201
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Lauer FM, Kaemmerer E, Meckel T. Single molecule microscopy in 3D cell cultures and tissues. Adv Drug Deliv Rev 2014; 79-80:79-94. [PMID: 25453259 DOI: 10.1016/j.addr.2014.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/20/2014] [Accepted: 10/03/2014] [Indexed: 12/19/2022]
Abstract
From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy.
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Affiliation(s)
- Florian M Lauer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany
| | - Elke Kaemmerer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany; Institute of Health and Biomedical Innovation, Science and Engineering Faculty, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, 4059 QLD, Brisbane, Australia
| | - Tobias Meckel
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany.
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202
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Cui Y, Irudayaraj J. Inside single cells: quantitative analysis with advanced optics and nanomaterials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:387-407. [PMID: 25430077 DOI: 10.1002/wnan.1321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/17/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023]
Abstract
Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
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203
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Ohno M, Karagiannis P, Taniguchi Y. Protein expression analyses at the single cell level. Molecules 2014; 19:13932-47. [PMID: 25197931 PMCID: PMC6270791 DOI: 10.3390/molecules190913932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/13/2014] [Accepted: 08/29/2014] [Indexed: 01/07/2023] Open
Abstract
The central dogma of molecular biology explains how genetic information is converted into its end product, proteins, which are responsible for the phenotypic state of the cell. Along with the protein type, the phenotypic state depends on the protein copy number. Therefore, quantification of the protein expression in a single cell is critical for quantitative characterization of the phenotypic states. Protein expression is typically a dynamic and stochastic phenomenon that cannot be well described by standard experimental methods. As an alternative, fluorescence imaging is being explored for the study of protein expression, because of its high sensitivity and high throughput. Here we review key recent progresses in fluorescence imaging-based methods and discuss their application to proteome analysis at the single cell level.
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Affiliation(s)
- Masae Ohno
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center, RIKEN Address, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Peter Karagiannis
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center, RIKEN Address, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Yuichi Taniguchi
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center, RIKEN Address, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
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204
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Coltharp C, Yang X, Xiao J. Quantitative analysis of single-molecule superresolution images. Curr Opin Struct Biol 2014; 28:112-21. [PMID: 25179006 DOI: 10.1016/j.sbi.2014.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
Abstract
This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10-50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images.
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Affiliation(s)
- Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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205
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Affiliation(s)
- Vasudha Aggarwal
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
| | - Taekjip Ha
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
- Department of Physics; University of Illinois Urbana Champaign; Urbana IL USA
- Howard Hughes Medical Institute; Urbana IL USA
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206
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Shcherbakova DM, Sengupta P, Lippincott-Schwartz J, Verkhusha VV. Photocontrollable fluorescent proteins for superresolution imaging. Annu Rev Biophys 2014; 43:303-29. [PMID: 24895855 DOI: 10.1146/annurev-biophys-051013-022836] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Superresolution fluorescence microscopy permits the study of biological processes at scales small enough to visualize fine subcellular structures that are unresolvable by traditional diffraction-limited light microscopy. Many superresolution techniques, including those applicable to live cell imaging, utilize genetically encoded photocontrollable fluorescent proteins. The fluorescence of these proteins can be controlled by light of specific wavelengths. In this review, we discuss the biochemical and photophysical properties of photocontrollable fluorescent proteins that are relevant to their use in superresolution microscopy. We then describe the recently developed photoactivatable, photoswitchable, and reversibly photoswitchable fluorescent proteins, and we detail their particular usefulness in single-molecule localization-based and nonlinear ensemble-based superresolution techniques. Finally, we discuss recent applications of photocontrollable proteins in superresolution imaging, as well as how these applications help to clarify properties of intracellular structures and processes that are relevant to cell and developmental biology, neuroscience, cancer biology and biomedicine.
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207
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Optimized two-color super resolution imaging of Drp1 during mitochondrial fission with a slow-switching Dronpa variant. Proc Natl Acad Sci U S A 2014; 111:13093-8. [PMID: 25149858 DOI: 10.1073/pnas.1320044111] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We studied the single-molecule photo-switching properties of Dronpa, a green photo-switchable fluorescent protein and a popular marker for photoactivated localization microscopy. We found the excitation light photoactivates as well as deactivates Dronpa single molecules, hindering temporal separation and limiting super resolution. To resolve this limitation, we have developed a slow-switching Dronpa variant, rsKame, featuring a V157L amino acid substitution proximal to the chromophore. The increased steric hindrance generated by the substitution reduced the excitation light-induced photoactivation from the dark to fluorescent state. To demonstrate applicability, we paired rsKame with PAmCherry1 in a two-color photoactivated localization microscopy imaging method to observe the inner and outer mitochondrial membrane structures and selectively labeled dynamin related protein 1 (Drp1), responsible for membrane scission during mitochondrial fission. We determined the diameter and length of Drp1 helical rings encircling mitochondria during fission and showed that, whereas their lengths along mitochondria were not significantly changed, their diameters decreased significantly. These results suggest support for the twistase model of Drp1 constriction, with potential loss of subunits at the helical ends.
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208
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Chozinski TJ, Gagnon LA, Vaughan JC. Twinkle, twinkle little star: photoswitchable fluorophores for super-resolution imaging. FEBS Lett 2014; 588:3603-12. [PMID: 25010263 DOI: 10.1016/j.febslet.2014.06.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 01/01/2023]
Abstract
Photoswitchable fluorescent probes are key elements of newly developed super-resolution fluorescence microscopy techniques that enable far-field interrogation of biological systems with a resolution of 50 nm or better. In contrast to most conventional fluorescence imaging techniques, the performance achievable by most super-resolution techniques is critically impacted by the photoswitching properties of the fluorophores. Here we review photoswitchable fluorophores for super-resolution imaging with discussion of the fundamental principles involved, a focus on practical implementation with available tools, and an outlook on future directions.
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Affiliation(s)
| | - Lauren A Gagnon
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
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209
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Habuchi S. Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science. Front Bioeng Biotechnol 2014; 2:20. [PMID: 25152893 PMCID: PMC4126472 DOI: 10.3389/fbioe.2014.00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.
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Affiliation(s)
- Satoshi Habuchi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Jeddah , Saudi Arabia
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210
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In cellulo evaluation of phototransformation quantum yields in fluorescent proteins used as markers for single-molecule localization microscopy. PLoS One 2014; 9:e98362. [PMID: 24915511 PMCID: PMC4051587 DOI: 10.1371/journal.pone.0098362] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule localization microscopy of biological samples requires a precise knowledge of the employed fluorescent labels. Photoactivation, photoblinking and photobleaching of phototransformable fluorescent proteins influence the data acquisition and data processing strategies to be used in (Fluorescence) Photoactivation Localization Microscopy ((F)-PALM), notably for reliable molecular counting. As these parameters might depend on the local environment, they should be measured in cellulo in biologically relevant experimental conditions. Here, we measured phototransformation quantum yields for Dendra2 fused to actin in fixed mammalian cells in typical (F)-PALM experiments. To this aim, we developed a data processing strategy based on the clustering optimization procedure proposed by Lee et al (PNAS 109, 17436–17441, 2012). Using simulations, we estimated the range of experimental parameters (molecular density, molecular orientation, background level, laser power, frametime) adequate for an accurate determination of the phototransformation yields. Under illumination at 561 nm in PBS buffer at pH 7.4, the photobleaching yield of Dendra2 fused to actin was measured to be (2.5±0.4)×10−5, whereas the blinking-off yield and thermally-activated blinking-on rate were measured to be (2.3±0.2)×10−5 and 11.7±0.5 s−1, respectively. These phototransformation yields differed from those measured in poly-vinyl alcohol (PVA) and were strongly affected by addition of the antifading agent 1,4-diazabicyclo[2.2.2]octane (DABCO). In the presence of DABCO, the photobleaching yield was reduced 2-fold, the blinking-off yield was decreased more than 3-fold, and the blinking-on rate was increased 2-fold. Therefore, DABCO largely improved Dendra2 photostability in fixed mammalian cells. These findings are consistent with redox-based bleaching and blinking mechanisms under (F)-PALM experimental conditions. Finally, the green-to-red photoconversion quantum yield of Dendra2 was estimated to be (1.4±0.6)×10−5in cellulo under 405 nm illumination.
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211
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Shivanandan A, Deschout H, Scarselli M, Radenovic A. Challenges in quantitative single molecule localization microscopy. FEBS Lett 2014; 588:3595-602. [PMID: 24928440 DOI: 10.1016/j.febslet.2014.06.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022]
Abstract
Single molecule localization microscopy (SMLM), which can provide up to an order of magnitude improvement in spatial resolution over conventional fluorescence microscopy, has the potential to be a highly useful tool for quantitative biological experiments. It has already been used for this purpose in varied fields in biology, ranging from molecular biology to neuroscience. In this review article, we briefly review the applications of SMLM in quantitative biology, and also the challenges involved and some of the solutions that have been proposed. Due to its advantages in labeling specificity and the relatively low overcounting caused by photoblinking when photo-activable fluorescent proteins (PA-FPs) are used as labels, we focus specifically on Photo-Activated Localization Microscopy (PALM), even though the ideas presented might be applicable to SMLM in general. Also, we focus on the following three quantitative measurements: single molecule counting, analysis of protein spatial distribution heterogeneity and co-localization analysis.
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Affiliation(s)
- A Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - H Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - M Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.
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212
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Adam V, Berardozzi R, Byrdin M, Bourgeois D. Phototransformable fluorescent proteins: Future challenges. Curr Opin Chem Biol 2014; 20:92-102. [DOI: 10.1016/j.cbpa.2014.05.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 01/28/2023]
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213
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Llorente-Garcia I, Lenn T, Erhardt H, Harriman OL, Liu LN, Robson A, Chiu SW, Matthews S, Willis NJ, Bray CD, Lee SH, Shin JY, Bustamante C, Liphardt J, Friedrich T, Mullineaux CW, Leake MC. Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:811-24. [DOI: 10.1016/j.bbabio.2014.01.020] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/22/2014] [Accepted: 01/30/2014] [Indexed: 02/04/2023]
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214
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Stracy M, Uphoff S, Garza de Leon F, Kapanidis AN. In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair. FEBS Lett 2014; 588:3585-94. [PMID: 24859634 DOI: 10.1016/j.febslet.2014.05.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/25/2022]
Abstract
In vivo single-molecule experiments offer new perspectives on the behaviour of DNA binding proteins, from the molecular level to the length scale of whole bacterial cells. With technological advances in instrumentation and data analysis, fluorescence microscopy can detect single molecules in live cells, opening the doors to directly follow individual proteins binding to DNA in real time. In this review, we describe key technical considerations for implementing in vivo single-molecule fluorescence microscopy. We discuss how single-molecule tracking and quantitative super-resolution microscopy can be adapted to extract DNA binding kinetics, spatial distributions, and copy numbers of proteins, as well as stoichiometries of protein complexes. We highlight experiments which have exploited these techniques to answer important questions in the field of bacterial gene regulation and transcription, as well as chromosome replication, organisation and repair. Together, these studies demonstrate how single-molecule imaging is transforming our understanding of DNA-binding proteins in cells.
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Affiliation(s)
- Mathew Stracy
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; Department of Systems Biology, Harvard Medical School, Boston, MA 02138, USA
| | - Federico Garza de Leon
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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215
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Wisniewski J, Hajj B, Chen J, Mizuguchi G, Xiao H, Wei D, Dahan M, Wu C. Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres. eLife 2014; 3:e02203. [PMID: 24844245 PMCID: PMC4067749 DOI: 10.7554/elife.02203] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.DOI: http://dx.doi.org/10.7554/eLife.02203.001.
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Affiliation(s)
- Jan Wisniewski
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Bassam Hajj
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jiji Chen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Gaku Mizuguchi
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Maxime Dahan
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Carl Wu
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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216
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Durisic N, Cuervo LL, Lakadamyali M. Quantitative super-resolution microscopy: pitfalls and strategies for image analysis. Curr Opin Chem Biol 2014; 20:22-8. [PMID: 24793374 DOI: 10.1016/j.cbpa.2014.04.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/04/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022]
Abstract
Super-resolution microscopy is an enabling technology that allows biologists to visualize cellular structures at nanometer length scales using far-field optics. To break the diffraction barrier, it is necessary to leverage the distinct molecular states of fluorescent probes. At the same time, the existence of these different molecular states and the photophysical properties of the fluorescent probes can complicate data quantification and interpretation. Here, we review the pitfalls in super-resolution data analysis that must be avoided for proper interpretation of images.
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Affiliation(s)
- Nela Durisic
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels (Barcelona), Spain
| | - Lara Laparra Cuervo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels (Barcelona), Spain
| | - Melike Lakadamyali
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels (Barcelona), Spain.
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217
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Art and artifacts in single-molecule localization microscopy: beyond attractive images. Nat Methods 2014; 11:235-8. [PMID: 24577272 DOI: 10.1038/nmeth.2852] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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218
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Jakobs S, Wurm CA. Super-resolution microscopy of mitochondria. Curr Opin Chem Biol 2014; 20:9-15. [PMID: 24769752 DOI: 10.1016/j.cbpa.2014.03.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 03/19/2014] [Accepted: 03/26/2014] [Indexed: 11/25/2022]
Abstract
Mitochondria, the powerhouses of the cell, are essential organelles in eukaryotic cells. With their complex inner architecture featuring a smooth outer and a highly convoluted inner membrane, they are challenging objects for microscopy. The diameter of mitochondria is generally close to the resolution limit of conventional light microscopy, rendering diffraction-unlimited super-resolution light microscopy (nanoscopy) for imaging submitochondrial protein distributions often mandatory. In this review, we discuss what can be expected when imaging mitochondria with conventional diffraction-limited and diffraction-unlimited microscopy. We provide an overview on recent studies using super-resolution microscopy to investigate mitochondria and discuss further developments and challenges in mitochondrial biology that might by addressed with these technologies in the future.
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Affiliation(s)
- Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany; Department of Neurology, University of Göttingen Medical School, 37073 Göttingen, Germany.
| | - Christian A Wurm
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany
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219
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Deschout H, Shivanandan A, Annibale P, Scarselli M, Radenovic A. Progress in quantitative single-molecule localization microscopy. Histochem Cell Biol 2014; 142:5-17. [PMID: 24748502 PMCID: PMC4072926 DOI: 10.1007/s00418-014-1217-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 01/10/2023]
Abstract
With the advent of single-molecule localization microscopy (SMLM) techniques, intracellular proteins can be imaged at unprecedented resolution with high specificity and contrast. These techniques can lead to a better understanding of cell functioning, as they allow, among other applications, counting the number of molecules of a protein specie in a single cell, studying the heterogeneity in protein spatial organization, and probing the spatial interactions between different protein species. However, the use of these techniques for accurate quantitative measurements requires corrections for multiple inherent sources of error, including: overcounting due to multiple localizations of a single fluorophore (i.e., photoblinking), undercounting caused by incomplete photoconversion, uncertainty in the localization of single molecules, sample drift during the long imaging time, and inaccurate image registration in the case of dual-color imaging. In this paper, we review recent efforts that address some of these sources of error in quantitative SMLM and give examples in the context of photoactivated localization microscopy (PALM).
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Affiliation(s)
- H. Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A. Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - P. Annibale
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Biomedical Engineering Department, University of California, Irvine, CA USA
| | - M. Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A. Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
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220
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Fukuoka H, Sagawa T, Inoue Y, Takahashi H, Ishijima A. Direct Imaging of Intracellular Signaling Components That Regulate Bacterial Chemotaxis. Sci Signal 2014; 7:ra32. [DOI: 10.1126/scisignal.2004963] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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221
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Genovese D, Rampazzo E, Bonacchi S, Montalti M, Zaccheroni N, Prodi L. Energy transfer processes in dye-doped nanostructures yield cooperative and versatile fluorescent probes. NANOSCALE 2014; 6:3022-3036. [PMID: 24531884 DOI: 10.1039/c3nr05599j] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fast and efficient energy transfer among dyes confined in nanocontainers provides the basis of outstanding functionalities in new-generation luminescent probes. This feature article provides an overview of recent research achievements on luminescent Pluronic-Silica NanoParticles (PluS NPs), a class of extremely monodisperse core-shell nanoparticles whose design can be easily tuned to match specific needs for diverse applications based on luminescence, and that have already been successfully tested in in vivo imaging. An outline of their outstanding properties, such as tuneability, bright and photoswitchable fluorescence and electrochemiluminescence, will be supported by a critical discussion of our recent works in this field. Furthermore, novel data and simulations will be presented to (i) thoroughly examine common issues arising from the inclusion of multiple dyes in a small silica core, and (ii) show the emergence of a cooperative behaviour among embedded dyes. Such cooperative behaviour provides a handle for fine control of brightness, emission colour and self-quenching phenomena in PluS NPs, leading to significantly enhanced signal to noise ratios.
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Affiliation(s)
- Damiano Genovese
- Dipartimento di Chimica "Giacomo Ciamician", via Selmi 2, Bologna 40126, Bologna, Italy.
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222
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Grove J. Super-resolution microscopy: a virus' eye view of the cell. Viruses 2014; 6:1365-78. [PMID: 24651030 PMCID: PMC3970155 DOI: 10.3390/v6031365] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/01/2014] [Accepted: 03/11/2014] [Indexed: 12/24/2022] Open
Abstract
It is difficult to observe the molecular choreography between viruses and host cell components, as they exist on a spatial scale beyond the reach of conventional microscopy. However, novel super-resolution microscopy techniques have cast aside technical limitations to reveal a nanoscale view of virus replication and cell biology. This article provides an introduction to super-resolution imaging; in particular, localisation microscopy, and explores the application of such technologies to the study of viruses and tetraspanins, the topic of this special issue.
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Affiliation(s)
- Joe Grove
- Institute of Immunity and Transplantation, University College London, London NW3 2PF, UK.
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223
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Uphoff S, Kapanidis AN. Studying the organization of DNA repair by single-cell and single-molecule imaging. DNA Repair (Amst) 2014; 20:32-40. [PMID: 24629485 PMCID: PMC4119245 DOI: 10.1016/j.dnarep.2014.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 12/26/2022]
Abstract
Single-cell experiments to study stochastic events and heterogeneity in DNA repair. Quantifying DNA repair protein concentration, diffusion, and localization in cells. Direct observation of DNA repair using photoactivated single-molecule tracking.
DNA repair safeguards the genome against a diversity of DNA damaging agents. Although the mechanisms of many repair proteins have been examined separately in vitro, far less is known about the coordinated function of the whole repair machinery in vivo. Furthermore, single-cell studies indicate that DNA damage responses generate substantial variation in repair activities across cells. This review focuses on fluorescence imaging methods that offer a quantitative description of DNA repair in single cells by measuring protein concentrations, diffusion characteristics, localizations, interactions, and enzymatic rates. Emerging single-molecule and super-resolution microscopy methods now permit direct visualization of individual proteins and DNA repair events in vivo. We expect much can be learned about the organization of DNA repair by linking cell heterogeneity to mechanistic observations at the molecular level.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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224
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Adam V. Phototransformable fluorescent proteins: which one for which application? Histochem Cell Biol 2014; 142:19-41. [PMID: 24522394 DOI: 10.1007/s00418-014-1190-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 01/10/2023]
Abstract
In these last two decades , fluorescent proteins (FPs) have become highly valued imaging tools for cell biology, owing to their compatibility with living samples, their low levels of invasiveness and the possibility to specifically fuse them to a variety of proteins of interest. Remarkably, the recent development of phototransformable fluorescent proteins (PTFPs) has made it possible to conceive optical imaging experiments that were unimaginable only a few years ago. For example, it is nowadays possible to monitor intra- or intercellular trafficking, to optically individualize single cells in tissues or to observe single molecules in live cells. The tagging specificity brought by these genetically encoded highlighters leads to constant progress in the engineering of increasingly powerful, versatile and non-cytotoxic FPs. This review is focused on the recent developments of PTFPs and highlights their contribution to studies within cells, tissues and even living organisms. The aspects of single-molecule localization microscopy, intracellular tracking of photoactivated molecules, applications of PTFPs in biotechnology/optobiology and complementarities between PTFPs and other microscopy techniques are particularly discussed.
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Affiliation(s)
- Virgile Adam
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, F-38000, Grenoble, France,
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225
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Fricke F, Malkusch S, Wangorsch G, Greiner JF, Kaltschmidt B, Kaltschmidt C, Widera D, Dandekar T, Heilemann M. Quantitative single-molecule localization microscopy combined with rule-based modeling reveals ligand-induced TNF-R1 reorganization toward higher-order oligomers. Histochem Cell Biol 2014; 142:91-101. [DOI: 10.1007/s00418-014-1195-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2014] [Indexed: 11/27/2022]
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226
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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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227
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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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228
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Zhang H, Guo P. Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation. Methods 2014; 67:169-76. [PMID: 24440482 DOI: 10.1016/j.ymeth.2014.01.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/28/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022] Open
Abstract
Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry of molecules or subunits within biocomplexes or nanomachines at nanometer scales. Stoichiometry is determined by real-time observation of the number of descending steps resulted from the photobleaching of individual fluorophore. This technology has now been used extensively for single molecule counting of protein, RNA, and other macromolecules in a variety of complexes or nanostructures. Here, we elucidate the SMPB technology, using the counting of RNA molecules within a bacteriophage phi29 DNA-packaging biomotor as an example. The method described here can be applied to the single molecule counting of other molecules in other systems. The construction of a concise, simple and economical single molecule total internal reflection fluorescence (TIRF) microscope combining prism-type and objective-type TIRF is described. The imaging system contains a deep-cooled sensitive EMCCD camera with single fluorophore detection sensitivity, a laser combiner for simultaneous dual-color excitation, and a Dual-View™ imager to split the multiple outcome signals to different detector channels based on their wavelengths. Methodology of the single molecule photobleaching assay used to elucidate the stoichiometry of RNA on phi29 DNA packaging motor and the mechanism of protein/RNA interaction are described. Different methods for single fluorophore labeling of RNA molecules are reviewed. The process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is also described.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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229
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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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230
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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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231
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Single-molecule and single-particle imaging of molecular motors in vitro and in vivo. EXPERIENTIA SUPPLEMENTUM (2012) 2014; 105:131-59. [PMID: 25095994 DOI: 10.1007/978-3-0348-0856-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Motor proteins are multi-potent molecular machines, whose localisation, function and regulation are achieved through tightly controlled processes involving conformational changes and interactions with their tracks, cargos and binding partners. Understanding how these complex machines work requires dissection of these processes both in space and time. Complementing the traditional ensemble measurements, single-molecule assays enable the detection of rare or short-lived intermediates and molecular heterogeneities, and the measurements of subpopulation dynamics. This chapter is focusing on the fluorescence imaging of single motors and their cargo. It discusses what is required in order to achieve single-molecule imaging with high temporal and spatial resolution and how these requirements are met both in vitro and in vivo. It also presents a general overview and applied examples of the major single-molecule imaging techniques and experimental assays which have been used to study motor proteins.
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232
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Watanabe S, Lehmann M, Hujber E, Fetter RD, Richards J, Söhl-Kielczynski B, Felies A, Rosenmund C, Schmoranzer J, Jorgensen EM. Nanometer-resolution fluorescence electron microscopy (nano-EM) in cultured cells. Methods Mol Biol 2014; 1117:503-526. [PMID: 24357377 DOI: 10.1007/978-1-62703-776-1_22] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nano-resolution fluorescence electron microscopy (nano-fEM) pinpoints the location of individual proteins in electron micrographs. Plastic sections are first imaged using a super-resolution fluorescence microscope and then imaged on an electron microscope. The two images are superimposed to correlate the position of labeled proteins relative to subcellular structures. Here, we describe the method in detail and present five technical advancements: the use of uranyl acetate during the freeze-substitution to enhance the contrast of tissues and reduce the loss of fluorescence, the use of ground-state depletion instead of photoactivation for temporal control of fluorescence, the use of organic fluorophores instead of fluorescent proteins to obtain brighter fluorescence signals, the use of tissue culture cells to broaden the utility of the method, and the use of a transmission electron microscope to achieve sharper images of ultrastructure.
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Affiliation(s)
- Shigeki Watanabe
- Department of Biology, University of Utah, Salt Lake City, UT, USA
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233
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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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234
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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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235
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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: 107] [Impact Index Per Article: 9.7] [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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236
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Kurz A, Schmied JJ, Grußmayer KS, Holzmeister P, Tinnefeld P, Herten DP. Counting fluorescent dye molecules on DNA origami by means of photon statistics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:4061-4068. [PMID: 23794455 DOI: 10.1002/smll.201300619] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 06/02/2023]
Abstract
Obtaining quantitative information about molecular assemblies with high spatial and temporal resolution is a challenging task in fluorescence microscopy. Single-molecule techniques build on the ability to count molecules one by one. Here, a method is presented that extends recent approaches to analyze the statistics of coincidently emitted photons to enable reliable counting of molecules in the range of 1-20. This method does not require photochemistry such as blinking or bleaching. DNA origami structures are labeled with up to 36 dye molecules as a new evaluation tool to characterize this counting by a photon statistics approach. Labeled DNA origami has a well-defined labeling stoichiometry and ensures equal brightness for all dyes incorporated. Bias and precision of the estimating algorithm are determined, along with the minimal acquisition time required for robust estimation. Complexes containing up to 18 molecules can be investigated non-invasively within 150 ms. The method might become a quantifying add-on for confocal microscopes and could be especially powerful in combination with STED/RESOLFT-type microscopy.
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Affiliation(s)
- Anton Kurz
- Cellnetworks Cluster und Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69210 Heidelberg, Germany
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237
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Super-resolution microscopy of live cells using single molecule localization. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-6088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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238
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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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239
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Cattoni DI, Fiche JB, Valeri A, Mignot T, Nöllmann M. Super-resolution imaging of bacteria in a microfluidics device. PLoS One 2013; 8:e76268. [PMID: 24146850 PMCID: PMC3797773 DOI: 10.1371/journal.pone.0076268] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/22/2013] [Indexed: 11/18/2022] Open
Abstract
Bacteria have evolved complex, highly-coordinated, multi-component cellular engines to achieve high degrees of efficiency, accuracy, adaptability, and redundancy. Super-resolution fluorescence microscopy methods are ideally suited to investigate the internal composition, architecture, and dynamics of molecular machines and large cellular complexes. These techniques require the long-term stability of samples, high signal-to-noise-ratios, low chromatic aberrations and surface flatness, conditions difficult to meet with traditional immobilization methods. We present a method in which cells are functionalized to a microfluidics device and fluorophores are injected and imaged sequentially. This method has several advantages, as it permits the long-term immobilization of cells and proper correction of drift, avoids chromatic aberrations caused by the use of different filter sets, and allows for the flat immobilization of cells on the surface. In addition, we show that different surface chemistries can be used to image bacteria at different time-scales, and we introduce an automated cell detection and image analysis procedure that can be used to obtain cell-to-cell, single-molecule localization and dynamic heterogeneity as well as average properties at the super-resolution level.
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Affiliation(s)
- Diego I. Cattoni
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Alessandro Valeri
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Centre National de la Recherche Scientifique, Aix-Marseille University, Unité Mixte de Recherche 7283, Marseille, France
| | - Marcelo Nöllmann
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Montpellier, France
- Institut Nationale de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
- * E-mail:
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240
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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: 114] [Impact Index Per Article: 10.4] [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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241
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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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242
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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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243
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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: 180] [Impact Index Per Article: 16.4] [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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Fiche JB, Cattoni DI, Diekmann N, Langerak JM, Clerte C, Royer CA, Margeat E, Doan T, Nöllmann M. Recruitment, assembly, and molecular architecture of the SpoIIIE DNA pump revealed by superresolution microscopy. PLoS Biol 2013; 11:e1001557. [PMID: 23667326 PMCID: PMC3646729 DOI: 10.1371/journal.pbio.1001557] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/27/2013] [Indexed: 11/18/2022] Open
Abstract
Super-resolution and fluctuation microscopy in a model DNA-segregation system reveal the architecture and assembly mechanism of the motor responsible for DNA translocation during bacterial cell division. ATP-fuelled molecular motors are responsible for rapid and specific transfer of double-stranded DNA during several fundamental processes, such as cell division, sporulation, bacterial conjugation, and viral DNA transport. A dramatic example of intercompartmental DNA transfer occurs during sporulation in Bacillus subtilis, in which two-thirds of a chromosome is transported across a division septum by the SpoIIIE ATPase. Here, we use photo-activated localization microscopy, structured illumination microscopy, and fluorescence fluctuation microscopy to investigate the mechanism of recruitment and assembly of the SpoIIIE pump and the molecular architecture of the DNA translocation complex. We find that SpoIIIE assembles into ∼45 nm complexes that are recruited to nascent sites of septation, and are subsequently escorted by the constriction machinery to the center of sporulation and division septa. SpoIIIE complexes contain 47±20 SpoIIIE molecules, a majority of which are assembled into hexamers. Finally, we show that directional DNA translocation leads to the establishment of a compartment-specific, asymmetric complex that exports DNA. Our data are inconsistent with the notion that SpoIIIE forms paired DNA conducting channels across fused membranes. Rather, our results support a model in which DNA translocation occurs through an aqueous DNA-conducting pore that could be structurally maintained by the divisional machinery, with SpoIIIE acting as a checkpoint preventing membrane fusion until completion of chromosome segregation. Our findings and proposed mechanism, and our unique combination of innovating methodologies, are relevant to the understanding of bacterial cell division, and may illuminate the mechanisms of other complex machineries involved in DNA conjugation and protein transport across membranes. Molecular motors are implicated in myriad cellular processes, notably in the transcription, replication, and segregation of DNA. Segregation or packaging of DNA is essential for production of viable viral particles, proper division of bacterial cells, and production of spores. A dramatic example of this process occurs during sporulation in Bacillus subtilis, in which a large proportion of the chromosome is actively transferred across a division septum by the SpoIIIE motor protein. Here, we use advanced microscopy methods to study the mechanism of recruitment and assembly of the SpoIIIE pump and the architecture of its complex with DNA. We found that SpoIIIE complexes are recruited before the beginning of cell division, and are subsequently escorted by the constriction machinery to the center of the septum. We show that the directionality of DNA transport by SpoIIIE results in the establishment of an asymmetric complex that exports DNA into the nascent spore. Our data are inconsistent with previous models that predicted the formation of a membrane-spanning DNA-conducting channel. Instead, the greater resolution afforded by our approach supports a model in which DNA movement occurs through an open pore structurally maintained by the division apparatus, with SpoIIIE working as a checkpoint preventing membrane fusion until completion of chromosome segregation. Our findings and proposed model may illuminate the mechanisms of other complex machineries involved in DNA conjugation and protein transport across membranes.
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Affiliation(s)
- Jean-Bernard Fiche
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Diego I. Cattoni
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Nele Diekmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Julio Mateos Langerak
- Centre National de la Recherche Scientifique, Institut de Génomique Humaine, Montpellier, France
| | - Caroline Clerte
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Catherine A. Royer
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Emmanuel Margeat
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Thierry Doan
- Laboratoire de Chimie Bactérienne, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7283, Marseille, France
| | - Marcelo Nöllmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
- * E-mail:
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Tiwari DK, Nagai T. Smart fluorescent proteins: Innovation for barrier-free superresolution imaging in living cells. Dev Growth Differ 2013; 55:491-507. [DOI: 10.1111/dgd.12064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 03/06/2013] [Accepted: 03/22/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Dhermendra K. Tiwari
- The Institute of Scientific and Industrial Research; Osaka University; Mihogaoka 8-1; Ibaraki; Osaka; 567-0047; Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research; Osaka University; Mihogaoka 8-1; Ibaraki; Osaka; 567-0047; Japan
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Fürstenberg A, Heilemann M. Single-molecule localization microscopy – near-molecular spatial resolution in light microscopy with photoswitchable fluorophores. Phys Chem Chem Phys 2013; 15:14919-30. [DOI: 10.1039/c3cp52289j] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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247
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Carroll AJ. The Arabidopsis Cytosolic Ribosomal Proteome: From form to Function. FRONTIERS IN PLANT SCIENCE 2013; 4:32. [PMID: 23459595 PMCID: PMC3585428 DOI: 10.3389/fpls.2013.00032] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/10/2013] [Indexed: 05/20/2023]
Abstract
The cytosolic ribosomal proteome of Arabidopsis thaliana has been studied intensively by a range of proteomics approaches and is now one of the most well characterized eukaryotic ribosomal proteomes. Plant cytosolic ribosomes are distinguished from other eukaryotic ribosomes by unique proteins, unique post-translational modifications and an abundance of ribosomal proteins for which multiple divergent paralogs are expressed and incorporated. Study of the A. thaliana ribosome has now progressed well beyond a simple cataloging of protein parts and is focused strongly on elucidating the functions of specific ribosomal proteins, their paralogous isoforms and covalent modifications. This review summarises current knowledge concerning the Arabidopsis cytosolic ribosomal proteome and highlights potentially fruitful areas of future research in this fast moving and important area.
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Affiliation(s)
- Adam J. Carroll
- Australian Research Council Centre of Excellence in Plant Energy Biology, Australian National UniversityCanberra, ACT, Australia
- *Correspondence: Adam J. Carroll, Australian Research Council Centre of Excellence in Plant Energy Biology, Australian National University, ACT 0200, Canberra, Australia. e-mail:
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