51
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Kirchweger P, Mullick D, Swain PP, Wolf SG, Elbaum M. Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap. J Struct Biol 2023; 215:107982. [PMID: 37268154 DOI: 10.1016/j.jsb.2023.107982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access 3D volumes on the scale of 1 micron with a resolution of nanometers, making it ideal for this task. Here we introduce two relevant advances: (a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and (b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy. Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to-isotropic resolution in the reconstruction without averaging. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.
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Affiliation(s)
- Peter Kirchweger
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Debakshi Mullick
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Prabhu Prasad Swain
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel; School of Physical Sciences, UM-DAE Centre for Excellence in Basic Sciences, Mumbai 400098, India
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michael Elbaum
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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52
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Habeck M. Bayesian methods in integrative structure modeling. Biol Chem 2023; 404:741-754. [PMID: 37505205 DOI: 10.1515/hsz-2023-0145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Abstract
There is a growing interest in characterizing the structure and dynamics of large biomolecular assemblies and their interactions within the cellular environment. A diverse array of experimental techniques allows us to study biomolecular systems on a variety of length and time scales. These techniques range from imaging with light, X-rays or electrons, to spectroscopic methods, cross-linking mass spectrometry and functional genomics approaches, and are complemented by AI-assisted protein structure prediction methods. A challenge is to integrate all of these data into a model of the system and its functional dynamics. This review focuses on Bayesian approaches to integrative structure modeling. We sketch the principles of Bayesian inference, highlight recent applications to integrative modeling and conclude with a discussion of current challenges and future perspectives.
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Affiliation(s)
- Michael Habeck
- Microscopic Image Analysis Group, Jena University Hospital, D-07743 Jena, Germany
- Max Planck Institute for Multidisciplinary Sciences, d-37077 Göttingen, Germany
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53
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Griswold JM, Bonilla-Quintana M, Pepper R, Lee CT, Raychaudhuri S, Ma S, Gan Q, Syed S, Zhu C, Bell M, Suga M, Yamaguchi Y, Chéreau R, Nägerl UV, Knott G, Rangamani P, Watanabe S. Membrane mechanics dictate axonal morphology and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549958. [PMID: 37503105 PMCID: PMC10370128 DOI: 10.1101/2023.07.20.549958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Axons are thought to be ultrathin membrane cables of a relatively uniform diameter, designed to conduct electrical signals, or action potentials. Here, we demonstrate that unmyelinated axons are not simple cylindrical tubes. Rather, axons have nanoscopic boutons repeatedly along their length interspersed with a thin cable with a diameter of ∼60 nm like pearls-on-a-string. These boutons are only ∼200 nm in diameter and do not have synaptic contacts or a cluster of synaptic vesicles, hence non-synaptic. Our in silico modeling suggests that axon pearling can be explained by the mechanical properties of the membrane including the bending modulus and tension. Consistent with modeling predictions, treatments that disrupt these parameters like hyper- or hypo-tonic solutions, cholesterol removal, and non-muscle myosin II inhibition all alter the degree of axon pearling, suggesting that axon morphology is indeed determined by the membrane mechanics. Intriguingly, neuronal activity modulates the cholesterol level of plasma membrane, leading to shrinkage of axon pearls. Consequently, the conduction velocity of action potentials becomes slower. These data reveal that biophysical forces dictate axon morphology and function and that modulation of membrane mechanics likely underlies plasticity of unmyelinated axons.
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54
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548468. [PMID: 37502991 PMCID: PMC10369871 DOI: 10.1101/2023.07.10.548468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI, 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53715, USA
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55
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Mätlik K, Govek EE, Paul MR, Allis CD, Hatten ME. Histone bivalency regulates the timing of cerebellar granule cell development. Genes Dev 2023; 37:570-589. [PMID: 37491148 PMCID: PMC10499015 DOI: 10.1101/gad.350594.123] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature neurons. Here we used RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in a specific type of CNS neuron: the mouse cerebellar granule cell (GC). We found that in proliferating GC progenitors (GCPs), H3K4me3/H3K27me3 bivalency is common at neuronal genes and undergoes dynamic changes that correlate with gene expression during migration and circuit formation. Expressing a fluorescent sensor for bivalent domains revealed subnuclear bivalent foci in proliferating GCPs. Inhibiting H3K27 methyltransferases EZH1 and EZH2 in vitro and in organotypic cerebellar slices dramatically altered the expression of bivalent genes, induced the down-regulation of migration-related genes and up-regulation of synaptic genes, inhibited glial-guided migration, and accelerated terminal differentiation. Thus, histone bivalency is required to regulate the timing of the progression from progenitor cells to mature neurons.
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Affiliation(s)
- Kärt Mätlik
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, Rockefeller University, New York, New York 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, New York, New York 10065, USA
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA;
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56
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Bharathan NK, Giang W, Hoffman CL, Aaron JS, Khuon S, Chew TL, Preibisch S, Trautman ET, Heinrich L, Bogovic J, Bennett D, Ackerman D, Park W, Petruncio A, Weigel AV, Saalfeld S, Wayne Vogl A, Stahley SN, Kowalczyk AP. Architecture and dynamics of a desmosome-endoplasmic reticulum complex. Nat Cell Biol 2023; 25:823-835. [PMID: 37291267 PMCID: PMC10960982 DOI: 10.1038/s41556-023-01154-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/24/2023] [Indexed: 06/10/2023]
Abstract
The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signalling and lipid transfer. Here, using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometre proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization, mobility and expression of ER stress transcripts. These findings indicate that desmosomes and the keratin cytoskeleton regulate the distribution, function and dynamics of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.
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Affiliation(s)
- Navaneetha Krishnan Bharathan
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - William Giang
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Coryn L Hoffman
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Satya Khuon
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Preibisch
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eric T Trautman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Larissa Heinrich
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - John Bogovic
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Davis Bennett
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - David Ackerman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Woohyun Park
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Alyson Petruncio
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Aubrey V Weigel
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Saalfeld
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - A Wayne Vogl
- Life Sciences Institute and the Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara N Stahley
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Andrew P Kowalczyk
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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57
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Mironov AA, Beznoussenko GV. The Regulated Secretion and Models of Intracellular Transport: The Goblet Cell as an Example. Int J Mol Sci 2023; 24:ijms24119560. [PMID: 37298509 DOI: 10.3390/ijms24119560] [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: 03/28/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
Transport models are extremely important to map thousands of proteins and their interactions inside a cell. The transport pathways of luminal and at least initially soluble secretory proteins synthesized in the endoplasmic reticulum can be divided into two groups: the so-called constitutive secretory pathway and regulated secretion (RS) pathway, in which the RS proteins pass through the Golgi complex and are accumulated into storage/secretion granules (SGs). Their contents are released when stimuli trigger the fusion of SGs with the plasma membrane (PM). In specialized exocrine, endocrine, and nerve cells, the RS proteins pass through the baso-lateral plasmalemma. In polarized cells, the RS proteins secrete through the apical PM. This exocytosis of the RS proteins increases in response to external stimuli. Here, we analyze RS in goblet cells to try to understand the transport model that can be used for the explanation of the literature data related to the intracellular transport of their mucins.
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Affiliation(s)
- Alexander A Mironov
- Department of Cell Biology, IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
| | - Galina V Beznoussenko
- Department of Cell Biology, IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
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58
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Rane L, Wulffele J, Bourgeois D, Glushonkov O, Mantovanelli AMR, Zala N, Byrdin M. Light-Induced Forward and Reverse Intersystem Crossing in Green Fluorescent Proteins at Cryogenic Temperatures. J Phys Chem B 2023. [PMID: 37235526 DOI: 10.1021/acs.jpcb.3c02971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Combining fluorescence and phosphorescence kinetics, we characterize forward and reverse intersystem crossing (FISC and RISC, respectively) between the singlet and triplet manifolds S ↔ T in photoswitchable (rsEGFP2) and non-photoswitchable (EGFP) green fluorescent proteins upon continuous 488 nm laser excitation at cryogenic temperatures (CTs). Both proteins behave very similarly, with T1 absorption spectra showing a visible peak at 490 nm (10 mM-1 cm-1) and a vibrational progression in the near-infrared (720 to 905 nm). The dark lifetime of T1 is 21-24 ms at 100 K and very weakly temperature-dependent up to 180 K. Above 180 K, T1 lifetimes reduce rapidly to few milliseconds as found at room temperature (RT). FISC and RISC quantum yields are 0.3 and 0.1%, respectively, for both proteins. The light-induced RISC channel becomes faster than the dark reversal at power densities as low as 20 W cm-2. We discuss implications for fluorescence (super resolution-) microscopy at CT and RT.
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Affiliation(s)
- Lukas Rane
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Jip Wulffele
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Oleksandr Glushonkov
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Angela M R Mantovanelli
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Ninon Zala
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Martin Byrdin
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
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59
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Last MGF, Tuijtel MW, Voortman LM, Sharp TH. Selecting optimal support grids for super-resolution cryogenic correlated light and electron microscopy. Sci Rep 2023; 13:8270. [PMID: 37217690 DOI: 10.1038/s41598-023-35590-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Cryogenic transmission electron microscopy (cryo-TEM) and super-resolution fluorescence microscopy are two popular and ever improving methods for high-resolution imaging of biological samples. In recent years, the combination of these two techniques into one correlated workflow has gained attention as a promising route towards contextualizing and enriching cryo-TEM imagery. A problem that is often encountered in the combination of these methods is that of light-induced damage to the sample during fluorescence imaging that renders the sample structure unsuitable for TEM imaging. In this paper, we describe how absorption of light by TEM sample support grids leads to sample damage, and we systematically explore the importance of parameters of grid design. We explain how, by changing the grid geometry and materials, one can increase the maximum illumination power density in fluorescence microscopy by up to an order of magnitude. Finally, we demonstrate the significant improvements in super-resolution image quality that are enabled by the selection of support grids that are optimally suited for correlated cryo-microscopy.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt Am Main, Germany
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands.
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60
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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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61
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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62
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Li S, Jia X, Niu T, Zhang X, Qi C, Xu W, Deng H, Sun F, Ji G. HOPE-SIM, a cryo-structured illumination fluorescence microscopy system for accurately targeted cryo-electron tomography. Commun Biol 2023; 6:474. [PMID: 37120442 PMCID: PMC10148829 DOI: 10.1038/s42003-023-04850-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
Cryo-focused ion beam (cryo-FIB) milling technology has been developed for the fabrication of cryo-lamella of frozen native specimens for study by in situ cryo-electron tomography (cryo-ET). However, the precision of the target of interest is still one of the major bottlenecks limiting application. Here, we have developed a cryo-correlative light and electron microscopy (cryo-CLEM) system named HOPE-SIM by incorporating a 3D structured illumination fluorescence microscopy (SIM) system and an upgraded high-vacuum stage to achieve efficiently targeted cryo-FIB. With the 3D super resolution of cryo-SIM as well as our cryo-CLEM software, 3D-View, the correlation precision of targeting region of interest can reach to 110 nm enough for the subsequent cryo-lamella fabrication. We have successfully utilized the HOPE-SIM system to prepare cryo-lamellae targeting mitochondria, centrosomes of HeLa cells and herpesvirus assembly compartment of infected BHK-21 cells, which suggests the high potency of the HOPE-SIM system for future in situ cryo-ET workflows.
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Affiliation(s)
- Shuoguo Li
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xing Jia
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaoyun Zhang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Chen Qi
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wei Xu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Hongyu Deng
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Gang Ji
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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63
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Abstract
The ability to view biomolecules in cells and measure changes in their structure, quantity, distribution, and interaction is fundamental to understanding biology. By coupling nano -scale resolution with meso and even macro scale volumes, the enhanced focused ion beam-scanning electron microscopy (FIB-SEM) pipeline has enabled numerous transformational discoveries in life science, many of which were major new landmarks in their fields. This pipeline consists of EM sample preparation, FIB-SEM sample preparation, FIB-SEM imaging, data alignment, and image analysis. While the EM sample preparation, data alignment, and image analysis are consistent with those from other volume Electron Microscopy (vEM) approaches, the enhanced FIB-SEM sample preparation and imaging are unique to the rest of comparable methods. We here illustrate the detailed methods of enhanced FIB-SEM sample preparation and image acquisition that have not been previously described. These methods can also be applied to the conventional FIB-SEM platforms for improved image acquisition quality and pipeline throughput.
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Affiliation(s)
- Song Pang
- Yale School of Medicine, New Haven, CT, United States.
| | - C Shan Xu
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, United States
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64
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Huang W, Hua C, Guo Y, Gao W, Li Y, Zheng Y. Super resolution imaging reconstruction reveals that gold standard methods may not correctly conclude neural/brain functional recovery. Comput Med Imaging Graph 2023; 105:102198. [PMID: 36805708 DOI: 10.1016/j.compmedimag.2023.102198] [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: 08/14/2022] [Revised: 12/17/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023]
Abstract
The status of cerebral perfusion and its restoration level play a vital role in the prognosis and clinical decision making of many neurosurgical diseases. As such, gold standard methods including CT, MR and ICP monitoring, which can indicate and measure cerebral perfusion and restoration, have been widely adopted to evaluate whether or not a patient has recovered from neurofunctional disabilities. This robust combination of methods, however, is confronted with a growing number of contradictions in recent years due to its inability to measure the status of cerebral reperfusion in microvasculature level, even though this has been shown to determine neurofunctional restoration as well or even better. To this date, nevertheless, we have very limited imaging methods that could evaluate human cerebral microperfusion both safely and accurately under most neurosurgical conditions. We herein report a new method of acquiring a patient's cerebral microperfusion status noninvasively which could display the precise distribution of microvasculature in deep cerebral regions with a resolution of ∼30 µm, using everyday bed-side ultrasonography combined with a computerized super-resolution reconstruction algorithm. Using this imaging modality, we found that a patient's cerebral microperfusion might not be improved by some routine administrations even though the gold standard method had yielded the opposite conclusions. Our imaging modality retains the safe, portable feature of ordinary ultrasonography while possesses the extraordinary super-resolution nature, which enables an efficient, precise diagnosis of cerebral perfusion. Most importantly, the super resolution nature of this method may also facilitate early-stage evaluation of a patient's neurofunctional restoration level and avoid overoptimistic conclusions from conventional angiography or ICP monitoring.
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Affiliation(s)
- Weifeng Huang
- Department of Critical Care Medicine, The Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Hua
- Department of Ultrasound, The Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Center for Brain Science, Shanghai, China.
| | - Yan Guo
- Department of Neurosurgery, The Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenwei Gao
- Department of Neurosurgery, The Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingchuan Li
- Department of Critical Care Medicine, The Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Critical Care Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Yuanyi Zheng
- Department of Ultrasound, The Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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65
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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66
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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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67
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Sartor A, Dahlberg PD, Perez D, Moerner WE. Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms. J Phys Chem B 2023; 127:2690-2700. [PMID: 36943356 PMCID: PMC10069424 DOI: 10.1021/acs.jpcb.2c08995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/01/2023] [Indexed: 03/23/2023]
Abstract
Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. We find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.
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Affiliation(s)
- Annina
M. Sartor
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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68
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Pope I, Tanner H, Masia F, Payne L, Arkill KP, Mantell J, Langbein W, Borri P, Verkade P. Correlative light-electron microscopy using small gold nanoparticles as single probes. LIGHT, SCIENCE & APPLICATIONS 2023; 12:80. [PMID: 36977682 PMCID: PMC10050153 DOI: 10.1038/s41377-023-01115-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 05/25/2023]
Abstract
Correlative light-electron microscopy (CLEM) requires the availability of robust probes which are visible both in light and electron microscopy. Here we demonstrate a CLEM approach using small gold nanoparticles as a single probe. Individual gold nanoparticles bound to the epidermal growth factor protein were located with nanometric precision background-free in human cancer cells by light microscopy using resonant four-wave mixing (FWM), and were correlatively mapped with high accuracy to the corresponding transmission electron microscopy images. We used nanoparticles of 10 nm and 5 nm radius, and show a correlation accuracy below 60 nm over an area larger than 10 µm size, without the need for additional fiducial markers. Correlation accuracy was improved to below 40 nm by reducing systematic errors, while the localisation precision is below 10 nm. Polarisation-resolved FWM correlates with nanoparticle shapes, promising for multiplexing by shape recognition in future applications. Owing to the photostability of gold nanoparticles and the applicability of FWM microscopy to living cells, FWM-CLEM opens up a powerful alternative to fluorescence-based methods.
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Affiliation(s)
- Iestyn Pope
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Hugh Tanner
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
- Department of Chemistry, Umeå University, Umeå, 90187, Sweden
| | - Francesco Masia
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lukas Payne
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Kenton Paul Arkill
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
- School of Medicine, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | - Wolfgang Langbein
- School of Physics and Astronomy, Cardiff University, The Parade, Cardiff, CF24 3AA, UK
| | - Paola Borri
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Paul Verkade
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK.
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69
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Chaiamarit T, Verhelle A, Chassefeyre R, Shukla N, Novak SW, Andrade LR, Manor U, Encalada SE. Mutant Prion Protein Endoggresomes are Hubs for Local Axonal Organelle-Cytoskeletal Remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533383. [PMID: 36993610 PMCID: PMC10055262 DOI: 10.1101/2023.03.19.533383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Dystrophic axons comprising misfolded mutant prion protein (PrP) aggregates are a characteristic pathological feature in the prionopathies. These aggregates form inside endolysosomes -called endoggresomes-, within swellings that line up the length of axons of degenerating neurons. The pathways impaired by endoggresomes that result in failed axonal and consequently neuronal health, remain undefined. Here, we dissect the local subcellular impairments that occur within individual mutant PrP endoggresome swelling sites in axons. Quantitative high-resolution light and electron microscopy revealed the selective impairment of the acetylated vs tyrosinated microtubule cytoskeleton, while micro-domain image analysis of live organelle dynamics within swelling sites revealed deficits uniquely to the MT-based active transport system that translocates mitochondria and endosomes toward the synapse. Cytoskeletal and defective transport results in the retention of mitochondria, endosomes, and molecular motors at swelling sites, enhancing mitochondria-Rab7 late endosome contacts that induce mitochondrial fission via the activity of Rab7, and render mitochondria dysfunctional. Our findings point to mutant Pr Pendoggresome swelling sites as selective hubs of cytoskeletal deficits and organelle retention that drive the remodeling of organelles along axons. We propose that the dysfunction imparted locally within these axonal micro-domains spreads throughout the axon over time, leading to axonal dysfunction in prionopathies.
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70
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Song DH, Song CW, Chung J, Jang EH, Kim H, Hur Y, Hur EM, Kim D, Chang JB. In situ silver nanoparticle development for molecular-specific biological imaging via highly accessible microscopies. NANOSCALE ADVANCES 2023; 5:1636-1650. [PMID: 36926569 PMCID: PMC10012848 DOI: 10.1039/d2na00449f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
In biological studies and diagnoses, brightfield (BF), fluorescence, and electron microscopy (EM) are used to image biomolecules inside cells. When compared, their relative advantages and disadvantages are obvious. BF microscopy is the most accessible of the three, but its resolution is limited to a few microns. EM provides a nanoscale resolution, but sample preparation is time-consuming. In this study, we present a new imaging technique, which we termed decoration microscopy (DecoM), and quantitative investigations to address the aforementioned issues in EM and BF microscopy. For molecular-specific EM imaging, DecoM labels proteins inside cells using antibodies bearing 1.4 nm gold nanoparticles (AuNPs) and grows silver layers on the AuNPs' surfaces. The cells are then dried without buffer exchange and imaged using scanning electron microscopy (SEM). Structures labeled with silver-grown AuNPs are clearly visible on SEM, even they are covered with lipid membranes. Using stochastic optical reconstruction microscopy, we show that the drying process causes negligible distortion of structures and that less structural deformation could be achieved through simple buffer exchange to hexamethyldisilazane. Using DecoM, we visualize the nanoscale alterations in microtubules by microtubule-severing proteins that cannot be observed with diffraction-limited fluorescence microscopy. We then combine DecoM with expansion microscopy to enable sub-micron resolution BF microscopy imaging. We first show that silver-grown AuNPs strongly absorb white light, and the structures labeled with them are clearly visible on BF microscopy. We then show that the application of AuNPs and silver development must follow expansion to visualize the labeled proteins clearly with sub-micron resolution.
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Affiliation(s)
- Dae-Hyeon Song
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Chang Woo Song
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | | | - Eun-Hae Jang
- Laboratory of Neuroscience, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University Seoul Korea
| | - Hyunwoo Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Yongsuk Hur
- BioMedical Research Center, Korea Advanced Institute of Science and Technology Daejeon Korea
| | - Eun-Mi Hur
- Laboratory of Neuroscience, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University Seoul Korea
- BK21 Four Future Veterinary Medicine Leading Education & Research Center, Seoul National University Seoul Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University Seoul Korea
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Daejeon Korea
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71
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Tan L, Shi J, Moghadami S, Wright CP, Parasar B, Seo Y, Vallejo K, Cobos I, Duncan L, Chen R, Deisseroth K. Cerebellar Granule Cells Develop Non-neuronal 3D Genome Architecture over the Lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530020. [PMID: 36865235 PMCID: PMC9980173 DOI: 10.1101/2023.02.25.530020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The cerebellum contains most of the neurons in the human brain, and exhibits unique modes of development, malformation, and aging. For example, granule cells-the most abundant neuron type-develop unusually late and exhibit unique nuclear morphology. Here, by developing our high-resolution single-cell 3D genome assay Dip-C into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we were able to resolve the first 3D genome structures of single cerebellar cells, create life-spanning 3D genome atlases for both human and mouse, and jointly measure transcriptome and chromatin accessibility during development. We found that while the transcriptome and chromatin accessibility of human granule cells exhibit a characteristic maturation pattern within the first year of postnatal life, 3D genome architecture gradually remodels throughout life into a non-neuronal state with ultra-long-range intra-chromosomal contacts and specific inter-chromosomal contacts. This 3D genome remodeling is conserved in mice, and robust to heterozygous deletion of chromatin remodeling disease-associated genes (Chd8 or Arid1b). Together these results reveal unexpected and evolutionarily-conserved molecular processes underlying the unique development and aging of the mammalian cerebellum.
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Affiliation(s)
- Longzhi Tan
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Jenny Shi
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Bioengineering, Stanford University, Stanford, CA
- Department of Chemistry, Stanford University, Stanford, CA
| | - Siavash Moghadami
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Cydney P. Wright
- Department of Neurobiology, Stanford University, Stanford, CA
- Department of Biology, Stanford University, Stanford, CA
| | - Bibudha Parasar
- Department of Neurobiology, Stanford University, Stanford, CA
| | - Yunji Seo
- Department of Neurobiology, Stanford University, Stanford, CA
| | | | - Inma Cobos
- Department of Pathology, Stanford University, Stanford, CA
| | - Laramie Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA
| | - Ritchie Chen
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford, CA
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72
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Galiani S, Eggeling C, Reglinski K. Super-resolution microscopy and studies of peroxisomes. Biol Chem 2023; 404:87-106. [PMID: 36698322 DOI: 10.1515/hsz-2022-0314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023]
Abstract
Fluorescence microscopy is an important tool for studying cellular structures such as organelles. Unfortunately, many details in the corresponding images are hidden due to the resolution limit of conventional lens-based far-field microscopy. An example is the study of peroxisomes, where important processes such as molecular organization during protein important can simply not be studied with conventional far-field microscopy methods. A remedy is super-resolution fluorescence microscopy, which is nowadays a well-established technique for the investigation of inner-cellular structures but has so far to a lesser extent been applied to the study of peroxisomes. To help advancing the latter, we here give an overview over the different super-resolution microscopy approaches and their potentials and challenges in cell-biological research, including labelling issues and a focus on studies on peroxisomes. Here, we also highlight experiments beyond simple imaging such as observations of diffusion dynamics of peroxisomal proteins.
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Affiliation(s)
- Silvia Galiani
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK.,Leibniz Institute of Photonic Technology e.V., Albert-Einstein Strasse 9, D-07745 Jena, Germany, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany.,Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, D-07743 Jena, Germany.,Jena Center for Soft Matter, Philosophenweg 7, D-07743 Jena, Germany
| | - Katharina Reglinski
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein Strasse 9, D-07745 Jena, Germany, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany.,Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, D-07743 Jena, Germany.,University Clinics Jena, Bachstraße 18, D-07743 Jena, Germany
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73
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Gallusser B, Maltese G, Di Caprio G, Vadakkan TJ, Sanyal A, Somerville E, Sahasrabudhe M, O’Connor J, Weigert M, Kirchhausen T. Deep neural network automated segmentation of cellular structures in volume electron microscopy. J Cell Biol 2023; 222:e202208005. [PMID: 36469001 PMCID: PMC9728137 DOI: 10.1083/jcb.202208005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/03/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Volume electron microscopy is an important imaging modality in contemporary cell biology. Identification of intracellular structures is a laborious process limiting the effective use of this potentially powerful tool. We resolved this bottleneck with automated segmentation of intracellular substructures in electron microscopy (ASEM), a new pipeline to train a convolutional neural network to detect structures of a wide range in size and complexity. We obtained dedicated models for each structure based on a small number of sparsely annotated ground truth images from only one or two cells. Model generalization was improved with a rapid, computationally effective strategy to refine a trained model by including a few additional annotations. We identified mitochondria, Golgi apparatus, endoplasmic reticulum, nuclear pore complexes, caveolae, clathrin-coated pits, and vesicles imaged by focused ion beam scanning electron microscopy. We uncovered a wide range of membrane-nuclear pore diameters within a single cell and derived morphological metrics from clathrin-coated pits and vesicles, consistent with the classical constant-growth assembly model.
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Affiliation(s)
- Benjamin Gallusser
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Giorgio Maltese
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | - Giuseppe Di Caprio
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Tegy John Vadakkan
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | - Anwesha Sanyal
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Elliott Somerville
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | - Mihir Sahasrabudhe
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Université Paris-Saclay, CentraleSupélec, Mathématiques et Informatique pour la Complexité et les Systèmes, Gif-sur-Yvette, France
| | - Justin O’Connor
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Martin Weigert
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Department of Cell Biology, Harvard Medical School, Boston, MA
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74
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Mätlik K, Govek EE, Paul MR, Allis CD, Hatten ME. Histone bivalency regulates the timing of cerebellar granule cell development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526881. [PMID: 36778390 PMCID: PMC9915618 DOI: 10.1101/2023.02.02.526881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature, multipolar neurons. Here we use RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in a specific type of CNS neuron, the mouse cerebellar granule cell (GC). We find that in proliferating GC progenitors (GCPs), H3K4me3/H3K27me3 bivalency is common at neuronal genes and undergoes dynamic changes that correlate with gene expression during migration and circuit formation. Expressing a fluorescent sensor for bivalent H3K4me3 and H3K27me3 domains revealed subnuclear bivalent foci in proliferating GCPs. Inhibiting H3K27 methyltransferases EZH1 and EZH2 in vitro and in organotypic cerebellar slices dramatically altered the expression of bivalent genes and induced the downregulation of migration-related genes and upregulation of synaptic genes, inhibited glial-guided migration, and accelerated terminal differentiation. Thus, histone bivalency is required to regulate the timing of the progression from progenitor cells to mature neurons.
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Affiliation(s)
- Kärt Mätlik
- Laboratory of Developmental Neurobiology, Rockefeller University, 10065, New York, NY, USA
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, Rockefeller University, 10065, New York, NY, USA
| | - Matthew R. Paul
- Bioinformatics Resource Center, Rockefeller University, 10065, New York, NY, USA
| | - C. David Allis
- Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, 10065, New York, NY, USA
| | - Mary E. Hatten
- Laboratory of Developmental Neurobiology, Rockefeller University, 10065, New York, NY, USA
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75
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Li S, Wang Z, Jia X, Niu T, Zhang J, Yin G, Zhang X, Zhu Y, Ji G, Sun F. ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study. Nat Methods 2023; 20:276-283. [PMID: 36646897 PMCID: PMC9911351 DOI: 10.1038/s41592-022-01748-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023]
Abstract
Cryo-electron tomography (cryo-ET) has become a powerful approach to study the high-resolution structure of cellular macromolecular machines in situ. However, the current correlative cryo-fluorescence and electron microscopy lacks sufficient accuracy and efficiency to precisely prepare cryo-lamellae of target locations for subsequent cryo-ET. Here we describe a precise cryogenic fabrication system, ELI-TriScope, which sets electron (E), light (L) and ion (I) beams at the same focal point to achieve accurate and efficient preparation of a target cryo-lamella. ELI-TriScope uses a commercial dual-beam scanning electron microscope modified to incorporate a cryo-holder-based transfer system and embed an optical imaging system just underneath the vitrified specimen. Cryo-focused ion beam milling can be accurately navigated by monitoring the real-time fluorescence signal of the target molecule. Using ELI-TriScope, we prepared a batch of cryo-lamellae of HeLa cells targeting the centrosome with a success rate of ~91% and discovered new in situ structural features of the human centrosome by cryo-ET.
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Affiliation(s)
- Shuoguo Li
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyan Wang
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xing Jia
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianguo Zhang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guoliang Yin
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyun Zhang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yun Zhu
- University of Chinese Academy of Sciences, Beijing, China.
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Gang Ji
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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76
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Kanchanawong P, Calderwood DA. Organization, dynamics and mechanoregulation of integrin-mediated cell-ECM adhesions. Nat Rev Mol Cell Biol 2023; 24:142-161. [PMID: 36168065 PMCID: PMC9892292 DOI: 10.1038/s41580-022-00531-5] [Citation(s) in RCA: 195] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 02/04/2023]
Abstract
The ability of animal cells to sense, adhere to and remodel their local extracellular matrix (ECM) is central to control of cell shape, mechanical responsiveness, motility and signalling, and hence to development, tissue formation, wound healing and the immune response. Cell-ECM interactions occur at various specialized, multi-protein adhesion complexes that serve to physically link the ECM to the cytoskeleton and the intracellular signalling apparatus. This occurs predominantly via clustered transmembrane receptors of the integrin family. Here we review how the interplay of mechanical forces, biochemical signalling and molecular self-organization determines the composition, organization, mechanosensitivity and dynamics of these adhesions. Progress in the identification of core multi-protein modules within the adhesions and characterization of rearrangements of their components in response to force, together with advanced imaging approaches, has improved understanding of adhesion maturation and turnover and the relationships between adhesion structures and functions. Perturbations of adhesion contribute to a broad range of diseases and to age-related dysfunction, thus an improved understanding of their molecular nature may facilitate therapeutic intervention in these conditions.
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Affiliation(s)
- Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.
| | - David A Calderwood
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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77
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Integrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation. Nat Methods 2023; 20:268-275. [PMID: 36646896 PMCID: PMC9911353 DOI: 10.1038/s41592-022-01749-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023]
Abstract
Cryo-electron tomography (cryo-ET) is a revolutionary technique for resolving the structure of subcellular organelles and macromolecular complexes in their cellular context. However, the application of the cryo-ET is hampered by the sample preparation step. Performing cryo-focused ion beam milling at an arbitrary position on the sample is inefficient, and the target of interest is not guaranteed to be preserved when thinning the cell from several micrometers to less than 300 nm thick. Here, we report a cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) technique that is capable of preparing cryo-lamellae under the guidance of three-dimensional confocal imaging. Moreover, we demonstrate a workflow to preselect and preserve nanoscale target regions inside the finished cryo-lamellae. By successfully preparing cryo-lamellae that contain a single centriole or contact sites between subcellular organelles, we show that this approach is generally applicable, and shall help in innovating more applications of cryo-ET.
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78
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Jadhav AC, Kounatidis I. Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues. Subcell Biochem 2023; 106:169-196. [PMID: 38159227 DOI: 10.1007/978-3-031-40086-5_6] [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
Viruses are obligate intracellular pathogens that depend on their host cell machinery and metabolism for their replicative life cycle. Virus entry, replication, and assembly are dynamic processes that lead to the reorganisation of host cell components. Therefore, a complete understanding of the viral processes requires their study in the cellular context where advanced imaging has been proven valuable in providing the necessary information. Among the available imaging techniques, soft X-ray tomography (SXT) at cryogenic temperatures can provide three-dimensional mapping to 25 nm resolution and is ideally suited to visualise the internal organisation of virus-infected cells. In this chapter, the principles and practices of synchrotron-based cryo-soft X-ray tomography (cryo-SXT) in virus research are presented. The potential of the cryo-SXT in correlative microscopy platforms is also demonstrated through working examples of reovirus and hepatitis research at Beamline B24 (Diamond Light Source Synchrotron, UK) and BL09-Mistral beamline (ALBA Synchrotron, Spain), respectively.
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Affiliation(s)
- Archana C Jadhav
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK.
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79
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Serra Lleti JM, Steyer AM, Schieber NL, Neumann B, Tischer C, Hilsenstein V, Holtstrom M, Unrau D, Kirmse R, Lucocq JM, Pepperkok R, Schwab Y. CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM. J Cell Biol 2022; 222:213779. [PMID: 36562752 PMCID: PMC9802685 DOI: 10.1083/jcb.202209127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
In recent years, Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) has emerged as a flexible method that enables semi-automated volume ultrastructural imaging. We present a toolset for adherent cells that enables tracking and finding cells, previously identified in light microscopy (LM), in the FIB-SEM, along with the automatic acquisition of high-resolution volume datasets. We detect the underlying grid pattern in both modalities (LM and EM), to identify common reference points. A combination of computer vision techniques enables complete automation of the workflow. This includes setting the coincidence point of both ion and electron beams, automated evaluation of the image quality and constantly tracking the sample position with the microscope's field of view reducing or even eliminating operator supervision. We show the ability to target the regions of interest in EM within 5 µm accuracy while iterating between different targets and implementing unattended data acquisition. Our results demonstrate that executing volume acquisition in multiple locations autonomously is possible in EM.
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Affiliation(s)
- José M. Serra Lleti
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna M. Steyer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Anna M. Steyer:
| | - Nicole L. Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Beate Neumann
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Tischer
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Volker Hilsenstein
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | - John M. Lucocq
- Medical and Biological Sciences, Schools of Medicine and Biology, University of St. Andrews, St. Andrews, UK
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Correspondence to Yannick Schwab:
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80
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Ito Y, Uemura T. Super resolution live imaging: The key for unveiling the true dynamics of membrane traffic around the Golgi apparatus in plant cells. FRONTIERS IN PLANT SCIENCE 2022; 13:1100757. [PMID: 36618665 PMCID: PMC9818705 DOI: 10.3389/fpls.2022.1100757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
In contrast to the relatively static image of the plants, the world inside each cell is surprisingly dynamic. Membrane-bounded organelles move actively on the cytoskeletons and exchange materials by vesicles, tubules, or direct contact between each other. In order to understand what is happening during those events, it is essential to visualize the working components in vivo. After the breakthrough made by the application of fluorescent proteins, the development of light microscopy enabled many discoveries in cell biology, including those about the membrane traffic in plant cells. Especially, super-resolution microscopy, which is becoming more and more accessible, is now one of the most powerful techniques. However, although the spatial resolution has improved a lot, there are still some difficulties in terms of the temporal resolution, which is also a crucial parameter for the visualization of the living nature of the intracellular structures. In this review, we will introduce the super resolution microscopy developed especially for live-cell imaging with high temporal resolution, and show some examples that were made by this tool in plant membrane research.
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Affiliation(s)
- Yoko Ito
- Institute for Human Life Science, Ochanomizu University, Tokyo, Japan
| | - Tomohiro Uemura
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
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81
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Mironov AA, Beznoussenko GV. Algorithm for Modern Electron Microscopic Examination of the Golgi Complex. Methods Mol Biol 2022; 2557:161-209. [PMID: 36512216 DOI: 10.1007/978-1-0716-2639-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Golgi complex (GC) is an essential organelle of the eukaryotic exocytic pathway. It has a very complexed structure and thus localization of its resident proteins is not trivial. Fast development of microscopic methods generates a huge difficulty for Golgi researchers to select the best protocol to use. Modern methods of light microscopy, such as super-resolution light microscopy (SRLM) and electron microscopy (EM), open new possibilities in analysis of various biological structures at organelle, cell, and organ levels. Nowadays, new generation of EM methods became available for the study of the GC; these include three-dimensional EM (3DEM), correlative light-EM (CLEM), immune EM, and new estimators within stereology that allow realization of maximal goal of any morphological study, namely, to achieve a three-dimensional model of the sample with optimal level of resolution and quantitative determination of its chemical composition. Methods of 3DEM have partially overlapping capabilities. This requires a careful comparison of these methods, identification of their strengths and weaknesses, and formulation of recommendations for their application to cell or tissue samples. Here, we present an overview of 3DEM methods for the study of the GC and some basics for how the images are formed and how the image quality can be improved.
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82
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Zhu Z, Xu W, Liu L. Ovarian aging: mechanisms and intervention strategies. MEDICAL REVIEW (BERLIN, GERMANY) 2022; 2:590-610. [PMID: 37724254 PMCID: PMC10471094 DOI: 10.1515/mr-2022-0031] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/25/2022] [Indexed: 09/20/2023]
Abstract
Ovarian reserve is essential for fertility and influences healthy aging in women. Advanced maternal age correlates with the progressive loss of both the quantity and quality of oocytes. The molecular mechanisms and various contributing factors underlying ovarian aging have been uncovered. In this review, we highlight some of critical factors that impact oocyte quantity and quality during aging. Germ cell and follicle reserve at birth determines reproductive lifespan and timing the menopause in female mammals. Accelerated diminishing ovarian reserve leads to premature ovarian aging or insufficiency. Poor oocyte quality with increasing age could result from chromosomal cohesion deterioration and misaligned chromosomes, telomere shortening, DNA damage and associated genetic mutations, oxidative stress, mitochondrial dysfunction and epigenetic alteration. We also discuss the intervention strategies to delay ovarian aging. Both the efficacy of senotherapies by antioxidants against reproductive aging and mitochondrial therapy are discussed. Functional oocytes and ovarioids could be rejuvenated from pluripotent stem cells or somatic cells. We propose directions for future interventions. As couples increasingly begin delaying parenthood in life worldwide, understanding the molecular mechanisms during female reproductive aging and potential intervention strategies could benefit women in making earlier choices about their reproductive health.
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Affiliation(s)
- Zhengmao Zhu
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, China
| | - Wanxue Xu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Lin Liu
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Tianjin Union Medical Center, Institute of Translational Medicine, Nankai University, Tianjin, China
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83
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Dahlberg PD, Perez D, Hecksel CW, Chiu W, Moerner WE. Metallic support films reduce optical heating in cryogenic correlative light and electron tomography. J Struct Biol 2022; 214:107901. [PMID: 36191745 PMCID: PMC9729463 DOI: 10.1016/j.jsb.2022.107901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/28/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022]
Abstract
Super-resolved cryogenic correlative light and electron tomography is an emerging method that provides both the single-molecule sensitivity and specificity of fluorescence imaging, and the molecular scale resolution and detailed cellular context of tomography, all in vitrified cells preserved in their native hydrated state. Technical hurdles that limit these correlative experiments need to be overcome for the full potential of this approach to be realized. Chief among these is sample heating due to optical excitation which leads to devitrification, a phase transition from amorphous to crystalline ice. Here we show that much of this heating is due to the material properties of the support film of the electron microscopy grid, specifically the absorptivity and thermal conductivity. We demonstrate through experiment and simulation that the properties of the standard holey carbon electron microscopy grid lead to substantial heating under optical excitation. In order to avoid devitrification, optical excitation intensities must be kept orders of magnitude lower than the intensities commonly employed in room temperature super-resolution experiments. We further show that the use of metallic films, either holey gold grids, or custom made holey silver grids, alleviate much of this heating. For example, the holey silver grids permit 20× the optical intensities used on the standard holey carbon grids. Super-resolution correlative experiments conducted on holey silver grids under these increased optical excitation intensities have a corresponding increase in the rate of single-molecule fluorescence localizations. This results in an increased density of localizations and improved correlative imaging without deleterious effects from sample heating.
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Affiliation(s)
- Peter D Dahlberg
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Davis Perez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Corey W Hecksel
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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84
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Zhang X, Zheng Y, Bai X, Cai L, Wang L, Wu S, Ke Q, Huang J. Femoral image segmentation based on two-stage convolutional network using 3D-DMFNet and 3D-ResUnet. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 226:107110. [PMID: 36167001 DOI: 10.1016/j.cmpb.2022.107110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/05/2022] [Accepted: 09/04/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE The femur is a typical human long bone with an irregular spatial structure. Femoral fractures are the most common occurrence in middle-aged and older adults. The structure of human bone tissue is very complex, and there are significant differences between individuals. Segmenting bone tissue is a challenging task and of great practical significance. METHODS Our research is based on segmenting and the three-dimensional reconstruction of femoral images using X-ray imaging. The currently commonly used two-dimensional fully convolutional network Unet has the problem of ignoring spatial position information and losing too much feature information. The commonly used three-dimensional fully convolutional network 3D Unet has the problem of ignoring spatial position information and losing too much feature information. For the problem of many model parameters, we proposes a two-stage network segmentation model composed of 3D-DMFNet and 3D-ResUnet networks and trains the network in stages to segment the femur. One stage is used to detect the coarse segmentation of the femur range, and one stage is used for the fine segmentation of the femur so that the training speed is fast and the segmentation accuracy is moderate, which is suitable for detecting the femur range. RESULTS The experimental dataset used in this paper is from The Second Affiliated Hospital of Fujian Medical University, which consists of 30 sets of femur X-ray images. The experiment compares the accuracy and loss value of Unet and the two-stage convolutional network. The image shows that the two-stage convolutional network has higher accuracy. At the same time, this paper shows the effect of the two-stage coarse segmentation and fine segmentation of medical images. Subsequently, this paper applies the model to practice and obtains the model's Dice, Sensitivity, Specificity and Pixel Accuracy values. After comparative analysis, the experimental results show that the two-stage network segmentation model composed of 3D-DMFNet and 3D-ResUnet network designed in this paper has higher accuracy, intuitiveness, and more application value than traditional image segmentation algorithms. CONCLUSION With the continuous application of X-ray images in clinical diagnosis using femoral images, the method in this paper is expected to become a diagnostic tool that can effectively improve the accuracy and loss of femoral image segmentation and the three-dimensional reconstruction.
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Affiliation(s)
- Xiaolu Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China.
| | - Yiqiang Zheng
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Xiaoming Bai
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Liquan Cai
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Liangming Wang
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Shiqiang Wu
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Qingfeng Ke
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Jianlong Huang
- Faculty of Mathematics and Computer Science, Quanzhou Normal University, Quanzhou, Fujian 362000, China; Fujian Provincial Key Laboratory of Data Intensive Computing, Quanzhou 362000, China; Key Laboratory of Intelligent Computing and Information Processing, Fujian Province University, Quanzhou 362000, China.
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85
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Fundamental roles for inter-organelle communication in aging. Biochem Soc Trans 2022; 50:1389-1402. [PMID: 36305642 PMCID: PMC9704535 DOI: 10.1042/bst20220519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/27/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Advances in public health have nearly doubled life expectancy over the last century, but this demographic shift has also changed the landscape of human illness. Today, chronic and age-dependent diseases dominate the leading causes of morbidity and mortality worldwide. Targeting the underlying molecular, genetic and cell biological drivers of the aging process itself appears to be an increasingly viable strategy for developing therapeutics against these diseases of aging. Towards this end, one of the most exciting developments in cell biology over the last decade is the explosion of research into organelle contact sites and related mechanisms of inter-organelle communication. Identification of the molecular mediators of inter-organelle tethering and signaling is now allowing the field to investigate the consequences of aberrant organelle interactions, which frequently seem to correlate with age-onset pathophysiology. This review introduces the major cellular roles for inter-organelle interactions, including the regulation of organelle morphology, the transfer of ions, lipids and other metabolites, and the formation of hubs for nutrient and stress signaling. We explore how these interactions are disrupted in aging and present findings that modulation of inter-organelle communication is a promising avenue for promoting longevity. Through this review, we propose that the maintenance of inter-organelle interactions is a pillar of healthy aging. Learning how to target the cellular mechanisms for sensing and controlling inter-organelle communication is a key next hurdle for geroscience.
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86
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Midorikawa K, Tateishi A, Toyooka K, Sato M, Imai T, Kodama Y, Numata K. Three-dimensional nanoscale analysis of light-dependent organelle changes in Arabidopsis mesophyll cells. PNAS NEXUS 2022; 1:pgac225. [PMID: 36712360 PMCID: PMC9802074 DOI: 10.1093/pnasnexus/pgac225] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/15/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022]
Abstract
Different organelles function coordinately in numerous intracellular processes. Photorespiration incidental to photosynthetic carbon fixation is organized across three subcellular compartments: chloroplasts, peroxisomes, and mitochondria. Under light conditions, these three organelles often form a ternary organellar complex in close proximity, suggesting a connection with metabolism during photorespiration. However, due to the heterogeneity of intercellular organelle localization and morphology, organelles' responses to changes in the external environment remain poorly understood. Here, we used array tomography by field emission scanning electron microscopy to image organelles inside the whole plant cell at nanometer resolution, generating a three-dimensional (3D) spatial map of the light-dependent positioning of chloroplasts, peroxisomes, nuclei, and vacuoles. Our results show, in light-treated cells, the volume of peroxisomes increased, and mitochondria were simplified. In addition, the population of free organelles decreased, and the ternary complex centered on chloroplasts increased. Moreover, our results emphasized the expansion of the proximity area rather than the increase in the number of proximity sites interorganelles. All of these phenomena were quantified for the first time on the basis of nanoscale spatial maps. In summary, we provide the first 3D reconstruction of Arabidopsis mesophyll cells, together with nanoscale quantified organelle morphology and their positioning via proximity areas, and then evidence of their light-dependent changes.
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Affiliation(s)
- Keiko Midorikawa
- Biomacromoleules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan,Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
| | - Ayaka Tateishi
- Biomacromoleules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan,Department of Material Chemistry, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan
| | - Takuto Imai
- Biomacromoleules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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87
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Abstract
Fluorescence microscopy is a highly effective tool for interrogating biological structure and function, particularly when imaging across multiple spatiotemporal scales. Here we survey recent innovations and applications in the relatively understudied area of multiscale fluorescence imaging of living samples. We discuss fundamental challenges in live multiscale imaging and describe successful examples that highlight the power of this approach. We attempt to synthesize general strategies from these test cases, aiming to help accelerate progress in this exciting area.
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Affiliation(s)
- Yicong Wu
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Hari Shroff
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
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88
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Abstract
Genomic DNA is organized three-dimensionally in the nucleus as chromatin. Recent accumulating evidence has demonstrated that chromatin organizes into numerous dynamic domains in higher eukaryotic cells, which act as functional units of the genome. These compacted domains facilitate DNA replication and gene regulation. Undamaged chromatin is critical for healthy cells to function and divide. However, the cellular genome is constantly threatened by many sources of DNA damage (e.g., radiation). How do cells maintain their genome integrity when subjected to DNA damage? This chapter describes how the compact state of chromatin safeguards the genome from radiation damage and chemical attacks. Together with recent genomics data, our finding suggests that DNA compaction, such as chromatin domain formation, plays a critical role in maintaining genome integrity. But does the formation of such domains limit DNA accessibility inside the domain and hinder the recruitment of repair machinery to the damaged site(s) during DNA repair? To approach this issue, we first describe a sensitive imaging method to detect changes in chromatin states in living cells (single-nucleosome imaging/tracking). We then use this method to explain how cells can overcome potential recruiting difficulties; cells can decompact chromatin domains following DNA damage and temporarily increase chromatin motion (∼DNA accessibility) to perform efficient DNA repair. We also speculate on how chromatin compaction affects DNA damage-resistance in the clinical setting.
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Affiliation(s)
- Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan.
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89
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Zhu C, Lee CT, Rangamani P. Mem3DG: Modeling membrane mechanochemical dynamics in 3D using discrete differential geometry. BIOPHYSICAL REPORTS 2022; 2:100062. [PMID: 36157269 PMCID: PMC9495267 DOI: 10.1016/j.bpr.2022.100062] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared with approximation-based methods (e.g., finite element method [FEM]), the class of discrete mesh models offers greater flexibility to simulate complex physics and shapes in three dimensions; its formulation produces an efficient algorithm while maintaining coordinate-free geometric descriptions. However, ambiguities in geometric definitions in the discrete context have led to a lack of consensus on which discrete mesh model is theoretically and numerically optimal; a bijective relationship between the terms contributing to both the energy and forces from the discrete and smooth geometric theories remains to be established. We address this and present an extensible framework, Mem3DG, for modeling 3D mechanochemical dynamics of membranes based on discrete differential geometry (DDG) on triangulated meshes. The formalism of DDG resolves the inconsistency and provides a unifying perspective on how to relate the smooth and discrete energy and forces. To demonstrate, Mem3DG is used to model a sequence of examples with increasing mechanochemical complexity: recovering classical shape transformations such as 1) biconcave disk, dumbbell, and unduloid; and 2) spherical bud on spherical, flat-patch membrane; investigating how the coupling of membrane mechanics with protein mobility jointly affects phase and shape transformation. As high-resolution 3D imaging of membrane ultrastructure becomes more readily available, we envision Mem3DG to be applied as an end-to-end tool to simulate realistic cell geometry under user-specified mechanochemical conditions.
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Affiliation(s)
- Cuncheng Zhu
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA 92093
| | - Christopher T. Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA 92093
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA 92093
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90
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Kievits AJ, Lane R, Carroll EC, Hoogenboom JP. How innovations in methodology offer new prospects for volume electron microscopy. J Microsc 2022; 287:114-137. [PMID: 35810393 PMCID: PMC9546337 DOI: 10.1111/jmi.13134] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
Abstract
Detailed knowledge of biological structure has been key in understanding biology at several levels of organisation, from organs to cells and proteins. Volume electron microscopy (volume EM) provides high resolution 3D structural information about tissues on the nanometre scale. However, the throughput rate of conventional electron microscopes has limited the volume size and number of samples that can be imaged. Recent improvements in methodology are currently driving a revolution in volume EM, making possible the structural imaging of whole organs and small organisms. In turn, these recent developments in image acquisition have created or stressed bottlenecks in other parts of the pipeline, like sample preparation, image analysis and data management. While the progress in image analysis is stunning due to the advent of automatic segmentation and server-based annotation tools, several challenges remain. Here we discuss recent trends in volume EM, emerging methods for increasing throughput and implications for sample preparation, image analysis and data management.
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Affiliation(s)
- Arent J. Kievits
- Department of Imaging PhysicsDelft University of TechnologyDelftThe Netherlands
| | - Ryan Lane
- Department of Imaging PhysicsDelft University of TechnologyDelftThe Netherlands
| | | | - Jacob P. Hoogenboom
- Department of Imaging PhysicsDelft University of TechnologyDelftThe Netherlands
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91
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Perez D, Dahlberg PD, Wang J, Sartor AM, Borden JS, Shapiro L, Moerner WE. Identification and demonstration of roGFP2 as an environmental sensor for cryogenic correlative light and electron microscopy. J Struct Biol 2022; 214:107881. [PMID: 35811036 PMCID: PMC9452478 DOI: 10.1016/j.jsb.2022.107881] [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: 02/22/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 10/17/2022]
Abstract
Cryogenic correlative light and electron microscopy (cryo-CLEM) seeks to leverage orthogonal information present in two powerful imaging modalities. While recent advances in cryogenic electron microscopy (cryo-EM) allow for the visualization and identification of structures within cells at the nanometer scale, information regarding the cellular environment, such as pH, membrane potential, ionic strength, etc., which influences the observed structures remains absent. Fluorescence microscopy can potentially be used to reveal this information when specific labels, known as fluorescent biosensors, are used, but there has been minimal use of such biosensors in cryo-CLEM to date. Here we demonstrate the applicability of one such biosensor, the fluorescent protein roGFP2, for cryo-CLEM experiments. At room temperature, the ratio of roGFP2 emission brightness when excited at 425 nm or 488 nm is known to report on the local redox potential. When samples containing roGFP2 are rapidly cooled to 77 K in a manner compatible with cryo-EM, the ratio of excitation peaks remains a faithful indicator of the redox potential at the time of freezing. Using purified protein in different oxidizing/reducing environments, we generate a calibration curve which can be used to analyze in situ measurements. As a proof-of-principle demonstration, we investigate the oxidation/reduction state within vitrified Caulobacter crescentus cells. The polar organizing protein Z (PopZ) localizes to the polar regions of C. crescentus where it is known to form a distinct microdomain. By expressing an inducible roGFP2-PopZ fusion we visualize individual microdomains in the context of their redox environment.
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Affiliation(s)
- Davis Perez
- Department of Chemistry, Stanford University, United States
| | - Peter D Dahlberg
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, United States
| | - Jiarui Wang
- Department of Chemistry, Stanford University, United States; Department of Developmental Biology, Stanford University, United States
| | | | - Julia S Borden
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, United States
| | - W E Moerner
- Department of Chemistry, Stanford University, United States
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92
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Wang Q, Wang Y, Li S, Zhou A, Qin Y. Organelle biogenesis: ribosomes as organizer and performer. Sci Bull (Beijing) 2022; 67:1614-1617. [PMID: 36546035 DOI: 10.1016/j.scib.2022.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Qi Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yibo Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shuoguo Li
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Aoqi Zhou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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93
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Bélanger S, Berensmann H, Baena V, Duncan K, Meyers BC, Narayan K, Czymmek KJ. A versatile enhanced freeze-substitution protocol for volume electron microscopy. Front Cell Dev Biol 2022; 10:933376. [PMID: 36003147 PMCID: PMC9393620 DOI: 10.3389/fcell.2022.933376] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Volume electron microscopy, a powerful approach to generate large three-dimensional cell and tissue volumes at electron microscopy resolutions, is rapidly becoming a routine tool for understanding fundamental and applied biological questions. One of the enabling factors for its adoption has been the development of conventional fixation protocols with improved heavy metal staining. However, freeze-substitution with organic solvent-based fixation and staining has not realized the same level of benefit. Here, we report a straightforward approach including osmium tetroxide, acetone and up to 3% water substitution fluid (compatible with traditional or fast freeze-substitution protocols), warm-up and transition from organic solvent to aqueous 2% osmium tetroxide. Once fully hydrated, samples were processed in aqueous based potassium ferrocyanide, thiocarbohydrazide, osmium tetroxide, uranyl acetate and lead acetate before resin infiltration and polymerization. We observed a consistent and substantial increase in heavy metal staining across diverse and difficult-to-fix test organisms and tissue types, including plant tissues (Hordeum vulgare), nematode (Caenorhabditis elegans) and yeast (Saccharomyces cerevisiae). Our approach opens new possibilities to combine the benefits of cryo-preservation with enhanced contrast for volume electron microscopy in diverse organisms.
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Affiliation(s)
| | - Heather Berensmann
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Valentina Baena
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Keith Duncan
- Donald Danforth Plant Science Center, Saint Louis, MO, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO, United States
- Division of Plant Science and Technology, University of Missouri–Columbia, Columbia, MO, United States
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Kirk J. Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO, United States
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO, United States
- *Correspondence: Kirk J. Czymmek,
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94
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Kiewisz R, Fabig G, Conway W, Baum D, Needleman DJ, Müller-Reichert T. Three-dimensional structure of kinetochore-fibers in human mitotic spindles. eLife 2022; 11:75459. [PMID: 35894209 PMCID: PMC9365394 DOI: 10.7554/elife.75459] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/24/2022] [Indexed: 11/13/2022] Open
Abstract
During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here, we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells.
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Affiliation(s)
- Robert Kiewisz
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - William Conway
- Department of Physics, Harvard University, Cambridge, United States
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Daniel J Needleman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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95
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Cao M, Zhu T, Zhao M, Meng F, Liu Z, Wang J, Niu G, Yu X. Structure Rigidification Promoted Ultrabright Solvatochromic Fluorescent Probes for Super-Resolution Imaging of Cytosolic and Nuclear Lipid Droplets. Anal Chem 2022; 94:10676-10684. [DOI: 10.1021/acs.analchem.2c00964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mingyue Cao
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P. R. China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, P. R. China
- Suzhou Research Institute, Shandong University, Suzhou 215123, P. R. China
| | - Ting Zhu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P. R. China
| | - Mengying Zhao
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P. R. China
| | - Fanda Meng
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, P. R. China
| | - Zhiqiang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P. R. China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, P. R. China
| | - Jianguo Wang
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
| | - Guangle Niu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P. R. China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, P. R. China
- Suzhou Research Institute, Shandong University, Suzhou 215123, P. R. China
| | - Xiaoqiang Yu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P. R. China
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96
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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: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [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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97
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Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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98
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Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
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Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
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99
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van den Dries K, Fransen J, Cambi A. Fluorescence CLEM in biology: historic developments and current super-resolution applications. FEBS Lett 2022; 596:2486-2496. [PMID: 35674424 DOI: 10.1002/1873-3468.14421] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a powerful imaging approach that allows the direct correlation of information obtained on a light and an electron microscope. There is a growing interest in the application of CLEM in biology, mainly attributable to technical advances in field of fluorescence microscopy in the past two decades. In this review, we summarize the important developments in CLEM for biological applications, focusing on the combination of fluorescence microscopy and electron microscopy. We first provide a brief overview of the early days of fluorescence CLEM usage starting with the initial rise in the late 1970s and the subsequent optimization of CLEM workflows during the following two decades. Next, we describe how the engineering of fluorescent proteins and the development of super-resolution fluorescence microscopy have significantly renewed the interest in CLEM resulting in the present application of fluorescence CLEM in many different areas of cellular and molecular biology. Lastly, we present the promises and challenges for the future of fluorescence CLEM discussing novel workflows, probe development and quantification possibilities.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
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Larocque G, Royle SJ. Integrating intracellular nanovesicles into integrin trafficking pathways and beyond. Cell Mol Life Sci 2022; 79:335. [PMID: 35657500 PMCID: PMC9166830 DOI: 10.1007/s00018-022-04371-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Membrane traffic controls the movement of proteins and lipids from one cellular compartment to another using a system of transport vesicles. Intracellular nanovesicles (INVs) are a newly described class of transport vesicles. These vesicles are small, carry diverse cargo, and are involved in multiple trafficking steps including anterograde traffic and endosomal recycling. An example of a biological process that they control is cell migration and invasion, due to their role in integrin recycling. In this review, we describe what is known so far about these vesicles. We discuss how INVs may integrate into established membrane trafficking pathways using integrin recycling as an example. We speculate where in the cell INVs have the potential to operate and we identify key questions for future investigation.
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Affiliation(s)
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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