201
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Miron E, Oldenkamp R, Brown JM, Pinto DMS, Xu CS, Faria AR, Shaban HA, Rhodes JDP, Innocent C, de Ornellas S, Hess HF, Buckle V, Schermelleh L. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. SCIENCE ADVANCES 2020; 6:eaba8811. [PMID: 32967822 PMCID: PMC7531892 DOI: 10.1126/sciadv.aba8811] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/06/2020] [Indexed: 05/05/2023]
Abstract
Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.
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Affiliation(s)
- Ezequiel Miron
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Roel Oldenkamp
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jill M Brown
- MRC Weatherall Institute of Molecular Medicine, Haematology Unit, University of Oxford, Oxford OX3 9DS, UK
| | - David M S Pinto
- Micron Oxford Advanced Bioimaging Unit, University of Oxford, Oxford OX1 3QU, UK
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ana R Faria
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Haitham A Shaban
- Spectroscopy Department, Physics Division, National Research Centre, 12622 Dokki, Cairo, Egypt
| | - James D P Rhodes
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Sara de Ornellas
- MRC Weatherall Institute of Molecular Medicine, Haematology Unit, University of Oxford, Oxford OX3 9DS, UK
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Veronica Buckle
- MRC Weatherall Institute of Molecular Medicine, Haematology Unit, University of Oxford, Oxford OX3 9DS, UK
| | - Lothar Schermelleh
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
- Micron Oxford Advanced Bioimaging Unit, University of Oxford, Oxford OX1 3QU, UK
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202
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Ravi RT, Leung MR, Zeev-Ben-Mordehai T. Looking back and looking forward: contributions of electron microscopy to the structural cell biology of gametes and fertilization. Open Biol 2020; 10:200186. [PMID: 32931719 PMCID: PMC7536082 DOI: 10.1098/rsob.200186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/25/2020] [Indexed: 01/22/2023] Open
Abstract
Mammalian gametes-the sperm and the egg-represent opposite extremes of cellular organization and scale. Studying the ultrastructure of gametes is crucial to understanding their interactions, and how to manipulate them in order to either encourage or prevent their union. Here, we survey the prominent electron microscopy (EM) techniques, with an emphasis on considerations for applying them to study mammalian gametes. We review how conventional EM has provided significant insight into gamete ultrastructure, but also how the harsh sample preparation methods required preclude understanding at a truly molecular level. We present recent advancements in cryo-electron tomography that provide an opportunity to image cells in a near-native state and at unprecedented levels of detail. New and emerging cellular EM techniques are poised to rekindle exploration of fundamental questions in mammalian reproduction, especially phenomena that involve complex membrane remodelling and protein reorganization. These methods will also allow novel lines of enquiry into problems of practical significance, such as investigating unexplained causes of human infertility and improving assisted reproductive technologies for biodiversity conservation.
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Affiliation(s)
- Ravi Teja Ravi
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Miguel Ricardo Leung
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
- Division of Structural Biology, Wellcome Centre for Human Genetics, The University of Oxford, Oxford OX3 7BN, UK
| | - Tzviya Zeev-Ben-Mordehai
- Cryo-Electron Microscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
- Division of Structural Biology, Wellcome Centre for Human Genetics, The University of Oxford, Oxford OX3 7BN, UK
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203
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Bryman GS, Liu A, Do MTH. Optimized Signal Flow through Photoreceptors Supports the High-Acuity Vision of Primates. Neuron 2020; 108:335-348.e7. [PMID: 32846139 DOI: 10.1016/j.neuron.2020.07.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/24/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
The fovea is a neural specialization that endows humans and other primates with the sharpest vision among mammals. This performance originates in the foveal cones, which are extremely narrow and long to form a high-resolution pixel array. Puzzlingly, this form is predicted to impede electrical conduction to an extent that appears incompatible with vision. We observe the opposite: signal flow through even the longest cones (0.4-mm axons) is essentially lossless. Unlike in most neurons, amplification and impulse generation by voltage-gated channels are dispensable. Rather, sparse channel activity preserves intracellular current, which flows as if unobstructed by organelles. Despite these optimizations, signaling would degrade if cones were lengthier. Because cellular packing requires that cone elongation accompanies foveal expansion, this degradation helps explain why the fovea is a constant, miniscule size despite multiplicative changes in eye size through evolution. These observations reveal how biophysical mechanisms tailor form-function relationships for primate behavioral performance.
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Affiliation(s)
- Gregory S Bryman
- F.M. Kirby Neurobiology Center and Department of Neurology, Boston Children's Hospital and Harvard Medical School, Center for Life Science 12061, 3 Blackfan Circle, Boston, MA 02115, USA.
| | - Andreas Liu
- F.M. Kirby Neurobiology Center and Department of Neurology, Boston Children's Hospital and Harvard Medical School, Center for Life Science 12061, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Michael Tri H Do
- F.M. Kirby Neurobiology Center and Department of Neurology, Boston Children's Hospital and Harvard Medical School, Center for Life Science 12061, 3 Blackfan Circle, Boston, MA 02115, USA.
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204
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Abstract
Extracellular vesicles mediate transfer of diverse molecular content to target cells in order to induce phenotypic changes, which has put them under the spotlight as likely major players in cell-to-cell communication. However, extracellular vesicle heterogeneity in terms of intracellular origin has only recently been recognized as a potential determinant of their activity. Recent work by Fan et al (2020) illustrates how lack of external resources that affect cellular homeostasis and signaling can also modulate EV biogenesis, by inducing the production of a novel subpopulation of exosomes enriched in Rab11a with context-dependent roles in Drosophila gland physiology and cancer cell aggressiveness.
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Affiliation(s)
- Guillaume van Niel
- Université de ParisInstitute of Psychiatry and Neuroscience of Paris (IPNP)INSERM U1266“Endosomal dynamic in neuropathies”ParisFrance
| | - Clotilde Théry
- INSERM U932Institut CuriePSL Research UniversityParisFrance
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205
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The In Situ Structure of Parkinson's Disease-Linked LRRK2. Cell 2020; 182:1508-1518.e16. [PMID: 32783917 DOI: 10.1016/j.cell.2020.08.004] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of familial Parkinson's disease. LRRK2 is a multi-domain protein containing a kinase and GTPase. Using correlative light and electron microscopy, in situ cryo-electron tomography, and subtomogram analysis, we reveal a 14-Å structure of LRRK2 bearing a pathogenic mutation that oligomerizes as a right-handed double helix around microtubules, which are left-handed. Using integrative modeling, we determine the architecture of LRRK2, showing that the GTPase and kinase are in close proximity, with the GTPase closer to the microtubule surface, whereas the kinase is exposed to the cytoplasm. We identify two oligomerization interfaces mediated by non-catalytic domains. Mutation of one of these abolishes LRRK2 microtubule-association. Our work demonstrates the power of cryo-electron tomography to generate models of previously unsolved structures in their cellular environment.
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206
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Reliable estimation of membrane curvature for cryo-electron tomography. PLoS Comput Biol 2020; 16:e1007962. [PMID: 32776920 PMCID: PMC7444595 DOI: 10.1371/journal.pcbi.1007962] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 08/20/2020] [Accepted: 05/18/2020] [Indexed: 01/01/2023] Open
Abstract
Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to-native state and molecular resolution. However, current curvature estimation methods cannot be applied directly to membrane segmentations in cryo-ET, as these methods cannot cope with some of the artifacts introduced during image acquisition and membrane segmentation, such as quantization noise and open borders. Here, we developed and implemented a Python package for membrane curvature estimation from tomogram segmentations, which we named PyCurv. From a membrane segmentation, a signed surface (triangle mesh) is first extracted. The triangle mesh is then represented by a graph, which facilitates finding neighboring triangles and the calculation of geodesic distances necessary for local curvature estimation. PyCurv estimates curvature based on tensor voting. Beside curvatures, this algorithm also provides robust estimations of surface normals and principal directions. We tested PyCurv and three well-established methods on benchmark surfaces and biological data. This revealed the superior performance of PyCurv not only for cryo-ET, but also for data generated by other techniques such as light microscopy and magnetic resonance imaging. Altogether, PyCurv is a versatile open-source software to reliably estimate curvature of membranes and other surfaces in a wide variety of applications. Membrane curvature plays a central role in many cellular processes like cell division, organelle shaping and membrane contact sites. While cryo-electron tomography (cryo-ET) allows the visualization of cellular membranes in 3D at molecular resolution and close-to-native conditions, there is a lack of computational methods to quantify membrane curvature from cryo-ET data. Therefore, we developed a computational procedure for membrane curvature estimation from tomogram segmentations and implemented it in a software package called PyCurv. PyCurv converts a membrane segmentation, i.e. a set of voxels, into a surface, i.e. a mesh of triangles. PyCurv uses the local geometrical information to reliably estimate the local surface orientation, the principal (maximum and minimum) curvatures and their directions. PyCurv outperforms well-established curvature estimation methods, and it can also be applied to data generated by other imaging techniques.
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207
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Nosov G, Kahms M, Klingauf J. The Decade of Super-Resolution Microscopy of the Presynapse. Front Synaptic Neurosci 2020; 12:32. [PMID: 32848695 PMCID: PMC7433402 DOI: 10.3389/fnsyn.2020.00032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 07/21/2020] [Indexed: 01/05/2023] Open
Abstract
The presynaptic compartment of the chemical synapse is a small, yet extremely complex structure. Considering its size, most methods of optical microscopy are not able to resolve its nanoarchitecture and dynamics. Thus, its ultrastructure could only be studied by electron microscopy. In the last decade, new methods of optical superresolution microscopy have emerged allowing the study of cellular structures and processes at the nanometer scale. While this is a welcome addition to the experimental arsenal, it has necessitated careful analysis and interpretation to ensure the data obtained remains artifact-free. In this article we review the application of nanoscopic techniques to the study of the synapse and the progress made over the last decade with a particular focus on the presynapse. We find to our surprise that progress has been limited, calling for imaging techniques and probes that allow dense labeling, multiplexing, longer imaging times, higher temporal resolution, while at least maintaining the spatial resolution achieved thus far.
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Affiliation(s)
- Georgii Nosov
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany.,CIM-IMPRS Graduate Program in Münster, Münster, Germany
| | - Martin Kahms
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Jurgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
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208
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Keevend K, Coenen T, Herrmann IK. Correlative cathodoluminescence electron microscopy bioimaging: towards single protein labelling with ultrastructural context. NANOSCALE 2020; 12:15588-15603. [PMID: 32677648 DOI: 10.1039/d0nr02563a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies heavily on the assessment of structure-function relationships at the nanoscale. Ever since the development of the first optical microscope, the reliance of scientists across disciplines on microscopy has increased. The development of the first electron microscope and with it the access to information at the nanoscale has prompted numerous disruptive discoveries. While fluorescence imaging allows identification of specific entities based on the labelling with fluorophores, the unlabelled constituents of the samples remain invisible. In electron microscopy on the other hand, structures can be comprehensively visualized based on their distinct electron density and geometry. Although electron microscopy is a powerful tool, it does not implicitly provide information on the location and activity of specific organic molecules. While correlative light and electron microscopy techniques have attempted to unify the two modalities, the resolution mismatch between the two data sets poses major challenges. Recent developments in optical super resolution microscopy enable high resolution correlative light and electron microscopy, however, with considerable constraints due to sample preparation requirements. Labelling of specific structures directly for electron microscopy using small gold nanoparticles (i.e. immunogold) has been used extensively. However, identification of specific entities solely based on electron contrast, and the differentiation from endogenous dense granules, remains challenging. Recently, the use of correlative cathodoluminescence electron microscopy (CCLEM) imaging based on luminescent inorganic nanocrystals has been proposed. While nanometric resolution can be reached for both the electron and the optical signal, high energy electron beams are potentially damaging to the sample. In this review, we discuss the opportunities of (volumetric) multi-color single protein labelling based on correlative cathodoluminescence electron microscopy, and its prospective impact on biomedical research in general. We elaborate on the potential challenges of correlative cathodoluminescence electron microscopy-based bioimaging and benchmark CCLEM against alternative high-resolution correlative imaging techniques.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St Gallen, Switzerland.
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209
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M'Saad O, Bewersdorf J. Light microscopy of proteins in their ultrastructural context. Nat Commun 2020; 11:3850. [PMID: 32737322 PMCID: PMC7395138 DOI: 10.1038/s41467-020-17523-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/03/2020] [Indexed: 11/09/2022] Open
Abstract
Resolving the distribution of specific proteins at the nanoscale in the ultrastructural context of the cell is a major challenge in fluorescence microscopy. We report the discovery of a new principle for an optical contrast equivalent to electron microscopy (EM) which reveals the ultrastructural context of the cells with a conventional confocal microscope. By decrowding the intracellular space through 13 to 21-fold physical expansion while simultaneously retaining the proteins, bulk (pan) labeling of the proteome resolves local protein densities and reveals the cellular nanoarchitecture by standard light microscopy.
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Affiliation(s)
- Ons M'Saad
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Nanobiology Institute, Yale University, West Haven, CT, USA.
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210
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Kounatidis I, Stanifer ML, Phillips MA, Paul-Gilloteaux P, Heiligenstein X, Wang H, Okolo CA, Fish TM, Spink MC, Stuart DI, Davis I, Boulant S, Grimes JM, Dobbie IM, Harkiolaki M. 3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway. Cell 2020; 182:515-530.e17. [PMID: 32610083 PMCID: PMC7391008 DOI: 10.1016/j.cell.2020.05.051] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 05/28/2020] [Indexed: 01/15/2023]
Abstract
Imaging of biological matter across resolution scales entails the challenge of preserving the direct and unambiguous correlation of subject features from the macroscopic to the microscopic level. Here, we present a correlative imaging platform developed specifically for imaging cells in 3D under cryogenic conditions by using X-rays and visible light. Rapid cryo-preservation of biological specimens is the current gold standard in sample preparation for ultrastructural analysis in X-ray imaging. However, cryogenic fluorescence localization methods are, in their majority, diffraction-limited and fail to deliver matching resolution. We addressed this technological gap by developing an integrated, user-friendly platform for 3D correlative imaging of cells in vitreous ice by using super-resolution structured illumination microscopy in conjunction with soft X-ray tomography. The power of this approach is demonstrated by studying the process of reovirus release from intracellular vesicles during the early stages of infection and identifying intracellular virus-induced structures.
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Affiliation(s)
- Ilias Kounatidis
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Michael A Phillips
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France; Nantes Université, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS3556, Nantes, France
| | | | - Hongchang Wang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Chidinma A Okolo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Thomas M Fish
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Matthew C Spink
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - David I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Ilan Davis
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; Research Group "Cellular polarity and viral infection," German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jonathan M Grimes
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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211
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Belmont AS, King MC. Going nuclear: Recent developments, cutting-edge tools, and new paradigms. Curr Opin Cell Biol 2020; 64:iii-v. [PMID: 32682519 DOI: 10.1016/j.ceb.2020.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, USA
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, USA.
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212
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Phillips MA, Harkiolaki M, Susano Pinto DM, Parton RM, Palanca A, Garcia-Moreno M, Kounatidis I, Sedat JW, Stuart DI, Castello A, Booth MJ, Davis I, Dobbie IM. CryoSIM: super-resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultrastructural imaging. OPTICA 2020; 7:802-812. [PMID: 34277893 PMCID: PMC8262592 DOI: 10.1364/optica.393203] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 05/19/2023]
Abstract
Rapid cryopreservation of biological specimens is the gold standard for visualizing cellular structures in their true structural context. However, current commercial cryo-fluorescence microscopes are limited to low resolutions. To fill this gap, we have developed cryoSIM, a microscope for 3D super-resolution fluorescence cryo-imaging for correlation with cryo-electron microscopy or cryo-soft X-ray tomography. We provide the full instructions for replicating the instrument mostly from off-the-shelf components and accessible, user-friendly, open-source Python control software. Therefore, cryoSIM democratizes the ability to detect molecules using super-resolution fluorescence imaging of cryopreserved specimens for correlation with their cellular ultrastructure.
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Affiliation(s)
- Michael A. Phillips
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
- STRUBI, Division of Structural Biology, Wellcome Centre for Human Genetics, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN,
UK
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - David Miguel Susano Pinto
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Richard M. Parton
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Ana Palanca
- Department of Anatomy and Cell Biology, Faculty of Medicine, Universidad de Cantabria, CP39011 Santander,
Spain
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Ilias Kounatidis
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - John W. Sedat
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143,
USA
| | - David I. Stuart
- STRUBI, Division of Structural Biology, Wellcome Centre for Human Genetics, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN,
UK
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
| | - Ilan Davis
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
- e-mail:
| | - Ian M. Dobbie
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
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213
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Zhao Q, Gao SM, Wang MC. Molecular Mechanisms of Lysosome and Nucleus Communication. Trends Biochem Sci 2020; 45:978-991. [PMID: 32624271 DOI: 10.1016/j.tibs.2020.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/11/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022]
Abstract
Lysosomes transcend the role of degradation stations, acting as key nodes for interorganelle crosstalk and signal transduction. Lysosomes communicate with the nucleus through physical proximity and functional interaction. In response to external and internal stimuli, lysosomes actively adjust their distribution between peripheral and perinuclear regions and modulate lysosome-nucleus signaling pathways; in turn, the nucleus fine-tunes lysosomal biogenesis and functions through transcriptional controls. Changes in coordination between these two essential organelles are associated with metabolic disorders, neurodegenerative diseases, and aging. In this review, we address recent advances in lysosome-nucleus communication by multi-tiered regulatory mechanisms and discuss how these regulations couple metabolic inputs with organellar motility, cellular signaling, and transcriptional network.
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Affiliation(s)
- Qian Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shihong Max Gao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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214
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Ganeva I, Kukulski W. Membrane Architecture in the Spotlight of Correlative Microscopy. Trends Cell Biol 2020; 30:577-587. [DOI: 10.1016/j.tcb.2020.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
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215
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Dahlberg PD, Saurabh S, Sartor AM, Wang J, Mitchell PG, Chiu W, Shapiro L, Moerner WE. Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter. Proc Natl Acad Sci U S A 2020; 117:13937-13944. [PMID: 32513734 PMCID: PMC7321984 DOI: 10.1073/pnas.2001849117] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus: McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.
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Affiliation(s)
- Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Annina M Sartor
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jiarui Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Patrick G Mitchell
- Division of Cryo-EM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Wah Chiu
- Division of Cryo-EM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305;
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216
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Nave C. The achievable resolution for X-ray imaging of cells and other soft biological material. IUCRJ 2020; 7:393-403. [PMID: 32431823 PMCID: PMC7201285 DOI: 10.1107/s2052252520002262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
X-ray imaging of soft materials is often difficult because of the low contrast of the components. This particularly applies to frozen hydrated biological cells where the feature of interest can have a similar density to the surroundings. As a consequence, a high dose is often required to achieve the desired resolution. However, the maximum dose that a specimen can tolerate is limited by radiation damage. Results from 3D coherent diffraction imaging (CDI) of frozen hydrated specimens have given resolutions of ∼80 nm compared with the expected resolution of 10 nm predicted from theoretical considerations for identifying a protein embedded in water. Possible explanations for this include the inapplicability of the dose-fractionation theorem, the difficulty of phase determination, an overall object-size dependence on the required fluence and dose, a low contrast within the biological cell, insufficient exposure, and a variety of practical difficulties such as scattering from surrounding material. A recent article [Villaneuva-Perez et al. (2018), Optica, 5, 450-457] concluded that imaging by Compton scattering gave a large dose advantage compared with CDI because of the object-size dependence for CDI. An object-size dependence would severely limit the applicability of CDI and perhaps related coherence-based methods for structural studies. This article specifically includes the overall object size in the analysis of the fluence and dose requirements for coherent imaging in order to investigate whether there is a dependence on object size. The applicability of the dose-fractionation theorem is also discussed. The analysis is extended to absorption-based imaging and imaging by incoherent scattering (Compton) and fluorescence. This article includes analysis of the dose required for imaging specific low-contrast cellular organelles as well as for protein against water. This article concludes that for both absorption-based and coherent diffraction imaging, the dose-fractionation theorem applies and the required dose is independent of the overall size of the object. For incoherent-imaging methods such as Compton scattering, the required dose depends on the X-ray path length through the specimen. For all three types of imaging, the dependence of fluence and dose on a resolution d goes as 1/d 4 when imaging uniform-density voxels. The independence of CDI on object size means that there is no advantage for Compton scattering over coherent-based imaging methods. The most optimistic estimate of achievable resolution is 3 nm for imaging protein molecules in water/ice using lensless imaging methods in the water window. However, the attainable resolution depends on a variety of assumptions including the model for radiation damage as a function of resolution, the efficiency of any phase-retrieval process, the actual contrast of the feature of interest within the cell and the definition of resolution itself. There is insufficient observational information available regarding the most appropriate model for radiation damage in frozen hydrated biological material. It is advocated that, in order to compare theory with experiment, standard methods of reporting results covering parameters such as the feature examined (e.g. which cellular organelle), resolution, contrast, depth of the material (for 2D), estimate of noise and dose should be adopted.
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Affiliation(s)
- Colin Nave
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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217
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Quarterly picks from the editors. Sci Transl Med 2020. [DOI: 10.1126/scitranslmed.abb4950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The
Science Translational Medicine
editors highlight interesting translational ties across select articles published recently in the
Science
family of journals.
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218
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219
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Hester SC, Kuriakose M, Nguyen CD, Mallidi S. Role of Ultrasound and Photoacoustic Imaging in Photodynamic Therapy for Cancer. Photochem Photobiol 2020; 96:260-279. [PMID: 31919853 PMCID: PMC7187279 DOI: 10.1111/php.13217] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022]
Abstract
Photodynamic therapy (PDT) is a phototoxic treatment with high spatial and temporal control and has shown tremendous promise in the management of cancer due to its high efficacy and minimal side effects. PDT efficacy is dictated by a complex relationship between dosimetry parameters such as the concentration of the photosensitizer at the tumor site, its spatial localization (intracellular or extracellular), light dose and distribution, oxygen distribution and concentration, and the heterogeneity of the inter- and intratumoral microenvironment. Studying and characterizing these parameters, along with monitoring tumor heterogeneity pre- and post-PDT, provides essential data for predicting therapeutic response and the design of subsequent therapies. In this review, we elucidate the role of ultrasound (US) and photoacoustic imaging in improving PDT-mediated outcomes in cancer-from tracking photosensitizer uptake and vascular destruction, to measuring oxygenation dynamics and the overall evaluation of tumor responses. We also present recent advances in multifunctional theranostic nanomaterials that can improve either US or photoacoustic imaging contrast, as well as deliver photosensitizers specifically to tumors. Given the wide availability, low-cost, portability and nonionizing nature of US and photoacoustic imaging, together with their capabilities of providing multiparametric morphological and functional information, these technologies are thusly inimitable when deployed in conjunction with PDT.
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Affiliation(s)
- Scott C. Hester
- Department of Biomedical EngineeringTufts UniversityMedfordMA
| | - Maju Kuriakose
- Department of Biomedical EngineeringTufts UniversityMedfordMA
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220
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Abstract
This article summarizes recent progress on biomimetic subcellular structures and discusses integration of these isolated systems.
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Affiliation(s)
- Shuying Yang
- College of Chemistry and Materials Science
- Jinan University
- Guangzhou 510632
- China
| | - Lingxiang Jiang
- College of Chemistry and Materials Science
- Jinan University
- Guangzhou 510632
- China
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