351
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Horrocks MH, Palayret M, Klenerman D, Lee SF. The changing point-spread function: single-molecule-based super-resolution imaging. Histochem Cell Biol 2014; 141:577-85. [PMID: 24509806 DOI: 10.1007/s00418-014-1186-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 11/29/2022]
Abstract
Over the past decade, many techniques for imaging systems at a resolution greater than the diffraction limit have been developed. These methods have allowed systems previously inaccessible to fluorescence microscopy to be studied and biological problems to be solved in the condensed phase. This brief review explains the basic principles of super-resolution imaging in both two and three dimensions, summarizes recent developments, and gives examples of how these techniques have been used to study complex biological systems.
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Affiliation(s)
- Mathew H Horrocks
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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352
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Quantitative analysis of three-dimensional fluorescence localization microscopy data. Biophys J 2014; 105:L05-7. [PMID: 23870275 DOI: 10.1016/j.bpj.2013.05.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/20/2013] [Accepted: 05/31/2013] [Indexed: 11/22/2022] Open
Abstract
Identifying the three-dimensional molecular organization of subcellular organelles in intact cells has been challenging to date. Here we present an analysis approach for three-dimensional localization microscopy that can not only identify subcellular objects below the diffraction limit but also quantify their shape and volume. This approach is particularly useful to map the topography of the plasma membrane and measure protein distribution within an undulating membrane.
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353
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Tabarin T, Pageon SV, Bach CTT, Lu Y, O'Neill GM, Gooding JJ, Gaus K. Insights into Adhesion Biology Using Single-Molecule Localization Microscopy. Chemphyschem 2014; 15:606-18. [DOI: 10.1002/cphc.201301041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Indexed: 01/07/2023]
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354
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Nanoscale effects of ethanol and naltrexone on protein organization in the plasma membrane studied by photoactivated localization microscopy (PALM). PLoS One 2014; 9:e87225. [PMID: 24503624 PMCID: PMC3913589 DOI: 10.1371/journal.pone.0087225] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 12/20/2013] [Indexed: 12/04/2022] Open
Abstract
Background Ethanol affects the signaling of several important neurotransmitter and neuromodulator systems in the CNS. It has been recently proposed that ethanol alters the dynamic lateral organization of proteins and lipids in the plasma membrane, thereby affecting surface receptor-mediated cellular signaling. Our aims are to establish whether pharmacologically relevant levels of ethanol can affect the lateral organization of plasma membrane and cytoskeletal proteins at the nanoscopic level, and investigate the relevance of such perturbations for mu-opioid receptor (MOP) function. Methodology/Principal Findings We used Photoactivated Localization Microscopy with pair-correlation analysis (pcPALM), a quantitative fluorescence imaging technique with high spatial resolution (15–25 nm) and single-molecule sensitivity, to study ethanol effects on protein organization in the plasma membrane. We observed that short (20 min) exposure to 20 and 40 mM ethanol alters protein organization in the plasma membrane of cells that harbor endogenous MOPs, causing a rearrangement of the lipid raft marker glycosylphosphatidylinositol (GPI). These effects could be largely occluded by pretreating the cells with the MOP antagonist naltrexone (200 nM for 3 hours). In addition, ethanol induced pronounced actin polymerization, leading to its partial co-localization with GPI. Conclusions/Significance Pharmacologically relevant levels of ethanol alter the lateral organization of GPI-linked proteins and induce actin cytoskeleton reorganization. Pretreatment with the MOP antagonist naltrexone is protective against ethanol action and significantly reduces the extent to which ethanol remodels the lateral organization of lipid-rafts-associated proteins in the plasma membrane. Super-resolution pcPALM reveals details of ethanol action at the nanoscale level, giving new mechanistic insight on the cellular and molecular mechanisms of its action.
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355
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Piehler J. Spectroscopic techniques for monitoring protein interactions in living cells. Curr Opin Struct Biol 2014; 24:54-62. [DOI: 10.1016/j.sbi.2013.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 12/21/2022]
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356
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Valley CC, Lidke KA, Lidke DS. The spatiotemporal organization of ErbB receptors: insights from microscopy. Cold Spring Harb Perspect Biol 2014; 6:cshperspect.a020735. [PMID: 24370847 DOI: 10.1101/cshperspect.a020735] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Signal transduction is regulated by protein-protein interactions. In the case of the ErbB family of receptor tyrosine kinases (RTKs), the precise nature of these interactions remains a topic of debate. In this review, we describe state-of-the-art imaging techniques that are providing new details into receptor dynamics, clustering, and interactions. We present the general principles of these techniques, their limitations, and the unique observations they provide about ErbB spatiotemporal organization.
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Affiliation(s)
- Christopher C Valley
- Department of Pathology and the Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico 87131
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357
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Long BR, Robinson DC, Zhong H. Subdiffractive microscopy: techniques, applications, and challenges. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014; 6:151-68. [PMID: 24443323 DOI: 10.1002/wsbm.1259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 01/30/2023]
Abstract
Cellular processes rely on the precise orchestration of signaling and effector molecules in space and time, yet it remains challenging to gain a comprehensive picture of the molecular organization underlying most basic biological functions. This organization often takes place at length scales below the resolving power of conventional microscopy. In recent years, several 'superresolution' fluorescence microscopic techniques have emerged that can surpass the diffraction limit of conventional microscopy by a factor of 2-20. These methods have been used to reveal previously unknown organization of macromolecular complexes and cytoskeletal structures. The resulting high-resolution view of molecular organization and dynamics is already changing our understanding of cellular processes at the systems level. However, current subdiffractive microscopic techniques are not without limitations; challenges remain to be overcome before these techniques achieve their full potential. Here, we introduce three primary types of subdiffractive microscopic techniques, consider their current limitations and challenges, and discuss recent biological applications.
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Affiliation(s)
- Brian R Long
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
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358
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Sengupta P, van Engelenburg SB, Lippincott-Schwartz J. Superresolution imaging of biological systems using photoactivated localization microscopy. Chem Rev 2014; 114:3189-202. [PMID: 24417572 DOI: 10.1021/cr400614m] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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359
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Durisic N, Laparra-Cuervo L, Sandoval-Álvarez Á, Borbely JS, Lakadamyali M. Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate. Nat Methods 2014; 11:156-62. [DOI: 10.1038/nmeth.2784] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 11/22/2013] [Indexed: 12/17/2022]
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360
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Truong-Quang BA, Lenne PF. Membrane microdomains: from seeing to understanding. FRONTIERS IN PLANT SCIENCE 2014; 5:18. [PMID: 24600455 PMCID: PMC3927121 DOI: 10.3389/fpls.2014.00018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/15/2014] [Indexed: 05/08/2023]
Abstract
The plasma membrane is a composite material, which forms a semi-permeable barrier and an interface for communication between the intracellular and extracellular environments. While the existence of membrane microdomains with nanoscale organization has been proved by the application of numerous biochemical and physical methods, direct observation of these heterogeneities using optical microscopy has remained challenging for decades, partly due to the optical diffraction limit, which restricts the resolution to ~200 nm. During the past years, new optical methods which circumvent this fundamental limit have emerged. Not only do these techniques allow direct visualization, but also quantitative characterization of nanoscopic structures. We discuss how these emerging optical methods have refined our knowledge of membrane microdomains and how they may shed light on the basic principles of the mesoscopic membrane organization.
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Affiliation(s)
| | - Pierre-François Lenne
- *Correspondence: Pierre-François Lenne, Developmental Biology Institute of Marseilles, UMR 7288 CNRS, Aix-Marseille Université, 13288 Marseille Cedex 9, France e-mail:
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361
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Visualizing the Ultrastructures and Dynamics of Synapses by Single-Molecule Nanoscopy. NEUROMETHODS 2014. [DOI: 10.1007/978-1-4614-9179-8_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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362
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Shtengel G, Wang Y, Zhang Z, Goh WI, Hess HF, Kanchanawong P. Imaging cellular ultrastructure by PALM, iPALM, and correlative iPALM-EM. Methods Cell Biol 2014; 123:273-94. [PMID: 24974033 DOI: 10.1016/b978-0-12-420138-5.00015-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Many biomolecules in cells can be visualized with high sensitivity and specificity by fluorescence microscopy. However, the resolution of conventional light microscopy is limited by diffraction to ~200-250 nm laterally and >500 nm axially. Here, we describe superresolution methods based on single-molecule localization analysis of photoswitchable fluorophores (PALM: photoactivated localization microscopy) as well as our recent three-dimensional (3D) method (iPALM: interferometric PALM) that allows imaging with a resolution better than 20 nm in all three dimensions. Considerations for their implementations, applications to multicolor imaging, and a recent development that extend the imaging depth of iPALM to ~750 nm are discussed. As the spatial resolution of superresolution fluorescence microscopy converges with that of electron microscopy (EM), direct imaging of the same specimen using both approaches becomes feasible. This could be particularly useful for cross validation of experiments, and thus, we also describe recent methods that were developed for correlative superresolution fluorescence and EM.
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Affiliation(s)
- Gleb Shtengel
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Yilin Wang
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Zhen Zhang
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Wah Ing Goh
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Harald F Hess
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore
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363
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Ishitsuka Y, Nienhaus K, Nienhaus GU. Photoactivatable fluorescent proteins for super-resolution microscopy. Methods Mol Biol 2014; 1148:239-60. [PMID: 24718806 DOI: 10.1007/978-1-4939-0470-9_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Super-resolution fluorescence microscopy techniques such as simulated emission depletion (STED) microscopy and photoactivated localization microscopy (PALM) allow substructures, organelles or even proteins within a cell to be imaged with a resolution far below the diffraction limit of ~200 nm. The development of advanced fluorescent proteins, especially photoactivatable fluorescent proteins of the GFP family, has greatly contributed to the successful application of these techniques to live-cell imaging. Here, we will illustrate how two fluorescent proteins with different photoactivation mechanisms can be utilized in high resolution dual color PALM imaging to obtain insights into a cellular process that otherwise would not be accessible. We will explain how to set up and perform the experiment and how to use our latest software "a-livePALM" for fast and efficient data analysis.
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Affiliation(s)
- Yuji Ishitsuka
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, Karlsruhe, 76131, Germany
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364
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van de Linde S, Sauer M. How to switch a fluorophore: from undesired blinking to controlled photoswitching. Chem Soc Rev 2014; 43:1076-87. [DOI: 10.1039/c3cs60195a] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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365
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Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc Natl Acad Sci U S A 2013; 111:681-6. [PMID: 24379392 DOI: 10.1073/pnas.1318496111] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy numbers of biomolecules in highly dense structures. Here we report a reflected light-sheet superresolution microscopy method capable of imaging inside the mammalian nucleus with superior signal-to-background ratio as well as molecular counting with single-copy accuracy. Using reflected light-sheet superresolution microscopy, we probed the spatial organization of transcription by RNA polymerase II (RNAP II) molecules and quantified their global extent of clustering inside the mammalian nucleus. Spatiotemporal clustering analysis that leverages on the blinking photophysics of specific organic dyes showed that the majority (>70%) of the transcription foci originate from single RNAP II molecules, and no significant clustering between RNAP II molecules was detected within the length scale of the reported diameter of "transcription factories." Colocalization measurements of RNAP II molecules equally labeled by two spectrally distinct dyes confirmed the primarily unclustered distribution, arguing against a prevalent existence of transcription factories in the mammalian nucleus as previously proposed. The methods developed in our study pave the way for quantitative mapping and stoichiometric characterization of key biomolecular species deep inside mammalian cells.
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366
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Gudheti MV, Curthoys NM, Gould TJ, Kim D, Gunewardene MS, Gabor KA, Gosse JA, Kim CH, Zimmerberg J, Hess ST. Actin mediates the nanoscale membrane organization of the clustered membrane protein influenza hemagglutinin. Biophys J 2013; 104:2182-92. [PMID: 23708358 DOI: 10.1016/j.bpj.2013.03.054] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 03/15/2013] [Accepted: 03/20/2013] [Indexed: 12/22/2022] Open
Abstract
The influenza viral membrane protein hemagglutinin (HA) is required at high concentrations on virion and host-cell membranes for infectivity. Because the role of actin in membrane organization is not completely understood, we quantified the relationship between HA and host-cell actin at the nanoscale. Results obtained using superresolution fluorescence photoactivation localization microscopy (FPALM) in nonpolarized cells show that HA clusters colocalize with actin-rich membrane regions (ARMRs). Individual molecular trajectories in live cells indicate restricted HA mobility in ARMRs, and actin disruption caused specific changes to HA clustering. Surprisingly, the actin-binding protein cofilin was excluded from some regions within several hundred nanometers of HA clusters, suggesting that HA clusters or adjacent proteins within the same clusters influence local actin structure. Thus, with the use of imaging, we demonstrate a dynamic relationship between glycoprotein membrane organization and the actin cytoskeleton at the nanoscale.
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Affiliation(s)
- Manasa V Gudheti
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
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367
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Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat Rev Genet 2013; 15:69-81. [PMID: 24342920 DOI: 10.1038/nrg3623] [Citation(s) in RCA: 333] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The interaction of regulatory proteins with the complex nucleoprotein structures that are found in mammalian cells involves chromatin reorganization at multiple levels. Mechanisms that support these transitions are complex on many timescales, which range from milliseconds to minutes or hours. In this Review, we discuss emerging concepts regarding the function of regulatory elements in living cells. We also explore the involvement of these dynamic and stochastic processes in the evolution of fluctuating transcriptional activity states that are now commonly reported in eukaryotic systems.
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368
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Owen DM, Gaus K. Imaging lipid domains in cell membranes: the advent of super-resolution fluorescence microscopy. FRONTIERS IN PLANT SCIENCE 2013; 4:503. [PMID: 24376453 PMCID: PMC3859905 DOI: 10.3389/fpls.2013.00503] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/24/2013] [Indexed: 05/08/2023]
Abstract
The lipid bilayer of model membranes, liposomes reconstituted from cell lipids, and plasma membrane vesicles and spheres can separate into two distinct liquid phases to yield lipid domains with liquid-ordered and liquid-disordered properties. These observations are the basis of the lipid raft hypothesis that postulates the existence of cholesterol-enriched ordered-phase lipid domains in cell membranes that could regulate protein mobility, localization and interaction. Here we review the evidence that nano-scaled lipid complexes and meso-scaled lipid domains exist in cell membranes and how new fluorescence microscopy techniques that overcome the diffraction limit provide new insights into lipid organization in cell membranes.
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Affiliation(s)
- Dylan M. Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College LondonLondon, UK
| | - Katharina Gaus
- Centre for Vascular Research and Australian Centre for Nanomedicine, University of New South WalesSydney, NSW, Australia
- *Correspondence: Katharina Gaus, Centre for Vascular Research, University of New South Wales, Sydney, NSW 2052, Australia e-mail:
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369
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Curthoys NM, Mlodzianoski MJ, Kim D, Hess ST. Simultaneous multicolor imaging of biological structures with fluorescence photoactivation localization microscopy. J Vis Exp 2013:e50680. [PMID: 24378721 DOI: 10.3791/50680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Localization-based super resolution microscopy can be applied to obtain a spatial map (image) of the distribution of individual fluorescently labeled single molecules within a sample with a spatial resolution of tens of nanometers. Using either photoactivatable (PAFP) or photoswitchable (PSFP) fluorescent proteins fused to proteins of interest, or organic dyes conjugated to antibodies or other molecules of interest, fluorescence photoactivation localization microscopy (FPALM) can simultaneously image multiple species of molecules within single cells. By using the following approach, populations of large numbers (thousands to hundreds of thousands) of individual molecules are imaged in single cells and localized with a precision of ~10-30 nm. Data obtained can be applied to understanding the nanoscale spatial distributions of multiple protein types within a cell. One primary advantage of this technique is the dramatic increase in spatial resolution: while diffraction limits resolution to ~200-250 nm in conventional light microscopy, FPALM can image length scales more than an order of magnitude smaller. As many biological hypotheses concern the spatial relationships among different biomolecules, the improved resolution of FPALM can provide insight into questions of cellular organization which have previously been inaccessible to conventional fluorescence microscopy. In addition to detailing the methods for sample preparation and data acquisition, we here describe the optical setup for FPALM. One additional consideration for researchers wishing to do super-resolution microscopy is cost: in-house setups are significantly cheaper than most commercially available imaging machines. Limitations of this technique include the need for optimizing the labeling of molecules of interest within cell samples, and the need for post-processing software to visualize results. We here describe the use of PAFP and PSFP expression to image two protein species in fixed cells. Extension of the technique to living cells is also described.
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370
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Wu J, Gao J, Qi M, Wang J, Cai M, Liu S, Hao X, Jiang J, Wang H. High-efficiency localization of Na(+)-K(+) ATPases on the cytoplasmic side by direct stochastic optical reconstruction microscopy. NANOSCALE 2013; 5:11582-6. [PMID: 24113832 DOI: 10.1039/c3nr03665k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We describe a concise and effective strategy towards precisely mapping Na(+)-K(+) ATPases on the cytoplasmic side of cell membranes by direct stochastic optical reconstruction microscopy (dSTORM). We found that most Na(+)-K(+) ATPases are localized in different sizes of clusters on human red blood cell (hRBC) membranes, revealed by Ripley's K-function analysis. Further evidence that cholesterol depletion causes the dispersion of Na(+)-K(+) ATPase clusters indicates that such clusters could be localized in cholesterol-enriched domains. Our results suggest that Na(+)-K(+) ATPases might aggregate within the lipid rafts to fulfill their functions.
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Affiliation(s)
- Jiazhen Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China.
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371
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Truan Z, Tarancón Díez L, Bönsch C, Malkusch S, Endesfelder U, Munteanu M, Hartley O, Heilemann M, Fürstenberg A. Quantitative morphological analysis of arrestin2 clustering upon G protein-coupled receptor stimulation by super-resolution microscopy. J Struct Biol 2013; 184:329-34. [DOI: 10.1016/j.jsb.2013.09.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 01/14/2023]
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372
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Zuidscherwoude M, de Winde CM, Cambi A, van Spriel AB. Microdomains in the membrane landscape shape antigen-presenting cell function. J Leukoc Biol 2013; 95:251-63. [PMID: 24168856 DOI: 10.1189/jlb.0813440] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The plasma membrane of immune cells is a highly organized cell structure that is key to the initiation and regulation of innate and adaptive immune responses. It is well-established that immunoreceptors embedded in the plasma membrane have a nonrandom spatial distribution that is important for coupling to components of intracellular signaling cascades. In the last two decades, specialized membrane microdomains, including lipid rafts and TEMs, have been identified. These domains are preformed structures ("physical entities") that compartmentalize proteins, lipids, and signaling molecules into multimolecular assemblies. In APCs, different microdomains containing immunoreceptors (MHC proteins, PRRs, integrins, among others) have been reported that are imperative for efficient pathogen recognition, the formation of the immunological synapse, and subsequent T cell activation. In addition, recent work has demonstrated that tetraspanin microdomains and lipid rafts are involved in BCR signaling and B cell activation. Research into the molecular mechanisms underlying membrane domain formation is fundamental to a comprehensive understanding of membrane-proximal signaling and APC function. This review will also discuss the advances in the microscopy field for the visualization of the plasma membrane, as well as the recent progress in targeting microdomains as novel, therapeutic approach for infectious and malignant diseases.
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Affiliation(s)
- Malou Zuidscherwoude
- 1.Nijmegen Centre for Molecular Life Sciences/278 TIL, Radboud University Medical Centre, Geert Grooteplein 28, 6525GA, Nijmegen, The Netherlands.
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373
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Dietz MS, Fricke F, Krüger CL, Niemann HH, Heilemann M. Receptor-Ligand Interactions: Binding Affinities Studied by Single-Molecule and Super-Resolution Microscopy on Intact Cells. Chemphyschem 2013; 15:671-6. [DOI: 10.1002/cphc.201300755] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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374
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Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling. Proc Natl Acad Sci U S A 2013; 110:18519-24. [PMID: 24158481 DOI: 10.1073/pnas.1318188110] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The RAF serine/threonine kinases regulate cell growth through the MAPK pathway, and are targeted by small-molecule RAF inhibitors (RAFis) in human cancer. It is now apparent that protein multimers play an important role in RAF activation and tumor response to RAFis. However, the exact stoichiometry and cellular location of these multimers remain unclear because of the lack of technologies to visualize them. In the present work, we demonstrate that photoactivated localization microscopy (PALM), in combination with quantitative spatial analysis, provides sufficient resolution to directly visualize protein multimers in cells. Quantitative PALM imaging showed that CRAF exists predominantly as cytoplasmic monomers under resting conditions but forms dimers as well as trimers and tetramers at the cell membrane in the presence of active RAS. In contrast, N-terminal truncated CRAF (CatC) lacking autoinhibitory domains forms constitutive dimers and occasional tetramers in the cytoplasm, whereas a CatC mutant with a disrupted CRAF-CRAF dimer interface does not. Finally, artificially forcing CRAF to the membrane by fusion to a RAS CAAX motif induces multimer formation but activates RAF/MAPK only if the dimer interface is intact. Together, these quantitative results directly confirm the existence of RAF dimers and potentially higher-order multimers and their involvement in cell signaling, and showed that RAF multimer formation can result from multiple mechanisms and is a critical but not sufficient step for RAF activation.
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375
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Soares H, Henriques R, Sachse M, Ventimiglia L, Alonso MA, Zimmer C, Thoulouze MI, Alcover A. Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse. ACTA ACUST UNITED AC 2013; 210:2415-33. [PMID: 24101378 PMCID: PMC3804939 DOI: 10.1084/jem.20130150] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of signaling nanoterritories at the T cell immunological synapse is controlled by the coordinated trafficking and fusion of specific vesicles containing the signaling molecules Lck, LAT, and TCRζ. How the vesicular traffic of signaling molecules contributes to T cell receptor (TCR) signal transduction at the immunological synapse remains poorly understood. In this study, we show that the protein tyrosine kinase Lck, the TCRζ subunit, and the adapter LAT traffic through distinct exocytic compartments, which are released at the immunological synapse in a differentially regulated manner. Lck vesicular release depends on MAL protein. Synaptic Lck, in turn, conditions the calcium- and synaptotagmin-7–dependent fusion of LAT and TCRζ containing vesicles. Fusion of vesicles containing TCRζ and LAT at the synaptic membrane determines not only the nanoscale organization of phosphorylated TCRζ, ZAP70, LAT, and SLP76 clusters but also the presence of phosphorylated LAT and SLP76 in interacting signaling nanoterritories. This mechanism is required for priming IL-2 and IFN-γ production and may contribute to fine-tuning T cell activation breadth in response to different stimulatory conditions.
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Affiliation(s)
- Helena Soares
- Institut Pasteur, Department of Immunology, Lymphocyte Cell Biology Unit, F-75724 Paris, France
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376
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Sahl SJ, Moerner WE. Super-resolution fluorescence imaging with single molecules. Curr Opin Struct Biol 2013; 23:778-87. [PMID: 23932284 PMCID: PMC3805708 DOI: 10.1016/j.sbi.2013.07.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 07/05/2013] [Indexed: 11/16/2022]
Abstract
The ability to detect, image and localize single molecules optically with high spatial precision by their fluorescence enables an emergent class of super-resolution microscopy methods which have overcome the longstanding diffraction barrier for far-field light-focusing optics. Achieving spatial resolutions of 20-40nm or better in both fixed and living cells, these methods are currently being established as powerful tools for minimally-invasive spatiotemporal analysis of structural details in cellular processes which benefit from enhanced resolution. Briefly covering the basic principles, this short review then summarizes key recent developments and application examples of two-dimensional and three-dimensional (3D) multi-color techniques and faster time-lapse schemes. The prospects for quantitative imaging - in terms of improved ability to correct for dipole-emission-induced systematic localization errors and to provide accurate counts of molecular copy numbers within nanoscale cellular domains - are discussed.
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Affiliation(s)
- Steffen J Sahl
- Department of Chemistry, Stanford University, Stanford, CA, USA
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377
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Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory. Proc Natl Acad Sci U S A 2013; 110:16015-20. [PMID: 24043832 DOI: 10.1073/pnas.1309676110] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cells tightly regulate trafficking of intracellular organelles, but a deeper understanding of this process is technically limited by our inability to track the molecular composition of individual organelles below the diffraction limit in size. Here we develop a technique for intracellularly calibrated superresolution microscopy that can measure the size of individual organelles as well as accurately count absolute numbers of molecules, by correcting for undercounting owing to immature fluorescent proteins and overcounting owing to fluorophore blinking. Using this technique, we characterized the size of individual vesicles in the yeast endocytic pathway and the number of accessible phosphatidylinositol 3-phosphate binding sites they contain. This analysis reveals a characteristic vesicle maturation trajectory of composition and size with both stochastic and regulated components. The trajectory displays some cell-to-cell variability, with smaller variation between organelles within the same cell. This approach also reveals mechanistic information on the order of events in this trajectory: Colocalization analysis with known markers of different vesicle maturation stages shows that phosphatidylinositol 3-phosphate production precedes fusion into larger endosomes. This single-organelle analysis can potentially be applied to a range of small organelles to shed light on their precise composition/structure relationships, the dynamics of their regulation, and the noise in these processes.
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378
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Buss J, Coltharp C, Huang T, Pohlmeyer C, Wang SC, Hatem C, Xiao J. In vivo organization of the FtsZ-ring by ZapA and ZapB revealed by quantitative super-resolution microscopy. Mol Microbiol 2013; 89:1099-120. [PMID: 23859153 PMCID: PMC3894617 DOI: 10.1111/mmi.12331] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2013] [Indexed: 12/13/2022]
Abstract
In most bacterial cells, cell division is dependent on the polymerization of the FtsZ protein to form a ring-like structure (Z-ring) at the midcell. Despite its essential role, the molecular architecture of the Z-ring remains elusive. In this work we examine the roles of two FtsZ-associated proteins, ZapA and ZapB, in the assembly dynamics and structure of the Z-ring in Escherichia coli cells. In cells deleted of zapA or zapB, we observed abnormal septa and highly dynamic FtsZ structures. While details of these FtsZ structures are difficult to discern under conventional fluorescence microscopy, single-molecule-based super-resolution imaging method Photoactivated Localization Microscopy (PALM) reveals that these FtsZ structures arise from disordered arrangements of FtsZ clusters. Quantitative analysis finds these clusters are larger and comprise more molecules than a single FtsZ protofilament, and likely represent a distinct polymeric species that is inherent to the assembly pathway of the Z-ring. Furthermore, we find these clusters are not due to the loss of ZapB-MatP interaction in ΔzapA and ΔzapB cells. Our results suggest that the main function of ZapA and ZapB in vivo may not be to promote the association of individual protofilaments but to align FtsZ clusters that consist of multiple FtsZ protofilaments.
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Affiliation(s)
- Jackson Buss
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Tao Huang
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Chris Pohlmeyer
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shih-Chin Wang
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christine Hatem
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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379
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Kim D, Curthoys NM, Parent MT, Hess ST. Bleed-through correction for rendering and correlation analysis in multi-colour localization microscopy. JOURNAL OF OPTICS (2010) 2013; 15:094011. [PMID: 26185614 PMCID: PMC4501387 DOI: 10.1088/2040-8978/15/9/094011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Multi-colour localization microscopy has enabled sub-diffraction studies of colocalization between multiple biological species and quantification of their correlation at length scales previously inaccessible with conventional fluorescence microscopy. However, bleed-through, or misidentification of probe species, creates false colocalization and artificially increases certain types of correlation between two imaged species, affecting the reliability of information provided by colocalization and quantified correlation. Despite the potential risk of these artefacts of bleed-through, neither the effect of bleed-through on correlation nor methods of its correction in correlation analyses has been systematically studied at typical rates of bleed-through reported to affect multi-colour imaging. Here, we present a reliable method of bleed-through correction applicable to image rendering and correlation analysis of multi-colour localization microscopy. Application of our bleed-through correction shows our method accurately corrects the artificial increase in both types of correlations studied (Pearson coefficient and pair correlation), at all rates of bleed-through tested, in all types of correlations examined. In particular, anti-correlation could not be quantified without our bleed-through correction, even at rates of bleed-through as low as 2%. Demonstrated with dichroic-based multi-colour FPALM here, our presented method of bleed-through correction can be applied to all types of localization microscopy (PALM, STORM, dSTORM, GSDIM, etc.), including both simultaneous and sequential multi-colour modalities, provided the rate of bleed-through can be reliably determined.
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Affiliation(s)
- Dahan Kim
- Department of Physics and Astronomy, 5709 Bennett Hall, University of Maine, Orono, Maine 04469, USA
| | - Nikki M. Curthoys
- Department of Physics and Astronomy, 5709 Bennett Hall, University of Maine, Orono, Maine 04469, USA
| | - Matthew T. Parent
- Department of Physics and Astronomy, 5709 Bennett Hall, University of Maine, Orono, Maine 04469, USA
| | - Samuel T. Hess
- Department of Physics and Astronomy, 5709 Bennett Hall, University of Maine, Orono, Maine 04469, USA
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380
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Enlightening G-protein-coupled receptors on the plasma membrane using super-resolution photoactivated localization microscopy. Biochem Soc Trans 2013; 41:191-6. [PMID: 23356282 DOI: 10.1042/bst20120250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The possibility to visualize and image the arrangement of proteins within the cell at the molecular level has always been an attraction for scientists in biological research. In particular, for signalling molecules such as GPCRs (G-protein-coupled receptors), the existence of protein aggregates such as oligomers or clusters has been the topic of extensive debate. One of the reasons for this lively argument is that the molecular size is below the diffraction-limited resolution of the conventional microscopy, precluding the direct visualization of protein super-structures. On the other hand, new super-resolution microscopy techniques, such as the PALM (photoactivated localization microscopy), allow the limit of the resolution power of conventional optics to be broken and the localization of single molecules to be determined with a precision of 10-20 nm, close to their molecular size. The application of super-resolution microscopy to study the spatial and temporal organization of GPCRs has brought new insights into receptor arrangement on the plasma membrane. Furthermore, the use of this powerful microscopy technique as a quantitative tool opens up the possibility for investigating and quantifying the number of molecules in biological assemblies and determining the protein stoichiometry in signalling complexes.
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381
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van de Linde S, Aufmkolk S, Franke C, Holm T, Klein T, Löschberger A, Proppert S, Wolter S, Sauer M. Investigating cellular structures at the nanoscale with organic fluorophores. ACTA ACUST UNITED AC 2013; 20:8-18. [PMID: 23352135 DOI: 10.1016/j.chembiol.2012.11.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 09/10/2012] [Accepted: 11/02/2012] [Indexed: 01/31/2023]
Abstract
Super-resolution fluorescence imaging can provide insights into cellular structure and organization with a spatial resolution approaching virtually electron microscopy. Among all the different super-resolution methods single-molecule-based localization microscopy could play an exceptional role in the future because it can provide quantitative information, for example, the absolute number of biomolecules interacting in space and time. Here, small organic fluorophores are a decisive factor because they exhibit high fluorescence quantum yields and photostabilities, thus enabling their localization with nanometer precision. Besides past progress, problems with high-density and specific labeling, especially in living cells, and the lack of suited standards and long-term continuous imaging methods with minimal photodamage render the exploitation of the full potential of the method currently challenging.
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Affiliation(s)
- Sebastian van de Linde
- Department of Biotechnology and Biophysics, Biozentrum, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
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382
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Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, Dugast-Darzacq C, Hajj B, Dahan M, Darzacq X. Real-time dynamics of RNA polymerase II clustering in live human cells. Science 2013; 341:664-7. [PMID: 23828889 DOI: 10.1126/science.1239053] [Citation(s) in RCA: 341] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 (± 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell's ability to effect rapid response to external signals. Our results suggest that transient crowding of enzymes may aid in rate-limiting steps of gene regulation.
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Affiliation(s)
- Ibrahim I Cisse
- Functional Imaging of Transcription, CNRS UMR8197, Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, 75005 France
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383
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Ultrahigh-resolution imaging reveals formation of neuronal SNARE/Munc18 complexes in situ. Proc Natl Acad Sci U S A 2013; 110:E2812-20. [PMID: 23821748 DOI: 10.1073/pnas.1310654110] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Membrane fusion is mediated by complexes formed by SNAP-receptor (SNARE) and Secretory 1 (Sec1)/mammalian uncoordinated-18 (Munc18)-like (SM) proteins, but it is unclear when and how these complexes assemble. Here we describe an improved two-color fluorescence nanoscopy technique that can achieve effective resolutions of up to 7.5-nm full width at half maximum (3.2-nm localization precision), limited only by stochastic photon emission from single molecules. We use this technique to dissect the spatial relationships between the neuronal SM protein Munc18-1 and SNARE proteins syntaxin-1 and SNAP-25 (25 kDa synaptosome-associated protein). Strikingly, we observed nanoscale clusters consisting of syntaxin-1 and SNAP-25 that contained associated Munc18-1. Rescue experiments with syntaxin-1 mutants revealed that Munc18-1 recruitment to the plasma membrane depends on the Munc18-1 binding to the N-terminal peptide of syntaxin-1. Our results suggest that in a primary neuron, SNARE/SM protein complexes containing syntaxin-1, SNAP-25, and Munc18-1 are preassembled in microdomains on the presynaptic plasma membrane. Our superresolution imaging method provides a framework for investigating interactions between the synaptic vesicle fusion machinery and other subcellular systems in situ.
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384
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Li Y, Ishitsuka Y, Hedde PN, Nienhaus GU. Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization. ACS NANO 2013; 7:5207-14. [PMID: 23647371 DOI: 10.1021/nn4009388] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In localization-based super-resolution microscopy, individual fluorescent markers are stochastically photoactivated and subsequently localized within a series of camera frames, yielding a final image with a resolution far beyond the diffraction limit. Yet, before localization can be performed, the subregions within the frames where the individual molecules are present have to be identified-oftentimes in the presence of high background. In this work, we address the importance of reliable molecule identification for the quality of the final reconstructed super-resolution image. We present a fast and robust algorithm (a-livePALM) that vastly improves the molecule detection efficiency while minimizing false assignments that can lead to image artifacts.
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Affiliation(s)
- Yiming Li
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
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385
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Lando D, Endesfelder U, Berger H, Subramanian L, Dunne PD, McColl J, Klenerman D, Carr AM, Sauer M, Allshire RC, Heilemann M, Laue ED. Quantitative single-molecule microscopy reveals that CENP-A(Cnp1) deposition occurs during G2 in fission yeast. Open Biol 2013; 2:120078. [PMID: 22870388 PMCID: PMC3411111 DOI: 10.1098/rsob.120078] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 06/08/2012] [Indexed: 11/30/2022] Open
Abstract
The inheritance of the histone H3 variant CENP-A in nucleosomes at centromeres following DNA replication is mediated by an epigenetic mechanism. To understand the process of epigenetic inheritance, or propagation of histones and histone variants, as nucleosomes are disassembled and reassembled in living eukaryotic cells, we have explored the feasibility of exploiting photo-activated localization microscopy (PALM). PALM of single molecules in living cells has the potential to reveal new concepts in cell biology, providing insights into stochastic variation in cellular states. However, thus far, its use has been limited to studies in bacteria or to processes occurring near the surface of eukaryotic cells. With PALM, one literally observes and ‘counts’ individual molecules in cells one-by-one and this allows the recording of images with a resolution higher than that determined by the diffraction of light (the so-called super-resolution microscopy). Here, we investigate the use of different fluorophores and develop procedures to count the centromere-specific histone H3 variant CENP-ACnp1 with single-molecule sensitivity in fission yeast (Schizosaccharomyces pombe). The results obtained are validated by and compared with ChIP-seq analyses. Using this approach, CENP-ACnp1 levels at fission yeast (S. pombe) centromeres were followed as they change during the cell cycle. Our measurements show that CENP-ACnp1 is deposited solely during the G2 phase of the cell cycle.
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Affiliation(s)
- David Lando
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1EW, UK
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386
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Phosphorylation of the Bin, Amphiphysin, and RSV161/167 (BAR) domain of ACAP4 regulates membrane tubulation. Proc Natl Acad Sci U S A 2013; 110:11023-8. [PMID: 23776207 DOI: 10.1073/pnas.1217727110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ArfGAP With Coiled-Coil, Ankyrin Repeat And PH Domains 4 (ACAP4) is an ADP-ribosylation factor 6 (ARF6) GTPase-activating protein essential for EGF-elicited cell migration. However, how ACAP4 regulates membrane dynamics and curvature in response to EGF stimulation is unknown. Here, we show that phosphorylation of the N-terminal region of ACAP4, named the Bin, Amphiphysin, and RSV161/167 (BAR) domain, at Tyr34 is necessary for EGF-elicited membrane remodeling. Domain structure analysis demonstrates that the BAR domain regulates membrane curvature. EGF stimulation of cells causes phosphorylation of ACAP4 at Tyr34, which subsequently promotes ACAP4 homodimer curvature. The phospho-mimicking mutant of ACAP4 demonstrates lipid-binding activity and tubulation in vitro, and ARF6 enrichment at the membrane is associated with ruffles of EGF-stimulated cells. Expression of the phospho-mimicking ACAP4 mutant promotes ARF6-dependent cell migration. Thus, the results present a previously undefined mechanism by which EGF-elicited phosphorylation of the BAR domain controls ACAP4 molecular plasticity and plasma membrane dynamics during cell migration.
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387
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Fluorescence nanoscopy. Methods and applications. J Chem Biol 2013; 6:97-120. [PMID: 24432127 DOI: 10.1007/s12154-013-0096-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/05/2013] [Indexed: 12/30/2022] Open
Abstract
Fluorescence nanoscopy refers to the experimental techniques and analytical methods used for fluorescence imaging at a resolution higher than conventional, diffraction-limited, microscopy. This review explains the concepts behind fluorescence nanoscopy and focuses on the latest and promising developments in acquisition techniques, labelling strategies to obtain highly detailed super-resolved images and in the quantitative methods to extract meaningful information from them.
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388
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Nieuwenhuizen RPJ, Lidke KA, Bates M, Puig DL, Grünwald D, Stallinga S, Rieger B. Measuring image resolution in optical nanoscopy. Nat Methods 2013; 10:557-62. [PMID: 23624665 PMCID: PMC4149789 DOI: 10.1038/nmeth.2448] [Citation(s) in RCA: 456] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 03/21/2013] [Indexed: 12/12/2022]
Abstract
Resolution in optical nanoscopy (or super-resolution microscopy) depends on the localization uncertainty and density of single fluorescent labels and on the sample's spatial structure. Currently there is no integral, practical resolution measure that accounts for all factors. We introduce a measure based on Fourier ring correlation (FRC) that can be computed directly from an image. We demonstrate its validity and benefits on two-dimensional (2D) and 3D localization microscopy images of tubulin and actin filaments. Our FRC resolution method makes it possible to compare achieved resolutions in images taken with different nanoscopy methods, to optimize and rank different emitter localization and labeling strategies, to define a stopping criterion for data acquisition, to describe image anisotropy and heterogeneity, and even to estimate the average number of localizations per emitter. Our findings challenge the current focus on obtaining the best localization precision, showing instead how the best image resolution can be achieved as fast as possible.
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389
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Banterle N, Bui KH, Lemke EA, Beck M. Fourier ring correlation as a resolution criterion for super-resolution microscopy. J Struct Biol 2013; 183:363-367. [PMID: 23684965 DOI: 10.1016/j.jsb.2013.05.004] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 05/07/2013] [Indexed: 11/16/2022]
Abstract
Optical nanoscopy techniques using localization based image reconstruction, also termed super-resolution microscopy (SRM), have become a standard tool to bypass the diffraction limit in fluorescence light microscopy. The localization precision measured for the detected fluorophores is commonly used to describe the maximal attainable resolution. However, this measure takes not all experimental factors, which impact onto the finally achieved resolution, into account. Several other methods to measure the resolution of super-resolved images were previously suggested, typically relying on intrinsic standards, such as molecular rulers, or on a priori knowledge about the specimen, e.g. its spatial frequency content. Here we show that Fourier ring correlation provides an easy-to-use, laboratory consistent standard for measuring the resolution of SRM images. We provide a freely available software tool that combines resolution measurement with image reconstruction.
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Affiliation(s)
- Niccolò Banterle
- EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Khanh Huy Bui
- EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Martin Beck
- EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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390
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Clustering and mobility of HIV-1 Env at viral assembly sites predict its propensity to induce cell-cell fusion. J Virol 2013; 87:7516-25. [PMID: 23637402 DOI: 10.1128/jvi.00790-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
HIV-1 Env mediates virus attachment to and fusion with target cell membranes, and yet, while Env is still situated at the plasma membrane of the producer cell and before its incorporation into newly formed particles, Env already interacts with the viral receptor CD4 on target cells, thus enabling the formation of transient cell contacts that facilitate the transmission of viral particles. During this first encounter with the receptor, Env must not induce membrane fusion, as this would prevent the producer cell and the target cell from separating upon virus transmission, but how Env's fusion activity is controlled remains unclear. To gain a better understanding of the Env regulation that precedes viral transmission, we examined the nanoscale organization of Env at the surface of producer cells. Utilizing superresolution microscopy (stochastic optical reconstruction microscopy [STORM]) and fluorescence recovery after photobleaching (FRAP), we quantitatively assessed the clustering and dynamics of Env upon its arrival at the plasma membrane. We found that Gag assembly induced the aggregation of small Env clusters into larger domains and that these domains were completely immobile. Truncation of the cytoplasmic tail (CT) of Env abrogated Gag's ability to induce Env clustering and restored Env mobility at assembly sites, both of which correlated with increased Env-induced fusion of infected and uninfected cells. Hence, while Env trapping by Gag secures Env incorporation into viral particles, Env clustering and its sequestration at assembly sites likely also leads to the repression of its fusion function, and thus, by preventing the formation of syncytia, Gag helps to secure efficient transfer of viral particles to target cells.
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391
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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392
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Alivisatos AP, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X. Nanotools for neuroscience and brain activity mapping. ACS NANO 2013; 7:1850-66. [PMID: 23514423 PMCID: PMC3665747 DOI: 10.1021/nn4012847] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.
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Affiliation(s)
- A. Paul Alivisatos
- Department of Chemistry, University of California, Berkeley, California 94720, and Lawrence Berkeley Laboratory, Berkeley, California 94720-1460
| | - Anne M. Andrews
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Psychiatry, and Semel Institute for Neuroscience & Human Behavior, Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095
| | - Edward S. Boyden
- Media Laboratory, Department of Biological Engineering, Brain and Cognitive Sciences, and McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | | | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University, Boston, Massachusetts 02115
| | - Karl Deisseroth
- Howard Hughes Medical Institute, Stanford University, Stanford California 94305
- Departments of Bioengineering and Psychiatry, Stanford University, Stanford California 94305
| | - John P. Donoghue
- Department of Neuroscience, Division of Engineering, Department of Computer Science, Brown University, Providence, Rhode Island 02912
| | - Scott E. Fraser
- Departments of Biological Sciences, Biomedical Engineering, Physiology and Biophysics, Stem Cell Biology and Regenerative Medicine, and Pediatrics, Radiology and Ophthalmology, University of Southern California, Los Angeles, California 90089
| | - Jennifer Lippincott-Schwartz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Sotiris Masmanidis
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Neurobiology, University of California, Los Angeles, California 90095
- Address correspondence to , , ,
| | - Paul L. McEuen
- Department of Physics, Laboratory of Atomic and Solid State Physics, and Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853
| | - Arto V. Nurmikko
- Department of Physics and Division of Engineering, Brown University, Providence, Rhode Island 02912
| | - Hongkun Park
- Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138
| | - Darcy S. Peterka
- Howard Hughes Medical Institute and Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Clay Reid
- Allen Institute for Brain Science, Seattle, Washington 98103
| | - Michael L. Roukes
- Kavli Nanoscience Institute, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Departments of Physics, Applied Physics, and Bioengineering, California Institute of Technology, MC 149-33, Pasadena, California 91125
| | - Axel Scherer
- Kavli Nanoscience Institute, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Departments of Electrical Engineering, Applied Physics, and Physics, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Address correspondence to , , ,
| | - Mark Schnitzer
- Howard Hughes Medical Institute, Stanford University, Stanford California 94305
- Departments of Applied Physics and Biology, James H. Clark Center, Stanford University, Stanford, California 94305
| | - Terrence J. Sejnowski
- Howard Hughes Medical Institute, Computational Neurobiology Laboratory, Salk Institute, La Jolla, California 92037, and Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, New York 10027
| | - Doris Tsao
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Gina Turrigiano
- Department of Biology and Center for Complex Systems, Brandeis University, Waltham, Massachusetts 02254
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Chemistry & Biochemistry, Department of Materials Science & Engineering, University of California, Los Angeles, California 90095
- Address correspondence to , , ,
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853
| | - Rafael Yuste
- Howard Hughes Medical Institute and Department of Biological Sciences, Columbia University, New York, New York 10027
- Kavli Institute for Brain Science, Columbia University, New York, New York 10027
- Address correspondence to , , ,
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Departments of Chemistry and Chemical Biology and Physics, Harvard University, Cambridge, Massachusetts 02138
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393
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Coelho M, Maghelli N, Tolić-Nørrelykke IM. Single-molecule imagingin vivo: the dancing building blocks of the cell. Integr Biol (Camb) 2013; 5:748-58. [DOI: 10.1039/c3ib40018b] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Miguel Coelho
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. Tel: +49 351 210 2691
| | - Nicola Maghelli
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. Tel: +49 351 210 2691
| | - Iva M. Tolić-Nørrelykke
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. Tel: +49 351 210 2691
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394
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Zooming in on biological processes with fluorescence nanoscopy. Curr Opin Biotechnol 2013; 24:646-53. [PMID: 23498844 DOI: 10.1016/j.copbio.2013.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 02/17/2013] [Accepted: 02/18/2013] [Indexed: 11/23/2022]
Abstract
Fluorescence nanoscopy enables the study of biological phenomena at nanometer scale spatial resolution. Recent biological studies using fluorescence nanoscopy have showcased the ability of these techniques to directly observe protein organization, subcellular molecular interactions, structural dynamics, electrical signaling, and diffusion of cytosolic proteins at unprecedented spatial resolution. Super-resolution imaging techniques critically rely on bright fluorescent probes such as organic dyes or fluorescent proteins. Recently, these methods have been extended to live cells and multicolor, three-dimensional imaging, thereby providing exquisite spatiotemporal resolutions of the order of 10-20 nm and 1-2 s for subcellular imaging. Further improvements in image processing algorithms, labeling techniques, correlative microscopy, and development of advanced fluorescent probes will be required to achieve true molecular-scale resolution using these techniques.
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395
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Sengupta P, Van Engelenburg S, Lippincott-Schwartz J. Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 2013; 23:1092-102. [PMID: 23237943 DOI: 10.1016/j.devcel.2012.09.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease.
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Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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396
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Kamiyama D, Huang B. Development in the STORM. Dev Cell 2013; 23:1103-10. [PMID: 23237944 DOI: 10.1016/j.devcel.2012.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/01/2012] [Accepted: 10/01/2012] [Indexed: 12/13/2022]
Abstract
The recent invention of superresolution microscopy has brought up much excitement in the biological research community. Here, we focus on stochastic optical reconstruction microscopy/photoactivated localization microscopy (STORM/PALM) to discuss the challenges in applying superresolution microscopy to the study of developmental biology, including tissue imaging, sample preparation artifacts, and image interpretation. We also summarize new opportunities that superresolution microscopy could bring to the field of developmental biology.
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Affiliation(s)
- Daichi Kamiyama
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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397
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Seong J, Wang Y, Kinoshita T, Maeda Y. Implications of lipid moiety in oligomerization and immunoreactivities of GPI-anchored proteins. J Lipid Res 2013; 54:1077-91. [PMID: 23378600 DOI: 10.1194/jlr.m034421] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI) enriches GPI-anchored proteins (GPI-AP) in lipid rafts by intimate interaction of its lipid moiety with sphingolipids and cholesterol. In addition to such lipid-lipid interactions, it has been reported that GPI may interact with protein moiety linked to GPI and affect protein conformations because GPI delipidation reduced immunoreactivities of protein. Here, we report that GPI-APs that have not undergone fatty acid remodeling exhibit reduced immunoreactivities in Western blotting, similar to delipidated proteins, compared with normal remodeled GPI-APs. In contrast, immunostaining in flow cytometry and immunoprecipitation did not show significant differences between remodeled and unremodeled GPI-APs. Moreover, detection with premixed primary/secondary antibody complexes or Fab fragments eliminated this difference in Western blotting. These results indicate that normally remodeled GPI enhanced oligomerization of GPI-APs and that inefficient oligomerization of unremodeled GPI-APs was responsible for reduced immunoreactivities. Moreover, the reduction in immunoreactivities of delipidated GPI-APs was most likely caused by the same effect. Finally, by chemical cross-linking of surface proteins in living cells and cell killing assay using a pore-forming bacterial toxin, we showed that enhanced oligomerization by GPI-remodeling occurs under a physiological membrane environment. Thus, this study clarifies the significance of GPI fatty acid remodeling in oligomerization of GPI-APs and provides useful information for technical studies of these cell components.
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Affiliation(s)
- Jihyoun Seong
- Department of Immunoregulation, Research Institute for Microbial Diseases, and Laboratory of Immunoglycobiology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
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398
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Sengupta P, Jovanovic-Talisman T, Lippincott-Schwartz J. Quantifying spatial organization in point-localization superresolution images using pair correlation analysis. Nat Protoc 2013; 8:345-54. [PMID: 23348362 PMCID: PMC3925398 DOI: 10.1038/nprot.2013.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The distinctive distributions of proteins within subcellular compartments both at steady state and during signaling events have essential roles in cell function. Here we describe a method for delineating the complex arrangement of proteins within subcellular structures visualized using point-localization superresolution (PL-SR) imaging. The approach, called pair correlation photoactivated localization microscopy (PC-PALM), uses a pair-correlation algorithm to precisely identify single molecules in PL-SR imaging data sets, and it is used to decipher quantitative features of protein organization within subcellular compartments, including the existence of protein clusters and the size, density and number of proteins in these clusters. We provide a step-by-step protocol for PC-PALM, illustrating its analysis capability for four plasma membrane proteins tagged with photoactivatable GFP (PAGFP). The experimental steps for PC-PALM can be carried out in 3 d and the analysis can be done in ∼6-8 h. Researchers need to have substantial experience in single-molecule imaging and statistical analysis to conduct the experiments and carry out this analysis.
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Affiliation(s)
- Prabuddha Sengupta
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tijana Jovanovic-Talisman
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jennifer Lippincott-Schwartz
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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399
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Abstract
Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures.
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Affiliation(s)
- Pakorn Kanchanawong
- Department of Bioengineering, Mechanobiology Institute, National University of Singapore, Singapore, Singapore
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400
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Biochemical and imaging methods to study receptor membrane organization and association with lipid rafts. Methods Cell Biol 2013; 117:105-22. [PMID: 24143974 DOI: 10.1016/b978-0-12-408143-7.00006-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lipid rafts, cell membrane domains with unique composition and properties, modulate the membrane distribution of receptors and signaling molecules facilitating the assembly of active signaling platforms. However, the underlying mechanisms that link signal transduction and lipid rafts are not fully understood, mainly because of the transient nature of these membrane assemblies. Several methods have been used to study the association of membrane receptors with lipid rafts. In the first part of this chapter, a description of how biochemical methods such as raft disruption by cholesterol depletion agents are useful in qualitatively establishing protein association with lipid rafts is presented. The second part of this chapter is dedicated to imaging techniques used to study membrane receptor organization and lipid rafts. We cover conventional approaches such as confocal microscopy to advanced imaging techniques such as homo-FRET microscopy and superresolution methods. For each technique described, their advantages and drawbacks are discussed.
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