1016/bs.mcb.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Rapidly changing features in an intact biological sample are challenging to efficiently trap and image by conventional electron microscopy (EM). For example, the model organism C. elegans is widely used to study embryonic development and differentiation, yet the fast kinetics of cell division makes the targeting of specific developmental stages for ultrastructural study difficult. We set out to image the condensed metaphase chromosomes of an early embryo in the intact worm in 3-D. To achieve this, one must capture this transient structure, then locate and subsequently image the corresponding volume by EM in the appropriate context of the organism, all while minimizing a variety of artifacts. In this methodological advance, we report on the high-pressure freezing of spatially constrained whole C. elegans hermaphrodites in a combination of cryoprotectants to identify embryonic cells in metaphase by in situ cryo-fluorescence microscopy. The screened worms were then freeze substituted, resin embedded and further prepared such that the targeted cells were successfully located and imaged by focused ion beam scanning electron microscopy (FIB-SEM). We reconstructed the targeted metaphase structure and also correlated an intriguing punctate fluorescence signal to a H2B-enriched putative polar body autophagosome in an adjacent cell undergoing telophase. By enabling cryo-fluorescence microscopy of thick samples, our workflow can thus be used to trap and image transient structures in C. elegans or similar organisms in a near-native state, and then reconstruct their corresponding cellular architectures at high resolution and in 3-D by correlative volume EM.
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Affiliation(s)
- Irene Y Chang
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Mohammad Rahman
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Orna Cohen-Fix
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.
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33
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Wu GH, Mitchell PG, Galaz-Montoya JG, Hecksel CW, Sontag EM, Gangadharan V, Marshman J, Mankus D, Bisher ME, Lytton-Jean AKR, Frydman J, Czymmek K, Chiu W. Multi-scale 3D Cryo-Correlative Microscopy for Vitrified Cells. Structure 2020; 28:1231-1237.e3. [PMID: 32814034 PMCID: PMC7642057 DOI: 10.1016/j.str.2020.07.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/10/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could be used for large-scale phenotypic studies of frozen-hydrated specimens in a variety of healthy and diseased conditions with and without treatments.
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Affiliation(s)
- Gong-Her Wu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Patrick G Mitchell
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jesus G Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Corey W Hecksel
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Emily M Sontag
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | | | - Jeffrey Marshman
- Zeiss Research Microscopy Solutions, White Plains, NY 10601, USA
| | - David Mankus
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Margaret E Bisher
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abigail K R Lytton-Jean
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Judith Frydman
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Kirk Czymmek
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
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34
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Rasse TM, Hollandi R, Horvath P. OpSeF: Open Source Python Framework for Collaborative Instance Segmentation of Bioimages. Front Bioeng Biotechnol 2020; 8:558880. [PMID: 33117778 PMCID: PMC7576117 DOI: 10.3389/fbioe.2020.558880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
Various pre-trained deep learning models for the segmentation of bioimages have been made available as developer-to-end-user solutions. They are optimized for ease of use and usually require neither knowledge of machine learning nor coding skills. However, individually testing these tools is tedious and success is uncertain. Here, we present the Open Segmentation Framework (OpSeF), a Python framework for deep learning-based instance segmentation. OpSeF aims at facilitating the collaboration of biomedical users with experienced image analysts. It builds on the analysts' knowledge in Python, machine learning, and workflow design to solve complex analysis tasks at any scale in a reproducible, well-documented way. OpSeF defines standard inputs and outputs, thereby facilitating modular workflow design and interoperability with other software. Users play an important role in problem definition, quality control, and manual refinement of results. OpSeF semi-automates preprocessing, convolutional neural network (CNN)-based segmentation in 2D or 3D, and postprocessing. It facilitates benchmarking of multiple models in parallel. OpSeF streamlines the optimization of parameters for pre- and postprocessing such, that an available model may frequently be used without retraining. Even if sufficiently good results are not achievable with this approach, intermediate results can inform the analysts in the selection of the most promising CNN-architecture in which the biomedical user might invest the effort of manually labeling training data. We provide Jupyter notebooks that document sample workflows based on various image collections. Analysts may find these notebooks useful to illustrate common segmentation challenges, as they prepare the advanced user for gradually taking over some of their tasks and completing their projects independently. The notebooks may also be used to explore the analysis options available within OpSeF in an interactive way and to document and share final workflows. Currently, three mechanistically distinct CNN-based segmentation methods, the U-Net implementation used in Cellprofiler 3.0, StarDist, and Cellpose have been integrated within OpSeF. The addition of new networks requires little; the addition of new models requires no coding skills. Thus, OpSeF might soon become both an interactive model repository, in which pre-trained models might be shared, evaluated, and reused with ease.
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Affiliation(s)
- Tobias M. Rasse
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Réka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Center (BRC), Szeged, Hungary
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Center (BRC), Szeged, Hungary
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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35
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Hayles MF, DE Winter DAM. An introduction to cryo-FIB-SEM cross-sectioning of frozen, hydrated Life Science samples. J Microsc 2020; 281:138-156. [PMID: 32737879 PMCID: PMC7891420 DOI: 10.1111/jmi.12951] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 12/31/2022]
Abstract
The introduction of cryo‐techniques to the focused ion‐beam scanning electron microscope (FIB‐SEM) has brought new opportunities to study frozen, hydrated samples from the field of Life Sciences. Cryo‐techniques have long been employed in electron microscopy. Thin electron transparent sections are produced by cryo‐ultramicrotomy for observation in a cryo‐transmission electron microscope (TEM). Cryo‐TEM is presently reaching the imaging of macromolecular structures. In parallel, cryo‐fractured surfaces from bulk materials have been investigated by cryo‐SEM. Both cryo‐TEM and cryo‐SEM have provided a wealth of information, despite being 2D techniques. Cryo‐TEM tomography does provide 3D information, but the thickness of the volume has a maximum of 200–300 nm, which limits the 3D information within the context of specific structures. FIB‐milling enables imaging additional planes by creating cross‐sections (e.g. cross‐sectioning or site‐specific X‐sectioning) perpendicular to the cryo‐fracture surface, thus adding a third imaging dimension to the cryo‐SEM. This paper discusses how to produce suitable cryo‐FIB‐SEM cross‐section results from frozen, hydrated Life Science samples with emphasis on ‘common knowledge’ and reoccurring observations. Lay Description Life Sciences studies life down to the smallest details. Visualising the smallest details requires electron microscopy, which utilises high‐vacuum chambers. One method to maintain the integrity of Life Sciences samples under vacuum conditions is freezing. Frozen samples can remain in a suspended state. As a result, research can be carried out without having to change the chemistry or internal physical structure of the samples. Two types of electron microscopes equipped with cryo‐sample handling facilities are used to investigate samples: The scanning electron microscope (SEM) which investigates surfaces and the transmission electron microscope (TEM) which investigates thin electron transparent sections (called lamellae). A third method of investigation combines a SEM with a focused ion beam (FIB) to form a cryo‐FIB‐SEM, which is the basis of this paper. The electron beam images the cryo‐sample surface while the ion beam mills into the surface to expose the interior of the sample. The latter is called cross‐sectioning and the result provides a way of investigating the 3rd dimension of the sample. This paper looks at the making of cross‐sections in this manner originating from knowledge and experience gained with this technique over many years. This information is meant for newcomers, and experienced researchers in cryo‐microscopy alike.
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Affiliation(s)
- M F Hayles
- Cryo-FIB-SEM Technologist, Eindhoven, the Netherlands
| | - D A M DE Winter
- Environmental Hydrogeology, Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
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Spehner D, Steyer AM, Bertinetti L, Orlov I, Benoit L, Pernet-Gallay K, Schertel A, Schultz P. Cryo-FIB-SEM as a promising tool for localizing proteins in 3D. J Struct Biol 2020; 211:107528. [PMID: 32387573 DOI: 10.1016/j.jsb.2020.107528] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/10/2020] [Accepted: 04/28/2020] [Indexed: 02/02/2023]
Abstract
Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) is an invaluable tool to visualize the 3D architecture of cell constituents and map cell networks. Recently, amorphous ice embedding techniques have been associated with FIB-SEM to ensure that the biological material remains as close as possible to its native state. Here we have vitrified human HeLa cells and directly imaged them by cryo-FIB-SEM with the secondary electron InLens detector at cryogenic temperature and without any staining. Image stacks were aligned and processed by denoising, removal of ion beam milling artefacts and local charge imbalance. Images were assembled into a 3D volume and the major cell constituents were modelled. The data illustrate the power of the workflow to provide a detailed view of the internal architecture of the fully hydrated, close-to-native, entire HeLa cell. In addition, we have studied the feasibility of combining cryo-FIB-SEM imaging with live-cell protein detection. We demonstrate that internalized gold particles can be visualized by detecting back scattered primary electrons at low kV while simultaneously acquiring signals from the secondary electron detector to image major cell features. Furthermore, gold-conjugated antibodies directed against RNA polymerase II could be observed in the endo-lysosomal pathway while labelling of the enzyme in the nucleus was not detected, a shortcoming likely due to the inadequacy between the size of the gold particles and the voxel size. With further refinements, this method promises to have a variety of applications where the goal is to localize cellular antigens while visualizing the entire native cell in three dimensions.
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Affiliation(s)
- Daniele Spehner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Anna M Steyer
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Luca Bertinetti
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14424 Potsdam, Germany
| | - Igor Orlov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Lucas Benoit
- University Grenoble Alpes; Institut National de la Santé et de la Recherche Médicale U1216, Grenoble, France; Grenoble Institut Neurosciences, GIN, Grenoble, France
| | - Karin Pernet-Gallay
- University Grenoble Alpes; Institut National de la Santé et de la Recherche Médicale U1216, Grenoble, France; Grenoble Institut Neurosciences, GIN, Grenoble, France
| | - Andreas Schertel
- Carl Zeiss Microscopy GmbH, Zeiss Customer Center Europe, Carl-Zeiss-Straße 22, D-73447 Oberkochen, Germany
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France; Université de Strasbourg, Illkirch, France
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37
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Zachs T, Schertel A, Medeiros J, Weiss GL, Hugener J, Matos J, Pilhofer M. Fully automated, sequential focused ion beam milling for cryo-electron tomography. eLife 2020; 9:e52286. [PMID: 32149604 PMCID: PMC7082125 DOI: 10.7554/elife.52286] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/07/2020] [Indexed: 11/13/2022] Open
Abstract
Cryo-electron tomography (cryoET) has become a powerful technique at the interface of structural biology and cell biology, due to its unique ability for imaging cells in their native state and determining structures of macromolecular complexes in their cellular context. A limitation of cryoET is its restriction to relatively thin samples. Sample thinning by cryo-focused ion beam (cryoFIB) milling has significantly expanded the range of samples that can be analyzed by cryoET. Unfortunately, cryoFIB milling is low-throughput, time-consuming and manual. Here, we report a method for fully automated sequential cryoFIB preparation of high-quality lamellae, including rough milling and polishing. We reproducibly applied this method to eukaryotic and bacterial model organisms, and show that the resulting lamellae are suitable for cryoET imaging and subtomogram averaging. Since our method reduces the time required for lamella preparation and minimizes the need for user input, we envision the technique will render previously inaccessible projects feasible.
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Affiliation(s)
- Tobias Zachs
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Andreas Schertel
- Carl Zeiss Microscopy GmbH, Zeiss Customer Center EuropeOberkochenGermany
| | - João Medeiros
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Gregor L Weiss
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Jannik Hugener
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
- Institute of Biochemistry, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Joao Matos
- Institute of Biochemistry, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
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Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, Stabley DR, Shirinifard A, Pang S, Peale D, Schaefer K, Pomp W, Chang CL, Lippincott-Schwartz J, Kirchhausen T, Solecki DJ, Betzig E, Hess HF. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science 2020; 367:eaaz5357. [PMID: 31949053 PMCID: PMC7339343 DOI: 10.1126/science.aaz5357] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
Abstract
Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam-milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum-associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.
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Affiliation(s)
- David P Hoffman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kirby R Campbell
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Melanie Freeman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Lei Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nirmala Iyer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - John A Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Daniel R Stabley
- Neuroimaging Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Abbas Shirinifard
- Bioimage Analysis Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - David Peale
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kathy Schaefer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wim Pomp
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chi-Lun Chang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - David J Solecki
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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39
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Smith ER, Hewitson TD, Holt SG. Diagnostic Tests for Vascular Calcification. Adv Chronic Kidney Dis 2019; 26:445-463. [PMID: 31831123 DOI: 10.1053/j.ackd.2019.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/22/2019] [Accepted: 07/28/2019] [Indexed: 02/06/2023]
Abstract
Vascular calcification (VC) is the heterogeneous endpoint of multiple vascular insults, which varies by arterial bed, the layer of the arterial wall affected, and is propagated by diverse cellular and biochemical mechanisms. A variety of in vivo and ex vivo techniques have been applied to the analysis of VC in preclinical studies, but clinical examination has principally relied on a number of noninvasive and invasive imaging modalities for detection and quantitation. Most imaging methods suffer from suboptimal spatial resolution, leading to the inability to distinguish medial from intimal VC and insufficient sensitivity to detect microcalcifications that are indicative of active mineral deposition and of vulnerable plaques which may be prone to rupture. Serum biomarkers lack specificity for VC and cannot discriminate pathology. Overall, uncertainties surrounding the sensitivity and specificity of different VC testing modalities, the absence of a clear cause-effect relationship, and lack of any evidence-based diagnostic or therapeutic protocols in relation to VC testing in chronic kidney disease has yielded weak or ungraded recommendations for their use in clinical practice. While VC is recognized as a key manifestation of chronic kidney disease-mineral and bone disorder and those with an increasing burden of VC are considered to be at higher cardiovascular risk, routine screening is not currently recommended.
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40
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Hörning M, Schertel A, Schneider R, Lemloh ML, Schweikert MR, Weiss IM. Mineralized scale patterns on the cell periphery of the chrysophyte Mallomonas determined by comparative 3D Cryo-FIB SEM data processing. J Struct Biol 2019; 209:107403. [PMID: 31614182 DOI: 10.1016/j.jsb.2019.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 11/26/2022]
Abstract
Unicellular protists can biomineralize spatially complex and functional shells. A typical cell of the photosynthetic synurophyte Mallomonas is covered by about 60-100 silica scales. Their geometric arrangement, the so-called scale case, mainly depends on the species and on the cell cycle. In this study, the scale case of the synurophyte Mallomonas was preserved in aqueous suspension using high-pressure freezing (HPF). From this specimen, a three-dimensional (3D) data set spanning a volume of about 25.6 μm × 19.2 μm × 4.2 μm with a voxel size of 12.5 nm × 12.5 nm × 25.0 nm was collected by Cryo-FIB SEM in 3 h and 24 min. SEM imaging using In-lens SE detection allowed to clearly differentiate between mineralized, curved scales of less than 0.2 μm thickness and organic cellular ultrastructure or vitrified ice. The three-dimensional spatial orientations and shapes of a minimum set of scales (N = 13) were identified by visual inspection, and manually segmented. Manual and automated segmentation approaches were comparatively applied to one arbitrarily selected reference scale using the differences in grey level between scales and other constituents. Computational automated routines and principal component analysis of the experimentally extracted data created a realistic mathematical model based on the Fibonacci pattern theory. A complete in silico scale case of Mallomonas was reconstructed showing an optimized scale coverage on the cell surface, similarly as it was observed experimentally. The minimum time requirements from harvesting the living cells to the final scale case determination by Cryo-FIB SEM and computational image processing are discussed.
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Affiliation(s)
- Marcel Hörning
- Institute of Biomaterials and Biomolecular Systems, Biobased Materials Group, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; AMICA - Stuttgart Research Focus (SRF), University of Stuttgart, Pfaffenwaldring 32, 70569 Stuttgart, Germany.
| | - Andreas Schertel
- Carl Zeiss Microscopy GmbH, Carl-Zeiss-Straße 22, 73447 Oberkochen, Germany
| | - Ralf Schneider
- High Performance Computing Center Stuttgart (HLRS), Nobelstr. 19, 70569 Stuttgart, Germany
| | - Marie-Louise Lemloh
- AMICA - Stuttgart Research Focus (SRF), University of Stuttgart, Pfaffenwaldring 32, 70569 Stuttgart, Germany; Materials Testing Institute (MPA), University of Stuttgart, Pfaffenwaldring 32, 70569 Stuttgart, Germany
| | - Michael R Schweikert
- Institute of Biomaterials and Biomolecular Systems, Biobased Materials Group, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; AMICA - Stuttgart Research Focus (SRF), University of Stuttgart, Pfaffenwaldring 32, 70569 Stuttgart, Germany
| | - Ingrid M Weiss
- Institute of Biomaterials and Biomolecular Systems, Biobased Materials Group, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; AMICA - Stuttgart Research Focus (SRF), University of Stuttgart, Pfaffenwaldring 32, 70569 Stuttgart, Germany; Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Stuttgart 70569, Germany
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41
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Abstract
Focused ion beam-scanning electron microscopy (FIB-SEM) has become a widely used technique in life sciences. To achieve the best data quality, sample preparation is important and has to be adapted to the specimen and the specific application. Here we illustrate three preparation procedures for mouse nervous tissue: First, the use of high-pressure freezing followed by direct imaging of vitrified tissue without any staining in the FIB-SEM under cryo-conditions as direct and fast procedure. Second, a slow procedure involving freeze substitution of frozen samples combined with additional staining for enhanced contrast and plastic embedding. Third, a fast preparation applying microwave-assisted chemical fixation and processing for resin embedding. All three methods of sample preparation are suitable for obtaining data stacks by FIB-SEM acquisition and 3D reconstruction.
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42
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Weiner A, Enninga J. The Pathogen–Host Interface in Three Dimensions: Correlative FIB/SEM Applications. Trends Microbiol 2019; 27:426-439. [DOI: 10.1016/j.tim.2018.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
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43
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Abstract
Electron cryo-tomography using the scanning transmission modality (STEM) enables 3D reconstruction of unstained, vitrified specimens as thick as 1μm or more. Contrast is related to mass/thickness and atomic number, providing quantifiable chemical characterization and mass mapping of intact prokaryotic and eukaryotic cells. Energy dispersive X-ray spectroscopy by STEM provides a simple, on-the-spot chemical identification of the elemental composition in sub-cellular organic bodies or mineral deposits. This chapter provides basic background and practical information for performing cryo-STEM tomography on vitrified biological cells.
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Affiliation(s)
- Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.
| | - Michael Elbaum
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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44
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Kizilyaprak C, Stierhof YD, Humbel BM. Volume microscopy in biology: FIB-SEM tomography. Tissue Cell 2019; 57:123-128. [DOI: 10.1016/j.tice.2018.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/30/2018] [Accepted: 09/20/2018] [Indexed: 01/10/2023]
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45
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Intercellular pathways from the vasculature to the forming bone in the zebrafish larval caudal fin: Possible role in bone formation. J Struct Biol 2019; 206:139-148. [PMID: 30858049 DOI: 10.1016/j.jsb.2019.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 11/20/2022]
Abstract
The pathway of ion supply from the source to the site of bone deposition in vertebrates is thought to involve transport through the vasculature, followed by ion concentration in osteoblasts. The cells deposit a precursor mineral phase in vesicles, which are then exocytosed into the extracellular matrix. We observed that the entire skeleton of zebrafish larvae, is labelled within minutes after injection of calcein or FITC-dextran into the blood. This raised the possibility that there is an additional pathway of solute transport that can account for the rapid labelling. We used cryo-FIB-SEM serial block face imaging to reconstruct at high resolution the 3D ultrastructure of the caudal tail of the zebrafish larva. This reconstruction clearly shows that there is a continuous intercellular pathway from the artery to the forming bone, and from the forming bone to the vein. Fluorescence light microscopy shows that calcein and FITC-dextran form a reticulate network pattern in this tissue, which we attribute to the dye being present in the intercellular space. We conclude that this intercellular continuous space may be a supply route for ions, mineral and other solute or particulate material to the fast forming bone.
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46
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Boey A, Rybakin V, Kalicharan D, Vints K, Gounko NV. Gold-substituted Silver-intensified Peroxidase Immunolabeling for FIB-SEM Imaging. J Histochem Cytochem 2019; 67:351-360. [PMID: 30624131 DOI: 10.1369/0022155418824335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Modern electron microscopy offers a wide variety of tools to investigate the ultrastructural organization of cells and tissues and to accurately pinpoint intracellular localizations of macromolecules of interest. New volumetric electron microscopy techniques and new instrumentation provide unique opportunities for high-throughput analysis of comparatively large volumes of tissue and their complete reconstitution in three-dimensional (3D) electron microscopy. However, due to a variety of technical issues such as the limited penetration of label into the tissue, low antigen preservation, substantial electron density of secondary detection reagents, and many others, the adaptation of immuno-detection techniques for use with such 3D imaging methods as focused ion beam-scanning electron microscopy (FIB-SEM) has been challenging. Here, we describe a sample preparation method for 3D FIB-SEM, which results in an optimal preservation and staining of ultrastructural details at a resolution necessary for tracing immunolabeled neuronal structures and detailed reconstruction of synapses. This technique is applicable to neuronal and non-neuronal cells, tissues, and a wide variety of antigens.
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Affiliation(s)
- Adrian Boey
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore
| | - Vasily Rybakin
- Laboratory of Immunobiology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dharamdajal Kalicharan
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Natalia V Gounko
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore.,VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
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47
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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48
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Studying biomineralization pathways in a 3D culture model of breast cancer microcalcifications. Biomaterials 2018; 179:71-82. [PMID: 29980076 DOI: 10.1016/j.biomaterials.2018.06.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/15/2022]
Abstract
Microcalcifications serve as diagnostic markers for breast cancer, yet their formation pathway(s) and role in cancer progression are debated due in part to a lack of relevant 3D culture models that allow studying the extent of cellular regulation over mineralization. Previous studies have suggested processes ranging from dystrophic mineralization associated with cell death to bone-like mineral deposition. Here, we evaluated microcalcification formation in 3D multicellular spheroids, generated from non-malignant, pre-cancer, and invasive cell lines from the MCF10A human breast tumor progression series. The spheroids with greater malignancy potential developed necrotic cores, thus recapitulating spatially distinct viable and non-viable areas known to regulate cellular behavior in tumors in vivo. The spatial distribution of the microcalcifications, as well as their compositions, were characterized using nanoCT, electron-microscopy, and X-ray spectroscopy. Apatite microcalcifications were primarily detected within the viable cell regions and their number and size increased with malignancy potential of the spheroids. Levels of alkaline phosphatase decreased with malignancy potential, whereas levels of osteopontin increased. These findings support a mineralization pathway in which cancer cells induce mineralization in a manner that is linked to their malignancy potential, but that is distinct from physiological osteogenic mineralization.
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New advances in scanning microscopy and its application to study parasitic protozoa. Exp Parasitol 2018; 190:10-33. [PMID: 29702111 DOI: 10.1016/j.exppara.2018.04.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 04/10/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022]
Abstract
Scanning electron microscopy has been used to observe and study parasitic protozoa for at least 40 years. However, field emission electron sources, as well as improvements in lenses and detectors, brought the resolution power of scanning electron microscopes (SEM) to a new level. Parallel to the refinement of instruments, protocols for preservation of the ultrastructure, immunolabeling, exposure of cytoskeleton and inner structures of parasites and host cells were developed. This review is focused on protozoan parasites of medical and veterinary relevance, e.g., Toxoplasma gondii, Tritrichomonas foetus, Giardia intestinalis, and Trypanosoma cruzi, compilating the main achievements in describing the fine ultrastructure of their surface, cytoskeleton and interaction with host cells. Two new resources, namely, Helium Ion Microscopy (HIM) and Slice and View, using either Focused Ion Beam (FIB) abrasion or Microtome Serial Sectioning (MSS) within the microscope chamber, combined to backscattered electron imaging of fixed (chemically or by quick freezing followed by freeze substitution and resin embedded samples is bringing an exponential amount of valuable information. In HIM there is no need of conductive coating and the depth of field is much higher than in any field emission SEM. As for FIB- and MSS-SEM, high resolution 3-D models of areas and volumes larger than any other technique allows can be obtained. The main results achieved with all these technological tools and some protocols for sample preparation are included in this review. In addition, we included some results obtained with environmental/low vacuum scanning microscopy and cryo-scanning electron microscopy, both promising, but not yet largely employed SEM modalities.
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