151
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Backlund MP, Joyner R, Moerner WE. Chromosomal locus tracking with proper accounting of static and dynamic errors. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:062716. [PMID: 26172745 PMCID: PMC4533921 DOI: 10.1103/physreve.91.062716] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 05/13/2023]
Abstract
The mean-squared displacement (MSD) and velocity autocorrelation (VAC) of tracked single particles or molecules are ubiquitous metrics for extracting parameters that describe the object's motion, but they are both corrupted by experimental errors that hinder the quantitative extraction of underlying parameters. For the simple case of pure Brownian motion, the effects of localization error due to photon statistics ("static error") and motion blur due to finite exposure time ("dynamic error") on the MSD and VAC are already routinely treated. However, particles moving through complex environments such as cells, nuclei, or polymers often exhibit anomalous diffusion, for which the effects of these errors are less often sufficiently treated. We present data from tracked chromosomal loci in yeast that demonstrate the necessity of properly accounting for both static and dynamic error in the context of an anomalous diffusion that is consistent with a fractional Brownian motion (FBM). We compare these data to analytical forms of the expected values of the MSD and VAC for a general FBM in the presence of these errors.
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Affiliation(s)
- Mikael P. Backlund
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, California 94305, USA
| | - Ryan Joyner
- Department of Cell and Developmental Biology, University of California, Berkeley, California, 94720, USA
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, California 94305, USA
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152
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Kempe D, Schöne A, Fitter J, Gabba M. Accurate Fluorescence Quantum Yield Determination by Fluorescence Correlation Spectroscopy. J Phys Chem B 2015; 119:4668-72. [DOI: 10.1021/acs.jpcb.5b02170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daryan Kempe
- AG
Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52062 Aachen, Germany
| | - Antonie Schöne
- Molecular
Biophysics, Institute of Complex Systems (ICS-5), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Jörg Fitter
- AG
Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52062 Aachen, Germany
- Molecular
Biophysics, Institute of Complex Systems (ICS-5), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Matteo Gabba
- Molecular
Biophysics, Institute of Complex Systems (ICS-5), Forschungszentrum Jülich, 52428 Jülich, Germany
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153
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Intergenerational continuity of cell shape dynamics in Caulobacter crescentus. Sci Rep 2015; 5:9155. [PMID: 25778096 PMCID: PMC4894450 DOI: 10.1038/srep09155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/11/2015] [Indexed: 01/15/2023] Open
Abstract
We investigate the intergenerational shape dynamics of single Caulobacter crescentus cells using a novel combination of imaging techniques and theoretical modeling. We determine the dynamics of cell pole-to-pole lengths, cross-sectional widths, and medial curvatures from high accuracy measurements of cell contours. Moreover, these shape parameters are determined for over 250 cells across approximately 10000 total generations, which affords high statistical precision. Our data and model show that constriction is initiated early in the cell cycle and that its dynamics are controlled by the time scale of exponential longitudinal growth. Based on our extensive and detailed growth and contour data, we develop a minimal mechanical model that quantitatively accounts for the cell shape dynamics and suggests that the asymmetric location of the division plane reflects the distinct mechanical properties of the stalked and swarmer poles. Furthermore, we find that the asymmetry in the division plane location is inherited from the previous generation. We interpret these results in terms of the current molecular understanding of shape, growth, and division of C. crescentus.
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154
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Abstract
An interesting concept in the organization of cellular membranes is the proposed existence of lipid rafts. Membranes of eukaryotic cells organize signal transduction proteins into membrane rafts or lipid rafts that are enriched in particular lipids such as cholesterol and are important for the correct functionality of diverse cellular processes. The assembly of lipid rafts in eukaryotes has been considered a fundamental step during the evolution of cellular complexity, suggesting that bacteria and archaea were organisms too simple to require such a sophisticated organization of their cellular membranes. However, it was recently discovered that bacteria organize many signal transduction, protein secretion, and transport processes in functional membrane microdomains, which are equivalent to the lipid rafts of eukaryotic cells. This review contains the most significant advances during the last 4 years in understanding the structural and biological role of lipid rafts in bacteria. Furthermore, this review shows a detailed description of a number of molecular and genetic approaches related to the discovery of bacterial lipid rafts as well as an overview of the group of tentative lipid-protein and protein-protein interactions that give consistency to these sophisticated signaling platforms. Additional data suggesting that lipid rafts are widely distributed in bacteria are presented in this review. Therefore, we discuss the available techniques and optimized protocols for the purification and analysis of raft-associated proteins in various bacterial species to aid in the study of bacterial lipid rafts in other laboratories that could be interested in this topic. Overall, the discovery of lipid rafts in bacteria reveals a new level of sophistication in signal transduction and membrane organization that was unexpected for bacteria and shows that bacteria are more complex than previously appreciated.
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Affiliation(s)
- Marc Bramkamp
- Department of Biology I, University of Munich (LMU), Planegg/Martinsried, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
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155
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Wu H, Iwai N, Nakano T, Ooi Y, Ishihara S, Sano K. Route of intrabacterial nanotransportation system for CagA in Helicobacter pylori. Med Mol Morphol 2015; 48:191-203. [PMID: 25707504 DOI: 10.1007/s00795-015-0097-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Helicobacter pylori (H. pylori) possesses an intrabacterial nanotransportation system (ibNoTS) for transporting CagA and urease within the bacterial cytoplasm; this system is controlled by the extrabacterial environment. The transportation routes of the system have not yet been studied in detail. In this study, we demonstrated by immunoelectron microscopy that CagA localizes closely with the MreB filament in the bacterium, and MreB polymerization inhibitor A22 obstructs ibNoTS for CagA. These findings indicate that the route of ibNoTS for CagA is closely associated with the MreB filament. Because these phenomena were not observed in ibNoTS for urease, the route of ibNoTS for CagA is different from that of ibNoTS for urease as previously suggested. We propose that the route of ibNoTS for CagA is associated with the MreB filament in H. pylori.
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Affiliation(s)
- Hong Wu
- Project Team for Study of Nanotransportation System, Central Research Center, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan. .,Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan.
| | - Noritaka Iwai
- Project Team for Study of Nanotransportation System, Central Research Center, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan.,Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Takashi Nakano
- Project Team for Study of Nanotransportation System, Central Research Center, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan.,Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Yukimasa Ooi
- Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan.,Infection Control Office, Osaka Medical College Hospital, Osaka, Japan
| | - Sonoko Ishihara
- Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Kouichi Sano
- Project Team for Study of Nanotransportation System, Central Research Center, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan.,Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
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156
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Botchway SW, Scherer KM, Hook S, Stubbs CD, Weston E, Bisby RH, Parker AW. A series of flexible design adaptations to the Nikon E-C1 and E-C2 confocal microscope systems for UV, multiphoton and FLIM imaging. J Microsc 2015; 258:68-78. [PMID: 25664385 DOI: 10.1111/jmi.12218] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/17/2014] [Indexed: 12/16/2022]
Abstract
Multiphoton microscopy is widely employed in the life sciences using extrinsic fluorescence of low- and high-molecular weight labels with excitation and emission spectra in the visible and near infrared regions. For imaging of intrinsic and extrinsic fluorophores with excitation spectra in the ultraviolet region, multiphoton excitation with one- or two-colour lasers avoids the need for ultraviolet-transmitting excitation optics and has advantages in terms of optical penetration in the sample and reduced phototoxicity. Excitation and detection of ultraviolet emission around 300 nm and below in a typical inverted confocal microscope is more difficult and requires the use of expensive quartz optics including the objective. In this technical note we describe the adaptation of a commercial confocal microscope (Nikon, Japan E-C1 or E-C2) for versatile use with Ti-sapphire and OPO laser sources and the addition of a second detection channel that enables detection of ultraviolet fluorescence and increases detection sensitivity in a typical fluorescence lifetime imaging microscopy experiment. Results from some experiments with this setup illustrate the resulting capabilities.
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Affiliation(s)
- Stanley W Botchway
- Central Laser Facility, STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell Oxford, Didcot, UK
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157
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The essential features and modes of bacterial polar growth. Trends Microbiol 2015; 23:347-53. [PMID: 25662291 DOI: 10.1016/j.tim.2015.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/19/2014] [Accepted: 01/07/2015] [Indexed: 01/25/2023]
Abstract
Polar growth represents a surprising departure from the canonical dispersed cell growth model. However, we know relatively little of the underlying mechanisms governing polar growth or the requisite suite of factors that direct polar growth. Underscoring how classic doctrine can be turned on its head, the peptidoglycan layer of polar-growing bacteria features unusual crosslinks and in some species the quintessential cell division proteins FtsA and FtsZ are recruited to the growing poles. Remarkably, numerous medically important pathogens utilize polar growth, accentuating the need for intensive research in this area. Here we review models of polar growth in bacteria based on recent research in the Actinomycetales and Rhizobiales, with emphasis on Mycobacterium and Agrobacterium species.
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158
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Mika JT, Vanhecke A, Dedecker P, Swings T, Vangindertael J, Van den Bergh B, Michiels J, Hofkens J. A study of SeqA subcellular localization in Escherichia coli using photo-activated localization microscopy. Faraday Discuss 2015; 184:425-50. [DOI: 10.1039/c5fd00058k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Escherichia coli (E. coli) cells replicate their genome once per cell cycle to pass on genetic information to the daughter cells. The SeqA protein binds the origin of replication, oriC, after DNA replication initiation and sequesters it from new initiations in order to prevent overinitiation. Conventional fluorescence microscopy studies of SeqA localization in bacterial cells have shown that the protein is localized to discrete foci. In this study we have used photo-activated localization microscopy (PALM) to determine the localization of SeqA molecules, tagged with fluorescent proteins, with a localization precision of 20–30 nm with the aim to visualize the SeqA subcellular structures in more detail than previously possible. SeqA–PAmCherry was imaged in wild type E. coli, expressed from plasmid or genetically engineered into the bacterial genome, replacing the native seqA gene. Unsynchronized cells as well as cells with a synchronized cell cycle were imaged at various time points, in order to investigate the evolution of SeqA localization during the cell cycle. We found that SeqA indeed localized into discrete foci but these were not the only subcellular localizations of the protein. A significant amount of SeqA–PAmCherry molecules was localized outside the foci and in a fraction of cells we saw patterns indicating localization at the membrane. Using quantitative PALM, we counted protein copy numbers per cell, protein copy numbers per focus, the numbers of foci per cell and the sizes of the SeqA clusters. The data showed broad cell-to-cell variation and we did not observe a correlation between SeqA–PAmCherry protein numbers and the cell cycle under the experimental conditions of this study. The numbers of SeqA–PAmCherry molecules per focus as well as the foci sizes also showed broad distributions indicating that the foci are likely not characterized by a fixed number of molecules. We also imaged an E. coli strain devoid of the dam methylase (Δdam) and observed that SeqA–PAmCherry no longer formed foci, and was dispersed throughout the cell and localized to the plasma membrane more readily. We discuss our results in the context of the limitations of the technique.
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Affiliation(s)
- Jacek T. Mika
- Department of Chemistry
- KU Leuven
- 3001 Heverlee
- Belgium
| | | | | | - Toon Swings
- Centre of Microbial and Plant Genetics (CMPG)
- KU Leuven
- 3001 Leuven
- Belgium
| | | | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics (CMPG)
- KU Leuven
- 3001 Leuven
- Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics (CMPG)
- KU Leuven
- 3001 Leuven
- Belgium
| | - Johan Hofkens
- Department of Chemistry
- KU Leuven
- 3001 Heverlee
- Belgium
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159
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Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells. Nat Commun 2014; 5:5820. [PMID: 25520215 PMCID: PMC4284645 DOI: 10.1038/ncomms6820] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/11/2014] [Indexed: 11/26/2022] Open
Abstract
The ubiquitous sliding clamp facilitates processivity of the replicative polymerase and acts as a platform to recruit proteins involved in replication, recombination and repair. While the dynamics of the E. coli β2-sliding clamp have been characterized in vitro, its in vivo stoichiometry and dynamics remain unclear. To probe both β2-clamp dynamics and stoichiometry in live E. coli cells, we use custom-built microfluidics in combination with single-molecule fluorescence microscopy and photoactivated fluorescence microscopy. We quantify the recruitment, binding and turnover of β2-sliding clamps on DNA during replication. These quantitative in vivo results demonstrate that numerous β2-clamps in E. coli remain on the DNA behind the replication fork for a protracted period of time, allowing them to form a docking platform for other enzymes involved in DNA metabolism. DNA replication is accomplished by the replisome, a multi-protein complex that comprises the sliding clamp. Here, Moolman et al. present quantitative and dynamic measurements of the number of β2-sliding clamps at the single-cell level in live E. coli cells to shed light on key aspects of DNA replication.
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160
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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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161
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Tuson HH, Biteen JS. Unveiling the inner workings of live bacteria using super-resolution microscopy. Anal Chem 2014; 87:42-63. [PMID: 25380480 DOI: 10.1021/ac5041346] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah H Tuson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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162
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Up against the wall: is yeast cell wall integrity ensured by mechanosensing in plasma membrane microdomains? Appl Environ Microbiol 2014; 81:806-11. [PMID: 25398859 DOI: 10.1128/aem.03273-14] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Yeast cell wall integrity (CWI) signaling serves as a model of the regulation of fungal cell wall synthesis and provides the basis for the development of antifungal drugs. A set of five membrane-spanning sensors (Wsc1 to Wsc3, Mid2, and Mtl1) detect cell surface stress and commence the signaling pathway upon perturbations of either the cell wall structure or the plasma membrane. We here summarize the latest advances in the structure/function relationship primarily of the Wsc1 sensor and critically review the evidence that it acts as a mechanosensor. The relevance and physiological significance of the information obtained for the function of the other CWI sensors, as well as expected future developments, are discussed.
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163
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Lew M, Moerner WE. Azimuthal polarization filtering for accurate, precise, and robust single-molecule localization microscopy. NANO LETTERS 2014; 14:6407-13. [PMID: 25272093 PMCID: PMC4245985 DOI: 10.1021/nl502914k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/26/2014] [Indexed: 05/08/2023]
Abstract
Many single nanoemitters such as fluorescent molecules produce dipole radiation that leads to systematic position errors in both particle tracking and super-resolution microscopy. Via vectorial diffraction equations and simulations, we show that imaging only azimuthally polarized light in the microscope naturally avoids emission from the z-component of the transition dipole moment, resulting in negligible localization errors for all emitter orientations and degrees of objective lens misfocus. Furthermore, localization accuracy is maintained even in the presence of aberrations resulting from imaging in mismatched media.
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Affiliation(s)
- Matthew
D. Lew
- Departments of Chemistry and Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Departments of Chemistry and Electrical Engineering, Stanford University, Stanford, California 94305, United States
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164
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Calderon CP. Data-driven techniques for detecting dynamical state changes in noisily measured 3D single-molecule trajectories. Molecules 2014; 19:18381-98. [PMID: 25397733 PMCID: PMC6271607 DOI: 10.3390/molecules191118381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 11/16/2022] Open
Abstract
Optical microscopes and nanoscale probes (AFM, optical tweezers, etc.) afford researchers tools capable of quantitatively exploring how molecules interact with one another in live cells. The analysis of in vivo single-molecule experimental data faces numerous challenges due to the complex, crowded, and time changing environments associated with live cells. Fluctuations and spatially varying systematic forces experienced by molecules change over time; these changes are obscured by "measurement noise" introduced by the experimental probe monitoring the system. In this article, we demonstrate how the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS) of Fox et al. [IEEE Transactions on Signal Processing 59] can be used to detect both subtle and abrupt state changes in time series containing "thermal" and "measurement" noise. The approach accounts for temporal dependencies induced by random and "systematic overdamped" forces. The technique does not require one to subjectively select the number of "hidden states" underlying a trajectory in an a priori fashion. The number of hidden states is simultaneously inferred along with change points and parameters characterizing molecular motion in a data-driven fashion. We use large scale simulations to study and compare the new approach to state-of-the-art Hidden Markov Modeling techniques. Simulations mimicking single particle tracking (SPT) experiments are the focus of this study.
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165
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Möckl L, Lamb DC, Bräuchle C. Superhochauflösende Mikroskopie: Nobelpreis in Chemie 2014 für Eric Betzig, Stefan Hell und William E. Moerner. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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166
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Möckl L, Lamb DC, Bräuchle C. Super-resolved fluorescence microscopy: Nobel Prize in Chemistry 2014 for Eric Betzig, Stefan Hell, and William E. Moerner. Angew Chem Int Ed Engl 2014; 53:13972-7. [PMID: 25371081 DOI: 10.1002/anie.201410265] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/22/2022]
Abstract
A big honor for small objects: The Nobel Prize in Chemistry 2014 was jointly awarded to Eric Betzig, Stefan Hell, and William E. Moerner "for the development of super-resolved fluorescence microscopy". This Highlight describes how the field of super-resolution microscopy developed from the first detection of a single molecule in 1989 to the sophisticated techniques of today.
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Affiliation(s)
- Leonhard Möckl
- Department for Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstrasse 5-13 (E), 81377 Munich (Germany)
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167
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Widom JR, Dhakal S, Heinicke LA, Walter NG. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Arch Toxicol 2014; 88:1965-85. [PMID: 25212907 PMCID: PMC4615698 DOI: 10.1007/s00204-014-1357-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 12/22/2022]
Abstract
Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy.
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Affiliation(s)
- Julia R Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109-1055, USA
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168
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Lee MK, Rai P, Williams J, Twieg RJ, Moerner WE. Small-molecule labeling of live cell surfaces for three-dimensional super-resolution microscopy. J Am Chem Soc 2014; 136:14003-6. [PMID: 25222297 PMCID: PMC4195381 DOI: 10.1021/ja508028h] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Precise
imaging of the cell surface of fluorescently labeled bacteria
requires super-resolution methods because the size-scale of these
cells is on the order of the diffraction limit. In this work, we present
a photocontrollable small-molecule rhodamine spirolactam
emitter suitable for non-toxic and specific labeling of the outer
surface of cells for three-dimensional (3D) super-resolution (SR)
imaging. Conventional rhodamine spirolactams photoswitch
to the emitting form with UV light; however, these wavelengths can
damage cells. We extended photoswitching to visible wavelengths
>400 nm by iterative synthesis and spectroscopic characterization
to optimize the substitution on the spirolactam. Further, an N-hydroxysuccinimide-functionalized derivative enabled
covalent labeling of amines on the surface of live Caulobacter
crescentus cells. Resulting 3D SR reconstructions of the
labeled cell surface reveal uniform and specific sampling with thousands
of localizations per cell and excellent localization precision in x, y, and z. The distribution
of cell stalk lengths (a sub-diffraction-sized cellular structure)
was quantified for a mixed population of cells. Pulse-chase experiments
identified sites of cell surface growth. Covalent labeling with the
optimized rhodamine spirolactam label provides a general
strategy to study the surfaces of living cells with high specificity
and resolution down to 10–20 nm.
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Affiliation(s)
- Marissa K Lee
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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169
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Rowland MM, Schonhoft JD, McKibbin PL, David SS, Stivers JT. Microscopic mechanism of DNA damage searching by hOGG1. Nucleic Acids Res 2014; 42:9295-303. [PMID: 25016526 PMCID: PMC4132736 DOI: 10.1093/nar/gku621] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/25/2014] [Accepted: 06/26/2014] [Indexed: 01/25/2023] Open
Abstract
The DNA backbone is often considered a track that allows long-range sliding of DNA repair enzymes in their search for rare damage sites in DNA. A proposed exemplar of DNA sliding is human 8-oxoguanine ((o)G) DNA glycosylase 1 (hOGG1), which repairs mutagenic (o)G lesions in DNA. Here we use our high-resolution molecular clock method to show that macroscopic 1D DNA sliding of hOGG1 occurs by microscopic 2D and 3D steps that masquerade as sliding in resolution-limited single-molecule images. Strand sliding was limited to distances shorter than seven phosphate linkages because attaching a covalent chemical road block to a single DNA phosphate located between two closely spaced damage sites had little effect on transfers. The microscopic parameters describing the DNA search of hOGG1 were derived from numerical simulations constrained by the experimental data. These findings support a general mechanism where DNA glycosylases use highly dynamic multidimensional diffusion paths to scan DNA.
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Affiliation(s)
- Meng M Rowland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Joseph D Schonhoft
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Paige L McKibbin
- Department of Chemistry, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Sheila S David
- Department of Chemistry, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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170
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Backer AS, Moerner WE. Extending single-molecule microscopy using optical Fourier processing. J Phys Chem B 2014; 118:8313-29. [PMID: 24745862 PMCID: PMC4317050 DOI: 10.1021/jp501778z] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/17/2014] [Indexed: 12/17/2022]
Abstract
This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules.
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Affiliation(s)
- Adam S. Backer
- Institute for Computational and
Mathematical Engineering and Department of
Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Institute for Computational and
Mathematical Engineering and Department of
Chemistry, Stanford University, Stanford, California 94305, United States
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171
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Prasad S. Asymptotics of Bayesian error probability and source super-localization in three dimensions. OPTICS EXPRESS 2014; 22:16008-16028. [PMID: 24977857 DOI: 10.1364/oe.22.016008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present an asymptotic analysis of the minimum probability of error (MPE) in inferring the correct hypothesis in a Bayesian multi-hypothesis testing (MHT) formalism using many pixels of data that are corrupted by signal dependent shot noise, sensor read noise, and background illumination. We perform our analysis for a variety of combined noise and background statistics, including a pseudo-Gaussian distribution that can be employed to treat approximately the photon-counting statistics of signal and background as well as purely Gaussian sensor read-out noise and more general, exponentially peaked distributions. We subsequently evaluate both the exact and asymptotic MPE expressions for the problem of three-dimensional (3D) point source localization. We focus specifically on a recently proposed rotating-PSF imager and compare, using the MPE metric, its 3D localization performance with that of conventional and astigmatic imagers in the presence of background and sensor-noise fluctuations.
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172
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Prasad S. Asymptotics of Bayesian error probability and 2D pair superresolution. OPTICS EXPRESS 2014; 22:16029-16047. [PMID: 24977858 DOI: 10.1364/oe.22.016029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper employs a recently developed asymptotic Bayesian multi-hypothesis testing (MHT) based error analysis to treat the problem of superresolution imaging of a pair of closely spaced, equally bright point sources. The analysis exploits the notion of the minimum probability of error (MPE) in discriminating between two competing equi-probable hypotheses, a single point source of a certain brightness at the origin vs. a pair of point sources, each of half the brightness of the single source and located symmetrically about the origin, as the distance between the source pair is changed. For a Gaussian point-spread function (PSF), the analysis makes predictions on the scaling of the minimum source strength, expressed in units of photon number, required to disambiguate the pair as a function of their separation in both the signal-dominated and background-dominated regimes. Certain logarithmic corrections to the quartic scaling of the minimum source strength with respect to the degree of superresolution characterize the signal-dominated regime, while the scaling is purely quadratic in the background-dominated regime. For the Gaussian PSF, general results for arbitrary strengths of the signal, background, and sensor noise levels are also presented.
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173
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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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174
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Calderon CP, Weiss LE, Moerner WE. Robust hypothesis tests for detecting statistical evidence of two-dimensional and three-dimensional interactions in single-molecule measurements. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052705. [PMID: 25353827 DOI: 10.1103/physreve.89.052705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Indexed: 06/04/2023]
Abstract
Experimental advances have improved the two- (2D) and three-dimensional (3D) spatial resolution that can be extracted from in vivo single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of forces experienced by biomolecules in their native environment. Situations where such force information is relevant range from mitosis to directed transport of protein cargo along cytoskeletal structures. Models commonly applied to quantify single-molecule dynamics assume that effective forces and velocity in the x,y (or x,y,z) directions are statistically independent, but this assumption is physically unrealistic in many situations. We present a hypothesis testing approach capable of determining if there is evidence of statistical dependence between positional coordinates in experimentally measured trajectories; if the hypothesis of independence between spatial coordinates is rejected, then a new model accounting for 2D (3D) interactions can and should be considered. Our hypothesis testing technique is robust, meaning it can detect interactions, even if the noise statistics are not well captured by the model. The approach is demonstrated on control simulations and on experimental data (directed transport of intraflagellar transport protein 88 homolog in the primary cilium).
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Affiliation(s)
| | - Lucien E Weiss
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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175
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Donczew R, Zakrzewska-Czerwińska J, Zawilak-Pawlik A. Beyond DnaA: the role of DNA topology and DNA methylation in bacterial replication initiation. J Mol Biol 2014; 426:2269-82. [PMID: 24747048 DOI: 10.1016/j.jmb.2014.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 12/31/2022]
Abstract
The replication of chromosomal DNA is a fundamental event in the life cycle of every cell. The first step of replication, initiation, is controlled by multiple factors to ensure only one round of replication per cell cycle. The process of initiation has been described most thoroughly for bacteria, especially Escherichia coli, and involves many regulatory proteins that vary considerably between different species. These proteins control the activity of the two key players of initiation in bacteria: the initiator protein DnaA and the origin of chromosome replication (oriC). Factors involved in the control of the availability, activity, or oligomerization of DnaA during initiation are generally regarded as the most important and thus have been thoroughly characterized. Other aspects of the initiation process, such as origin accessibility and susceptibility to unwinding, have been less explored. However, recent findings indicate that these factors have a significant role. This review focuses on DNA topology, conformation, and methylation as important factors that regulate the initiation process in bacteria. We present a comprehensive summary of the factors involved in the modulation of DNA topology, both locally at oriC and more globally at the level of the entire chromosome. We show clearly that the conformation of oriC dynamically changes, and control of this conformation constitutes another, important factor in the regulation of bacterial replication initiation. Furthermore, the process of initiation appears to be associated with the dynamics of the entire chromosome and this association is an important but largely unexplored phenomenon.
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Affiliation(s)
- Rafał Donczew
- Institute of Immunology and Experimental Therapy, Department of Microbiology, Polish Academy of Sciences, Weigla 12, 53-114 Wrocław, Poland.
| | - Jolanta Zakrzewska-Czerwińska
- Institute of Immunology and Experimental Therapy, Department of Microbiology, Polish Academy of Sciences, Weigla 12, 53-114 Wrocław, Poland; Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-138 Wrocław, Poland.
| | - Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy, Department of Microbiology, Polish Academy of Sciences, Weigla 12, 53-114 Wrocław, Poland.
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