1
|
Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CK. Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.576943. [PMID: 38370628 PMCID: PMC10871237 DOI: 10.1101/2024.02.05.576943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.
Collapse
Affiliation(s)
- Johannes Stein
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maria Ericsson
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Michel Nofal
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Lorenzo Magni
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Sarah Aufmkolk
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan B. McMillan
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Laura Breimann
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Norway
| | - Laura Arguedas-Jimenez
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Peng Yin
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - George M. Church
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chao-Kng Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
Albrecht NE, Jiang D, Akhanov V, Hobson R, Speer CM, Robichaux MA, Samuel MA. Rapid 3D-STORM imaging of diverse molecular targets in tissue. CELL REPORTS METHODS 2022; 2:100253. [PMID: 35880013 PMCID: PMC9308169 DOI: 10.1016/j.crmeth.2022.100253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/22/2022] [Accepted: 06/17/2022] [Indexed: 11/25/2022]
Abstract
Fine-scale molecular architecture is critical for nervous system and other biological functions. Methods to visualize these nanoscale structures would benefit from enhanced accessibility, throughput, and tissue compatibility. Here, we report RAIN-STORM, a rapid and scalable nanoscopic imaging optimization approach that improves three-dimensional visualization for subcellular targets in tissue at depth. RAIN-STORM uses conventional tissue samples and readily available reagents and is suitable for commercial instrumentation. To illustrate the efficacy of RAIN-STORM, we utilized the retina. We show that RAIN-STORM imaging is versatile and provide 3D nanoscopic data for over 20 synapse, neuron, glia, and vasculature targets. Sample preparation is also rapid, with a 1-day turnaround from tissue to image, and parameters are suitable for multiple tissue sources. Finally, we show that this method can be applied to clinical samples to reveal nanoscale features of human cells and synapses. RAIN-STORM thus paves the way for high-throughput studies of nanoscopic targets in tissue.
Collapse
Affiliation(s)
- Nicholas E. Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Viktor Akhanov
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert Hobson
- Bruker Nano Surfaces Division, Salt Lake City, UT 84108, USA
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Michael A. Robichaux
- Departments of Ophthalmology and Biochemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Melanie A. Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
3
|
Three-dimensional SEM, TEM, and STEM for analysis of large-scale biological systems. Histochem Cell Biol 2022; 158:203-211. [PMID: 35829815 PMCID: PMC9399040 DOI: 10.1007/s00418-022-02117-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2022] [Indexed: 12/12/2022]
Abstract
A major aim in structural cell biology is to analyze intact cells in three dimensions, visualize subcellular structures, and even localize proteins at the best possible resolution in three dimensions. Though recently developed electron microscopy tools such as electron tomography, or three-dimensional (3D) scanning electron microscopy, offer great resolution in three dimensions, the challenge is that, the better the resolution, usually the smaller the volume under investigation. Several different approaches to overcome this challenge were presented at the Microscopy Conference in Vienna in 2021. These tools include array tomography, batch tomography, or scanning transmission electron tomography, all of which can nowadays be extended toward correlative light and electron tomography, with greatly increased 3D information. Here, we review these tools, describe the underlying procedures, and discuss their advantages and limits.
Collapse
|
4
|
Brenna C, Simioni C, Varano G, Conti I, Costanzi E, Melloni M, Neri LM. Optical tissue clearing associated with 3D imaging: application in preclinical and clinical studies. Histochem Cell Biol 2022; 157:497-511. [PMID: 35235045 PMCID: PMC9114043 DOI: 10.1007/s00418-022-02081-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2022] [Indexed: 12/23/2022]
Abstract
Understanding the inner morphology of intact tissues is one of the most competitive challenges in modern biology. Since the beginning of the twentieth century, optical tissue clearing (OTC) has provided solutions for volumetric imaging, allowing the microscopic visualization of thick sections of tissue, organoids, up to whole organs and organisms (for example, mouse or rat). Recently, tissue clearing has also been introduced in clinical settings to achieve a more accurate diagnosis with the support of 3D imaging. This review aims to give an overview of the most recent developments in OTC and 3D imaging and to illustrate their role in the field of medical diagnosis, with a specific focus on clinical applications.
Collapse
Affiliation(s)
- Cinzia Brenna
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy.,Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Carolina Simioni
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy.,LTTA - Electron Microscopy Center, University of Ferrara, 44121, Ferrara, Italy
| | - Gabriele Varano
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Ilaria Conti
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Eva Costanzi
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Mattia Melloni
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Luca Maria Neri
- Department of Translational Medicine, University of Ferrara, 44121, Ferrara, Italy. .,LTTA - Electron Microscopy Center, University of Ferrara, 44121, Ferrara, Italy.
| |
Collapse
|
5
|
Bhattacharya U, Jhou JF, Zou YF, Abrigo G, Lin SW, Chen YH, Chien FC, Tai HC. Surface charge manipulation and electrostatic immobilization of synaptosomes for super-resolution imaging: a study on tau compartmentalization. Sci Rep 2021; 11:18583. [PMID: 34545174 PMCID: PMC8452691 DOI: 10.1038/s41598-021-98142-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/30/2021] [Indexed: 12/31/2022] Open
Abstract
Synaptosomes are subcellular fractions prepared from brain tissues that are enriched in synaptic terminals, widely used for the study of neural transmission and synaptic dysfunction. Immunofluorescence imaging is increasingly applied to synaptosomes to investigate protein localization. However, conventional methods for imaging synaptosomes over glass coverslips suffer from formaldehyde-induced aggregation. Here, we developed a facile strategy to capture and image synaptosomes without aggregation artefacts. First, ethylene glycol bis(succinimidyl succinate) (EGS) is chosen as the chemical fixative to replace formaldehyde. EGS/glycine treatment makes the zeta potential of synaptosomes more negative. Second, we modified glass coverslips with 3-aminopropyltriethoxysilane (APTES) to impart positive charges. EGS-fixed synaptosomes spontaneously attach to modified glasses via electrostatic attraction while maintaining good dispersion. Individual synaptic terminals are imaged by conventional fluorescence microscopy or by super-resolution techniques such as direct stochastic optical reconstruction microscopy (dSTORM). We examined tau protein by two-color and three-color dSTORM to understand its spatial distribution within mouse cortical synapses, observing tau colocalization with synaptic vesicles as well postsynaptic densities.
Collapse
Affiliation(s)
| | - Jia-Fong Jhou
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Fong Zou
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Gerald Abrigo
- Department of Optics and Photonics, National Central University, Taoyuan, Taiwan
| | - Shu-Wei Lin
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Yun-Hsuan Chen
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Taoyuan, Taiwan
| | - Hwan-Ching Tai
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
| |
Collapse
|
6
|
Carvalhais LG, Martinho VC, Ferreiro E, Pinheiro PS. Unraveling the Nanoscopic Organization and Function of Central Mammalian Presynapses With Super-Resolution Microscopy. Front Neurosci 2021; 14:578409. [PMID: 33584169 PMCID: PMC7874199 DOI: 10.3389/fnins.2020.578409] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022] Open
Abstract
The complex, nanoscopic scale of neuronal function, taking place at dendritic spines, axon terminals, and other minuscule structures, cannot be adequately resolved using standard, diffraction-limited imaging techniques. The last couple of decades saw a rapid evolution of imaging methods that overcome the diffraction limit imposed by Abbe's principle. These techniques, including structured illumination microscopy (SIM), stimulated emission depletion (STED), photo-activated localization microscopy (PALM), and stochastic optical reconstruction microscopy (STORM), among others, have revolutionized our understanding of synapse biology. By exploiting the stochastic nature of fluorophore light/dark states or non-linearities in the interaction of fluorophores with light, by using modified illumination strategies that limit the excitation area, these methods can achieve spatial resolutions down to just a few tens of nm or less. Here, we review how these advanced imaging techniques have contributed to unprecedented insight into the nanoscopic organization and function of mammalian neuronal presynapses, revealing new organizational principles or lending support to existing views, while raising many important new questions. We further discuss recent technical refinements and newly developed tools that will continue to expand our ability to delve deeper into how synaptic function is orchestrated at the nanoscopic level.
Collapse
Affiliation(s)
- Lia G Carvalhais
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Vera C Martinho
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Elisabete Ferreiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Paulo S Pinheiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
7
|
Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
Collapse
Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
| |
Collapse
|
8
|
Anoop V, Bipin PR. Super-Resolution Based Automatic Diagnosis of Retinal Disease Detection for Clinical Applications. Neural Process Lett 2020. [DOI: 10.1007/s11063-020-10292-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
Klevanski M, Herrmannsdoerfer F, Sass S, Venkataramani V, Heilemann M, Kuner T. Automated highly multiplexed super-resolution imaging of protein nano-architecture in cells and tissues. Nat Commun 2020; 11:1552. [PMID: 32214101 PMCID: PMC7096454 DOI: 10.1038/s41467-020-15362-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/04/2020] [Indexed: 11/23/2022] Open
Abstract
Understanding the nano-architecture of protein machines in diverse subcellular compartments remains a challenge despite rapid progress in super-resolution microscopy. While single-molecule localization microscopy techniques allow the visualization and identification of cellular structures with near-molecular resolution, multiplex-labeling of tens of target proteins within the same sample has not yet been achieved routinely. However, single sample multiplexing is essential to detect patterns that threaten to get lost in multi-sample averaging. Here, we report maS3TORM (multiplexed automated serial staining stochastic optical reconstruction microscopy), a microscopy approach capable of fully automated 3D direct STORM (dSTORM) imaging and solution exchange employing a re-staining protocol to achieve highly multiplexed protein localization within individual biological samples. We demonstrate 3D super-resolution images of 15 targets in single cultured cells and 16 targets in individual neuronal tissue samples with <10 nm localization precision, allowing us to define distinct nano-architectural features of protein distribution within the presynaptic nerve terminal. Super-resolution imaging of multiple target proteins in the same sample can provide important information of cellular nanostructure, but has not been routinely achieved. Here, the authors present a fully automated 3D STORM approach using a re-staining protocol to image 15 targets in single cells and 16 targets in neuronal tissue.
Collapse
Affiliation(s)
- Maja Klevanski
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Frank Herrmannsdoerfer
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Steffen Sass
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Varun Venkataramani
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Mike Heilemann
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.,Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Thomas Kuner
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
| |
Collapse
|
10
|
mmSTORM: Multimodal localization based super-resolution microscopy. Sci Rep 2019; 9:798. [PMID: 30692575 PMCID: PMC6349879 DOI: 10.1038/s41598-018-37341-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/04/2018] [Indexed: 11/09/2022] Open
Abstract
Super-resolution localization microscopy provides a powerful tool to study biochemical mechanisms at single molecule level. Although the lateral position of the fluorescent dye molecules can be determined routinely with high precision, measurement of other modalities such as 3D and multicolor without the degradation of the original super-resolved image is still in the focus. In this paper a dual-objective multimodal single molecule localization microscopy (SMLM) technique has been developed, optimized and tested. The proposed optical arrangement can be implemented onto a conventional inverted microscope without serious system modification. The performance of the method was tested using fluorescence beads, F-actin filaments and sarcomere structures. It was shown that the proposed imaging method does not degrade the image quality of the original SMLM 2D image but could provide information on the axial position or emission spectra of the dye molecules.
Collapse
|
11
|
Gruβmayer KS, Yserentant K, Herten DP. Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting. Methods Appl Fluoresc 2019; 7:012003. [DOI: 10.1088/2050-6120/aaf2eb] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
12
|
Abstract
Array tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore three-dimensional cellular architectures in extremely fine structural and molecular detail. Fluorescence array tomography achieves much higher resolution and molecular multiplexing than most other fluorescence microscopy methods, while electron array tomography can capture three-dimensional ultrastructure much more easily and rapidly than traditional serial-section electron microscopy methods. A correlative fluorescence/electron microscopy mode of array tomography furthermore offers a unique capacity to merge the molecular discrimination strengths of multichannel fluorescence microscopy with the ultrastructural imaging strengths of electron microscopy. This essay samples the first decade of array tomography, highlighting applications in neuroscience.
Collapse
|
13
|
New advances in scanning microscopy and its application to study parasitic protozoa. Exp Parasitol 2018; 190:10-33. [PMID: 29702111 DOI: 10.1016/j.exppara.2018.04.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 04/10/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022]
Abstract
Scanning electron microscopy has been used to observe and study parasitic protozoa for at least 40 years. However, field emission electron sources, as well as improvements in lenses and detectors, brought the resolution power of scanning electron microscopes (SEM) to a new level. Parallel to the refinement of instruments, protocols for preservation of the ultrastructure, immunolabeling, exposure of cytoskeleton and inner structures of parasites and host cells were developed. This review is focused on protozoan parasites of medical and veterinary relevance, e.g., Toxoplasma gondii, Tritrichomonas foetus, Giardia intestinalis, and Trypanosoma cruzi, compilating the main achievements in describing the fine ultrastructure of their surface, cytoskeleton and interaction with host cells. Two new resources, namely, Helium Ion Microscopy (HIM) and Slice and View, using either Focused Ion Beam (FIB) abrasion or Microtome Serial Sectioning (MSS) within the microscope chamber, combined to backscattered electron imaging of fixed (chemically or by quick freezing followed by freeze substitution and resin embedded samples is bringing an exponential amount of valuable information. In HIM there is no need of conductive coating and the depth of field is much higher than in any field emission SEM. As for FIB- and MSS-SEM, high resolution 3-D models of areas and volumes larger than any other technique allows can be obtained. The main results achieved with all these technological tools and some protocols for sample preparation are included in this review. In addition, we included some results obtained with environmental/low vacuum scanning microscopy and cryo-scanning electron microscopy, both promising, but not yet largely employed SEM modalities.
Collapse
|
14
|
Aβ mediates F-actin disassembly in dendritic spines leading to cognitive deficits in Alzheimer's disease. J Neurosci 2018; 38:1085-1099. [PMID: 29246925 PMCID: PMC5792472 DOI: 10.1523/jneurosci.2127-17.2017] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023] Open
Abstract
Dendritic spine loss is recognized as an early feature of Alzheimer's disease (AD), but the underlying mechanisms are poorly understood. Dendritic spine structure is defined by filamentous actin (F-actin) and we observed depolymerization of synaptosomal F-actin accompanied by increased globular-actin (G-actin) at as early as 1 month of age in a mouse model of AD (APPswe/PS1ΔE9, male mice). This led to recall deficit after contextual fear conditioning (cFC) at 2 months of age in APPswe/PS1ΔE9 male mice, which could be reversed by the actin-polymerizing agent jasplakinolide. Further, the F-actin-depolymerizing agent latrunculin induced recall deficit after cFC in WT mice, indicating the importance of maintaining F-/G-actin equilibrium for optimal behavioral response. Using direct stochastic optical reconstruction microscopy (dSTORM), we show that F-actin depolymerization in spines leads to a breakdown of the nano-organization of outwardly radiating F-actin rods in cortical neurons from APPswe/PS1ΔE9 mice. Our results demonstrate that synaptic dysfunction seen as F-actin disassembly occurs very early, before onset of pathological hallmarks in AD mice, and contributes to behavioral dysfunction, indicating that depolymerization of F-actin is causal and not consequent to decreased spine density. Further, we observed decreased synaptosomal F-actin levels in postmortem brain from mild cognitive impairment and AD patients compared with subjects with normal cognition. F-actin decrease correlated inversely with increasing AD pathology (Braak score, Aβ load, and tangle density) and directly with performance in episodic and working memory tasks, suggesting its role in human disease pathogenesis and progression.SIGNIFICANCE STATEMENT Synaptic dysfunction underlies cognitive deficits in Alzheimer's disease (AD). The cytoskeletal protein actin plays a critical role in maintaining structure and function of synapses. Using cultured neurons and an AD mouse model, we show for the first time that filamentous actin (F-actin) is lost selectively from synapses early in the disease process, long before the onset of classical AD pathology. We also demonstrate that loss of synaptic F-actin contributes directly to memory deficits. Loss of synaptosomal F-actin in human postmortem tissue correlates directly with decreased performance in memory test and inversely with AD pathology. Our data highlight that synaptic cytoarchitectural changes occur early in AD and they may be targeted for the development of therapeutics.
Collapse
|
15
|
Collinson LM, Carroll EC, Hoogenboom JP. Correlating 3D light to 3D electron microscopy for systems biology. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
16
|
Yi J, Manna A, Barr VA, Hong J, Neuman KC, Samelson LE. Highly Multiplexed, Super-resolution Imaging of T Cells Using madSTORM. J Vis Exp 2017. [PMID: 28671659 DOI: 10.3791/55997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Imaging heterogeneous cellular structures using single molecule localization microscopy has been hindered by inadequate localization precision and multiplexing ability. Using fluorescent nano-diamond fiducial markers, we describe the drift correction and alignment procedures required to obtain high precision in single molecule localization microscopy. In addition, a new multiplexing strategy, madSTORM, is described in which multiple molecules are targeted in the same cell using sequential binding and elution of fluorescent antibodies. madSTORM is demonstrated on an activated T cell to visualize the locations of different components within a membrane-bound, multi-protein structure called the T cell receptor microcluster. In addition, application of madSTORM as a general tool for visualization of multi-protein structures is discussed.
Collapse
Affiliation(s)
- Jason Yi
- Laboratory of Cellular & Molecular Biology, National Cancer Institute, National Institutes of Health
| | - Asit Manna
- Laboratory of Cellular & Molecular Biology, National Cancer Institute, National Institutes of Health
| | - Valarie A Barr
- Laboratory of Cellular & Molecular Biology, National Cancer Institute, National Institutes of Health
| | - Jennifer Hong
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood, Institute, National Institutes of Health
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood, Institute, National Institutes of Health
| | - Lawrence E Samelson
- Laboratory of Cellular & Molecular Biology, National Cancer Institute, National Institutes of Health;
| |
Collapse
|
17
|
Markert SM, Bauer V, Muenz TS, Jones NG, Helmprobst F, Britz S, Sauer M, Rössler W, Engstler M, Stigloher C. 3D subcellular localization with superresolution array tomography on ultrathin sections of various species. Methods Cell Biol 2017; 140:21-47. [PMID: 28528634 DOI: 10.1016/bs.mcb.2017.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Array Tomography (AT) is a relatively easy-to-use and yet powerful method to put molecular identity in its full ultrastructural context. Ultrathin sections are stained with fluorophores and then imaged by light and afterward by electron microscopy to obtain a correlated view of a region of interest: its ultrastructure and specific staining. By combining AT with high-pressure freezing for superior structural preservation and superresolution light microscopy, even small subcellular structures can be mapped in 3D. We established protocols for the application of superresolution AT on ultrathin plastic sections of Caenorhabditis elegans, Trypanosoma brucei, and brain tissue of Cataglyphis fortis and Apis mellifera. All steps are described in detail from sample preparation to 3D reconstruction, including species-specific modifications. We thus showcase the versatility of our protocol and give some examples for biological questions that can be answered with this technique. We offer a step-by-step recipe for superresolution AT that can be easily applied for C. elegans, T. brucei, C. fortis, and A. mellifera and adapted for other model systems.
Collapse
|
18
|
Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples. Nat Protoc 2017; 12:916-946. [PMID: 28384138 DOI: 10.1038/nprot.2017.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM data sets for aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. The choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replication creates high-contrast, 3D images of the cytoplasmic surface of the plasma membrane but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (∼10-50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2-7 d, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology.
Collapse
|
19
|
Gang Y, Zhou H, Jia Y, Liu L, Liu X, Rao G, Li L, Wang X, Lv X, Xiong H, Yang Z, Luo Q, Gong H, Zeng S. Embedding and Chemical Reactivation of Green Fluorescent Protein in the Whole Mouse Brain for Optical Micro-Imaging. Front Neurosci 2017; 11:121. [PMID: 28352214 PMCID: PMC5349086 DOI: 10.3389/fnins.2017.00121] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/27/2017] [Indexed: 02/02/2023] Open
Abstract
Resin embedding has been widely applied to fixing biological tissues for sectioning and imaging, but has long been regarded as incompatible with green fluorescent protein (GFP) labeled sample because it reduces fluorescence. Recently, it has been reported that resin-embedded GFP-labeled brain tissue can be imaged with high resolution. In this protocol, we describe an optimized protocol for resin embedding and chemical reactivation of fluorescent protein labeled mouse brain, we have used mice as experiment model, but the protocol should be applied to other species. This method involves whole brain embedding and chemical reactivation of the fluorescent signal in resin-embedded tissue. The whole brain embedding process takes a total of 7 days. The duration of chemical reactivation is ~2 min for penetrating 4 μm below the surface in the resin-embedded brain. This protocol provides an efficient way to prepare fluorescent protein labeled sample for high-resolution optical imaging. This kind of sample was demonstrated to be imaged by various optical micro-imaging methods. Fine structures labeled with GFP across a whole brain can be detected.
Collapse
Affiliation(s)
- Yadong Gang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Hongfu Zhou
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Yao Jia
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Ling Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Xiuli Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Gong Rao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Longhui Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Xiaojun Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Xiaohua Lv
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Hanqing Xiong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Zhongqin Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan, China
- Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and TechnologyWuhan, China
| |
Collapse
|
20
|
Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
Collapse
Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
| |
Collapse
|
21
|
Abstract
Central nervous system tissue contains a high density of synapses each composed of an intricate molecular machinery mediating precise transmission of information. Deciphering the molecular nanostructure of pre- and postsynaptic specializations within such a complex tissue architecture poses a particular challenge for light microscopy. Here, we describe two approaches suitable to examine the molecular nanostructure of synapses at 20-30 nm lateral and 50-70 nm axial resolution within an area of 500 μm × 500 μm and a depth of 0.6 μm to several micrometers. We employ single-molecule localization microscopy (SMLM) on immunolabeled fixed brain tissue slices. tomoSTORM utilizes array tomography to achieve SMLM in 40 nm thick resin-embedded sections. dSTORM of cryo-sectioned slices uses optical sectioning in 0.1-4 μm thick hydrated sections. Both approaches deliver 3D nanolocalization of two or more labeled proteins within a defined tissue volume. We review sample preparation, data acquisition, analysis, and interpretation.
Collapse
|
22
|
German CL, Gudheti MV, Fleckenstein AE, Jorgensen EM. Brain Slice Staining and Preparation for Three-Dimensional Super-Resolution Microscopy. Methods Mol Biol 2017; 1663:153-162. [PMID: 28924666 DOI: 10.1007/978-1-4939-7265-4_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Localization microscopy techniques-such as photoactivation localization microscopy (PALM), fluorescent PALM (FPALM), ground state depletion (GSD), and stochastic optical reconstruction microscopy (STORM)-provide the highest precision for single-molecule localization currently available. However, localization microscopy has been largely limited to cell cultures due to the difficulties that arise in imaging thicker tissue sections. Sample fixation and antibody staining, background fluorescence, fluorophore photoinstability, light scattering in thick sections, and sample movement create significant challenges for imaging intact tissue. We have developed a sample preparation and image acquisition protocol to address these challenges in rat brain slices. The sample preparation combined multiple fixation steps, saponin permeabilization, and tissue clarification. Together, these preserve intracellular structures, promote antibody penetration, reduce background fluorescence and light scattering, and allow acquisition of images deep in a 30 μm thick slice. Image acquisition challenges were resolved by overlaying samples with a permeable agarose pad and custom-built stainless-steel imaging adapter, and sealing the imaging chamber. This approach kept slices flat, immobile, bathed in imaging buffer, and prevented buffer oxidation during imaging. Using this protocol, we consistently obtained single-molecule localizations of synaptic vesicle and active zone proteins in three dimensions within individual synaptic terminals of the striatum in rat brain slices. These techniques may be easily adapted to the preparation and imaging of other tissues, substantially broadening the application of super-resolution imaging.
Collapse
Affiliation(s)
- Christopher L German
- School of Dentistry, University of Utah, 530 Wakara Way, Room 3857, Salt Lake City, UT, 84108, USA.
| | - Manasa V Gudheti
- Department of Biology, University of Utah, Salt Lake City, UT, USA.,Bruker, Salt Lake City, UT, USA
| | | | - Erik M Jorgensen
- Department of Biology, University of Utah, Salt Lake City, UT, USA.,Howard Hughes Medical Institute, Silver Springs, MD, USA
| |
Collapse
|
23
|
Light-Microscopy-Based Sparse Neural Circuit Reconstruction: Array Tomography and Other Methods. Appl Microsc 2016. [DOI: 10.9729/am.2016.46.4.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
24
|
Wacker I, Spomer W, Hofmann A, Thaler M, Hillmer S, Gengenbach U, Schröder RR. Hierarchical imaging: a new concept for targeted imaging of large volumes from cells to tissues. BMC Cell Biol 2016; 17:38. [PMID: 27955619 PMCID: PMC5154069 DOI: 10.1186/s12860-016-0122-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/29/2016] [Indexed: 11/30/2022] Open
Abstract
Background Imaging large volumes such as entire cells or small model organisms at nanoscale resolution seemed an unrealistic, rather tedious task so far. Now, technical advances have lead to several electron microscopy (EM) large volume imaging techniques. One is array tomography, where ribbons of ultrathin serial sections are deposited on solid substrates like silicon wafers or glass coverslips. Results To ensure reliable retrieval of multiple ribbons from the boat of a diamond knife we introduce a substrate holder with 7 axes of translation or rotation specifically designed for that purpose. With this device we are able to deposit hundreds of sections in an ordered way in an area of 22 × 22 mm, the size of a coverslip. Imaging such arrays in a standard wide field fluorescence microscope produces reconstructions with 200 nm lateral resolution and 100 nm (the section thickness) resolution in z. By hierarchical imaging cascades in the scanning electron microscope (SEM), using a new software platform, we can address volumes from single cells to complete organs. In our first example, a cell population isolated from zebrafish spleen, we characterize different cell types according to their organelle inventory by segmenting 3D reconstructions of complete cells imaged with nanoscale resolution. In addition, by screening large numbers of cells at decreased resolution we can define the percentage at which different cell types are present in our preparation. With the second example, the root tip of cress, we illustrate how combining information from intermediate resolution data with high resolution data from selected regions of interest can drastically reduce the amount of data that has to be recorded. By imaging only the interesting parts of a sample considerably less data need to be stored, handled and eventually analysed. Conclusions Our custom-designed substrate holder allows reproducible generation of section libraries, which can then be imaged in a hierarchical way. We demonstrate, that EM volume data at different levels of resolution can yield comprehensive information, including statistics, morphology and organization of cells and tissue. We predict, that hierarchical imaging will be a first step in tackling the big data issue inevitably connected with volume EM. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0122-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Irene Wacker
- Cryo Electron Microscopy, Centre for Advanced Materials, Universität Heidelberg, Im Neuenheimer Feld 267, D-691120, Heidelberg, Germany. .,HEiKA, Heidelberg Karlsruhe Research Partnership, Heidelberg, Germany.
| | - Waldemar Spomer
- HEiKA, Heidelberg Karlsruhe Research Partnership, Heidelberg, Germany.,Institute for Applied Computer Science, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Andreas Hofmann
- HEiKA, Heidelberg Karlsruhe Research Partnership, Heidelberg, Germany.,Institute for Applied Computer Science, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Marlene Thaler
- Carl Zeiss Microscopy GmbH, Carl-Zeiss Str. 22, D-73447, Oberkochen, Germany
| | - Stefan Hillmer
- Electron Microscopy Core Facility, Universität Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany
| | - Ulrich Gengenbach
- HEiKA, Heidelberg Karlsruhe Research Partnership, Heidelberg, Germany.,Institute for Applied Computer Science, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Rasmus R Schröder
- Cryo Electron Microscopy, Centre for Advanced Materials, Universität Heidelberg, Im Neuenheimer Feld 267, D-691120, Heidelberg, Germany.,HEiKA, Heidelberg Karlsruhe Research Partnership, Heidelberg, Germany.,Cryo Electron Microscopy, CellNetworks, BioQuant, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 267, D-691120, Heidelberg, Germany
| |
Collapse
|
25
|
Delvendahl I, Hallermann S. The Cerebellar Mossy Fiber Synapse as a Model for High-Frequency Transmission in the Mammalian CNS. Trends Neurosci 2016; 39:722-737. [DOI: 10.1016/j.tins.2016.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022]
|
26
|
Yi J, Manna A, Barr VA, Hong J, Neuman KC, Samelson LE. madSTORM: a superresolution technique for large-scale multiplexing at single-molecule accuracy. Mol Biol Cell 2016; 27:3591-3600. [PMID: 27708141 PMCID: PMC5221591 DOI: 10.1091/mbc.e16-05-0330] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/27/2016] [Indexed: 12/15/2022] Open
Abstract
A highly multiplexed superresolution imaging strategy with single-molecule accuracy enabled by fluorescent nanodiamonds called madSTORM affords the ability to define spatial relationships among constituent molecules within structures. It makes it possible to probe the molecular topology of complex signaling cascades and other heterogeneous networks. Investigation of heterogeneous cellular structures using single-molecule localization microscopy has been limited by poorly defined localization accuracy and inadequate multiplexing capacity. Using fluorescent nanodiamonds as fiducial markers, we define and achieve localization precision required for single-molecule accuracy in dSTORM images. Coupled with this advance, our new multiplexing strategy, madSTORM, allows accurate targeting of multiple molecules using sequential binding and elution of fluorescent antibodies. madSTORM is used on an activated T-cell to localize 25 epitopes, 14 of which are on components of the same multimolecular T-cell receptor complex. We obtain an average localization precision of 2.6 nm, alignment error of 2.0 nm, and <0.01% cross-talk. Combining these technical advances affords the ability to move beyond obtaining superresolved structures to defining spatial relationships among constituent molecules within structures. Probing the molecular topology of complex signaling cascades and other heterogeneous networks is feasible with madSTORM.
Collapse
Affiliation(s)
- Jason Yi
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Asit Manna
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Valarie A Barr
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jennifer Hong
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
27
|
Markert SM, Britz S, Proppert S, Lang M, Witvliet D, Mulcahy B, Sauer M, Zhen M, Bessereau JL, Stigloher C. Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome. NEUROPHOTONICS 2016; 3:041802. [PMID: 27175373 PMCID: PMC4855082 DOI: 10.1117/1.nph.3.4.041802] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/08/2016] [Indexed: 06/02/2023]
Abstract
Correlating molecular labeling at the ultrastructural level with high confidence remains challenging. Array tomography (AT) allows for a combination of fluorescence and electron microscopy (EM) to visualize subcellular protein localization on serial EM sections. Here, we describe an application for AT that combines near-native tissue preservation via high-pressure freezing and freeze substitution with super-resolution light microscopy and high-resolution scanning electron microscopy (SEM) analysis on the same section. We established protocols that combine SEM with structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). We devised a method for easy, precise, and unbiased correlation of EM images and super-resolution imaging data using endogenous cellular landmarks and freely available image processing software. We demonstrate that these methods allow us to identify and label gap junctions in Caenorhabditis elegans with precision and confidence, and imaging of even smaller structures is feasible. With the emergence of connectomics, these methods will allow us to fill in the gap-acquiring the correlated ultrastructural and molecular identity of electrical synapses.
Collapse
Affiliation(s)
| | - Sebastian Britz
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
| | - Sven Proppert
- University of Würzburg, Department of Biotechnology and Biophysics, Am Hubland, Würzburg 97074, Germany
- University of Würzburg, Department of Neurophysiology, Institute of Physiology, Röntgenring 9, Würzburg 97070, Germany
| | - Marietta Lang
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
| | - Daniel Witvliet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Markus Sauer
- University of Würzburg, Department of Biotechnology and Biophysics, Am Hubland, Würzburg 97074, Germany
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Jean-Louis Bessereau
- Institut NeuroMyoGene, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, 16 rue R. Dubois, Villeurbanne Cedex F-69622, France
| | - Christian Stigloher
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
| |
Collapse
|
28
|
Laine RF, Kaminski Schierle GS, van de Linde S, Kaminski CF. From single-molecule spectroscopy to super-resolution imaging of the neuron: a review. Methods Appl Fluoresc 2016; 4:022004. [PMID: 28809165 PMCID: PMC5390958 DOI: 10.1088/2050-6120/4/2/022004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/09/2016] [Accepted: 05/19/2016] [Indexed: 12/03/2022]
Abstract
For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.
Collapse
Affiliation(s)
- Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Gabriele S Kaminski Schierle
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Julius-Maximilians-University, Am Hubland, D-97074 Würzburg, Germany
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| |
Collapse
|
29
|
Spühler IA, Conley GM, Scheffold F, Sprecher SG. Super Resolution Imaging of Genetically Labeled Synapses in Drosophila Brain Tissue. Front Cell Neurosci 2016; 10:142. [PMID: 27303270 PMCID: PMC4880563 DOI: 10.3389/fncel.2016.00142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
Understanding synaptic connectivity and plasticity within brain circuits and their relationship to learning and behavior is a fundamental quest in neuroscience. Visualizing the fine details of synapses using optical microscopy remains however a major technical challenge. Super resolution microscopy opens the possibility to reveal molecular features of synapses beyond the diffraction limit. With direct stochastic optical reconstruction microscopy, dSTORM, we image synaptic proteins in the brain tissue of the fruit fly, Drosophila melanogaster. Super resolution imaging of brain tissue harbors difficulties due to light scattering and the density of signals. In order to reduce out of focus signal, we take advantage of the genetic tools available in the Drosophila and have fluorescently tagged synaptic proteins expressed in only a small number of neurons. These neurons form synapses within the calyx of the mushroom body, a distinct brain region involved in associative memory formation. Our results show that super resolution microscopy, in combination with genetically labeled synaptic proteins, is a powerful tool to investigate synapses in a quantitative fashion providing an entry point for studies on synaptic plasticity during learning and memory formation.
Collapse
Affiliation(s)
- Isabelle A Spühler
- Department of Physics, University of FribourgFribourg, Switzerland; Department of Biology, University of FribourgFribourg, Switzerland
| | | | - Frank Scheffold
- Department of Physics, University of Fribourg Fribourg, Switzerland
| | - Simon G Sprecher
- Department of Biology, University of Fribourg Fribourg, Switzerland
| |
Collapse
|
30
|
High-density three-dimensional localization microscopy across large volumes. Nat Methods 2016; 13:359-65. [PMID: 26950745 PMCID: PMC4889433 DOI: 10.1038/nmeth.3797] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022]
Abstract
Extending three-dimensional (3D) single molecule localization microscopy away from the coverslip and into thicker specimens will greatly broaden its biological utility. However, localizing molecules in 3D with high precision in such samples, while simultaneously achieving the extreme labeling densities required for high resolution of densely crowded structures is challenging due to the limitations both of conventional imaging modalities and of conventional labeling techniques. Here, we combine lattice light sheet microscopy with newly developed, freely diffusing, cell permeable chemical probes with targeted affinity towards either DNA, intracellular membranes, or the plasma membrane. We use this combination to perform high localization precision, ultra-high labeling density, multicolor localization microscopy in samples up to 20 microns thick, including dividing cells and the neuromast organ of a zebrafish embryo. We also demonstrate super-resolution correlative imaging with protein specific photoactivable fluorophores, providing a mutually compatible, single platform alternative to correlative light-electron microscopy over large volumes.
Collapse
|
31
|
Sigal YM, Speer CM, Babcock HP, Zhuang X. Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging. Cell 2015; 163:493-505. [PMID: 26435106 PMCID: PMC4733473 DOI: 10.1016/j.cell.2015.08.033] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 07/22/2015] [Accepted: 08/12/2015] [Indexed: 01/28/2023]
Abstract
As a basic functional unit in neural circuits, each neuron integrates input signals from hundreds to thousands of synapses. Knowledge of the synaptic input fields of individual neurons, including the identity, strength, and location of each synapse, is essential for understanding how neurons compute. Here, we developed a volumetric super-resolution reconstruction platform for large-volume imaging and automated segmentation of neurons and synapses with molecular identity information. We used this platform to map inhibitory synaptic input fields of On-Off direction-selective ganglion cells (On-Off DSGCs), which are important for computing visual motion direction in the mouse retina. The reconstructions of On-Off DSGCs showed a GABAergic, receptor subtype-specific input field for generating direction selective responses without significant glycinergic inputs for mediating monosynaptic crossover inhibition. These results demonstrate unique capabilities of this super-resolution platform for interrogating neural circuitry.
Collapse
Affiliation(s)
- Yaron M Sigal
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Colenso M Speer
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hazen P Babcock
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
32
|
Koho S, Deguchi T, Hänninen PE. A software tool for tomographic axial superresolution in STED microscopy. J Microsc 2015; 260:208-18. [PMID: 26258639 DOI: 10.1111/jmi.12287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/09/2015] [Indexed: 11/29/2022]
Abstract
A method for generating three-dimensional tomograms from multiple three-dimensional axial projections in STimulated Emission Depletion (STED) superresolution microscopy is introduced. Our STED< method, based on the use of a micromirror placed on top of a standard microscopic sample, is used to record a three-dimensional projection at an oblique angle in relation to the main optical axis. Combining the STED< projection with the regular STED image into a single view by tomographic reconstruction, is shown to result in a tomogram with three-to-four-fold improved apparent axial resolution. Registration of the different projections is based on the use of a mutual-information histogram similarity metric. Fusion of the projections into a single view is based on Richardson-Lucy iterative deconvolution algorithm, modified to work with multiple projections. Our tomographic reconstruction method is demonstrated to work with real biological STED superresolution images, including a data set with a limited signal-to-noise ratio (SNR); the reconstruction software (SuperTomo) and its source code will be released under BSD open-source license.
Collapse
Affiliation(s)
- S Koho
- Department of Cell Biology and Anatomy, Laboratory of Biophysics, Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Tykistökatu 6A, Turku, Finland
| | - T Deguchi
- Department of Cell Biology and Anatomy, Laboratory of Biophysics, Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Tykistökatu 6A, Turku, Finland
| | - P E Hänninen
- Department of Cell Biology and Anatomy, Laboratory of Biophysics, Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Tykistökatu 6A, Turku, Finland
| |
Collapse
|
33
|
Jacak J, Schaller S, Borgmann D, Winkler SM. Characterization of the Distance Relationship Between Localized Serotonin Receptors and Glia Cells on Fluorescence Microscopy Images of Brain Tissue. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:826-836. [PMID: 26173412 DOI: 10.1017/s1431927615013513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We here present two new methods for the characterization of fluorescent localization microscopy images obtained from immunostained brain tissue sections. Direct stochastic optical reconstruction microscopy images of 5-HT1A serotonin receptors and glial fibrillary acidic proteins in healthy cryopreserved brain tissues are analyzed. In detail, we here present two image processing methods for characterizing differences in receptor distribution on glial cells and their distribution on neural cells: One variant relies on skeleton extraction and adaptive thresholding, the other on k-means based discrete layer segmentation. Experimental results show that both methods can be applied for distinguishing classes of images with respect to serotonin receptor distribution. Quantification of nanoscopic changes in relative protein expression on particular cell types can be used to analyze degeneration in tissues caused by diseases or medical treatment.
Collapse
Affiliation(s)
- Jaroslaw Jacak
- 1Department of Medical Engineering,University of Applied Sciences Upper Austria,Garnisonstraße 21,4020 Linz,Austria
| | - Susanne Schaller
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
| | - Daniela Borgmann
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
| | - Stephan M Winkler
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
| |
Collapse
|
34
|
Rah JC, Feng L, Druckmann S, Lee H, Kim J. From a meso- to micro-scale connectome: array tomography and mGRASP. Front Neuroanat 2015; 9:78. [PMID: 26089781 PMCID: PMC4454886 DOI: 10.3389/fnana.2015.00078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/21/2015] [Indexed: 11/21/2022] Open
Abstract
Mapping mammalian synaptic connectivity has long been an important goal of neuroscience because knowing how neurons and brain areas are connected underpins an understanding of brain function. Meeting this goal requires advanced techniques with single synapse resolution and large-scale capacity, especially at multiple scales tethering the meso- and micro-scale connectome. Among several advanced LM-based connectome technologies, Array Tomography (AT) and mammalian GFP-Reconstitution Across Synaptic Partners (mGRASP) can provide relatively high-throughput mapping synaptic connectivity at multiple scales. AT- and mGRASP-assisted circuit mapping (ATing and mGRASPing), combined with techniques such as retrograde virus, brain clearing techniques, and activity indicators will help unlock the secrets of complex neural circuits. Here, we discuss these useful new tools to enable mapping of brain circuits at multiple scales, some functional implications of spatial synaptic distribution, and future challenges and directions of these endeavors.
Collapse
Affiliation(s)
- Jong-Cheol Rah
- Korea Brain Research InstituteDaegu, South Korea
- Department of Brain Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST)Daegu, South Korea
| | - Linqing Feng
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST)Seoul, South Korea
| | - Shaul Druckmann
- Janelia Farm Research Campus, Howard Hugh Medical InstituteAshburn, VA, USA
| | - Hojin Lee
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST)Seoul, South Korea
- Neuroscience Program, University of Science and TechnologyDaejeon, South Korea
| | - Jinhyun Kim
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST)Seoul, South Korea
- Neuroscience Program, University of Science and TechnologyDaejeon, South Korea
| |
Collapse
|
35
|
Valley CC, Liu S, Lidke DS, Lidke KA. Sequential superresolution imaging of multiple targets using a single fluorophore. PLoS One 2015; 10:e0123941. [PMID: 25860558 PMCID: PMC4393115 DOI: 10.1371/journal.pone.0123941] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/09/2015] [Indexed: 12/11/2022] Open
Abstract
Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique.
Collapse
Affiliation(s)
- Christopher C. Valley
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Sheng Liu
- Department of Physics & Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Diane S. Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Keith A. Lidke
- Department of Physics & Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail:
| |
Collapse
|
36
|
Ehmann N, Sauer M, Kittel RJ. Super-resolution microscopy of the synaptic active zone. Front Cell Neurosci 2015; 9:7. [PMID: 25688186 PMCID: PMC4311638 DOI: 10.3389/fncel.2015.00007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/07/2015] [Indexed: 12/31/2022] Open
Abstract
Brain function relies on accurate information transfer at chemical synapses. At the presynaptic active zone (AZ) a variety of specialized proteins are assembled to complex architectures, which set the basis for speed, precision and plasticity of synaptic transmission. Calcium channels are pivotal for the initiation of excitation-secretion coupling and, correspondingly, capture a central position at the AZ. Combining quantitative functional studies with modeling approaches has provided predictions of channel properties, numbers and even positions on the nanometer scale. However, elucidating the nanoscopic organization of the surrounding protein network requires direct ultrastructural access. Without this information, knowledge of molecular synaptic structure-function relationships remains incomplete. Recently, super-resolution microscopy (SRM) techniques have begun to enter the neurosciences. These approaches combine high spatial resolution with the molecular specificity of fluorescence microscopy. Here, we discuss how SRM can be used to obtain information on the organization of AZ proteins.
Collapse
Affiliation(s)
- Nadine Ehmann
- Department of Neurophysiology, Institute of Physiology, University of Würzburg Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg Würzburg, Germany
| | - Robert J Kittel
- Department of Neurophysiology, Institute of Physiology, University of Würzburg Würzburg, Germany
| |
Collapse
|
37
|
Fornasiero EF, Opazo F. Super-resolution imaging for cell biologists: concepts, applications, current challenges and developments. Bioessays 2015; 37:436-51. [PMID: 25581819 DOI: 10.1002/bies.201400170] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The recent 2014 Nobel Prize in chemistry honored an era of discoveries and technical advancements in the field of super-resolution microscopy. However, the applications of diffraction-unlimited imaging in biology have a long road ahead and persistently engage scientists with new challenges. Some of the bottlenecks that restrain the dissemination of super-resolution techniques are tangible, and include the limited performance of affinity probes and the yet not capillary diffusion of imaging setups. Likewise, super-resolution microscopy has introduced new paradigms in the design of projects that require imaging with nanometer-resolution and in the interpretation of biological images. Besides structural or morphological characterization, super-resolution imaging is quickly expanding towards interaction mapping, multiple target detection and live imaging. Here we review the recent progress of biologists employing super-resolution imaging, some pitfalls, implications and new trends, with the purpose of animating the field and spurring future developments.
Collapse
Affiliation(s)
- Eugenio F Fornasiero
- STED Microscopy Group, European Neuroscience Institute, Göttingen, Germany; Department of Neuro- and Sensory-physiology, University of Göttingen, Göttingen, Germany
| | | |
Collapse
|
38
|
Abstract
Single-molecule localization-based super-resolution microscopy can be performed with regular, bright, and photostable organic fluorophores. We review a concept termed direct stochastic optical reconstruction microscopy (dSTORM), which operates conventional fluorophores as photoswitches and provides an optical resolution of ~20 nm. We introduce the principle of dSTORM, illustrate experimental schemes, and discuss approaches for data analysis.
Collapse
Affiliation(s)
- Ulrike Endesfelder
- Institute of Physical & Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Street 7, Frankfurt, 60438, Germany
| | | |
Collapse
|
39
|
Peng K, Muranyi W, Glass B, Laketa V, Yant SR, Tsai L, Cihlar T, Müller B, Kräusslich HG. Quantitative microscopy of functional HIV post-entry complexes reveals association of replication with the viral capsid. eLife 2014; 3:e04114. [PMID: 25517934 PMCID: PMC4293571 DOI: 10.7554/elife.04114] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022] Open
Abstract
The steps from HIV-1 cytoplasmic entry until integration of the reverse transcribed genome are currently enigmatic. They occur in ill-defined reverse-transcription- and pre-integration-complexes (RTC, PIC) with various host and viral proteins implicated. In this study, we report quantitative detection of functional RTC/PIC by labeling nascent DNA combined with detection of viral integrase. We show that the viral CA (capsid) protein remains associated with cytoplasmic RTC/PIC but is lost on nuclear PIC in a HeLa-derived cell line. In contrast, nuclear PIC were almost always CA-positive in primary human macrophages, indicating nuclear import of capsids or capsid-like structures. We further show that the CA-targeted inhibitor PF74 exhibits a bimodal mechanism, blocking RTC/PIC association with the host factor CPSF6 and nuclear entry at low, and abrogating reverse transcription at high concentrations. The newly developed system is ideally suited for studying retroviral post-entry events and the roles of host factors including DNA sensors and signaling molecules.
Collapse
Affiliation(s)
- Ke Peng
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Walter Muranyi
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Bärbel Glass
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | | | - Luong Tsai
- Gilead Sciences Inc., Foster City, United States
| | - Tomas Cihlar
- Gilead Sciences Inc., Foster City, United States
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| |
Collapse
|
40
|
Löschberger A, Franke C, Krohne G, van de Linde S, Sauer M. Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution. J Cell Sci 2014; 127:4351-5. [PMID: 25146397 DOI: 10.1242/jcs.156620] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Here, we combine super-resolution fluorescence localization microscopy with scanning electron microscopy to map the position of proteins of nuclear pore complexes in isolated Xenopus laevis oocyte nuclear envelopes with molecular resolution in both imaging modes. We use the periodic molecular structure of the nuclear pore complex to superimpose direct stochastic optical reconstruction microscopy images with a precision of <20 nm on electron micrographs. The correlative images demonstrate quantitative molecular labeling and localization of nuclear pore complex proteins by standard immunocytochemistry with primary and secondary antibodies and reveal that the nuclear pore complex is composed of eight gp210 (also known as NUP210) protein homodimers. In addition, we find subpopulations of nuclear pore complexes with ninefold symmetry, which are found occasionally among the more typical eightfold symmetrical structures.
Collapse
Affiliation(s)
- Anna Löschberger
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christian Franke
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Georg Krohne
- Department of Electron Microscopy, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| |
Collapse
|
41
|
STED super-resolution microscopy of clinical paraffin-embedded human rectal cancer tissue. PLoS One 2014; 9:e101563. [PMID: 25025184 PMCID: PMC4099123 DOI: 10.1371/journal.pone.0101563] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/09/2014] [Indexed: 01/29/2023] Open
Abstract
Formalin fixed and paraffin-embedded human tissue resected during cancer surgery is indispensable for diagnostic and therapeutic purposes and represents a vast and largely unexploited resource for research. Optical microscopy of such specimen is curtailed by the diffraction-limited resolution of conventional optical microscopy. To overcome this limitation, we used STED super-resolution microscopy enabling optical resolution well below the diffraction barrier. We visualized nanoscale protein distributions in sections of well-annotated paraffin-embedded human rectal cancer tissue stored in a clinical repository. Using antisera against several mitochondrial proteins, STED microscopy revealed distinct sub-mitochondrial protein distributions, suggesting a high level of structural preservation. Analysis of human tissues stored for up to 17 years demonstrated that these samples were still amenable for super-resolution microscopy. STED microscopy of sections of HER2 positive rectal adenocarcinoma revealed details in the surface and intracellular HER2 distribution that were blurred in the corresponding conventional images, demonstrating the potential of super-resolution microscopy to explore the thus far largely untapped nanoscale regime in tissues stored in biorepositories.
Collapse
|
42
|
Peddie CJ, Collinson LM. Exploring the third dimension: Volume electron microscopy comes of age. Micron 2014; 61:9-19. [DOI: 10.1016/j.micron.2014.01.009] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 12/12/2022]
|
43
|
Jakobs S, Wurm CA. Super-resolution microscopy of mitochondria. Curr Opin Chem Biol 2014; 20:9-15. [PMID: 24769752 DOI: 10.1016/j.cbpa.2014.03.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 03/19/2014] [Accepted: 03/26/2014] [Indexed: 11/25/2022]
Abstract
Mitochondria, the powerhouses of the cell, are essential organelles in eukaryotic cells. With their complex inner architecture featuring a smooth outer and a highly convoluted inner membrane, they are challenging objects for microscopy. The diameter of mitochondria is generally close to the resolution limit of conventional light microscopy, rendering diffraction-unlimited super-resolution light microscopy (nanoscopy) for imaging submitochondrial protein distributions often mandatory. In this review, we discuss what can be expected when imaging mitochondria with conventional diffraction-limited and diffraction-unlimited microscopy. We provide an overview on recent studies using super-resolution microscopy to investigate mitochondria and discuss further developments and challenges in mitochondrial biology that might by addressed with these technologies in the future.
Collapse
Affiliation(s)
- Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany; Department of Neurology, University of Göttingen Medical School, 37073 Göttingen, Germany.
| | - Christian A Wurm
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany
| |
Collapse
|
44
|
Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau VV, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. Correlative light- and electron microscopy with chemical tags. J Struct Biol 2014; 186:205-13. [PMID: 24698954 DOI: 10.1016/j.jsb.2014.03.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x-y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.
Collapse
Affiliation(s)
- Mario Perkovic
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Michael Kunz
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Ulrike Endesfelder
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Stefanie Bunse
- Max-Planck-Institute for Brain Research, Max-von-Laue Str. 4, 60438 Frankfurt am Main, Germany
| | - Christoph Wigge
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Zhou Yu
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Victor-Valentin Hodirnau
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Margot P Scheffer
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Anja Seybert
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Sebastian Malkusch
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Erin M Schuman
- Max-Planck-Institute for Brain Research, Max-von-Laue Str. 4, 60438 Frankfurt am Main, Germany
| | - Mike Heilemann
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Achilleas S Frangakis
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
45
|
Alekseev A, Efimov A, Loos J, Matsko N, Syurik J. Three-dimensional imaging of polymer materials by Scanning Probe Tomography. Eur Polym J 2014. [DOI: 10.1016/j.eurpolymj.2014.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
46
|
|
47
|
Kopek BG, Shtengel G, Grimm JB, Clayton DA, Hess HF. Correlative photoactivated localization and scanning electron microscopy. PLoS One 2013; 8:e77209. [PMID: 24204771 PMCID: PMC3808397 DOI: 10.1371/journal.pone.0077209] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/03/2013] [Indexed: 11/26/2022] Open
Abstract
The ability to localize proteins precisely within subcellular space is crucial to understanding the functioning of biological systems. Recently, we described a protocol that correlates a precise map of fluorescent fusion proteins localized using three-dimensional super-resolution optical microscopy with the fine ultrastructural context of three-dimensional electron micrographs. While it achieved the difficult simultaneous objectives of high photoactivated fluorophore preservation and ultrastructure preservation, it required a super-resolution optical and specialized electron microscope that is not available to many researchers. We present here a faster and more practical protocol with the advantage of a simpler two-dimensional optical (Photoactivated Localization Microscopy (PALM)) and scanning electron microscope (SEM) system that retains the often mutually exclusive attributes of fluorophore preservation and ultrastructure preservation. As before, cryosections were prepared using the Tokuyasu protocol, but the staining protocol was modified to be amenable for use in a standard SEM without the need for focused ion beam ablation. We show the versatility of this technique by labeling different cellular compartments and structures including mitochondrial nucleoids, peroxisomes, and the nuclear lamina. We also demonstrate simultaneous two-color PALM imaging with correlated electron micrographs. Lastly, this technique can be used with small-molecule dyes as demonstrated with actin labeling using phalloidin conjugated to a caged dye. By retaining the dense protein labeling expected for super-resolution microscopy combined with ultrastructural preservation, simplifying the tools required for correlative microscopy, and expanding the number of useful labels we expect this method to be accessible and valuable to a wide variety of researchers.
Collapse
Affiliation(s)
- Benjamin G. Kopek
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail:
| | - Gleb Shtengel
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Jonathan B. Grimm
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - David A. Clayton
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Harald F. Hess
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| |
Collapse
|
48
|
Abstract
In array tomography ordered, ribbon-like assemblies of ultrathin serial sections are deposited on a solid substrate and imaged afterwards. The resulting images are then aligned and reconstructed into a three-dimensional representation of the object. Depending on the preparation and labelling regime, different imaging modalities can be applied. When using light microscopy, the labelling with fluorescent markers would be the obvious choice, whereas the imaging in a scanning electron microscope would require impregnation with heavy metals. Depending on preparative constraints, the combination of diverse imaging modalities or truly correlative imaging is possible.
Collapse
Affiliation(s)
- I Wacker
- Institute for Biological Interfaces 1, Karlsruhe Institute of Technology, Karlsruhe, Germany; HEiKA, Heidelberg-Karlsruhe Research Partnership, Correlative Imaging Platform
| | | |
Collapse
|
49
|
Seeing the forest tree by tree: super-resolution light microscopy meets the neurosciences. Nat Neurosci 2013; 16:790-7. [PMID: 23799471 DOI: 10.1038/nn.3403] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/16/2013] [Indexed: 02/07/2023]
Abstract
Light microscopy can be applied in vivo and can sample large tissue volumes, features crucial for the study of single neurons and neural circuits. However, light microscopy per se is diffraction-limited in resolution, and the substructure of core signaling compartments of neuronal circuits--axons, presynaptic active zones, postsynaptic densities and dendritic spines-can be only insufficiently characterized by standard light microscopy. Recently, several forms of super-resolution light microscopy breaking the diffraction-imposed resolution limit have started to allow highly resolved, dynamic imaging in the cell-biologically highly relevant 10-100 nanometer range ('mesoscale'). New, sometimes surprising answers concerning how protein mobility and protein architectures shape neuronal communication have already emerged. Here we start by briefly introducing super-resolution microscopy techniques, before we describe their use in the analysis of neuronal compartments. We conclude with long-term prospects for super-resolution light microscopy in the molecular and cellular neurosciences.
Collapse
|
50
|
Kay KR, Smith C, Wright AK, Serrano-Pozo A, Pooler AM, Koffie R, Bastin ME, Bak TH, Abrahams S, Kopeikina KJ, McGuone D, Frosch MP, Gillingwater TH, Hyman BT, Spires-Jones TL. Studying synapses in human brain with array tomography and electron microscopy. Nat Protoc 2013; 8:1366-80. [PMID: 23787894 DOI: 10.1038/nprot.2013.078] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Postmortem studies of synapses in human brain are problematic because of the axial resolution limit of light microscopy and the difficulty in preserving and analyzing ultrastructure with electron microscopy (EM). Array tomography (AT) overcomes these problems by embedding autopsy tissue in resin and cutting ribbons of ultrathin serial sections. Ribbons are imaged with immunofluorescence, allowing high-throughput imaging of tens of thousands of synapses to assess synapse density and protein composition. The protocol takes ~3 d per case, excluding image analysis, which is done at the end of the study. Parallel processing for transmission electron microscopy (TEM) using a protocol modified to preserve the structure in human samples allows complementary ultrastructural studies. Incorporation of AT and TEM into brain banking is a potent way of phenotyping synapses in well-characterized clinical cohorts in order to develop clinicopathological correlations at the synapse level. This will be important for research in neurodegenerative disease, developmental disease and psychiatric illness.
Collapse
Affiliation(s)
- Kevin R Kay
- Massachusetts General Hospital and Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|