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Sharma N, van Oijen AM, Spenkelink LM, Mueller SH. Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:595-614. [PMID: 39328428 PMCID: PMC11423410 DOI: 10.1021/cbmi.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 09/28/2024]
Abstract
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
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Affiliation(s)
- Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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2
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Zulueta Diaz YDLM, Arnspang EC. Super-resolution microscopy to study membrane nanodomains and transport mechanisms in the plasma membrane. Front Mol Biosci 2024; 11:1455153. [PMID: 39290992 PMCID: PMC11405310 DOI: 10.3389/fmolb.2024.1455153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Biological membranes are complex, heterogeneous, and dynamic systems that play roles in the compartmentalization and protection of cells from the environment. It is still a challenge to elucidate kinetics and real-time transport routes for molecules through biological membranes in live cells. Currently, by developing and employing super-resolution microscopy; increasing evidence indicates channels and transporter nano-organization and dynamics within membranes play an important role in these regulatory mechanisms. Here we review recent advances and discuss the major advantages and disadvantages of using super-resolution microscopy to investigate protein organization and transport within plasma membranes.
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Affiliation(s)
| | - Eva C Arnspang
- Department of Green Technology, SDU Biotechnology, University of Southern Denmark, Odense, Denmark
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3
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Maillard J, Grassin E, Bestsennaia E, Silaghi M, Straková K, García-Calvo J, Sakai N, Matile S, Fürstenberg A. Single-Molecule Localization Microscopy and Tracking with a Fluorescent Mechanosensitive Probe. J Phys Chem B 2024; 128:7997-8006. [PMID: 39119910 DOI: 10.1021/acs.jpcb.4c02506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
A milestone in optical imaging of mechanical forces in cells has been the development of the family of flipper fluorescent probes able to report membrane tension noninvasively in living cells through their fluorescence lifetime. The specifically designed Flipper-CF3 probe with an engineered inherent blinking mechanism was recently introduced for super-resolution fluorescence microscopy of lipid ordered membranes but was too dim to be detected in lipid disordered membranes at the single-molecule level (García-Calvo, J. J. Am. Chem. Soc. 2020, 142(28), 12034-12038). We show here that the original and commercially available probe Flipper-TR is compatible with single-molecule based super-resolution imaging and resolves both liquid ordered and liquid disordered membranes of giant unilamellar vesicles below the diffraction limit. Single probe molecules were additionally tracked in lipid bilayers, enabling to distinguish membranes of varying composition from the diffusion coefficient of the probe. Differences in brightness between Flipper-CF3 and Flipper-TR originate in their steady-state absorption and fluorescence properties. The general compatibility of the Flipper-TR scaffold with single-molecule detection is further shown in super-resolution experiments with targetable Flipper-TR derivatives.
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Affiliation(s)
- Jimmy Maillard
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Ewa Grassin
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Ekaterina Bestsennaia
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Melinda Silaghi
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Karolina Straková
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - José García-Calvo
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Alexandre Fürstenberg
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
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4
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Liu Y, van den Ent F, Löwe J. Filament structure and subcellular organization of the bacterial intermediate filament-like protein crescentin. Proc Natl Acad Sci U S A 2024; 121:e2309984121. [PMID: 38324567 PMCID: PMC10873595 DOI: 10.1073/pnas.2309984121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/28/2023] [Indexed: 02/09/2024] Open
Abstract
The protein crescentin is required for the crescent shape of the freshwater bacterium Caulobacter crescentus (vibrioides). Crescentin forms a filamentous structure on the inner, concave side of the curved cells. It shares features with eukaryotic intermediate filament (IF) proteins, including the formation of static filaments based on long and parallel coiled coils, the protein's length, structural roles in cell and organelle shape determination and the presence of a coiled coil discontinuity called the "stutter." Here, we have used electron cryomicroscopy (cryo-EM) to determine the structure of the full-length protein and its filament, exploiting a crescentin-specific nanobody. The filament is formed by two strands, related by twofold symmetry, that each consist of two dimers, resulting in an octameric assembly. Crescentin subunits form longitudinal contacts head-to-head and tail-to-tail, making the entire filament non-polar. Using in vivo site-directed cysteine cross-linking, we demonstrated that contacts observed in the in vitro filament structure exist in cells. Electron cryotomography (cryo-ET) of cells expressing crescentin showed filaments on the concave side of the curved cells, close to the inner membrane, where they form a band. When comparing with current models of IF proteins and their filaments, which are also built from parallel coiled coil dimers and lack overall polarity, it emerges that IF proteins form head-to-tail longitudinal contacts in contrast to crescentin and hence several inter-dimer contacts in IFs have no equivalents in crescentin filaments. Our work supports the idea that intermediate filament-like proteins achieve their shared polymerization and mechanical properties through a variety of filament architectures.
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Affiliation(s)
- Yue Liu
- Medical Research Council Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, CambridgeCB2 0QH, United Kingdom
| | - Fusinita van den Ent
- Medical Research Council Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, CambridgeCB2 0QH, United Kingdom
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, CambridgeCB2 0QH, United Kingdom
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5
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Wu T, King MR, Farag M, Pappu RV, Lew MD. Single fluorogen imaging reveals distinct environmental and structural features of biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525727. [PMID: 36747818 PMCID: PMC9900924 DOI: 10.1101/2023.01.26.525727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Recent computations suggest that biomolecular condensates that form via macromolecular phase separation are network fluids featuring spatially inhomogeneous organization of the underlying molecules. Computations also point to unique conformations of molecules at condensate interfaces. Here, we test these predictions using high-resolution structural characterizations of condensates formed by intrinsically disordered prion-like low complexity domains (PLCDs). We leveraged the localization and orientational preferences of freely diffusing fluorogens and the solvatochromic effect whereby specific fluorogens are turned on in response to the physic-chemical properties of condensate microenvironments to facilitate single-molecule tracking and super-resolution imaging. We deployed three different fluorogens to probe internal microenvironments and molecular organization of PLCD condensates. The spatiotemporal resolution and environmental sensitivity afforded by single-fluorogen imaging shows that the internal environments of condensates are more hydrophobic than coexisting dilute phases. Molecules within condensates are organized in a spatially inhomogeneous manner featuring slow-moving nanoscale molecular clusters or hubs that coexist with fast-moving molecules. Finally, molecules at interfaces of condensates are found to have distinct orientational preferences when compared to the interiors. Our findings, which affirm computational predictions, help provide a structural basis for condensate viscoelasticity and dispel the notion of protein condensates being isotropic liquids defined by uniform internal densities.
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Affiliation(s)
- Tingting Wu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Matthew R King
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Mina Farag
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
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6
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Ahmed YM, Bowman GR. Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain in C. crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553945. [PMID: 37645878 PMCID: PMC10462113 DOI: 10.1101/2023.08.19.553945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Asymmetric cell division in bacteria is achieved through cell polarization, where regulatory proteins are directed to specific cell poles. Curiously, both poles contain a membraneless microdomain, established by the polar assembly hub PopZ, through most of the cell cycle, yet many PopZ clients are unipolar and transiently localized. We find that PopZ's interaction with the response regulator CpdR is controlled by phosphorylation, via the histidine kinase CckA. Phosphorylated CpdR does not interact with PopZ and is not localized to cell poles. At poles where CckA acts as a phosphatase, de-phosphorylated CpdR binds directly with PopZ and subsequently recruits ClpX, substrates, and other members of a protease complex to the cell pole. We also find that co-recruitment of protease components and substrates to polar microdomains enhances their coordinated activity. This study connects phosphosignaling with polar assembly and the activity of a protease that triggers cell cycle progression and cell differentiation.
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Affiliation(s)
- Yasin M Ahmed
- Department of Molecular Biology, University of Wyoming, Laramie Wyoming 82071
| | - Grant R Bowman
- Department of Molecular Biology, University of Wyoming, Laramie Wyoming 82071
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Gao J, Wang P, Li W, Zhang X, Song C, Liu Z, Han S, Liu H. Imaging and positioning through scattering media with double-helix point spread function engineering. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:046008. [PMID: 37114201 PMCID: PMC10127513 DOI: 10.1117/1.jbo.28.4.046008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/17/2023] [Accepted: 04/12/2023] [Indexed: 05/18/2023]
Abstract
Significance Double-helix point spread function (DH-PSF) microscopy has been developed for three-dimensional (3D) localization and imaging at super-resolution but usually in environments with no or weak scattering. To date, super-resolution imaging through turbid media has not been reported. Aim We aim to explore the potential of DH-PSF microscopy in the imaging and localization of targets in scattering environments for improved 3D localization accuracy and imaging quality. Approach The conventional DH-PSF method was modified to accommodate the scanning strategy combined with a deconvolution algorithm. The localization of a fluorescent microsphere is determined by the center of the corresponding double spot, and the image is reconstructed from the scanned data by deconvoluting the DH-PSF. Results The resolution, i.e., the localization accuracy, was calibrated to 13 nm in the transverse plane and 51 nm in the axial direction. Penetration thickness could reach an optical thickness (OT) of 5. Proof-of-concept imaging and the 3D localization of fluorescent microspheres through an eggshell membrane and an inner epidermal membrane of an onion are presented to demonstrate the super-resolution and optical sectioning capabilities. Conclusions Modified DH-PSF microscopy can image and localize targets buried in scattering media using super-resolution. Combining fluorescent dyes, nanoparticles, and quantum dots, among other fluorescent probes, the proposed method may provide a simple solution for visualizing deeper and clearer in/through scattering media, making in situ super-resolution microscopy possible for various demanding applications.
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Affiliation(s)
- Jingjing Gao
- Chinese Academy of Sciences, Shanghai Institute of Optics and Fine Mechanics, Key Laboratory of Quantum Optics, Shanghai, China
- University of Chinese Academy of Sciences, Center of Materials Science and Optoelectronics Engineering, Beijing, China
| | - Pengwei Wang
- Chinese Academy of Sciences, Shanghai Institute of Optics and Fine Mechanics, Key Laboratory of Quantum Optics, Shanghai, China
| | - Wenwen Li
- University of Science and Technology of China, Hefei National Laboratory, Hefei, China
| | - Xuyu Zhang
- Chinese Academy of Sciences, Shanghai Institute of Optics and Fine Mechanics, Key Laboratory of Quantum Optics, Shanghai, China
| | - Chunyuan Song
- Chinese Academy of Sciences, Shanghai Institute of Optics and Fine Mechanics, Key Laboratory of Quantum Optics, Shanghai, China
- University of Chinese Academy of Sciences, Center of Materials Science and Optoelectronics Engineering, Beijing, China
| | - Zhentao Liu
- Chinese Academy of Sciences, Shanghai Institute of Optics and Fine Mechanics, Key Laboratory of Quantum Optics, Shanghai, China
- University of Chinese Academy of Sciences, Center of Materials Science and Optoelectronics Engineering, Beijing, China
| | - Shensheng Han
- Chinese Academy of Sciences, Shanghai Institute of Optics and Fine Mechanics, Key Laboratory of Quantum Optics, Shanghai, China
- University of Chinese Academy of Sciences, Center of Materials Science and Optoelectronics Engineering, Beijing, China
- University of Chinese Academy of Sciences, Hangzhou Institute for Advanced Study, Hangzhou, China
| | - Honglin Liu
- Chinese Academy of Sciences, Shanghai Institute of Optics and Fine Mechanics, Key Laboratory of Quantum Optics, Shanghai, China
- University of Chinese Academy of Sciences, Center of Materials Science and Optoelectronics Engineering, Beijing, China
- Address all correspondence to Honglin Liu,
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8
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Aparin IO, Yan R, Pelletier R, Choi AA, Danylchuk DI, Xu K, Klymchenko AS. Fluorogenic Dimers as Bright Switchable Probes for Enhanced Super-Resolution Imaging of Cell Membranes. J Am Chem Soc 2022; 144:18043-18053. [PMID: 36153973 DOI: 10.1021/jacs.2c07542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Super-resolution fluorescence imaging based on single-molecule localization microscopy (SMLM) enables visualizing cellular structures with nanometric precision. However, its spatial and temporal resolution largely relies on the brightness of ON/OFF switchable fluorescent dyes. Moreover, in cell plasma membranes, the single-molecule localization is hampered by the fast lateral diffusion of membrane probes. Here, to address these two fundamental problems, we propose a concept of ON/OFF switchable probes for SMLM (points accumulation for imaging in nanoscale topography, PAINT) based on fluorogenic dimers of bright cyanine dyes. In these probes, the two cyanine units connected with a linker were modified at their extremities with low-affinity membrane anchors. Being self-quenched in water due to intramolecular dye H-aggregation, they displayed light up on reversible binding to lipid membranes. The charged group in the linker further decreased the probe affinity to the lipid membranes, thus accelerating its dynamic reversible ON/OFF switching. The concept was validated on cyanines 3 and 5. SMLM of live cells revealed that the new probes provided higher brightness and ∼10-fold slower diffusion at the cell surface, compared to reference probes Nile Red and DiD, which boosted axial localization precision >3-fold down to 31 nm. The new probe allowed unprecedented observation of nanoscale fibrous protrusions on plasma membranes of live cells with 40 s time resolution, revealing their fast dynamics. Thus, going beyond the brightness limit of single switchable dyes by cooperative dequenching in fluorogenic dimers and slowing down probe diffusion in biomembranes open the route to significant enhancement of super-resolution fluorescence microscopy of live cells.
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Affiliation(s)
- Ilya O Aparin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
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9
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Mukherjee S, Jimenez R. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies. J Phys Chem B 2022; 126:735-750. [DOI: 10.1021/acs.jpcb.1c05629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
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10
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Yang J, Du H, Chai Z, Ling Z, Li BQ, Mei X. Targeted Nanoscale 3D Thermal Imaging of Tumor Cell Surface with Functionalized Quantum Dots. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102807. [PMID: 34390313 DOI: 10.1002/smll.202102807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Indexed: 06/13/2023]
Abstract
Measuring the changes in tumor cell surface temperature can provide insights into cellular metabolism and pathological features, which is significant for targeted chemotherapy and hyperthermic therapy. However, conventional micro-nano scale methods are invasive and can only measure the temperature of cells across a single plane, which excludes specific organelles. In this study, fluorescence quantum dots (QDs) are functionalized with the membrane transport protein transferrin (Tf) as a thermo-sensor specific for tumor cell membrane. The covalent conjugation is optimized to maintain the relative fluorescence intensity of the Tf-QDs to >90%. In addition, the Tf-QDs undergo changes in the fluorescence spectra as a function of temperature, underscoring its thermo-sensor function. Double helix point spread function imaging optical path is designed to locate the probe at nanoscale, and 3D thermal imaging technology is proposed to measure the local temperature distribution and direction of heat flux on the tumor cell surface. This novel targeted nanoscale 3D thermometry method can be a highly promising tool for measuring the local and global temperature distribution across intracellular organelles.
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Affiliation(s)
- Jun Yang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- Shaanxi Key Laboratory of Intelligent Robots, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Hanliang Du
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- Shaanxi Key Laboratory of Intelligent Robots, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhenhao Chai
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- Shaanxi Key Laboratory of Intelligent Robots, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zheng Ling
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- Shaanxi Key Laboratory of Intelligent Robots, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ben Q Li
- Department of Mechanical Engineering, College of Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48128, USA
| | - Xuesong Mei
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- Shaanxi Key Laboratory of Intelligent Robots, Xi'an Jiaotong University, Xi'an, 710049, China
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11
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Wang H, Xiong W. Vibrational Sum-Frequency Generation Hyperspectral Microscopy for Molecular Self-Assembled Systems. Annu Rev Phys Chem 2021; 72:279-306. [PMID: 33441031 DOI: 10.1146/annurev-physchem-090519-050510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this review, we discuss the recent developments and applications of vibrational sum-frequency generation (VSFG) microscopy. This hyperspectral imaging technique can resolve systems without inversion symmetry, such as surfaces, interfaces and noncentrosymmetric self-assembled materials, in the spatial, temporal, and spectral domains. We discuss two common VSFG microscopy geometries: wide-field and confocal point-scanning. We then introduce the principle of VSFG and the relationships between hyperspectral imaging with traditional spectroscopy, microscopy, and time-resolved measurements. We further highlight crucial applications of VSFG microscopy in self-assembled monolayers, cellulose in plants, collagen fibers, and lattice self-assembled biomimetic materials. In these systems, VSFG microscopy reveals relationships between physical properties that would otherwise be hidden without being spectrally, spatially, and temporally resolved. Lastly, we discuss the recent development of ultrafast transient VSFG microscopy, which can spatially measure the ultrafast vibrational dynamics of self-assembled materials. The review ends with an outlook on the technical challenges of and scientific potential for VSFG microscopy.
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Affiliation(s)
- Haoyuan Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA; ,
| | - Wei Xiong
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA; , .,Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, USA
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12
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Arista-Romero M, Pujals S, Albertazzi L. Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design. Front Bioeng Biotechnol 2021; 9:647874. [PMID: 33842446 PMCID: PMC8033170 DOI: 10.3389/fbioe.2021.647874] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
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13
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Andrian T, Riera R, Pujals S, Albertazzi L. Nanoscopy for endosomal escape quantification. NANOSCALE ADVANCES 2021; 3:10-23. [PMID: 36131870 PMCID: PMC9419860 DOI: 10.1039/d0na00454e] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/26/2020] [Indexed: 05/04/2023]
Abstract
The successful cytosolic delivery of nanoparticles is hampered by their endosomal entrapment and degradation. To push forward the smart development of nanoparticles we must reliably detect and quantify their endosomal escape process. However, the current methods employed are not quantitative enough at the nanoscale to achieve this. Nanoscopy is a rapidly evolving field that has developed a diverse set of powerful techniques in the last two decades, opening the door to explore nanomedicine with an unprecedented resolution and specificity. The understanding of key steps in the drug delivery process - such as endosomal escape - would benefit greatly from the implementation of the most recent advances in microscopy. In this review, we provide the latest insights into endosomal escape of nanoparticles obtained by nanoscopy, and we discuss the features that would allow these techniques to make a great impact in the field.
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Affiliation(s)
- Teodora Andrian
- Nanoscopy for Nanomedicine, Institute for Bioengineering of Catalonia Barcelona Spain
| | - Roger Riera
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology Eindhoven Netherlands
| | - Silvia Pujals
- Nanoscopy for Nanomedicine, Institute for Bioengineering of Catalonia Barcelona Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona Av. Diagonal 647 08028 Barcelona Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine, Institute for Bioengineering of Catalonia Barcelona Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology Eindhoven Netherlands
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14
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 298] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
;
;
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15
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Liang J. Punching holes in light: recent progress in single-shot coded-aperture optical imaging. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2020; 83:116101. [PMID: 33125347 DOI: 10.1088/1361-6633/abaf43] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-shot coded-aperture optical imaging physically captures a code-aperture-modulated optical signal in one exposure and then recovers the scene via computational image reconstruction. Recent years have witnessed dazzling advances in various modalities in this hybrid imaging scheme in concomitant technical improvement and widespread applications in physical, chemical and biological sciences. This review comprehensively surveys state-of-the-art single-shot coded-aperture optical imaging. Based on the detected photon tags, this field is divided into six categories: planar imaging, depth imaging, light-field imaging, temporal imaging, spectral imaging, and polarization imaging. In each category, we start with a general description of the available techniques and design principles, then provide two representative examples of active-encoding and passive-encoding approaches, with a particular emphasis on their methodology and applications as well as their advantages and challenges. Finally, we envision prospects for further technical advancement in this field.
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Affiliation(s)
- Jinyang Liang
- Laboratory of Applied Computational Imaging, Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes, Québec J3X1S2, Canada
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16
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Yan R, Chen K, Xu K. Probing Nanoscale Diffusional Heterogeneities in Cellular Membranes through Multidimensional Single-Molecule and Super-Resolution Microscopy. J Am Chem Soc 2020; 142:18866-18873. [PMID: 33084318 DOI: 10.1021/jacs.0c08426] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diffusion properties notably determine the behavior of biomembranes. Here we report the concurrent nanoscale fine-mapping of membrane topography, diffusivity, and packing order in live mammalian cells through a synergy of single-molecule and super-resolution methods. By identifying a bright, lipophilic fluorescence turn-on probe that enables sustained single-molecule imaging of cellular membranes under stroboscopic excitation, we accumulate the positions and transient displacements of >106 probe molecules to achieve super-resolution topography and diffusivity mapping. We thus determine a trend that the membrane diffusivity drops with increased lipid packing order when comparing the endoplasmic reticulum (ER) membrane, plasma membrane, and nanodomains induced by cholera toxin B. Utilizing our nanoscale mapping capability, we further unveil reduced diffusivity in the ER membrane at ER-plasma membrane contact sites. By next integrating spectrally resolved single-molecule imaging, we show that this localized diffusion slowdown is not due to altered lipid packing order but may instead be attributed to local protein crowding. Our integrated multidimensional single-molecule approach thus unveils and differentiates between nanoscale diffusional heterogeneities of different origins in live-cell membranes.
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Affiliation(s)
- Rui Yan
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Kun Chen
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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17
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García-Calvo J, Maillard J, Fureraj I, Strakova K, Colom A, Mercier V, Roux A, Vauthey E, Sakai N, Fürstenberg A, Matile S. Fluorescent Membrane Tension Probes for Super-Resolution Microscopy: Combining Mechanosensitive Cascade Switching with Dynamic-Covalent Ketone Chemistry. J Am Chem Soc 2020; 142:12034-12038. [PMID: 32609500 DOI: 10.1021/jacs.0c04942] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report the design, synthesis, and evaluation of fluorescent flipper probes for single-molecule super-resolution imaging of membrane tension in living cells. Reversible switching from bright-state ketones to dark-state hydrates, hemiacetals, and hemithioacetals is demonstrated for twisted and planarized mechanophores in solution and membranes. Broadband femtosecond fluorescence up-conversion spectroscopy evinces ultrafast chalcogen-bonding cascade switching in the excited state in solution. According to fluorescence lifetime imaging microscopy, the new flippers image membrane tension in live cells with record red shifts and photostability. Single-molecule localization microscopy with the new tension probes resolves membranes well below the diffraction limit.
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Affiliation(s)
- José García-Calvo
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Jimmy Maillard
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Ina Fureraj
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Karolina Strakova
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Adai Colom
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Vincent Mercier
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Aurelien Roux
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Eric Vauthey
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Naomi Sakai
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Alexandre Fürstenberg
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Stefan Matile
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
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18
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Purohit A, Centeno SP, Wypysek SK, Richtering W, Wöll D. Microgel PAINT - nanoscopic polarity imaging of adaptive microgels without covalent labelling. Chem Sci 2019; 10:10336-10342. [PMID: 32110321 PMCID: PMC6984396 DOI: 10.1039/c9sc03373d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Polymer nanostructures have enormous potential for various applications in materials and life sciences. In order to exploit and understand their full capabilities, a detailed analysis of their structures and the environmental conditions in them is essential on the nanoscopic scale. With a super-resolution fluorescence microscopy technique known as PAINT (Points Accumulation for Imaging in Nanoscale Topography), we imaged colloidal hydrogel networks, so-called microgels, having a hydrodynamic radius smaller than the diffraction limit, gaining unprecedented insight into their full 3D structure which is not accessible in this much detail with any other experimental method. In addition to imaging of the microgel structure, the use of Nile Red as the solvatochromic fluorophore allowed us to resolve the polarity conditions within the investigated microgels, thus providing nanoscopic information on the x,y,z-position of labels including their polarity without the need of covalent labelling. With this imaging approach, we give a detailed insight into adapting structural and polarity properties of temperature-responsive microgels when changing the temperature beyond the volume phase transition.
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Affiliation(s)
- Ashvini Purohit
- Institute of Physical Chemistry , RWTH Aachen University , Landoltweg 2 , 52074 Aachen , Germany .
| | - Silvia P Centeno
- Institute of Physical Chemistry , RWTH Aachen University , Landoltweg 2 , 52074 Aachen , Germany .
| | - Sarah K Wypysek
- Institute of Physical Chemistry , RWTH Aachen University , Landoltweg 2 , 52074 Aachen , Germany .
| | - Walter Richtering
- Institute of Physical Chemistry , RWTH Aachen University , Landoltweg 2 , 52074 Aachen , Germany .
| | - Dominik Wöll
- Institute of Physical Chemistry , RWTH Aachen University , Landoltweg 2 , 52074 Aachen , Germany .
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19
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Gao MY, Chen Q, Li W, Shen AG, Hu JM. Combined Surface-Enhanced Raman Scattering Emissions for High-Throughput Optical Labels on Micrometer-Scale Objects. Anal Chem 2019; 91:13866-13873. [DOI: 10.1021/acs.analchem.9b03357] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Meng-Yue Gao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Qiao Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Wei Li
- Hubei Key Laboratory of Biomass Fiber and Eco-dyeing & Finishing, College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan 430073, People’s Republic of China
| | - Ai-Guo Shen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Ji-Ming Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
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20
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Achimovich AM, Ai H, Gahlmann A. Enabling technologies in super-resolution fluorescence microscopy: reporters, labeling, and methods of measurement. Curr Opin Struct Biol 2019; 58:224-232. [PMID: 31175034 PMCID: PMC6778497 DOI: 10.1016/j.sbi.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 04/26/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022]
Abstract
Super-resolution fluorescence microscopy continues to experience a period of extraordinary development. New instrumentation and fluorescent labeling strategies provide access to molecular and cellular processes that occur on length scales ranging from nanometers to millimeters and on time scales ranging from milliseconds to hours. At the shortest length scales, single-molecule imaging methods now allow measurement of nanoscale localization, motion, and binding kinetics of individual biomolecules. At cellular and intercellular length scales, super-resolution microscopy allows structural and functional imaging of individual cells in tissues and even in whole animals. Here, we review recent advances that have enabled entirely new types of experiments and greatly potentiated existing technologies.
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Affiliation(s)
- Alecia Marie Achimovich
- Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Huiwang Ai
- Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Andreas Gahlmann
- Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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21
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Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods 2019; 174:27-41. [PMID: 31344404 DOI: 10.1016/j.ymeth.2019.07.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/28/2019] [Accepted: 07/17/2019] [Indexed: 12/17/2022] Open
Abstract
Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.
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22
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Visualizing the inner life of microbes: practices of multi-color single-molecule localization microscopy in microbiology. Biochem Soc Trans 2019; 47:1041-1065. [PMID: 31296734 DOI: 10.1042/bst20180399] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 12/28/2022]
Abstract
In this review, we discuss multi-color single-molecule imaging and tracking strategies for studying microbial cell biology. We first summarize and compare the methods in a detailed literature review of published studies conducted in bacteria and fungi. We then introduce a guideline on which factors and parameters should be evaluated when designing a new experiment, from fluorophore and labeling choices to imaging routines and data analysis. Finally, we give some insight into some of the recent and promising applications and developments of these techniques and discuss the outlook for this field.
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23
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Wollman AJM, Hedlund EG, Shashkova S, Leake MC. Towards mapping the 3D genome through high speed single-molecule tracking of functional transcription factors in single living cells. Methods 2019; 170:82-89. [PMID: 31252059 PMCID: PMC6971689 DOI: 10.1016/j.ymeth.2019.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022] Open
Abstract
How genomic DNA is organized in the nucleus is a long-standing question. We describe a single-molecule bioimaging method utilizing super-localization precision coupled to fully quantitative image analysis tools, towards determining snapshots of parts of the 3D genome architecture of model eukaryote budding yeast Saccharomyces cerevisiae with exceptional millisecond time resolution. We employ astigmatism imaging to enable robust extraction of 3D position data on genomically encoded fluorescent protein reporters that bind to DNA. Our relatively straightforward method enables snippets of 3D architectures of likely single genome conformations to be resolved captured via DNA-sequence specific binding proteins in single functional living cells.
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Affiliation(s)
- Adam J M Wollman
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Erik G Hedlund
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Sviatlana Shashkova
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Mark C Leake
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
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24
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Taylor JA, Sichel SR, Salama NR. Bent Bacteria: A Comparison of Cell Shape Mechanisms in Proteobacteria. Annu Rev Microbiol 2019; 73:457-480. [PMID: 31206344 DOI: 10.1146/annurev-micro-020518-115919] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Helical cell shape appears throughout the bacterial phylogenetic tree. Recent exciting work characterizing cell shape mutants in a number of curved and helical Proteobacteria is beginning to suggest possible mechanisms and provide tools to assess functional significance. We focus here on Caulobacter crescentus, Vibrio cholerae, Helicobacter pylori, and Campylobacter jejuni, organisms from three classes of Proteobacteria that live in diverse environments, from freshwater and saltwater to distinct compartments within the gastrointestinal tract of humans and birds. Comparisons among these bacteria reveal common themes as well as unique solutions to the task of maintaining cell curvature. While motility appears to be influenced in all these bacteria when cell shape is perturbed, consequences on niche colonization are diverse, suggesting the need to consider additional selective pressures.
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Affiliation(s)
- Jennifer A Taylor
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA; .,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sophie R Sichel
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Molecular Medicine and Mechanisms of Disease Graduate Program, University of Washington, Seattle, Washington 98195, USA
| | - Nina R Salama
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA; .,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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25
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Ruba A, Luo W, Kelich J, Tingey M, Yang W. 3D Tracking-Free Approach for Obtaining 3D Super-Resolution Information in Rotationally Symmetric Biostructures. J Phys Chem B 2019; 123:5107-5120. [PMID: 31117612 DOI: 10.1021/acs.jpcb.9b02979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, it is highly desirable but still challenging to obtain high-resolution (<50 nm) three-dimensional (3D) super-resolution information on structures in fixed specimens as well as for dynamic processes in live cells. Here we introduce a simple approach, without using 3D super-resolution microscopy or real-time 3D particle tracking, to estimate 3D sub-diffraction-limited structural or dynamic information in rotationally symmetric biostructures. This is a postlocalization analysis that transforms 2D super-resolution images or 2D single-molecule localization distributions into their corresponding 3D spatial probability distributions on the basis of prior known structural knowledge. This analysis is ideal in cases where the ultrastructure of a cellular structure is known but the substructural localization of a particular (usually mobile) protein is not. The method has been successfully applied to achieve 3D structural and functional sub-diffraction-limited information for 25-300 nm subcellular organelles that meet the rotational symmetry requirement, such as nuclear pore complex, primary cilium, and microtubule. In this Article, we will provide comprehensive analyses of this method by using experimental data and computational simulations. Finally, open source code of the 2D to 3D transformation algorithm (MATLAB) and simulations (Python) have also been developed.
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Affiliation(s)
- Andrew Ruba
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Wangxi Luo
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Joseph Kelich
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Mark Tingey
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
| | - Weidong Yang
- Department of Biology , Temple University , 1900 North 12th Street , Philadelphia , Pennsylvania , United States
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26
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Yoon J, Comerci CJ, Weiss LE, Milenkovic L, Stearns T, Moerner WE. Revealing Nanoscale Morphology of the Primary Cilium Using Super-Resolution Fluorescence Microscopy. Biophys J 2018; 116:319-329. [PMID: 30598282 PMCID: PMC6349968 DOI: 10.1016/j.bpj.2018.11.3136] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/20/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
Super-resolution (SR) microscopy has been used to observe structural details beyond the diffraction limit of ∼250 nm in a variety of biological and materials systems. By combining this imaging technique with both computer-vision algorithms and topological methods, we reveal and quantify the nanoscale morphology of the primary cilium, a tiny tubular cellular structure (∼2-6 μm long and 200-300 nm in diameter). The cilium in mammalian cells protrudes out of the plasma membrane and is important in many signaling processes related to cellular differentiation and disease. After tagging individual ciliary transmembrane proteins, specifically Smoothened, with single fluorescent labels in fixed cells, we use three-dimensional (3D) single-molecule SR microscopy to determine their positions with a precision of 10-25 nm. We gain a dense, pointillistic reconstruction of the surfaces of many cilia, revealing large heterogeneity in membrane shape. A Poisson surface reconstruction algorithm generates a fine surface mesh, allowing us to characterize the presence of deformations by quantifying the surface curvature. Upon impairment of intracellular cargo transport machinery by genetic knockout or small-molecule treatment of cells, our quantitative curvature analysis shows significant morphological differences not visible by conventional fluorescence microscopy techniques. Furthermore, using a complementary SR technique, two-color, two-dimensional stimulated emission depletion microscopy, we find that the cytoskeleton in the cilium, the axoneme, also exhibits abnormal morphology in the mutant cells, similar to our 3D results on the Smoothened-measured ciliary surface. Our work combines 3D SR microscopy and computational tools to quantitatively characterize morphological changes of the primary cilium under different treatments and uses stimulated emission depletion to discover correlated changes in the underlying structure. This approach can be useful for studying other biological or nanoscale structures of interest.
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Affiliation(s)
- Joshua Yoon
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California
| | - Colin J Comerci
- Biophysics Program, Stanford University, Stanford, California
| | - Lucien E Weiss
- Department of Chemistry, Stanford University, Stanford, California
| | | | - Tim Stearns
- Department of Biology, Stanford University, Stanford, California
| | - W E Moerner
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California.
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27
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Ponjavic A, Ye Y, Laue E, Lee SF, Klenerman D. Sensitive light-sheet microscopy in multiwell plates using an AFM cantilever. BIOMEDICAL OPTICS EXPRESS 2018; 9:5863-5880. [PMID: 31065399 PMCID: PMC6490997 DOI: 10.1364/boe.9.005863] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 06/01/2023]
Abstract
We present a sensitive inverted light sheet microscope, capable of single-molecule fluorescence imaging of cells in 96-well plates. Light sheet microscope designs are often complex and costly, requiring custom-made sample chambers that are incompatible with standard cell culture samples. To overcome this limitation, we have developed single-objective cantilever selective plane illumination microscopy (socSPIM), which introduces a light sheet through the objective lens of an inverted microscope using an AFM tip. We demonstrate the effectiveness of this setup by performing 3D imaging of nuclear pore complexes, as well as live whole-cell 3D imaging of lysosomes and super-resolution imaging of the T-cell membrane. The unique advantage offered by socSPIM is the minimal footprint of the cantilever, which allowed us to perform super-resolution reflected light-sheet microscopy by PAINT in 96-well plates, paving the way for high-throughput studies.
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Affiliation(s)
- Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Yu Ye
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Cell Biology, Harvard Medical School, Longwood Avenue, Boston, 02115 MA, USA
| | - Ernest Laue
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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28
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Lukeš T, Pospíšil J, Fliegel K, Lasser T, Hagen GM. Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors. Gigascience 2018; 7:1-10. [PMID: 29361123 PMCID: PMC5841371 DOI: 10.1093/gigascience/giy002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/10/2018] [Indexed: 01/22/2023] Open
Abstract
Background Super-resolution single molecule localization microscopy (SMLM) is a method for achieving resolution beyond the classical limit in optical microscopes (approx. 200 nm laterally). Yellow fluorescent protein (YFP) has been used for super-resolution single molecule localization microscopy, but less frequently than other fluorescent probes. Working with YFP in SMLM is a challenge because a lower number of photons are emitted per molecule compared with organic dyes, which are more commonly used. Publically available experimental data can facilitate development of new data analysis algorithms. Findings Four complete, freely available single molecule super-resolution microscopy datasets on YFP-tagged growth factor receptors expressed in a human cell line are presented, including both raw and analyzed data. We report methods for sample preparation, for data acquisition, and for data analysis, as well as examples of the acquired images. We also analyzed the SMLM datasets using a different method: super-resolution optical fluctuation imaging (SOFI). The 2 modes of analysis offer complementary information about the sample. A fifth single molecule super-resolution microscopy dataset acquired with the dye Alexa 532 is included for comparison purposes. Conclusions This dataset has potential for extensive reuse. Complete raw data from SMLM experiments have typically not been published. The YFP data exhibit low signal-to-noise ratios, making data analysis a challenge. These datasets will be useful to investigators developing their own algorithms for SMLM, SOFI, and related methods. The data will also be useful for researchers investigating growth factor receptors such as ErbB3.
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Affiliation(s)
- Tomáš Lukeš
- Laboratoire d'Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Route Cantonale, CH-1015 Lausanne, Switzerland
| | - Jakub Pospíšil
- Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 16627 Prague 6, Czech Republic
| | - Karel Fliegel
- Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 16627 Prague 6, Czech Republic
| | - Theo Lasser
- Laboratoire d'Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Route Cantonale, CH-1015 Lausanne, Switzerland
| | - Guy M Hagen
- UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USA
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29
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Spahn CK, Glaesmann M, Grimm JB, Ayala AX, Lavis LD, Heilemann M. A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels. Sci Rep 2018; 8:14768. [PMID: 30282984 PMCID: PMC6170473 DOI: 10.1038/s41598-018-33052-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/21/2018] [Indexed: 11/09/2022] Open
Abstract
Maintenance of the bacterial homeostasis initially emanates from interactions between proteins and the bacterial nucleoid. Investigating their spatial correlation requires high spatial resolution, especially in tiny, highly confined and crowded bacterial cells. Here, we present super-resolution microscopy using a palette of fluorescent labels that bind transiently to either the membrane or the nucleoid of fixed E. coli cells. The presented labels are easily applicable, versatile and allow long-term single-molecule super-resolution imaging independent of photobleaching. The different spectral properties allow for multiplexed imaging in combination with other localisation-based super-resolution imaging techniques. As examples for applications, we demonstrate correlated super-resolution imaging of the bacterial nucleoid with the position of genetic loci, of nascent DNA in correlation to the entire nucleoid, and of the nucleoid of metabolically arrested cells. We furthermore show that DNA- and membrane-targeting labels can be combined with photoactivatable fluorescent proteins and visualise the nano-scale distribution of RNA polymerase relative to the nucleoid in drug-treated E. coli cells.
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Affiliation(s)
- Christoph K Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Anthony X Ayala
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA.
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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30
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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31
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Baddeley D, Bewersdorf J. Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. Annu Rev Biochem 2018; 87:965-989. [PMID: 29272143 DOI: 10.1146/annurev-biochem-060815-014801] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution optical imaging based on the switching and localization of individual fluorescent molecules [photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), etc.] has evolved remarkably over the last decade. Originally driven by pushing technological limits, it has become a tool of biological discovery. The initial demand for impressive pictures showing well-studied biological structures has been replaced by a need for quantitative, reliable data providing dependable evidence for specific unresolved biological hypotheses. In this review, we highlight applications that showcase this development, identify the features that led to their success, and discuss remaining challenges and difficulties. In this context, we consider the complex topic of defining resolution for this imaging modality and address some of the more common analytical methods used with this data.
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Affiliation(s)
- David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Auckland Bioengineering Institute, University of Auckland, Auckland 1010, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
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32
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Gustavsson AK, Petrov PN, Moerner WE. Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. OPTICS EXPRESS 2018; 26:13122-13147. [PMID: 29801343 PMCID: PMC6005674 DOI: 10.1364/oe.26.013122] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/30/2018] [Indexed: 05/08/2023]
Abstract
The development of imaging techniques beyond the diffraction limit has paved the way for detailed studies of nanostructures and molecular mechanisms in biological systems. Imaging thicker samples, such as mammalian cells and tissue, in all three dimensions, is challenging due to increased background and volumes to image. Light sheet illumination is a method that allows for selective irradiation of the image plane, and its inherent optical sectioning capability allows for imaging of biological samples with reduced background, photobleaching, and photodamage. In this review, we discuss the advantage of combining single-molecule imaging with light sheet illumination. We begin by describing the principles of single-molecule localization microscopy and of light sheet illumination. Finally, we present examples of designs that successfully have married single-molecule super-resolution imaging with light sheet illumination for improved precision in mammalian cells.
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33
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Xiang L, Wojcik M, Kenny SJ, Yan R, Moon S, Li W, Xu K. Optical characterization of surface adlayers and their compositional demixing at the nanoscale. Nat Commun 2018; 9:1435. [PMID: 29650981 PMCID: PMC5897338 DOI: 10.1038/s41467-018-03820-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Under ambient conditions, the behavior of a solid surface is often dominated by a molecularly thin adsorbed layer (adlayer) of small molecules. Here we develop an optical approach to unveil the nanoscale structure and composition of small-molecule adlayers on glass surfaces through spectrally resolved super-resolution microscopy. By recording the images and emission spectra of millions of individual solvatochromic molecules that turn fluorescent in the adlayer phase, we obtain ~30 nm spatial resolution and achieve concurrent measurement of local polarity. This allows us to establish that the adlayer dimensionality gradually increases through a sequence of 0D (nanodroplets), 1D (nano-lines), and 2D (films) for liquids of increasing polarity. Moreover, we find that in adlayers, a solution of two miscible liquids spontaneously demixes into nanodroplets of different compositions that correlate strongly with droplet size and location. We thus reveal unexpectedly rich structural and compositional behaviors of surface adlayers at the nanoscale. Characterization of adsorbed molecular layers on surfaces is the key to wide-ranging applications, but elucidating the structure and composition of such adlayers remains challenging. Here the authors develop an approach to unveil the nanoscale structure and composition of adlayers through spectrally resolved super-resolution microscopy.
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Affiliation(s)
- Limin Xiang
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Michal Wojcik
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Samuel J Kenny
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Seonah Moon
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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34
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Venkataramani V, Kardorff M, Herrmannsdörfer F, Wieneke R, Klein A, Tampé R, Heilemann M, Kuner T. Enhanced labeling density and whole-cell 3D dSTORM imaging by repetitive labeling of target proteins. Sci Rep 2018; 8:5507. [PMID: 29615726 PMCID: PMC5882651 DOI: 10.1038/s41598-018-23818-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022] Open
Abstract
With continuing advances in the resolving power of super-resolution microscopy, the inefficient labeling of proteins with suitable fluorophores becomes a limiting factor. For example, the low labeling density achieved with antibodies or small molecule tags limits attempts to reveal local protein nano-architecture of cellular compartments. On the other hand, high laser intensities cause photobleaching within and nearby an imaged region, thereby further reducing labeling density and impairing multi-plane whole-cell 3D super-resolution imaging. Here, we show that both labeling density and photobleaching can be addressed by repetitive application of trisNTA-fluorophore conjugates reversibly binding to a histidine-tagged protein by a novel approach called single-epitope repetitive imaging (SERI). For single-plane super-resolution microscopy, we demonstrate that, after multiple rounds of labeling and imaging, the signal density is increased. Using the same approach of repetitive imaging, washing and re-labeling, we demonstrate whole-cell 3D super-resolution imaging compensated for photobleaching above or below the imaging plane. This proof-of-principle study demonstrates that repetitive labeling of histidine-tagged proteins provides a versatile solution to break the ‘labeling barrier’ and to bypass photobleaching in multi-plane, whole-cell 3D experiments.
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Affiliation(s)
- Varun Venkataramani
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Markus Kardorff
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Frank Herrmannsdörfer
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Alina Klein
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Mike Heilemann
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany. .,Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - Thomas Kuner
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
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35
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Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE. Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2018; 10500:105000M. [PMID: 29681676 PMCID: PMC5906058 DOI: 10.1117/12.2288443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To obtain a complete picture of subcellular nanostructures, cells must be imaged with high resolution in all three dimensions (3D). Here, we present tilted light sheet microscopy with 3D point spread functions (TILT3D), an imaging platform that combines a novel, tilted light sheet illumination strategy with engineered long axial range point spread functions (PSFs) for low-background, 3D super localization of single molecules as well as 3D super-resolution imaging in thick cells. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The axial positions of the single molecules are encoded in the shape of the PSF rather than in the position or thickness of the light sheet, and the light sheet can therefore be formed using simple optics. The result is flexible and user-friendly 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validated TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed Tetrapod PSF for fiducial bead tracking and live axial drift correction. We envision TILT3D to become an important tool not only for 3D super-resolution imaging, but also for live whole-cell single-particle and single-molecule tracking.
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Affiliation(s)
- Anna-Karin Gustavsson
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
- Dept. of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden 17111
| | - Petar N. Petrov
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
| | - Maurice Y. Lee
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
- Biophysics Program, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
| | - Yoav Shechtman
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
| | - W. E. Moerner
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
- Biophysics Program, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
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36
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37
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Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat Commun 2018; 9:123. [PMID: 29317629 PMCID: PMC5760554 DOI: 10.1038/s41467-017-02563-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/11/2017] [Indexed: 12/24/2022] Open
Abstract
Tilted light sheet microscopy with 3D point spread functions (TILT3D) combines a novel, tilted light sheet illumination strategy with long axial range point spread functions (PSFs) for low-background, 3D super-localization of single molecules as well as 3D super-resolution imaging in thick cells. Because the axial positions of the single emitters are encoded in the shape of each single-molecule image rather than in the position or thickness of the light sheet, the light sheet need not be extremely thin. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The result is simple and flexible 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validate TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed tetrapod PSFs for fiducial bead tracking and live axial drift correction.
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Affiliation(s)
- Anna-Karin Gustavsson
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Maurice Y Lee
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.,Biomedical Engineering Department, Technion, Israel Institute of Technology, Haifa, 3200003, Israel
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA. .,Biophysics Program, Stanford University, Stanford, CA, 94305, USA.
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38
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Lippert A, Janeczek AA, Fürstenberg A, Ponjavic A, Moerner WE, Nusse R, Helms JA, Evans ND, Lee SF. Single-Molecule Imaging of Wnt3A Protein Diffusion on Living Cell Membranes. Biophys J 2017; 113:2762-2767. [PMID: 29262368 PMCID: PMC5925569 DOI: 10.1016/j.bpj.2017.08.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/13/2017] [Accepted: 08/02/2017] [Indexed: 01/31/2023] Open
Abstract
Wnt proteins are secreted, hydrophobic, lipidated proteins found in all animals that play essential roles in development and disease. Lipid modification is thought to facilitate the interaction of the protein with its receptor, Frizzled, but may also regulate the transport of Wnt protein and its localization at the cell membrane. Here, by employing single-molecule fluorescence techniques, we show that Wnt proteins associate with and diffuse on the plasma membranes of living cells in the absence of any receptor binding. We find that labeled Wnt3A transiently and dynamically associates with the membranes of Drosophila Schneider 2 cells, diffuses with Brownian kinetics on flattened membranes and on cellular protrusions, and does not transfer between cells in close contact. In S2 receptor-plus (S2R+) cells, which express Frizzled receptors, membrane diffusion rate is reduced and membrane residency time is increased. These results provide direct evidence of Wnt3A interaction with living cell membranes, and represent, to our knowledge, a new system for investigating the dynamics of Wnt transport.
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Affiliation(s)
- Anna Lippert
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Agnieszka A Janeczek
- Centre for Human Development, Stem Cells and Regeneration, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Alexandre Fürstenberg
- Department of Chemistry, Stanford University, Palo Alto, California; Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, Genève, Switzerland
| | - Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - W E Moerner
- Department of Chemistry, Stanford University, Palo Alto, California
| | - Roel Nusse
- Department of Developmental Biology, Stanford University, Palo Alto, California
| | - Jill A Helms
- Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, California
| | - Nicholas D Evans
- Centre for Human Development, Stem Cells and Regeneration, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Chemistry, Stanford University, Palo Alto, California.
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39
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Moon S, Yan R, Kenny SJ, Shyu Y, Xiang L, Li W, Xu K. Spectrally Resolved, Functional Super-Resolution Microscopy Reveals Nanoscale Compositional Heterogeneity in Live-Cell Membranes. J Am Chem Soc 2017; 139:10944-10947. [DOI: 10.1021/jacs.7b03846] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Seonah Moon
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Rui Yan
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Samuel J. Kenny
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Yennie Shyu
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Limin Xiang
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Wan Li
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ke Xu
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Division
of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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40
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Mollazade M, Tabarin T, Nicovich PR, Soeriyadi A, Nieves DJ, Gooding JJ, Gaus K. Can single molecule localization microscopy be used to map closely spaced RGD nanodomains? PLoS One 2017; 12:e0180871. [PMID: 28723958 PMCID: PMC5516992 DOI: 10.1371/journal.pone.0180871] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/22/2017] [Indexed: 11/22/2022] Open
Abstract
Cells sense and respond to nanoscale variations in the distribution of ligands to adhesion receptors. This makes single molecule localization microscopy (SMLM) an attractive tool to map the distribution of ligands on nanopatterned surfaces. We explore the use of SMLM spatial cluster analysis to detect nanodomains of the cell adhesion-stimulating tripeptide arginine-glycine-aspartic acid (RGD). These domains were formed by the phase separation of block copolymers with controllable spacing on the scale of tens of nanometers. We first determined the topology of the block copolymer with atomic force microscopy (AFM) and then imaged the localization of individual RGD peptides with direct stochastic optical reconstruction microscopy (dSTORM). To compare the data, we analyzed the dSTORM data with DBSCAN (density-based spatial clustering application with noise). The ligand distribution and polymer topology are not necessary identical since peptides may attach to the polymer outside the nanodomains and/or coupling and detection of peptides within the nanodomains is incomplete. We therefore performed simulations to explore the extent to which nanodomains could be mapped with dSTORM. We found that successful detection of nanodomains by dSTORM was influenced by the inter-domain spacing and the localization precision of individual fluorophores, and less by non-specific absorption of ligands to the substratum. For example, under our imaging conditions, DBSCAN identification of nanodomains spaced further than 50 nm apart was largely independent of background localisations, while nanodomains spaced closer than 50 nm required a localization precision of ~11 nm to correctly estimate the modal nearest neighbor distance (NDD) between nanodomains. We therefore conclude that SMLM is a promising technique to directly map the distribution and nanoscale organization of ligands and would benefit from an improved localization precision.
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Affiliation(s)
- Mahdie Mollazade
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Thibault Tabarin
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Philip R Nicovich
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Alexander Soeriyadi
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Daniel J Nieves
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
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41
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von Diezmann A, Shechtman Y, Moerner WE. Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking. Chem Rev 2017; 117:7244-7275. [PMID: 28151646 PMCID: PMC5471132 DOI: 10.1021/acs.chemrev.6b00629] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information on single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems.
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Affiliation(s)
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
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Carr AR, Ponjavic A, Basu S, McColl J, Santos AM, Davis S, Laue ED, Klenerman D, Lee SF. Three-Dimensional Super-Resolution in Eukaryotic Cells Using the Double-Helix Point Spread Function. Biophys J 2017; 112:1444-1454. [PMID: 28402886 PMCID: PMC5390298 DOI: 10.1016/j.bpj.2017.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/07/2017] [Accepted: 02/21/2017] [Indexed: 02/02/2023] Open
Abstract
Single-molecule localization microscopy, typically based on total internal reflection illumination, has taken our understanding of protein organization and dynamics in cells beyond the diffraction limit. However, biological systems exist in a complicated three-dimensional environment, which has required the development of new techniques, including the double-helix point spread function (DHPSF), to accurately visualize biological processes. The application of the DHPSF approach has so far been limited to the study of relatively small prokaryotic cells. By matching the refractive index of the objective lens immersion liquid to that of the sample media, we demonstrate DHPSF imaging of up to 15-μm-thick whole eukaryotic cell volumes in three to five imaging planes. We illustrate the capabilities of the DHPSF by exploring large-scale membrane reorganization in human T cells after receptor triggering, and by using single-particle tracking to image several mammalian proteins, including membrane, cytoplasmic, and nuclear proteins in T cells and embryonic stem cells.
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Affiliation(s)
- Alexander R. Carr
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - James McColl
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ana Mafalda Santos
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- Radcliffe Department of Clinical Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven F. Lee
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom,Corresponding author
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43
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Nicovich PR, Owen DM, Gaus K. Turning single-molecule localization microscopy into a quantitative bioanalytical tool. Nat Protoc 2017; 12:453-460. [DOI: 10.1038/nprot.2016.166] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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44
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Hauser M, Wojcik M, Kim D, Mahmoudi M, Li W, Xu K. Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities. Chem Rev 2017; 117:7428-7456. [PMID: 28045508 DOI: 10.1021/acs.chemrev.6b00604] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.
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Affiliation(s)
- Meghan Hauser
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Michal Wojcik
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Doory Kim
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Morteza Mahmoudi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Wan Li
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California , Berkeley, California 94720, United States.,Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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45
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Spahn C, Glaesmann M, Gao Y, Foo YH, Lampe M, Kenney LJ, Heilemann M. Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells. Methods Mol Biol 2017; 1624:269-289. [PMID: 28842890 DOI: 10.1007/978-1-4939-7098-8_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Despite their small size and the lack of compartmentalization, bacteria exhibit a striking degree of cellular organization, both in time and space. During the last decade, a group of new microscopy techniques emerged, termed super-resolution microscopy or nanoscopy, which facilitate visualizing the organization of proteins in bacteria at the nanoscale. Single-molecule localization microscopy (SMLM) is especially well suited to reveal a wide range of new information regarding protein organization, interaction, and dynamics in single bacterial cells. Recent developments in click chemistry facilitate the visualization of bacterial chromatin with a resolution of ~20 nm, providing valuable information about the ultrastructure of bacterial nucleoids, especially at short generation times. In this chapter, we describe a simple-to-realize protocol that allows determining precise structural information of bacterial nucleoids in fixed cells, using direct stochastic optical reconstruction microscopy (dSTORM). In combination with quantitative photoactivated localization microscopy (PALM), the spatial relationship of proteins with the bacterial chromosome can be studied. The position of a protein of interest with respect to the nucleoids and the cell cylinder can be visualized by super-resolving the membrane using point accumulation for imaging in nanoscale topography (PAINT). The combination of the different SMLM techniques in a sequential workflow maximizes the information that can be extracted from single cells, while maintaining optimal imaging conditions for each technique.
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Affiliation(s)
- Christoph Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Yunfeng Gao
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Otto-Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Linda J Kenney
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore.
- University of Illinois, Chicago, Chicago, IL, 60612, USA.
- Jesse Brown VA Medical Center, Chicago, IL, 60612, USA.
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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46
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Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping. Nat Commun 2016; 7:13544. [PMID: 27929085 PMCID: PMC5155161 DOI: 10.1038/ncomms13544] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/13/2016] [Indexed: 12/20/2022] Open
Abstract
Super-resolution microscopy allows biological systems to be studied at the nanoscale, but has been restricted to providing only positional information. Here, we show that it is possible to perform multi-dimensional super-resolution imaging to determine both the position and the environmental properties of single-molecule fluorescent emitters. The method presented here exploits the solvatochromic and fluorogenic properties of nile red to extract both the emission spectrum and the position of each dye molecule simultaneously enabling mapping of the hydrophobicity of biological structures. We validated this by studying synthetic lipid vesicles of known composition. We then applied both to super-resolve the hydrophobicity of amyloid aggregates implicated in neurodegenerative diseases, and the hydrophobic changes in mammalian cell membranes. Our technique is easily implemented by inserting a transmission diffraction grating into the optical path of a localization-based super-resolution microscope, enabling all the information to be extracted simultaneously from a single image plane.
Many super-resolution imaging techniques use fluorescence emission intensity to obtain precise positional information, but other spectral information is ignored. Here, the authors develop a method that records the spectrum and position of single dye molecules to map the hydrophobicity of a surface.
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47
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Wang W, Shen H, Shuang B, Hoener BS, Tauzin LJ, Moringo NA, Kelly KF, Landes CF. Super Temporal-Resolved Microscopy (STReM). J Phys Chem Lett 2016; 7:4524-4529. [PMID: 27797527 DOI: 10.1021/acs.jpclett.6b02098] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Super-resolution microscopy typically achieves high spatial resolution, but the temporal resolution remains low. We report super temporal-resolved microscopy (STReM) to improve the temporal resolution of 2D super-resolution microscopy by a factor of 20 compared to that of the traditional camera-limited frame rate. This is achieved by rotating a phase mask in the Fourier plane during data acquisition and then recovering the temporal information by fitting the point spread function (PSF) orientations. The feasibility of this technique is verified with both simulated and experimental 2D adsorption/desorption and 2D emitter transport. When STReM is applied to measure protein adsorption at a glass surface, previously unseen dynamics are revealed.
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Affiliation(s)
- Wenxiao Wang
- Department of Electrical and Computer Engineering, Rice University , MS 366, Houston, Texas 77251-1892, United States
| | - Hao Shen
- Department of Chemistry, Rice University , MS 60, Houston, Texas 77251-1892, United States
| | - Bo Shuang
- Department of Chemistry, Rice University , MS 60, Houston, Texas 77251-1892, United States
| | - Benjamin S Hoener
- Department of Chemistry, Rice University , MS 60, Houston, Texas 77251-1892, United States
| | - Lawrence J Tauzin
- Department of Chemistry, Rice University , MS 60, Houston, Texas 77251-1892, United States
| | - Nicholas A Moringo
- Department of Chemistry, Rice University , MS 60, Houston, Texas 77251-1892, United States
| | - Kevin F Kelly
- Department of Electrical and Computer Engineering, Rice University , MS 366, Houston, Texas 77251-1892, United States
| | - Christy F Landes
- Department of Electrical and Computer Engineering, Rice University , MS 366, Houston, Texas 77251-1892, United States
- Department of Chemistry, Rice University , MS 60, Houston, Texas 77251-1892, United States
- Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
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48
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Gelissen APH, Oppermann A, Caumanns T, Hebbeker P, Turnhoff SK, Tiwari R, Eisold S, Simon U, Lu Y, Mayer J, Richtering W, Walther A, Wöll D. 3D Structures of Responsive Nanocompartmentalized Microgels. NANO LETTERS 2016; 16:7295-7301. [PMID: 27701865 DOI: 10.1021/acs.nanolett.6b03940] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Compartmentalization in soft matter is important for segregating and coordinating chemical reactions, sequestering (re)active components, and integrating multifunctionality. Advances depend crucially on quantitative 3D visualization in situ with high spatiotemporal resolution. Here, we show the direct visualization of different compartments within adaptive microgels using a combination of in situ electron and super-resolved fluorescence microscopy. We unravel new levels of structural details and address the challenge of reconstructing 3D information from 2D projections for nonuniform soft matter as opposed to monodisperse proteins. Moreover, we visualize the thermally induced shrinkage of responsive core-shell microgels live in water. This strategy opens doors for systematic in situ studies of soft matter systems and their application as smart materials.
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Affiliation(s)
- Arjan P H Gelissen
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Alex Oppermann
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Tobias Caumanns
- GFE Central Facility for Electron Microscopy, RWTH Aachen University , Mies-van-der-Rohe-Straße 59, D-52074 Aachen, Germany
| | - Pascal Hebbeker
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Sarah K Turnhoff
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Rahul Tiwari
- DWI - Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, D-52074 Aachen, Germany
| | - Sabine Eisold
- Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Ulrich Simon
- Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Yan Lu
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
| | - Joachim Mayer
- GFE Central Facility for Electron Microscopy, RWTH Aachen University , Mies-van-der-Rohe-Straße 59, D-52074 Aachen, Germany
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Andreas Walther
- DWI - Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, D-52074 Aachen, Germany
| | - Dominik Wöll
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
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49
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Xiao J, Dufrêne YF. Optical and force nanoscopy in microbiology. Nat Microbiol 2016; 1:16186. [PMID: 27782138 PMCID: PMC5839876 DOI: 10.1038/nmicrobiol.2016.186] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.
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Affiliation(s)
- Jie Xiao
- Department of Biophysics &Biophysical Chemistry, The Johns Hopkins School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21212, USA
| | - Yves F Dufrêne
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), Belgium
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50
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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