151
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Di Rienzo C, Gratton E, Beltram F, Cardarelli F. Spatiotemporal Fluctuation Analysis: A Powerful Tool for the Future Nanoscopy of Molecular Processes. Biophys J 2017; 111:679-685. [PMID: 27558712 PMCID: PMC5002078 DOI: 10.1016/j.bpj.2016.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/01/2016] [Accepted: 07/14/2016] [Indexed: 11/29/2022] Open
Abstract
The enormous wealth of information available today from optical microscopy measurements on living samples is often underexploited. We argue that spatiotemporal analysis of fluorescence fluctuations using multiple detection channels can enhance the performance of current nanoscopy methods and provide further insight into dynamic molecular processes of high biological relevance.
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Affiliation(s)
- Carmine Di Rienzo
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Pisa, Italy; Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Fabio Beltram
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Pisa, Italy; Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy
| | - Francesco Cardarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy.
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152
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Dixon CL, Sah P, Keramidas A, Lynch JW, Durisic N. γ1-Containing GABA-A Receptors Cluster at Synapses Where they Mediate Slower Synaptic Currents than γ2-Containing GABA-A Receptors. Front Mol Neurosci 2017. [PMID: 28642681 PMCID: PMC5462899 DOI: 10.3389/fnmol.2017.00178] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
GABA-A receptors (GABAARs) are pentameric ligand-gated ion channels that are assembled mainly from α (α1–6), β (β1–3) and γ (γ1–3) subunits. Although GABAARs containing γ2L subunits mediate most of the inhibitory neurotransmission in the brain, significant expression of γ1 subunits is seen in the amygdala, pallidum and substantia nigra. However, the location and function of γ1-containing GABAARs in these regions remains unclear. In “artificial” synapses, where the subunit composition of postsynaptic receptors is specifically controlled, γ1 incorporation slows the synaptic current decay rate without affecting channel deactivation, suggesting that γ1-containing receptors are not clustered and therefore activated by diffuse neurotransmitter. However, we show that γ1-containing receptors are localized at neuronal synapses and form clusters in both synaptic and extrasynaptic regions. In addition, they exhibit rapid membrane diffusion and a higher frequency of exchange between synaptic and perisynaptic populations compared to γ2L-containing GABAARs. A point mutation in the large intracellular domain and a pharmacological analysis reveal that when a single non-conserved γ2L residue is mutated to its γ1 counterpart (T349L), the synaptic current decay is slowed from γ2L- to γ1-like without changing the clustering or diffusion properties of the receptors. In addition, previous fast perfusion and single channel kinetic experiments revealed no difference in the intrinsic closing rates of γ2L- and γ1-containing receptors when expressed in HEK293 cells. These observations together with Monte Carlo simulations of synaptic function confirm that decreased clustering does not control γ1-containing GABAAR kinetics. Rather, they suggest that γ1- and γ2L-containing receptors exhibit differential synaptic current decay rates due to differential gating dynamics when localized at the synapse.
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Affiliation(s)
- Christine L Dixon
- Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Pankaj Sah
- Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Angelo Keramidas
- Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
| | - Joseph W Lynch
- Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia.,School of Biomedical Sciences, The University of QueenslandBrisbane, QLD, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of QueenslandBrisbane, QLD, Australia
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153
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Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y. Nucleic Acid-Based Nanodevices in Biological Imaging. Annu Rev Biochem 2017; 85:349-73. [PMID: 27294440 DOI: 10.1146/annurev-biochem-060815-014244] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.
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Affiliation(s)
- Kasturi Chakraborty
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Aneesh T Veetil
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York 10065;
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , , .,Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637
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154
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155
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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.
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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
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156
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Chamma I, Rossier O, Giannone G, Thoumine O, Sainlos M. Optimized labeling of membrane proteins for applications to super-resolution imaging in confined cellular environments using monomeric streptavidin. Nat Protoc 2017; 12:748-763. [DOI: 10.1038/nprot.2017.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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157
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Nicovich PR, Owen DM, Gaus K. Turning single-molecule localization microscopy into a quantitative bioanalytical tool. Nat Protoc 2017; 12:453-460. [DOI: 10.1038/nprot.2016.166] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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158
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Agasti SS, Wang Y, Schueder F, Sukumar A, Jungmann R, Yin P. DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging. Chem Sci 2017; 8:3080-3091. [PMID: 28451377 PMCID: PMC5380918 DOI: 10.1039/c6sc05420j] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 01/28/2017] [Indexed: 12/19/2022] Open
Abstract
We report the development of multiplexed cellular super-resolution imaging using DNA-barcoded binders.
Recent advances in super-resolution fluorescence imaging allow researchers to overcome the classical diffraction limit of light, and are already starting to make an impact in biology. However, a key challenge for traditional super-resolution methods is their limited multiplexing capability, which prevents a systematic understanding of multi-protein interactions on the nanoscale. Exchange-PAINT, a recently developed DNA-based multiplexing approach, in theory facilitates spectrally-unlimited multiplexing by sequentially imaging target molecules using orthogonal dye-labeled ‘imager’ strands. While this approach holds great promise for the bioimaging community, its widespread application has been hampered by the availability of DNA-conjugated ligands for protein labeling. Herein, we report a universal approach for the creation of DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging, using a variety of affinity reagents such as primary and secondary antibodies, nanobodies, and small molecule binders. Furthermore, we extend the availability of orthogonal imager strands for Exchange-PAINT to over 50 and assay their orthogonality in a novel DNA origami-based crosstalk assay. Using our optimized conjugation and labeling strategies, we demonstrate nine-color super-resolution imaging in situ in fixed cells.
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Affiliation(s)
- Sarit S Agasti
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts , USA . ; .,Department of Systems Biology , Harvard Medical School , Boston , Massachusetts , USA.,New Chemistry Unit and Chemistry & Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) , Bangalore , India
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts , USA . ; .,Department of Systems Biology , Harvard Medical School , Boston , Massachusetts , USA.,Program of Biological and Biomedical Science , Harvard Medical School , Boston , Massachusetts , USA
| | - Florian Schueder
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts , USA . ; .,Department of Systems Biology , Harvard Medical School , Boston , Massachusetts , USA.,Department of Physics and Center for Nanoscience , Ludwig Maximilian University , 80539 Munich , Germany.,Max Planck Institute of Biochemistry , 82152 Martinsried near Munich , Germany
| | - Aishwarya Sukumar
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts , USA . ;
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts , USA . ; .,Department of Systems Biology , Harvard Medical School , Boston , Massachusetts , USA.,Department of Physics and Center for Nanoscience , Ludwig Maximilian University , 80539 Munich , Germany.,Max Planck Institute of Biochemistry , 82152 Martinsried near Munich , Germany
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts , USA . ; .,Department of Systems Biology , Harvard Medical School , Boston , Massachusetts , USA
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159
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Lambert TJ, Waters JC. Navigating challenges in the application of superresolution microscopy. J Cell Biol 2017; 216:53-63. [PMID: 27920217 PMCID: PMC5223610 DOI: 10.1083/jcb.201610011] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 11/22/2022] Open
Abstract
In 2014, the Nobel Prize in Chemistry was awarded to three scientists who have made groundbreaking contributions to the field of superresolution (SR) microscopy (SRM). The first commercial SR microscope came to market a decade earlier, and many other commercial options have followed. As commercialization has lowered the barrier to using SRM and the awarding of the Nobel Prize has drawn attention to these methods, biologists have begun adopting SRM to address a wide range of questions in many types of specimens. There is no shortage of reviews on the fundamental principles of SRM and the remarkable achievements made with these methods. We approach SRM from another direction: we focus on the current practical limitations and compromises that must be made when designing an SRM experiment. We provide information and resources to help biologists navigate through common pitfalls in SRM specimen preparation and optimization of image acquisition as well as errors and artifacts that may compromise the reproducibility of SRM data.
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Affiliation(s)
- Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Jennifer C Waters
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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160
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Barr VA, Yi J, Samelson LE. Super-resolution Analysis of TCR-Dependent Signaling: Single-Molecule Localization Microscopy. Methods Mol Biol 2017; 1584:183-206. [PMID: 28255704 PMCID: PMC6676910 DOI: 10.1007/978-1-4939-6881-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-molecule localization microscopy (SMLM) comprises methods that produce super-resolution images from molecular locations of single molecules. These techniques mathematically determine the center of a diffraction-limited spot produced by a fluorescent molecule, which represents the most likely location of the molecule. Only a small cohort of well-separated molecules is visualized in a single image, and then many images are obtained from a single sample. The localizations from all the images are combined to produce a super-resolution picture of the sample. Here we describe the application of two methods, photoactivation localization microscopy (PALM) and direct stochastic optical reconstruction microscopy (dSTORM), to the study of signaling microclusters in T cells.
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Affiliation(s)
- Valarie A Barr
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Jason Yi
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA.
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161
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Czöndör K, Thoumine O. Synaptogenic Assays Using Neurons Cultured on Micropatterned Substrates. Methods Mol Biol 2017; 1538:29-44. [PMID: 27943181 DOI: 10.1007/978-1-4939-6688-2_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
One of the difficulties for studying the mechanisms of synaptogenesis stems from the spatial unpredictability of contact formation between neurons, and the involvement of many parallel adhesive pathways mediating axon/dendrite recognition. To circumvent these limitations, we describe here a method allowing the investigation of synaptic contacts at controlled locations with high precision and statistics. Specifically, primary neurons are cultured on micropatterned substrates comprising arrays of micron-scale dots coated with purified synaptogenic adhesion molecules. Coating the substrates with the homophilic adhesion molecule SynCAM triggers the formation of functional presynaptic structures in axons, while neurexin elicits postsynapses in dendrites from neurons expressing the counter receptor neuroligin. This assay can be combined with various imaging techniques including immunocytochemistry to screen the accumulation of synaptic components, long-term live cell recordings to probe the kinetics of neurite growth and synapse differentiation, as well as high resolution single molecule tracking.
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Affiliation(s)
- Katalin Czöndör
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, UMR 5297, 146 rue Leo Saignat, F-33000, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, F-33000, Bordeaux, France
| | - Olivier Thoumine
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, UMR 5297, 146 rue Leo Saignat, F-33000, Bordeaux, France. .,Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, F-33000, Bordeaux, France.
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162
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Zhao ZW, White MD, Bissiere S, Levi V, Plachta N. Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos. BMC Biol 2016; 14:115. [PMID: 28010727 PMCID: PMC5180410 DOI: 10.1186/s12915-016-0331-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.
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Affiliation(s)
- Ziqing W Zhao
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Melanie D White
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Stephanie Bissiere
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Valeria Levi
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Conicet, Buenos Aires, C1428EHA, Argentina
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
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163
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Monachino E, Spenkelink LM, van Oijen AM. Watching cellular machinery in action, one molecule at a time. J Cell Biol 2016; 216:41-51. [PMID: 27979907 PMCID: PMC5223611 DOI: 10.1083/jcb.201610025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 12/03/2022] Open
Abstract
Monachino et al. review recent developments in single-molecule biophysical approaches and the cell biological advances they allow. Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.
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Affiliation(s)
- Enrico Monachino
- Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute and University of Wollongong, New South Wales 2522, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, Netherlands
| | - Lisanne M Spenkelink
- Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute and University of Wollongong, New South Wales 2522, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, Netherlands
| | - Antoine M van Oijen
- Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
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164
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El Beheiry M, Türkcan S, Richly MU, Triller A, Alexandrou A, Dahan M, Masson JB. A Primer on the Bayesian Approach to High-Density Single-Molecule Trajectories Analysis. Biophys J 2016; 110:1209-15. [PMID: 27028631 DOI: 10.1016/j.bpj.2016.01.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 10/22/2022] Open
Abstract
Tracking single molecules in living cells provides invaluable information on their environment and on the interactions that underlie their motion. New experimental techniques now permit the recording of large amounts of individual trajectories, enabling the implementation of advanced statistical tools for data analysis. In this primer, we present a Bayesian approach toward treating these data, and we discuss how it can be fruitfully employed to infer physical and biochemical parameters from single-molecule trajectories.
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Affiliation(s)
- Mohamed El Beheiry
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, Paris, France; Department of Radiation Oncology, Sorbonne Universités, Paris, France; Physics of Biological Systems, Institut Pasteur, Paris, France
| | - Silvan Türkcan
- Division of Medical Physics, Stanford University School of Medicine, Palo Alto, California
| | - Maximilian U Richly
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Université Paris-Saclay, Palaiseau, France
| | - Antoine Triller
- Biologie Cellulaire de la Synapse, École Normale Supérieure, PSL Research University, Paris, France
| | - Antigone Alexandrou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Université Paris-Saclay, Palaiseau, France
| | - Maxime Dahan
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, Paris, France; Department of Radiation Oncology, Sorbonne Universités, Paris, France; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Jean-Baptiste Masson
- Physics of Biological Systems, Institut Pasteur, Paris, France; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia.
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165
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Joensuu M, Padmanabhan P, Durisic N, Bademosi ATD, Cooper-Williams E, Morrow IC, Harper CB, Jung W, Parton RG, Goodhill GJ, Papadopulos A, Meunier FA. Subdiffractional tracking of internalized molecules reveals heterogeneous motion states of synaptic vesicles. J Cell Biol 2016; 215:277-292. [PMID: 27810917 PMCID: PMC5080683 DOI: 10.1083/jcb.201604001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/30/2016] [Indexed: 11/23/2022] Open
Abstract
Joensuu et al. describe a tool for subdiffractional tracking of internalized molecules. They reveal that synaptic vesicles exhibit stochastic switching between heterogeneous diffusive and transport states in live hippocampal nerve terminals. Our understanding of endocytic pathway dynamics is severely restricted by the diffraction limit of light microscopy. To address this, we implemented a novel technique based on the subdiffractional tracking of internalized molecules (sdTIM). This allowed us to image anti–green fluorescent protein Atto647N-tagged nanobodies trapped in synaptic vesicles (SVs) from live hippocampal nerve terminals expressing vesicle-associated membrane protein 2 (VAMP2)–pHluorin with 36-nm localization precision. Our results showed that, once internalized, VAMP2–pHluorin/Atto647N–tagged nanobodies exhibited a markedly lower mobility than on the plasma membrane, an effect that was reversed upon restimulation in presynapses but not in neighboring axons. Using Bayesian model selection applied to hidden Markov modeling, we found that SVs oscillated between diffusive states or a combination of diffusive and transport states with opposite directionality. Importantly, SVs exhibiting diffusive motion were relatively less likely to switch to the transport motion. These results highlight the potential of the sdTIM technique to provide new insights into the dynamics of endocytic pathways in a wide variety of cellular settings.
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Affiliation(s)
- Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Pranesh Padmanabhan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adekunle T D Bademosi
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Isabel C Morrow
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Callista B Harper
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - WooRam Jung
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andreas Papadopulos
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia .,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia .,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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166
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Albrecht D, Winterflood CM, Sadeghi M, Tschager T, Noé F, Ewers H. Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J Cell Biol 2016; 215:37-46. [PMID: 27697928 PMCID: PMC5057285 DOI: 10.1083/jcb.201603108] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/16/2016] [Indexed: 12/31/2022] Open
Abstract
A diffusion barrier impeding membrane molecule motion between the axon and the somatodendritic compartment develops as neurons mature and the axon initial segment (AIS) is enriched in specific molecules. Albrecht et al. analyze the mobility of lipid-anchored molecules in the AIS using single-particle tracking time course experiments and propose a new mechanistic model for the AIS diffusion barrier. The axon initial segment (AIS) is enriched in specific adaptor, cytoskeletal, and transmembrane molecules. During AIS establishment, a membrane diffusion barrier is formed between the axonal and somatodendritic domains. Recently, an axonal periodic pattern of actin, spectrin, and ankyrin forming 190-nm-spaced, ring-like structures has been discovered. However, whether this structure is related to the diffusion barrier function is unclear. Here, we performed single-particle tracking time-course experiments on hippocampal neurons during AIS development. We analyzed the mobility of lipid-anchored molecules by high-speed single-particle tracking and correlated positions of membrane molecules with the nanoscopic organization of the AIS cytoskeleton. We observe a strong reduction in mobility early in AIS development. Membrane protein motion in the AIS plasma membrane is confined to a repetitive pattern of ∼190-nm-spaced segments along the AIS axis as early as day in vitro 4, and this pattern alternates with actin rings. Mathematical modeling shows that diffusion barriers between the segments significantly reduce lateral diffusion along the axon.
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Affiliation(s)
- David Albrecht
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195 Berlin, Germany Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, England, UK Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Christian M Winterflood
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, England, UK Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mohsen Sadeghi
- Department of Mathematics and Computer Science, Free University Berlin, 14195 Berlin, Germany
| | - Thomas Tschager
- Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Frank Noé
- Department of Mathematics and Computer Science, Free University Berlin, 14195 Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195 Berlin, Germany Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, England, UK Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
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167
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Tafteh R, Abraham L, Seo D, Lu HY, Gold MR, Chou KC. Real-time 3D stabilization of a super-resolution microscope using an electrically tunable lens. OPTICS EXPRESS 2016; 24:22959-22970. [PMID: 27828362 DOI: 10.1364/oe.24.022959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule localization microscopy (SMLM) has become an essential tool for examining a wide variety of biological structures and processes. However, the relatively long acquisition time makes SMLM prone to drift-induced artifacts. Here we report an optical design with an electrically tunable lens (ETL) that actively stabilizes a SMLM in three dimensions and nearly eliminates the mechanical drift (RMS ~0.7 nm lateral and ~2.7 nm axial). The bifocal design that employed fiducial markers on the coverslip was able to stabilize the sample regardless of the imaging depth. The effectiveness of the ETL was demonstrated by imaging endosomal transferrin receptors near the apical surface of B-lymphocytes at a depth of 8 µm. The drift-free images obtained with the stabilization system showed that the transferrin receptors were present in distinct but heterogeneous clusters with a bimodal size distribution. In contrast, the images obtained without the stabilization system showed a broader unimodal size distribution. Thus, this stabilization system enables a more accurate analysis of cluster topology. Additionally, this ETL-based stabilization system is cost-effective and can be integrated into existing microscopy systems.
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168
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Chamma I, Levet F, Sibarita JB, Sainlos M, Thoumine O. Nanoscale organization of synaptic adhesion proteins revealed by single-molecule localization microscopy. NEUROPHOTONICS 2016; 3:041810. [PMID: 27872870 PMCID: PMC5093229 DOI: 10.1117/1.nph.3.4.041810] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/11/2016] [Indexed: 06/06/2023]
Abstract
The advent of superresolution imaging has created a strong need for both optimized labeling strategies and analysis methods to probe the nanoscale organization of complex biological structures. We present a thorough description of the distribution of synaptic adhesion proteins at the nanoscopic scale, namely presynaptic neurexin-[Formula: see text] ([Formula: see text]), and its two postsynaptic binding partners neuroligin-1 (Nlg1) and leucine-rich-repeat transmembrane protein 2 (LRRTM2). We monitored these proteins in the membrane of neurons by direct stochastic optical reconstruction microscopy, after live surface labeling with Alexa647-conjugated monomeric streptavidin. The small probe ([Formula: see text]) efficiently penetrates into crowded synaptic junctions and reduces the distance to target. We quantified the organization of the single-molecule localization data using a tesselation-based analysis technique. We show that Nlg1 exhibits a fairly disperse organization within dendritic spines, while LRRTM2 is organized in compact domains, and [Formula: see text] in presynaptic terminals displays a dual-organization pattern intermediate between that of Nlg1 and LRRTM2. These results suggest that part of [Formula: see text] interacts transsynaptically with Nlg1 and the other part with LRRTM2.
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Affiliation(s)
- Ingrid Chamma
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
| | - Florian Levet
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
| | - Jean-Baptiste Sibarita
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
| | - Matthieu Sainlos
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
| | - Olivier Thoumine
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, 147 rue Léo-Saignat, Bordeaux Cedex 33077, France
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169
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Compans B, Choquet D, Hosy E. Review on the role of AMPA receptor nano-organization and dynamic in the properties of synaptic transmission. NEUROPHOTONICS 2016; 3:041811. [PMID: 27981061 PMCID: PMC5109202 DOI: 10.1117/1.nph.3.4.041811] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Receptor trafficking and its regulation have appeared in the last two decades to be a major controller of basal synaptic transmission and its activity-dependent plasticity. More recently, considerable advances in super-resolution microscopy have begun deciphering the subdiffraction organization of synaptic elements and their functional roles. In particular, the dynamic nanoscale organization of neurotransmitter receptors in the postsynaptic membrane has recently been suggested to play a major role in various aspects of synapstic function. We here review the recent advances in our understanding of alpha-amino-3-hydroxy-5-méthyl-4-isoxazolepropionic acid subtype glutamate receptors subsynaptic organization and their role in short- and long-term synaptic plasticity.
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Affiliation(s)
- Benjamin Compans
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
| | - Daniel Choquet
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
- University of Bordeaux, Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM, France
| | - Eric Hosy
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
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170
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Varela JA, Ferreira JS, Dupuis JP, Durand P, Bouchet D, Groc L. Single nanoparticle tracking of [Formula: see text]-methyl-d-aspartate receptors in cultured and intact brain tissue. NEUROPHOTONICS 2016; 3:041808. [PMID: 27429996 PMCID: PMC4940612 DOI: 10.1117/1.nph.3.4.041808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/22/2016] [Indexed: 06/01/2023]
Abstract
Recent developments in single-molecule imaging have revealed many biological mechanisms, providing high spatial and temporal resolution maps of molecular events. In neurobiology, these techniques unveiled that plasma membrane neurotransmitter receptors and transporters laterally diffuse at the surface of cultured brain cells. The photostability of bright nanoprobes, such as quantum dots (QDs), has given access to neurotransmitter receptor tracking over long periods of time with a high spatial resolution. However, our knowledge has been restricted to cultured systems, i.e., neurons and organotypic slices, therefore lacking several aspects of the intact brain rheology and connectivity. Here, we used QDs to track single glutamatergic [Formula: see text]-methyl-d-aspartate receptors (NMDAR) in acute brain slices. By delivering functionalized nanoparticles in vivo through intraventricular injections to rats expressing genetically engineered-tagged NMDAR, we successfully tracked the receptors in native brain tissue. Comparing NMDAR tracking to different classical brain preparations (acute brain slices, cultured organotypic brain slices, and cultured neurons) revealed that the surface diffusion properties shared several features and are also influenced by the nature of the extracellular environment. Together, we describe the experimental procedures to track plasma membrane NMDAR in dissociated and native brain tissue, paving the way for investigations aiming at characterizing receptor diffusion biophysics in intact tissue and exploring the physiopathological roles of receptor surface dynamics.
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Affiliation(s)
- Juan A. Varela
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, 146 rue Leo Saignat, 33077 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Joana S. Ferreira
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, 146 rue Leo Saignat, 33077 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Julien P. Dupuis
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, 146 rue Leo Saignat, 33077 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Pauline Durand
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, 146 rue Leo Saignat, 33077 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Delphine Bouchet
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, 146 rue Leo Saignat, 33077 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Laurent Groc
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, 146 rue Leo Saignat, 33077 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
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171
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Kasula R, Chai YJ, Bademosi AT, Harper CB, Gormal RS, Morrow IC, Hosy E, Collins BM, Choquet D, Papadopulos A, Meunier FA. The Munc18-1 domain 3a hinge-loop controls syntaxin-1A nanodomain assembly and engagement with the SNARE complex during secretory vesicle priming. J Cell Biol 2016; 214:847-58. [PMID: 27646276 PMCID: PMC5037406 DOI: 10.1083/jcb.201508118] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 08/24/2016] [Indexed: 12/12/2022] Open
Abstract
Kasula et al. use single-molecule imaging to reveal the diffusional signature for the SNARE proteins Munc18-1 and syntaxin-1A during secretory vesicle priming. The authors show that a conformational change in the Munc18-1 domain 3a hinge-loop regulates engagement of syntaxin-1A in the SNARE complex. Munc18-1 and syntaxin-1A control SNARE-dependent neuroexocytosis and are organized in nanodomains on the plasma membrane of neurons and neurosecretory cells. Deciphering the intra- and intermolecular steps via which they prepare secretory vesicles (SVs) for fusion is key to understanding neuronal and hormonal communication. Here, we demonstrate that expression of a priming-deficient mutant lacking 17 residues of the domain 3a hinge-loop (Munc18-1Δ317-333) in PC12 cells engineered to knockdown Munc18-1/2 markedly prolonged SV docking. Single-molecule analysis revealed nonhomogeneous diffusion of Munc18-1 and syntaxin-1A in and out of partially overlapping nanodomains. Whereas Munc18-1WT mobility increased in response to stimulation, syntaxin-1A became less mobile. These Munc18-1 and syntaxin-1A diffusional switches were blocked by the expression of Munc18-1Δ317-333, suggesting that a conformational change in the Munc18-1 hinge-loop controls syntaxin-1A and subsequent SNARE complex assembly. Accordingly, syntaxin-1A confinement was prevented by expression of botulinum neurotoxin type E. The Munc18-1 domain 3a hinge-loop therefore controls syntaxin-1A engagement into SNARE complex formation during priming.
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Affiliation(s)
- Ravikiran Kasula
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ye Jin Chai
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adekunle T Bademosi
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Callista B Harper
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rachel S Gormal
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Isabel C Morrow
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eric Hosy
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, 33077 Bordeaux, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5297, 33077 Bordeaux, France
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel Choquet
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, 33077 Bordeaux, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5297, 33077 Bordeaux, France Bordeaux Imaging Center, Unité Mixte de Service 3420, Centre National de la Recherche Scientifique, US4 Institut National de la Santé et de la Recherche Médicale, University of Bordeaux, 33077 Bordeaux, France
| | - Andreas Papadopulos
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Frédéric A Meunier
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
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172
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Protein Crowding within the Postsynaptic Density Can Impede the Escape of Membrane Proteins. J Neurosci 2016; 36:4276-95. [PMID: 27076425 DOI: 10.1523/jneurosci.3154-15.2016] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/19/2016] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED Mechanisms regulating lateral diffusion and positioning of glutamate receptors within the postsynaptic density (PSD) determine excitatory synaptic strength. Scaffold proteins in the PSD are abundant receptor binding partners, yet electron microscopy suggests that the PSD is highly crowded, potentially restricting the diffusion of receptors regardless of binding. However, the contribution of macromolecular crowding to receptor retention remains poorly understood. We combined experimental and computational approaches to test the effect of synaptic crowding on receptor movement and positioning in Sprague Dawley rat hippocampal neurons. We modeled AMPA receptor diffusion in synapses where the distribution of scaffold proteins was determined from photoactivated localization microscopy experiments, and receptor-scaffold association and dissociation rates were adjusted to fit single-molecule tracking and fluorescence recovery measurements. Simulations predicted that variation of receptor size strongly influences the fractional synaptic area the receptor may traverse, and the proportion that may exchange in and out of the synapse. To test the model experimentally, we designed a set of novel transmembrane (TM) probes. A single-pass TM protein with one PDZ binding motif concentrated in the synapse as do AMPARs yet was more mobile there than the much larger AMPAR. Furthermore, either the single binding motif or an increase in cytoplasmic bulk through addition of a single GFP slowed synaptic movement of a small TM protein. These results suggest that both crowding and binding limit escape of AMPARs from the synapse. Moreover, tight protein packing within the PSD may modulate the synaptic dwell time of many TM proteins important for synaptic function. SIGNIFICANCE STATEMENT Small alterations to the distribution within synapses of key transmembrane proteins, such as receptors, can dramatically change synaptic strength. Indeed, many diseases are thought to unbalance neural circuit function in this manner. Processes that regulate this in healthy synapses are unclear, however. By combining computer simulations with imaging methods that examined protein dynamics at multiple scales in space and time, we showed that both steric effects and protein-protein binding each regulate the mobility of receptors in the synapse. Our findings extend our knowledge of the synapse as a crowded environment that counteracts molecular diffusion, and support the idea that both molecular collisions and biochemical binding can be involved in the regulation of neural circuit performance.
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173
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Dai M, Jungmann R, Yin P. Optical imaging of individual biomolecules in densely packed clusters. NATURE NANOTECHNOLOGY 2016; 11:798-807. [PMID: 27376244 PMCID: PMC5014615 DOI: 10.1038/nnano.2016.95] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/09/2016] [Indexed: 05/15/2023]
Abstract
Recent advances in fluorescence super-resolution microscopy have allowed subcellular features and synthetic nanostructures down to 10-20 nm in size to be imaged. However, the direct optical observation of individual molecular targets (∼5 nm) in a densely packed biomolecular cluster remains a challenge. Here, we show that such discrete molecular imaging is possible using DNA-PAINT (points accumulation for imaging in nanoscale topography)-a super-resolution fluorescence microscopy technique that exploits programmable transient oligonucleotide hybridization-on synthetic DNA nanostructures. We examined the effects of a high photon count, high blinking statistics and an appropriate blinking duty cycle on imaging quality, and developed a software-based drift correction method that achieves <1 nm residual drift (root mean squared) over hours. This allowed us to image a densely packed triangular lattice pattern with ∼5 nm point-to-point distance and to analyse the DNA origami structural offset with ångström-level precision (2 Å) from single-molecule studies. By combining the approach with multiplexed exchange-PAINT imaging, we further demonstrated an optical nanodisplay with 5 × 5 nm pixel size and three distinct colours with <1 nm cross-channel registration accuracy.
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Affiliation(s)
- Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Biophysics Program, Harvard University, Boston, MA 02115
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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174
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Holcman D, Hoze N, Schuss Z. Analysis and Interpretation of Superresolution Single-Particle Trajectories. Biophys J 2016; 109:1761-71. [PMID: 26536253 DOI: 10.1016/j.bpj.2015.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/29/2015] [Accepted: 09/01/2015] [Indexed: 01/30/2023] Open
Abstract
A large number (tens of thousands) of single molecular trajectories on a cell membrane can now be collected by superresolution methods. The data contains information about the diffusive motion of molecule, proteins, or receptors and here we review methods for its recovery by statistical analysis of the data. The information includes the forces, organization of the membrane, the diffusion tensor, the long-time behavior of the trajectories, and more. To recover the long-time behavior and statistics of long trajectories, a stochastic model of their nonequilibrium motion is required. Modeling and data analysis serve extracting novel biophysical features at an unprecedented spatiotemporal resolution. The review presents data analysis, modeling, and stochastic simulations applied in particular on surface receptors evolving in neuronal cells.
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Affiliation(s)
- D Holcman
- Applied Mathematics and Computational Biology, IBENS Ecole Normale Supérieure, Paris, France; Churchill College, Cambridge University, Cambridge, United Kingdom.
| | - N Hoze
- ETH Zürich, Institute of Integrative Biology, ETH-Zentrum CHN, Universitätsstrasse 16, Zürich, Switzerland
| | - Z Schuss
- Department of Applied Mathematics, Tel-Aviv University, Tel-Aviv, Israel
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175
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Huang F, Sirinakis G, Allgeyer ES, Schroeder LK, Duim WC, Kromann EB, Phan T, Rivera-Molina FE, Myers JR, Irnov I, Lessard M, Zhang Y, Handel MA, Jacobs-Wagner C, Lusk CP, Rothman JE, Toomre D, Booth MJ, Bewersdorf J. Ultra-High Resolution 3D Imaging of Whole Cells. Cell 2016; 166:1028-1040. [PMID: 27397506 PMCID: PMC5005454 DOI: 10.1016/j.cell.2016.06.016] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/02/2016] [Accepted: 06/03/2016] [Indexed: 12/23/2022]
Abstract
Fluorescence nanoscopy, or super-resolution microscopy, has become an important tool in cell biological research. However, because of its usually inferior resolution in the depth direction (50-80 nm) and rapidly deteriorating resolution in thick samples, its practical biological application has been effectively limited to two dimensions and thin samples. Here, we present the development of whole-cell 4Pi single-molecule switching nanoscopy (W-4PiSMSN), an optical nanoscope that allows imaging of three-dimensional (3D) structures at 10- to 20-nm resolution throughout entire mammalian cells. We demonstrate the wide applicability of W-4PiSMSN across diverse research fields by imaging complex molecular architectures ranging from bacteriophages to nuclear pores, cilia, and synaptonemal complexes in large 3D cellular volumes.
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Affiliation(s)
- Fang Huang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - George Sirinakis
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Edward S Allgeyer
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Lena K Schroeder
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Whitney C Duim
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Harvey Mudd College, Claremont, CA 91711, USA
| | - Emil B Kromann
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, CT 06520, USA
| | - Thomy Phan
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Felix E Rivera-Molina
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Jordan R Myers
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Mark Lessard
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Yongdeng Zhang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | | | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - C Patrick Lusk
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - James E Rothman
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Derek Toomre
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Martin J Booth
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK; Centre for Neural Circuits and Behaviour, University of Oxford, Oxford OX1 3SR, UK
| | - Joerg Bewersdorf
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, CT 06520, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA.
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176
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Li TP, Blanpied TA. Control of Transmembrane Protein Diffusion within the Postsynaptic Density Assessed by Simultaneous Single-Molecule Tracking and Localization Microscopy. Front Synaptic Neurosci 2016; 8:19. [PMID: 27499742 PMCID: PMC4956670 DOI: 10.3389/fnsyn.2016.00019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/05/2016] [Indexed: 11/13/2022] Open
Abstract
Postsynaptic transmembrane proteins are critical elements of synapses, mediating trans-cellular contact, sensitivity to neurotransmitters and other signaling molecules, and flux of Ca and other ions. Positioning and mobility of each member of this large class of proteins is critical to their individual function at the synapse. One critical example is that the position of glutamate receptors within the postsynaptic density (PSD) strongly modulates their function by aligning or misaligning them with sites of presynaptic vesicle fusion. In addition, the regulated ability of receptors to move in or out of the synapse is critical for activity-dependent plasticity. However, factors that control receptor mobility within the boundaries of the synapse are not well understood. Notably, PSD scaffold molecules accumulate in domains much smaller than the synapse. Within these nanodomains, the density of proteins is considerably higher than that of the synapse as a whole, so high that steric hindrance is expected to reduce receptor mobility substantially. However, while numerical modeling has demonstrated several features of how the varying protein density across the face of a single PSD may modulate receptor motion, there is little experimental information about the extent of this influence. To address this critical aspect of synaptic organizational dynamics, we performed single-molecule tracking of transmembrane proteins using universal point accumulation-for-imaging-in-nanoscale-topography (uPAINT) over PSDs whose internal structure was simultaneously resolved using photoactivated localization microscopy (PALM). The results provide important experimental confirmation that PSD scaffold protein density strongly influences the mobility of transmembrane proteins. A protein with a cytosolic domain that does not bind PSD-95 was still slowed in regions of high PSD-95 density, suggesting that crowding by scaffold molecules and perhaps other proteins is sufficient to stabilize receptors even in the absence of binding. Because numerous proteins thought to be involved in establishing PSD structure are linked to disorders including autism and depression, this motivates further exploration of how PSD nanostructure is created. The combined application PALM and uPAINT should be invaluable for distinguishing the interactions of mobile proteins with their nano-environment both in synapses and other cellular compartments.
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Affiliation(s)
- Tuo P. Li
- Department of Physiology and Program in Neuroscience, University of Maryland School of MedicineBaltimore, MD, USA
| | - Thomas A. Blanpied
- Department of Physiology and Program in Neuroscience, University of Maryland School of MedicineBaltimore, MD, USA
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177
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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.
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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
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178
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179
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Residence times of receptors in dendritic spines analyzed by stochastic simulations in empirical domains. Biophys J 2016; 107:3008-3017. [PMID: 25517165 DOI: 10.1016/j.bpj.2014.10.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/23/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023] Open
Abstract
Analysis of high-density superresolution imaging of receptors reveals the organization of dendrites at nanoscale resolution. We present here an apparently novel method that uses local statistics extracted from short-range trajectories for the simulations of long-range trajectories in empirical live cell images. Based on these empirical simulations, we compute the residence time of a receptor in dendritic spines that accounts for receptors' local interactions and geometrical membrane organization. We report here that depending on the type of the spine, the residence time varies from 1 to 5 min. Moreover, we show that there exists transient organized structures, previously described as potential wells that can regulate the trafficking of receptors to dendritic spine: the simulation results suggest that receptor trafficking is regulated by transient structures.
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180
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Dosset P, Rassam P, Fernandez L, Espenel C, Rubinstein E, Margeat E, Milhiet PE. Automatic detection of diffusion modes within biological membranes using back-propagation neural network. BMC Bioinformatics 2016; 17:197. [PMID: 27141816 PMCID: PMC4855490 DOI: 10.1186/s12859-016-1064-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 04/29/2016] [Indexed: 12/17/2022] Open
Abstract
Background Single particle tracking (SPT) is nowadays one of the most popular technique to probe spatio-temporal dynamics of proteins diffusing within the plasma membrane. Indeed membrane components of eukaryotic cells are very dynamic molecules and can diffuse according to different motion modes. Trajectories are often reconstructed frame-by-frame and dynamic properties often evaluated using mean square displacement (MSD) analysis. However, to get statistically significant results in tracking experiments, analysis of a large number of trajectories is required and new methods facilitating this analysis are still needed. Results In this study we developed a new algorithm based on back-propagation neural network (BPNN) and MSD analysis using a sliding window. The neural network was trained and cross validated with short synthetic trajectories. For simulated and experimental data, the algorithm was shown to accurately discriminate between Brownian, confined and directed diffusion modes within one trajectory, the 3 main of diffusion encountered for proteins diffusing within biological membranes. It does not require a minimum number of observed particle displacements within the trajectory to infer the presence of multiple motion states. The size of the sliding window was small enough to measure local behavior and to detect switches between different diffusion modes for segments as short as 20 frames. It also provides quantitative information from each segment of these trajectories. Besides its ability to detect switches between 3 modes of diffusion, this algorithm is able to analyze simultaneously hundreds of trajectories with a short computational time. Conclusion This new algorithm, implemented in powerful and handy software, provides a new conceptual and versatile tool, to accurately analyze the dynamic behavior of membrane components. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1064-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrice Dosset
- Inserm, U1054, Montpellier, France.,Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - Patrice Rassam
- Inserm, U1054, Montpellier, France.,Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - Laurent Fernandez
- Inserm, U1054, Montpellier, France.,Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - Cedric Espenel
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Eric Rubinstein
- Inserm, U1004, Villejuif, France.,Institut André Lwoff, Université Paris 11, Villejuif, France
| | - Emmanuel Margeat
- Inserm, U1054, Montpellier, France.,Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - Pierre-Emmanuel Milhiet
- Inserm, U1054, Montpellier, France. .,Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France. .,Centre de Biochimie Structurale, 29, rue de Navacelles, 34090, Montpellier, France.
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181
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Aloi A, Vilanova N, Albertazzi L, Voets IK. iPAINT: a general approach tailored to image the topology of interfaces with nanometer resolution. NANOSCALE 2016; 8:8712-6. [PMID: 27055489 PMCID: PMC5050559 DOI: 10.1039/c6nr00445h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/09/2016] [Indexed: 05/24/2023]
Abstract
Understanding interfacial phenomena in soft materials such as wetting, colloidal stability, coalescence, and friction warrants non-invasive imaging with nanometer resolution. Super-resolution microscopy has emerged as an attractive method to visualize nanostructures labeled covalently with fluorescent tags, but this is not amenable to all interfaces. Inspired by PAINT we developed a simple and general strategy to overcome this limitation, which we coin 'iPAINT: interface Point Accumulation for Imaging in Nanoscale Topography'. It enables three-dimensional, sub-diffraction imaging of interfaces irrespective of their nature via reversible adsorption of polymer chains end-functionalized with photo-activatable moieties. We visualized model dispersions, emulsions, and foams with ∼20 nm and ∼3° accuracy demonstrating the general applicability of iPAINT to study solid/liquid, liquid/liquid and liquid/air interfaces. iPAINT thus broadens the scope of super-resolution microscopy paving the way for non-invasive, high-resolution imaging of complex soft materials.
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Affiliation(s)
- A. Aloi
- Institute for Complex Molecular Systems , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands .
- Laboratory of Macromolecular and Organic Chemistry , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands
| | - N. Vilanova
- Institute for Complex Molecular Systems , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands .
- Laboratory of Macromolecular and Organic Chemistry , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands
| | - L. Albertazzi
- Institute for Complex Molecular Systems , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands .
| | - I. K. Voets
- Institute for Complex Molecular Systems , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands .
- Laboratory of Macromolecular and Organic Chemistry , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands
- Laboratory of Physical Chemistry , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , Post Office Box 513 , 5600 MD Eindhoven , The Netherlands .
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182
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Rossier O, Giannone G. The journey of integrins and partners in a complex interactions landscape studied by super-resolution microscopy and single protein tracking. Exp Cell Res 2016; 343:28-34. [DOI: 10.1016/j.yexcr.2015.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/05/2015] [Indexed: 10/24/2022]
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183
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Mapping the dynamics and nanoscale organization of synaptic adhesion proteins using monomeric streptavidin. Nat Commun 2016; 7:10773. [PMID: 26979420 PMCID: PMC4799371 DOI: 10.1038/ncomms10773] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/17/2016] [Indexed: 12/12/2022] Open
Abstract
The advent of super-resolution imaging (SRI) has created a need for optimized labelling strategies. We present a new method relying on fluorophore-conjugated monomeric streptavidin (mSA) to label membrane proteins carrying a short, enzymatically biotinylated tag, compatible with SRI techniques including uPAINT, STED and dSTORM. We demonstrate efficient and specific labelling of target proteins in confined intercellular and organotypic tissues, with reduced steric hindrance and no crosslinking compared with multivalent probes. We use mSA to decipher the dynamics and nanoscale organization of the synaptic adhesion molecules neurexin-1β, neuroligin-1 (Nlg1) and leucine-rich-repeat transmembrane protein 2 (LRRTM2) in a dual-colour configuration with GFP nanobody, and show that these proteins are diffusionally trapped at synapses where they form apposed trans-synaptic adhesive structures. Furthermore, Nlg1 is dynamic, disperse and sensitive to synaptic stimulation, whereas LRRTM2 is organized in compact and stable nanodomains. Thus, mSA is a versatile tool to image membrane proteins at high resolution in complex live environments, providing novel information about the nano-organization of biological structures. The advent of fluorescence-based super-resolution microscopy has created a need for labeling strategies relying on small probes that minimally perturb protein function. Here the authors describe a labeling method that reduces protein tag and label sizes, allowing for accurate protein targeting and measurements of protein dynamics in tight cellular spaces.
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184
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Heine M, Ciuraszkiewicz A, Voigt A, Heck J, Bikbaev A. Surface dynamics of voltage-gated ion channels. Channels (Austin) 2016; 10:267-81. [PMID: 26891382 DOI: 10.1080/19336950.2016.1153210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Neurons encode information in fast changes of the membrane potential, and thus electrical membrane properties are critically important for the integration and processing of synaptic inputs by a neuron. These electrical properties are largely determined by ion channels embedded in the membrane. The distribution of most ion channels in the membrane is not spatially uniform: they undergo activity-driven changes in the range of minutes to days. Even in the range of milliseconds, the composition and topology of ion channels are not static but engage in highly dynamic processes including stochastic or activity-dependent transient association of the pore-forming and auxiliary subunits, lateral diffusion, as well as clustering of different channels. In this review we briefly discuss the potential impact of mobile sodium, calcium and potassium ion channels and the functional significance of this for individual neurons and neuronal networks.
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Affiliation(s)
- Martin Heine
- a RG Molecular Physiology, Leibniz Institute for Neurobiology, Center for Behavioral Brain Science, Otto-von-Guericke-University of Magdeburg , Magdeburg , Germany
| | - Anna Ciuraszkiewicz
- a RG Molecular Physiology, Leibniz Institute for Neurobiology, Center for Behavioral Brain Science, Otto-von-Guericke-University of Magdeburg , Magdeburg , Germany
| | - Andreas Voigt
- b Lehrstuhl Systemverfahrenstechnik, Otto-von-Guericke-University of Magdeburg , Magdeburg , Germany
| | - Jennifer Heck
- a RG Molecular Physiology, Leibniz Institute for Neurobiology, Center for Behavioral Brain Science, Otto-von-Guericke-University of Magdeburg , Magdeburg , Germany
| | - Arthur Bikbaev
- a RG Molecular Physiology, Leibniz Institute for Neurobiology, Center for Behavioral Brain Science, Otto-von-Guericke-University of Magdeburg , Magdeburg , Germany
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185
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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186
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Hogstrom LJ, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales. Interface Focus 2016; 6:20150081. [PMID: 26855758 DOI: 10.1098/rsfs.2015.0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Brain function emerges from hierarchical neuronal structure that spans orders of magnitude in length scale, from the nanometre-scale organization of synaptic proteins to the macroscopic wiring of neuronal circuits. Because the synaptic electrochemical signal transmission that drives brain function ultimately relies on the organization of neuronal circuits, understanding brain function requires an understanding of the principles that determine hierarchical neuronal structure in living or intact organisms. Recent advances in fluorescence imaging now enable quantitative characterization of neuronal structure across length scales, ranging from single-molecule localization using super-resolution imaging to whole-brain imaging using light-sheet microscopy on cleared samples. These tools, together with correlative electron microscopy and magnetic resonance imaging at the nanoscopic and macroscopic scales, respectively, now facilitate our ability to probe brain structure across its full range of length scales with cellular and molecular specificity. As these imaging datasets become increasingly accessible to researchers, novel statistical and computational frameworks will play an increasing role in efforts to relate hierarchical brain structure to its function. In this perspective, we discuss several prominent experimental advances that are ushering in a new era of quantitative fluorescence-based imaging in neuroscience along with novel computational and statistical strategies that are helping to distil our understanding of complex brain structure.
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Affiliation(s)
- L J Hogstrom
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - S M Guo
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - K Murugadoss
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - M Bathe
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
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187
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Kollmannsperger A, Sharei A, Raulf A, Heilemann M, Langer R, Jensen KF, Wieneke R, Tampé R. Live-cell protein labelling with nanometre precision by cell squeezing. Nat Commun 2016; 7:10372. [PMID: 26822409 PMCID: PMC4740111 DOI: 10.1038/ncomms10372] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/30/2015] [Indexed: 11/08/2022] Open
Abstract
Live-cell labelling techniques to visualize proteins with minimal disturbance are important; however, the currently available methods are limited in their labelling efficiency, specificity and cell permeability. We describe high-throughput protein labelling facilitated by minimalistic probes delivered to mammalian cells by microfluidic cell squeezing. High-affinity and target-specific tracing of proteins in various subcellular compartments is demonstrated, culminating in photoinduced labelling within live cells. Both the fine-tuned delivery of subnanomolar concentrations and the minimal size of the probe allow for live-cell super-resolution imaging with very low background and nanometre precision. This method is fast in probe delivery (∼ 1,000,000 cells per second), versatile across cell types and can be readily transferred to a multitude of proteins. Moreover, the technique succeeds in combination with well-established methods to gain multiplexed labelling and has demonstrated potential to precisely trace target proteins, in live mammalian cells, by super-resolution microscopy.
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Affiliation(s)
- Alina Kollmannsperger
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
| | - Armon Sharei
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), 500 Main Street, Building 76-661, Cambridge, Massachusetts 02139, USA
| | - Anika Raulf
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Robert Langer
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), 500 Main Street, Building 76-661, Cambridge, Massachusetts 02139, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), 500 Main Street, Building 76-661, Cambridge, Massachusetts 02139, USA
| | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
- Cluster of Excellence—Macromolecular Complexes, Goethe-University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt/Main, Germany
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188
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Superresolution microscopy with transient binding. Curr Opin Biotechnol 2016; 39:8-16. [PMID: 26773299 DOI: 10.1016/j.copbio.2015.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/12/2015] [Accepted: 12/16/2015] [Indexed: 01/05/2023]
Abstract
For single-molecule localization based superresolution, the concentration of fluorescent labels has to be thinned out. This is commonly achieved by photophysically or photochemically deactivating subsets of molecules. Alternatively, apparent switching of molecules can be achieved by transient binding of fluorescent labels. Here, a diffusing dye yields bright fluorescent spots when binding to the structure of interest. As the binding interaction is weak, the labeling is reversible and the dye ligand construct diffuses back into solution. This approach of achieving superresolution by transient binding (STB) is reviewed in this manuscript. Different realizations of STB are discussed and compared to other localization-based superresolution modalities. We propose the development of labeling strategies that will make STB a highly versatile tool for superresolution microscopy at highest resolution.
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189
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Jang S, Oh D, Lee Y, Hosy E, Shin H, van Riesen C, Whitcomb D, Warburton JM, Jo J, Kim D, Kim SG, Um SM, Kwon SK, Kim MH, Roh JD, Woo J, Jun H, Lee D, Mah W, Kim H, Kaang BK, Cho K, Rhee JS, Choquet D, Kim E. Synaptic adhesion molecule IgSF11 regulates synaptic transmission and plasticity. Nat Neurosci 2016; 19:84-93. [PMID: 26595655 PMCID: PMC5010778 DOI: 10.1038/nn.4176] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/20/2015] [Indexed: 12/11/2022]
Abstract
Synaptic adhesion molecules regulate synapse development and plasticity through mechanisms that include trans-synaptic adhesion and recruitment of diverse synaptic proteins. We found that the immunoglobulin superfamily member 11 (IgSF11), a homophilic adhesion molecule that preferentially expressed in the brain, is a dual-binding partner of the postsynaptic scaffolding protein PSD-95 and AMPA glutamate receptors (AMPARs). IgSF11 required PSD-95 binding for its excitatory synaptic localization. In addition, IgSF11 stabilized synaptic AMPARs, as determined by IgSF11 knockdown-induced suppression of AMPAR-mediated synaptic transmission and increased surface mobility of AMPARs, measured by high-throughput, single-molecule tracking. IgSF11 deletion in mice led to the suppression of AMPAR-mediated synaptic transmission in the dentate gyrus and long-term potentiation in the CA1 region of the hippocampus. IgSF11 did not regulate the functional characteristics of AMPARs, including desensitization, deactivation or recovery. These results suggest that IgSF11 regulates excitatory synaptic transmission and plasticity through its tripartite interactions with PSD-95 and AMPARs.
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Affiliation(s)
- Seil Jang
- Department of Biological Sciences, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Daeyoung Oh
- Department of Biomedical Sciences, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 305-701, Korea
- Department of Psychiatry, CHA Bundang Medical Center, CHA
University, Seoul, Korea
| | - Yeunkum Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science
(IBS), Daejeon 305-701, Korea
| | - Eric Hosy
- University of Bordeaux, Interdisciplinary Institute for
Neuroscience, France; CNRS UMR 5297, F-33000 Bordeaux, France
| | - Hyewon Shin
- Department of Biomedical Sciences, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Christoph van Riesen
- Department of Molecular Neurobiology, Max Planck Institute of
Experimental Medicine, D-37075 Göttingen, Germany
| | - Daniel Whitcomb
- School of Clinical Sciences, Faculty of Medicine and Dentistry,
University of Bristol, Whitson street, Bristol, UK
- Centre for Synaptic Plasticity, University of Bristol, Whitson
street, Bristol, UK
| | - Julia M. Warburton
- School of Clinical Sciences, Faculty of Medicine and Dentistry,
University of Bristol, Whitson street, Bristol, UK
| | - Jihoon Jo
- School of Clinical Sciences, Faculty of Medicine and Dentistry,
University of Bristol, Whitson street, Bristol, UK
- Department of Biomedical Sciences, Chonnam National University
Medical School, Gwangju, South Korea
| | - Doyoun Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science
(IBS), Daejeon 305-701, Korea
| | - Sun Gyun Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science
(IBS), Daejeon 305-701, Korea
| | - Seung Min Um
- Department of Biological Sciences, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Seok-kyu Kwon
- Department of Biological Sciences, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Myoung-Hwan Kim
- Department of Physiology, Seoul National University College of
Medicine, Seoul 110-799, Republic of Korea
- Seoul National University Bundang Hospital, Seongnam, Gyeonggi
463-707, Republic of Korea
| | - Junyeop Daniel Roh
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science
(IBS), Daejeon 305-701, Korea
| | - Jooyeon Woo
- Department of Biological Sciences, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Heejung Jun
- Brain and Cognitive Sciences, College of Natural Sciences, Seoul
National University, Seoul 151-747, Korea
| | - Dongmin Lee
- Department of Anatomy and Division of Brain Korea 21 Biomedical
Science, College of Medicine, Korea University, 126-1, 5-Ka, Anam-Dong, Seongbuk-Gu,
Seoul 136-705, Korea
| | - Won Mah
- Department of Anatomy and Neurobiology, School of Dentistry,
Kyungpook National University, Daegu 700-412, Korea
| | - Hyun Kim
- Department of Anatomy and Division of Brain Korea 21 Biomedical
Science, College of Medicine, Korea University, 126-1, 5-Ka, Anam-Dong, Seongbuk-Gu,
Seoul 136-705, Korea
| | - Bong-Kiun Kaang
- Brain and Cognitive Sciences, College of Natural Sciences, Seoul
National University, Seoul 151-747, Korea
| | - Kwangwook Cho
- School of Clinical Sciences, Faculty of Medicine and Dentistry,
University of Bristol, Whitson street, Bristol, UK
- Centre for Synaptic Plasticity, University of Bristol, Whitson
street, Bristol, UK
| | - Jeong-Seop Rhee
- Department of Molecular Neurobiology, Max Planck Institute of
Experimental Medicine, D-37075 Göttingen, Germany
| | - Daniel Choquet
- University of Bordeaux, Interdisciplinary Institute for
Neuroscience, France; CNRS UMR 5297, F-33000 Bordeaux, France
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of
Science and Technology (KAIST), Daejeon 305-701, Korea
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science
(IBS), Daejeon 305-701, Korea
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190
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Manzo C, Garcia-Parajo MF. A review of progress in single particle tracking: from methods to biophysical insights. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:124601. [PMID: 26511974 DOI: 10.1088/0034-4885/78/12/124601] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness. The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems. Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences. SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study. In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels. We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function. The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells.
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Affiliation(s)
- Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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191
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Abstract
The local structure and composition of the outer membrane of an animal cell are important factors in the control of many membrane processes and mechanisms. These include signaling, sorting, and exo- and endocytic processes that are occurring all the time in a living cell. Paradoxically, not only are the local structure and composition of the membrane matters of much debate and discussion, the mechanisms that govern its genesis remain highly controversial. Here, we discuss a swathe of new technological advances that may be applied to understand the local structure and composition of the membrane of a living cell from the molecular scale to the scale of the whole membrane.
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Affiliation(s)
- Thomas S van Zanten
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
| | - Satyajit Mayor
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
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192
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Harkes R, Keizer VIP, Schaaf MJM, Schmidt T. Depth-of-Focus Correction in Single-Molecule Data Allows Analysis of 3D Diffusion of the Glucocorticoid Receptor in the Nucleus. PLoS One 2015; 10:e0141080. [PMID: 26555072 PMCID: PMC4640500 DOI: 10.1371/journal.pone.0141080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022] Open
Abstract
Single-molecule imaging of proteins in a 2D environment like membranes has been frequently used to extract diffusive properties of multiple fractions of receptors. In a 3D environment the apparent fractions however change with observation time due to the movements of molecules out of the depth-of-field of the microscope. Here we developed a mathematical framework that allowed us to correct for the change in fraction size due to the limited detection volume in 3D single-molecule imaging. We applied our findings on the mobility of activated glucocorticoid receptors in the cell nucleus, and found a freely diffusing fraction of 0.49±0.02. Our analysis further showed that interchange between this mobile fraction and an immobile fraction does not occur on time scales shorter than 150 ms.
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Affiliation(s)
- Rolf Harkes
- Physics of Life Processes, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
| | - Veer I. P. Keizer
- Institute of Biology Leiden (IBL), Leiden University, Leiden, The Netherlands
| | - Marcel J. M. Schaaf
- Institute of Biology Leiden (IBL), Leiden University, Leiden, The Netherlands
| | - Thomas Schmidt
- Physics of Life Processes, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands
- * E-mail:
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193
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Platonova E, Winterflood CM, Junemann A, Albrecht D, Faix J, Ewers H. Single-molecule microscopy of molecules tagged with GFP or RFP derivatives in mammalian cells using nanobody binders. Methods 2015; 88:89-97. [PMID: 26123185 DOI: 10.1016/j.ymeth.2015.06.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/03/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022] Open
Abstract
With the recent development of single-molecule localization-based superresolution microscopy, the imaging of cellular structures at a resolution below the diffraction-limit of light has become a widespread technique. While single fluorescent molecules can be resolved in the nanometer range, the delivery of these molecules to the authentic structure in the cell via traditional antibody-mediated techniques can add substantial error due to the size of the antibodies. Accurate and quantitative labeling of cellular molecules has thus become one of the bottlenecks in the race for highest resolution of target structures. Here we illustrate in detail how to use small, high affinity nanobody binders against GFP and RFP family proteins for highly generic labeling of fusion constructs with bright organic dyes. We provide detailed protocols and examples for their application in superresolution imaging and single particle tracking and demonstrate advantages over conventional labeling approaches.
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Affiliation(s)
- Evgenia Platonova
- Randall Division of Cell and Molecular Biophysics, King's College London, SE1 1UL, United Kingdom; Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Christian M Winterflood
- Randall Division of Cell and Molecular Biophysics, King's College London, SE1 1UL, United Kingdom; Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - David Albrecht
- Randall Division of Cell and Molecular Biophysics, King's College London, SE1 1UL, United Kingdom; Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Jan Faix
- Hannover Medical School, Hannover, Germany
| | - Helge Ewers
- Randall Division of Cell and Molecular Biophysics, King's College London, SE1 1UL, United Kingdom; Institute of Biochemistry, ETH Zurich, Zurich, Switzerland; Institut für Biochemie und Chemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.
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194
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Yang B, Fang CY, Chang HC, Treussart F, Trebbia JB, Lounis B. Polarization effects in lattice-STED microscopy. Faraday Discuss 2015; 184:37-49. [PMID: 26407019 DOI: 10.1039/c5fd00092k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Massive parallelization of STED-like nanoscopies is now achievable using well-designed optical lattices for state depletion. Yet, only the lattice intensity distribution was considered for the description of the super-resolved point spread function. This holds for fast-rotating fluorescent emitters. Here, we study the effects of electric field topography in lattice-STED microscopy. The dependence of the super-resolved point spread function on the number of dipoles and their orientation is investigated. Single fluorescent nano-diamonds are imaged using different optical lattice configurations and the measured resolutions are compared to theoretical simulations.
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Affiliation(s)
- B Yang
- Univ Bordeaux, LP2N, F-33405 Talence, France.
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195
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Levet F, Hosy E, Kechkar A, Butler C, Beghin A, Choquet D, Sibarita JB. SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat Methods 2015; 12:1065-71. [DOI: 10.1038/nmeth.3579] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/03/2015] [Indexed: 12/18/2022]
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196
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Wieneke R, Raulf A, Kollmannsperger A, Heilemann M, Tampé R. SLAP: Small Labeling Pair for Single-Molecule Super-Resolution Imaging. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201503215] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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197
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Wieneke R, Raulf A, Kollmannsperger A, Heilemann M, Tampé R. SLAP: Small Labeling Pair for Single-Molecule Super-Resolution Imaging. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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198
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Super-resolution microscopy approaches for live cell imaging. Biophys J 2015; 107:1777-1784. [PMID: 25418158 DOI: 10.1016/j.bpj.2014.08.028] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 11/21/2022] Open
Abstract
By delivering optical images with spatial resolutions below the diffraction limit, several super-resolution fluorescence microscopy techniques opened new opportunities to study biological structures with details approaching molecular structure sizes. They have now become methods of choice for imaging proteins and their nanoscale dynamic organizations in live cells. In this mini-review, we describe and compare the main far-field super-resolution approaches that allow studying endogenous or overexpressed proteins in live cells.
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199
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Maiti P, Manna J, McDonald MP. Merging advanced technologies with classical methods to uncover dendritic spine dynamics: A hot spot of synaptic plasticity. Neurosci Res 2015; 96:1-13. [DOI: 10.1016/j.neures.2015.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 01/08/2023]
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200
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Beheiry ME, Dahan M, Masson JB. InferenceMAP: mapping of single-molecule dynamics with Bayesian inference. Nat Methods 2015; 12:594-5. [DOI: 10.1038/nmeth.3441] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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