1
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Tholen MME, Tas RP, Wang Y, Albertazzi L. Beyond DNA: new probes for PAINT super-resolution microscopy. Chem Commun (Camb) 2023; 59:8332-8342. [PMID: 37306078 PMCID: PMC10318573 DOI: 10.1039/d3cc00757j] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/26/2023] [Indexed: 06/13/2023]
Abstract
In the last decade, point accumulation for imaging in nanoscale topography (PAINT) has emerged as a versatile tool for single-molecule localization microscopy (SMLM). Currently, DNA-PAINT is the most widely used, in which a transient stochastically binding DNA docking-imaging pair is used to reconstruct specific characteristics of biological or synthetic materials on a single-molecule level. Slowly, the need for PAINT probes that are not dependent on DNA has emerged. These probes can be based on (i) endogenous interactions, (ii) engineered binders, (iii) fusion proteins, or (iv) synthetic molecules and provide complementary applications for SMLM. Therefore, researchers have been expanding the PAINT toolbox with new probes. In this review, we provide an overview of the currently existing probes that go beyond DNA and their applications and challenges.
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Affiliation(s)
- Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Roderick P Tas
- Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing Soft Matter, Eindhoven University of Technology, Eindhoven, 5612 AP, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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2
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Single-cell extracellular vesicle analysis by microfluidics and beyond. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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3
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Iwasaki H, Ichinose S, Tajika Y, Murakami T. Recent technological advances in correlative light and electron microscopy for the comprehensive analysis of neural circuits. Front Neuroanat 2022; 16:1061078. [PMID: 36530521 PMCID: PMC9748091 DOI: 10.3389/fnana.2022.1061078] [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: 10/04/2022] [Accepted: 11/16/2022] [Indexed: 11/04/2023] Open
Abstract
Light microscopy (LM) covers a relatively wide area and is suitable for observing the entire neuronal network. However, resolution of LM is insufficient to identify synapses and determine whether neighboring neurons are connected via synapses. In contrast, the resolution of electron microscopy (EM) is sufficiently high to detect synapses and is useful for identifying neuronal connectivity; however, serial images cannot easily show the entire morphology of neurons, as EM covers a relatively narrow region. Thus, covering a large area requires a large dataset. Furthermore, the three-dimensional (3D) reconstruction of neurons by EM requires considerable time and effort, and the segmentation of neurons is laborious. Correlative light and electron microscopy (CLEM) is an approach for correlating images obtained via LM and EM. Because LM and EM are complementary in terms of compensating for their shortcomings, CLEM is a powerful technique for the comprehensive analysis of neural circuits. This review provides an overview of recent advances in CLEM tools and methods, particularly the fluorescent probes available for CLEM and near-infrared branding technique to match LM and EM images. We also discuss the challenges and limitations associated with contemporary CLEM technologies.
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Affiliation(s)
- Hirohide Iwasaki
- Department of Anatomy, Gunma University Graduate School of Medicine, Maebashi, Japan
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4
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Jensen LG, Williamson DJ, Hahn U. Semiparametric point process modeling of blinking artifacts in PALM. Ann Appl Stat 2022. [DOI: 10.1214/21-aoas1553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | - Ute Hahn
- Department of Mathematics, Aarhus University
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5
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SUPER-RESOLUTION MICROSCOPY FOR THE STUDY OF STORE-OPERATED CALCIUM ENTRY. Cell Calcium 2022; 104:102595. [DOI: 10.1016/j.ceca.2022.102595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022]
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6
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Shabairou N, Tiferet M, Zalevsky Z, Sinvani M. Dynamics of laser-induced tunable focusing in silicon. Sci Rep 2022; 12:6342. [PMID: 35428805 PMCID: PMC9012861 DOI: 10.1038/s41598-022-10112-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/16/2022] [Indexed: 11/09/2022] Open
Abstract
We report here on focusing of a probe IR (λ = 1.55 μm) laser beam in silicon. The focusing is done by a second pump laser beam, at λ = 0.775 μm and 30 ps pulse width, with a donut shape that is launched collinearly and simultaneously (with some delay time) with the IR beam pulse. The pump beam pulse is absorbed in the silicon and creates, temporally, a free charge carriers (FCCs) donut pattern in the silicon. Following the plasma dispersion effect, the donut FCCs shapes a complex index of refraction pattern in the silicon that serves as a sort of dynamic GRIN lens for the probe beam due to the diffusion of the FCCs towards the donut center. This lens can be tuned to its focal point by the pump-probe delay time to reduce the point spread function (PSF) of the IR probe beam. We start seeing the focusing of the probe beam at pump-probe delay time of \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm{\Delta t }\approx 100\mathrm{ ps}$$\end{document}Δt≈100ps. The best focusing (results in PSF \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm{\Delta t}\approx 350\mathrm{ ps}$$\end{document}Δt≈350ps and it slowly degrades before the FCCs full recombination at \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm{\Delta t }\sim 12\mathrm{ ns}$$\end{document}Δt∼12ns. We propose this beam shaping method to overcome the diffraction resolution limit in silicon microscopy on and deep under the silicon surface dependent on the pump wavelength and the pulse width. We also proposed this technique for direct measurement of the FCCs dynamics.
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Affiliation(s)
- Nadav Shabairou
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, 52900, Ramat Gan, Israel
| | - Maor Tiferet
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, 52900, Ramat Gan, Israel
| | - Zeev Zalevsky
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, 52900, Ramat Gan, Israel
| | - Moshe Sinvani
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, 52900, Ramat Gan, Israel.
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7
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Abrashitova K, Amitonova LV. High-speed label-free multimode-fiber-based compressive imaging beyond the diffraction limit. OPTICS EXPRESS 2022; 30:10456-10469. [PMID: 35473012 DOI: 10.1364/oe.444796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Glass fibers are miniature optical components that serve as ultra-narrow endoscopy probes. Ideally, one would want to perform imaging through a fiber at the highest achievable resolution and speed. State-of-the-art super-resolution techniques have shattered the diffraction limit, but more than twofold improvement requires fluorescent labeling and a long acquisition time. Moreover, it is challenging to implement super-resolution microscopy in a fiber format. Here we present fiber-based label-free video-rate imaging at more than 2-fold higher resolution than the diffraction limit. Our work paves the way to rapid, sub-wavelength endo-microscopy in unlabeled live specimens.
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8
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Dhiman S, Andrian T, Gonzalez BS, Tholen MME, Wang Y, Albertazzi L. Can super-resolution microscopy become a standard characterization technique for materials chemistry? Chem Sci 2022; 13:2152-2166. [PMID: 35310478 PMCID: PMC8864713 DOI: 10.1039/d1sc05506b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
The characterization of newly synthesized materials is a cornerstone of all chemistry and nanotechnology laboratories. For this purpose, a wide array of analytical techniques have been standardized and are used routinely by laboratories across the globe. With these methods we can understand the structure, dynamics and function of novel molecular architectures and their relations with the desired performance, guiding the development of the next generation of materials. Moreover, one of the challenges in materials chemistry is the lack of reproducibility due to improper publishing of the sample preparation protocol. In this context, the recent adoption of the reporting standard MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature) for material characterization and details of experimental protocols aims to provide complete, reproducible and reliable sample preparation for the scientific community. Thus, MIRIBEL should be immediately adopted in publications by scientific journals to overcome this challenge. Besides current standard spectroscopy and microscopy techniques, there is a constant development of novel technologies that aim to help chemists unveil the structure of complex materials. Among them super-resolution microscopy (SRM), an optical technique that bypasses the diffraction limit of light, has facilitated the study of synthetic materials with multicolor ability and minimal invasiveness at nanometric resolution. Although still in its infancy, the potential of SRM to unveil the structure, dynamics and function of complex synthetic architectures has been highlighted in pioneering reports during the last few years. Currently, SRM is a sophisticated technique with many challenges in sample preparation, data analysis, environmental control and automation, and moreover the instrumentation is still expensive. Therefore, SRM is currently limited to expert users and is not implemented in characterization routines. This perspective discusses the potential of SRM to transition from a niche technique to a standard routine method for material characterization. We propose a roadmap for the necessary developments required for this purpose based on a collaborative effort from scientists and engineers across disciplines.
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Affiliation(s)
- Shikha Dhiman
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Teodora Andrian
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
| | - Beatriz Santiago Gonzalez
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Department of Applied Physics, Eindhoven University of Technology Postbus 513 5600 MB Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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9
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Huang D, Haddad L, Rahman F, Palma M, Sapelkin A. Engineering a DNA origami mediated multicolour quantum dot platform for sub-diffraction spectral separation imaging. RSC Adv 2022; 12:23778-23785. [PMID: 36093241 PMCID: PMC9394590 DOI: 10.1039/d2ra04316e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
The validation of super-resolution optical imaging techniques requires well-defined reference samples that can be used repeatedly and reliably as model standards. Here, we engineer a DNA origami scaffold-mediated multicolour quantum dot hybrid nanostructure and test it using a recently proposed Quantum Dot-based spectral separation technique. We show that multivalent DNA structures offer a robust and precise nanoscale quantum dot placement scaffold, while the spectral resolution method provides relatively simple and fast image acquisition capabilities using any standard confocal or fluorescence microscope capable of spectral signal separation and a single excitation laser wavelength. The validation of super-resolution optical imaging techniques requires well-defined reference samples that can be used repeatedly and reliably as model standards.![]()
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Affiliation(s)
- Da Huang
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Lucy Haddad
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Fahmida Rahman
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - Matteo Palma
- Department of Chemistry, Queen Mary University of London, London E1 4NS, UK
| | - Andrei Sapelkin
- Department of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
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10
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Chen X, Wang Y, Zhang X, Liu C. Advances in super-resolution fluorescence microscopy for the study of nano-cell interactions. Biomater Sci 2021; 9:5484-5496. [PMID: 34286716 DOI: 10.1039/d1bm00676b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the interactions between nanomaterials and biological systems plays an essential role in enhancing the efficacy of nanomedicines and deepening the understanding of the biological domain. Fluorescence microscopy is a powerful optical imaging technique that allows direct visualization of the behavior of fluorescent-labeled nanomaterials in the intracellular microenvironment. However, conventional fluorescence microscopy, such as confocal microscopy, has limited optical resolution due to the diffraction of light and therefore cannot provide the precise details of nanomaterials with diameters of less than ∼250 nm. Fortunately, the development of super-resolution fluorescence microscopy has overcome the resolution limitation, enabling more comprehensive studies of nano-cell interactions. Herein, we have summarized the recent advances in nano-cell interactions investigated by a variety of super-resolution microscopic techniques, which may benefit researchers in this multi-disciplinary area by providing a guideline to select appropriate platforms for studying materiobiology.
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Affiliation(s)
- Xi Chen
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Engineering Research Center for Biomaterials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Xuewei Zhang
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Engineering Research Center for Biomaterials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
| | - Changsheng Liu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Engineering Research Center for Biomaterials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
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11
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Lu J, Zong S, Wang Z, Chen C, Zhang Y, Wang H, Cui Y. Dual-Labeled Graphene Quantum Dot-Based Förster Resonance Energy Transfer Nanoprobes for Single-Molecule Localization Microscopy. ACS OMEGA 2021; 6:8808-8815. [PMID: 33842752 PMCID: PMC8028002 DOI: 10.1021/acsomega.0c05417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Single-molecule localization microscopy (SMLM)-based super-resolution imaging techniques (e.g., photoactivated localization microscopy (PALM)/stochastic optical reconstruction microscopy (STORM)) require that the employed optical nanoprobes possess fluorescence intensity fluctuations under certain excitation conditions. Here, we present a dual-labeled graphene quantum dot (GQD)-based Förster resonance energy transfer (FRET) nanoprobe, which is suitable for SMLM imaging. The nanoprobe is constructed by attaching Alexa Fluor 488 (AF488) and Alexa Fluor 568 (AF568) dye molecules onto GQDs. Experimental results confirmed the FRET effect of the nanoprobes. Moreover, under a single 405 nm excitation, the FRET nanoprobe exhibits excellent blinking behavior. SMLM imaging of microtubules in MRC-5 cells is realized. The presented nanoprobe shows great potential in multicolor SMLM-based super-resolution imaging.
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Affiliation(s)
- Ju Lu
- Advanced
Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China
| | - Shenfei Zong
- Advanced
Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China
| | - Zhuyuan Wang
- Advanced
Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China
| | - Chen Chen
- Advanced
Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China
| | - Yizhi Zhang
- Advanced
Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China
| | - Hong Wang
- Department
of Laboratory Medicine, The First Affiliated
Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yiping Cui
- Advanced
Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China
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12
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Delgadillo RF, Carnes KA, Zaleta-Rivera K, Olmos O, Parkhurst LJ. A FLIM Microscopy Based on Acceptor-Detected Förster Resonance Energy Transfer. Anal Chem 2021; 93:4841-4849. [PMID: 33691398 PMCID: PMC7992049 DOI: 10.1021/acs.analchem.0c04492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Time-resolved donor-detected
Förster resonance energy transfer
(trDDFRET) allows the observation of molecular interactions of dye-labeled
biomolecules in the ∼10–100 Å region. However,
we can observe longer-range interactions when using time-resolved
acceptor-detected FRET (trADFRET), since the signal/noise ratio can
be improved when observing the acceptor emission. Therefore, we propose
a new methodology based on trADFRET to construct a new fluorescence
lifetime microscopy (FLIM-trADFRET) technique to observe biological
machinery in the range of 100–300 Å in vivo, the last
frontier in biomolecular medicine. The integrated trADFRET signal
is extracted in such a way that noise is canceled, and more photons
are collected, even though trADFRET and trDDFRET have the same rate
of transfer. To assess our new methodology, proof of concept was demonstrated
with a set of well-defined DNA scaffolds.
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Affiliation(s)
- Roberto F Delgadillo
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States.,Tecnologico de Monterrey, School of Engineering and Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico.,BASF Enzymes LLC, 3550 John Hopkins Ct, San Diego, California 92121, United States
| | - Katie A Carnes
- GlaxoSmithKline, Medicinal Science and Technology, CMC Analytical - Drug Substance and Product Analysis, King of Prussia, Pennsylvania, 19406, United States
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, California, 92093-0412, United States
| | - Omar Olmos
- Tecnologico de Monterrey, School of Engineering and Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico
| | - Lawrence J Parkhurst
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States
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13
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Lu Y, Son T, Kim TH, Le D, Yao X. Virtually structured detection enables super-resolution ophthalmoscopy of rod and cone photoreceptors in human retina. Quant Imaging Med Surg 2021; 11:1060-1069. [PMID: 33654677 PMCID: PMC7829177 DOI: 10.21037/qims-20-542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/26/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND High resolution imaging is desirable for advanced study and clinical management of retinal diseases. However, spatial resolution of retinal imaging has been limited due to available numerical aperture and optical aberration of the ocular optics. This study is to develop and validate virtually structured detection (VSD) to surpass diffraction limit for resolution improvement in in vivo retinal imaging of awake human. METHODS A rapid line scanning laser ophthalmoscope (SLO) was constructed for in vivo retinal imaging. A high speed (25,000 kHz) camera was used for recording the two-dimensional (2D) light reflectance profile, corresponding to each focused line illumination. VSD was implemented to the 2D light reflectance profiles for super-resolution reconstruction. Because each 2D light reflectance profile was recorded within 40 μs, the intra-frame blur due to eye movements can be ignored. Digital registration was implemented to further compensate for inter-frame eye movements, before the VSD processing. Based on digital processing, the modulation transfer function (MTF) of the imaging system was derived for objective identification of the cut-off frequency of ocular optics, which is essential for robust VSD processing to ensure reliable super-resolution imaging. Dynamic motility analysis of the super-resolution images was implemented to further enhance the imaging contrast of retinal rod and cone photoreceptors. RESULTS The VSD based super-resolution SLO significantly improved image quality compared with equivalent wide-field imaging. In vivo observation of individual retinal photoreceptors has been demonstrated unambiguously. Dynamic motility analysis of the super-resolution images enhanced the contrast of retinal rod and cone photoreceptors, and revealed sub-cellular structures in cone photoreceptors. CONCLUSIONS In conjunction with rapid line-scan imaging and digital registration to minimize the effect of eye movements, VSD enabled resolution improvement to observe individual retinal photoreceptors without the involvement of adaptive optics (AO). An objective method has been developed to identify MTF to enable quantitative estimation of the cut-off frequency required for robust VSD processing.
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Affiliation(s)
- Yiming Lu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Taeyoon Son
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Tae-Hoon Kim
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - David Le
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Xincheng Yao
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
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14
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15
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Self-Labeling Enzyme Tags for Translocation Analyses of Salmonella Effector Proteins. Methods Mol Biol 2020. [PMID: 32894488 DOI: 10.1007/978-1-0716-0791-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Salmonella enterica is an invasive, facultative intracellular pathogen with a highly sophisticated intracellular lifestyle. Invasion and intracellular proliferation are dependent on the translocation of effector proteins by two distinct type III secretion systems (T3SS) into the host cell. To unravel host-pathogen interactions, dedicated imaging techniques visualizing Salmonella effector proteins during the infection are essential. Here we describe a new approach utilizing self-labeling enzyme (SLE) tags as a universal labeling tool for tracing effector proteins. This method is able to resolve the temporal and spatial dynamics of effector proteins in living cells. The method is applicable to conventional confocal fluorescence microscopy, but also to tracking and localization microscopy (TALM), and super-resolution microscopy (SRM) of single molecules, allowing the visualization of effector proteins beyond the optical diffraction limit.
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16
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Tröger J, Hoischen C, Perner B, Monajembashi S, Barbotin A, Löschberger A, Eggeling C, Kessels MM, Qualmann B, Hemmerich P. Comparison of Multiscale Imaging Methods for Brain Research. Cells 2020; 9:E1377. [PMID: 32492970 PMCID: PMC7349602 DOI: 10.3390/cells9061377] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022] Open
Abstract
A major challenge in neuroscience is how to study structural alterations in the brain. Even small changes in synaptic composition could have severe outcomes for body functions. Many neuropathological diseases are attributable to disorganization of particular synaptic proteins. Yet, to detect and comprehensively describe and evaluate such often rather subtle deviations from the normal physiological status in a detailed and quantitative manner is very challenging. Here, we have compared side-by-side several commercially available light microscopes for their suitability in visualizing synaptic components in larger parts of the brain at low resolution, at extended resolution as well as at super-resolution. Microscopic technologies included stereo, widefield, deconvolution, confocal, and super-resolution set-ups. We also analyzed the impact of adaptive optics, a motorized objective correction collar and CUDA graphics card technology on imaging quality and acquisition speed. Our observations evaluate a basic set of techniques, which allow for multi-color brain imaging from centimeter to nanometer scales. The comparative multi-modal strategy we established can be used as a guide for researchers to select the most appropriate light microscopy method in addressing specific questions in brain research, and we also give insights into recent developments such as optical aberration corrections.
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Affiliation(s)
- Jessica Tröger
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Christian Hoischen
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
| | - Birgit Perner
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
- Molecular Genetics Lab, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Shamci Monajembashi
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
| | - Aurélien Barbotin
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX13PJ, UK;
| | - Anna Löschberger
- Advanced Development Light Microscopy, Carl Zeiss Microscopy GmbH, Carl-Zeiss-Promenade 10, 07745 Jena, Germany;
| | - Christian Eggeling
- MRC Human Immunology Unit & Wolfson Imaging Center Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX39DS, UK;
- Dep. Biophysical Imaging, Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, and Institute for Applied Optics and Biophysics, Faculty of Physics and Astronomy, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Michael M. Kessels
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Peter Hemmerich
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
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17
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Sharma R, Singh M, Sharma R. Recent advances in STED and RESOLFT super-resolution imaging techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:117715. [PMID: 31748155 DOI: 10.1016/j.saa.2019.117715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/15/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Stimulated emission depletion (STED) and reversible saturable optical fluorescence transition (RESOLFT) microscopy are the super-resolution imaging techniques that can acquire nanoscale spatial resolution. The spatial resolution of the other far-field optical microscopic techniques is bound by diffraction limit, however, STED/RESOLFT techniques eliminate the diffraction barrier. These microscopic techniques have taken the limits of optical image resolution down to the nanometer scale and opened new paths for biomedical and nanophosphor research. In this paper, we review the recent advancements of these techniques in the field of nanoscopy using continuous wave (CW) laser sources. Further, we discuss the main limitation of the STED microscopy in terms of essential requirements of higher depletion beam power and photobleaching issues. The RESOLFT microscopic technique can be considered as an alternate technique to overcome limitations of existing STED microscopy. Moreover, the Bessel and Gaussian-Bessel beam STED microscopic techniques are also reviewed to produce deep images with faster scanning of the samples. The organic molecules as well as the fluorescent doped nanoparticles like ZnSe:Mn having characteristics of excited state absorption can be investigated using RESOLFT microscopy.
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Affiliation(s)
- Reena Sharma
- Department of Physics, University Institute of Sciences, Chandigarh University, Mohali, Punjab, 140413, India
| | - Manjot Singh
- Department of Physics, University Institute of Sciences, Chandigarh University, Mohali, Punjab, 140413, India
| | - Rajesh Sharma
- Department of Physics, University Institute of Sciences, Chandigarh University, Mohali, Punjab, 140413, India.
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18
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Sun J, Tárnok A, Su X. Deep Learning-Based Single-Cell Optical Image Studies. Cytometry A 2020; 97:226-240. [PMID: 31981309 DOI: 10.1002/cyto.a.23973] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/03/2020] [Accepted: 01/10/2020] [Indexed: 12/17/2022]
Abstract
Optical imaging technology that has the advantages of high sensitivity and cost-effectiveness greatly promotes the progress of nondestructive single-cell studies. Complex cellular image analysis tasks such as three-dimensional reconstruction call for machine-learning technology in cell optical image research. With the rapid developments of high-throughput imaging flow cytometry, big data cell optical images are always obtained that may require machine learning for data analysis. In recent years, deep learning has been prevalent in the field of machine learning for large-scale image processing and analysis, which brings a new dawn for single-cell optical image studies with an explosive growth of data availability. Popular deep learning techniques offer new ideas for multimodal and multitask single-cell optical image research. This article provides an overview of the basic knowledge of deep learning and its applications in single-cell optical image studies. We explore the feasibility of applying deep learning techniques to single-cell optical image analysis, where popular techniques such as transfer learning, multimodal learning, multitask learning, and end-to-end learning have been reviewed. Image preprocessing and deep learning model training methods are then summarized. Applications based on deep learning techniques in the field of single-cell optical image studies are reviewed, which include image segmentation, super-resolution image reconstruction, cell tracking, cell counting, cross-modal image reconstruction, and design and control of cell imaging systems. In addition, deep learning in popular single-cell optical imaging techniques such as label-free cell optical imaging, high-content screening, and high-throughput optical imaging cytometry are also mentioned. Finally, the perspectives of deep learning technology for single-cell optical image analysis are discussed. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Jing Sun
- Institute of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Attila Tárnok
- Department of Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
| | - Xuantao Su
- Institute of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, 250061, China
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19
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Schmidl L, Schmidl G, Gawlik A, Dellith J, Hübner U, Tympel V, Schmidl F, Plentz J, Geis C, Haselmann H. Combining super-resolution microscopy with neuronal network recording using magnesium fluoride thin films as cover layer for multi-electrode array technology. Sci Rep 2019; 9:16110. [PMID: 31695073 PMCID: PMC6834630 DOI: 10.1038/s41598-019-52397-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
We present an approach for fabrication of reproducible, chemically and mechanically robust functionalized layers based on MgF2 thin films on thin glass substrates. These show great advantages for use in super-resolution microscopy as well as for multi-electrode-array fabrication and are especially suited for combination of these techniques. The transparency of the coated substrates with the low refractive index material is adjustable by the layer thickness and can be increased above 92%. Due to the hydrophobic and lipophilic properties of the thin crystalline MgF2 layers, the temporal stable adhesion needed for fixation of thin tissue, e.g. cryogenic brain slices is given. This has been tested using localization-based super-resolution microscopy with currently highest spatial resolution in light microscopy. We demonstrated that direct stochastic optical reconstruction microscopy revealed in reliable imaging of structures of central synapses by use of double immunostaining of post- (homer1 and GluA2) and presynaptic (bassoon) marker structure in a 10 µm brain slice without additional fixing of the slices. Due to the proven additional electrical insulating effect of MgF2 layers, surfaces of multi-electrode-arrays were coated with this material and tested by voltage-current-measurements. MgF2 coated multi-electrode-arrays can be used as a functionalized microscope cover slip for combination with live-cell super-resolution microscopy.
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Affiliation(s)
- L Schmidl
- University Hospital Jena, Hans-Berger Department of Neurology, Section Translational Neuroimmunology, Am Klinikum 1, 07747, Jena, Germany
| | - G Schmidl
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany.
| | - A Gawlik
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - J Dellith
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - U Hübner
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - V Tympel
- Helmholtz Institute Jena, Froebelstieg 3, 07743, Jena, Germany
| | - F Schmidl
- Friedrich Schiller University Jena, Institute of solid state physics, Helmholtzweg 5, 07743, Jena, Germany
| | - J Plentz
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - C Geis
- University Hospital Jena, Hans-Berger Department of Neurology, Section Translational Neuroimmunology, Am Klinikum 1, 07747, Jena, Germany
| | - H Haselmann
- University Hospital Jena, Hans-Berger Department of Neurology, Section Translational Neuroimmunology, Am Klinikum 1, 07747, Jena, Germany.,Center for Sepsis Control and Care (CSCC), University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany
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20
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Karlsson JKG, Laude A, Hall MJ, Harriman A. Photo-isomerization of the Cyanine Dye Alexa-Fluor 647 (AF-647) in the Context of dSTORM Super-Resolution Microscopy. Chemistry 2019; 25:14983-14998. [PMID: 31515919 DOI: 10.1002/chem.201904117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Indexed: 02/06/2023]
Abstract
Cyanine dyes, as used in super-resolution fluorescence microscopy, undergo light-induced "blinking", enabling localization of fluorophores with spatial resolution beyond the optical diffraction limit. Despite a plethora of studies, the molecular origins of this blinking are not well understood. Here, we examine the photophysical properties of a bio-conjugate cyanine dye (AF-647), used extensively in dSTORM imaging. In the absence of a potent sacrificial reductant, light-induced electron transfer and intermediates formed via the metastable, triplet excited state are considered unlikely to play a significant role in the blinking events. Instead, it is found that, under conditions appropriate to dSTORM microscopy, AF-647 undergoes reversible photo-induced isomerization to at least two long-lived dark species. These photo-isomers are characterized spectroscopically and their interconversion probed by computational means. The first-formed isomer is light sensitive and transforms to a longer-lived species in modest yield that could be involved in dSTORM related blinking. Permanent photobleaching of AF-647 occurs with very low quantum yield and is partially suppressed by the anaerobic redox buffer.
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Affiliation(s)
- Joshua K G Karlsson
- Molecular Photonics Laboratory, SNES, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alex Laude
- Bio-Imaging Unit, Medical School, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Michael J Hall
- School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, SNES, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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21
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Cell type–specific super-resolution imaging reveals an increase in calcium-permeable AMPA receptors at spinal peptidergic terminals as an anatomical correlate of inflammatory pain. Pain 2019; 160:2641-2650. [DOI: 10.1097/j.pain.0000000000001672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Kanoulas E, Butler M, Rowley C, Voulgaridou V, Diamantis K, Duncan WC, McNeilly A, Averkiou M, Wijkstra H, Mischi M, Wilson RS, Lu W, Sboros V. Super-Resolution Contrast-Enhanced Ultrasound Methodology for the Identification of In Vivo Vascular Dynamics in 2D. Invest Radiol 2019; 54:500-516. [PMID: 31058661 PMCID: PMC6661242 DOI: 10.1097/rli.0000000000000565] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The aim of this study was to provide an ultrasound-based super-resolution methodology that can be implemented using clinical 2-dimensional ultrasound equipment and standard contrast-enhanced ultrasound modes. In addition, the aim is to achieve this for true-to-life patient imaging conditions, including realistic examination times of a few minutes and adequate image penetration depths that can be used to scan entire organs without sacrificing current super-resolution ultrasound imaging performance. METHODS Standard contrast-enhanced ultrasound was used along with bolus or infusion injections of SonoVue (Bracco, Geneva, Switzerland) microbubble (MB) suspensions. An image analysis methodology, translated from light microscopy algorithms, was developed for use with ultrasound contrast imaging video data. New features that are tailored for ultrasound contrast image data were developed for MB detection and segmentation, so that the algorithm can deal with single and overlapping MBs. The method was tested initially on synthetic data, then with a simple microvessel phantom, and then with in vivo ultrasound contrast video loops from sheep ovaries. Tracks detailing the vascular structure and corresponding velocity map of the sheep ovary were reconstructed. Images acquired from light microscopy, optical projection tomography, and optical coherence tomography were compared with the vasculature network that was revealed in the ultrasound contrast data. The final method was applied to clinical prostate data as a proof of principle. RESULTS Features of the ovary identified in optical modalities mentioned previously were also identified in the ultrasound super-resolution density maps. Follicular areas, follicle wall, vessel diameter, and tissue dimensions were very similar. An approximately 8.5-fold resolution gain was demonstrated in vessel width, as vessels of width down to 60 μm were detected and verified (λ = 514 μm). Best agreement was found between ultrasound measurements and optical coherence tomography with 10% difference in the measured vessel widths, whereas ex vivo microscopy measurements were significantly lower by 43% on average. The results were mostly achieved using video loops of under 2-minute duration that included respiratory motion. A feasibility study on a human prostate showed good agreement between density and velocity ultrasound maps with the histological evaluation of the location of a tumor. CONCLUSIONS The feasibility of a 2-dimensional contrast-enhanced ultrasound-based super-resolution method was demonstrated using in vitro, synthetic and in vivo animal data. The method reduces the examination times to a few minutes using state-of-the-art ultrasound equipment and can provide super-resolution maps for an entire prostate with similar resolution to that achieved in other studies.
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Affiliation(s)
- Evangelos Kanoulas
- From the Institute of Biochemistry, Biological Physics, and Bio Engineering, and
| | - Mairead Butler
- From the Institute of Biochemistry, Biological Physics, and Bio Engineering, and
| | - Caitlin Rowley
- Department of Physics, Heriot-Watt University, Riccarton
| | - Vasiliki Voulgaridou
- From the Institute of Biochemistry, Biological Physics, and Bio Engineering, and
| | | | - William Colin Duncan
- Center for Reproductive Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan McNeilly
- Center for Reproductive Health, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Massimo Mischi
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; and
| | - Rhodri Simon Wilson
- **Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Weiping Lu
- From the Institute of Biochemistry, Biological Physics, and Bio Engineering, and
| | - Vassilis Sboros
- From the Institute of Biochemistry, Biological Physics, and Bio Engineering, and
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23
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Dobek K, Baranowski M. Multi-planar imaging using the thermal lensing effect. APPLIED OPTICS 2019; 58:5883-5891. [PMID: 31503895 DOI: 10.1364/ao.58.005883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The application of a thermal lens, formed by a laser beam, in the imaging of objects lying in three different planes is reported for the first time, to the best of our knowledge. The objects' planes are separated by a distance surpassing the depth-of-field of the imaging setup. It is the local formation of two thermal lenses near the intermediate image plane in a thermo-optical material that allows for the observation of two additional objects.
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24
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Altinoglu I, Merrifield CJ, Yamaichi Y. Single molecule super-resolution imaging of bacterial cell pole proteins with high-throughput quantitative analysis pipeline. Sci Rep 2019; 9:6680. [PMID: 31040310 PMCID: PMC6491441 DOI: 10.1038/s41598-019-43051-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/05/2019] [Indexed: 12/17/2022] Open
Abstract
Bacteria show sophisticated control of their cellular organization, and many bacteria deploy different polar landmark proteins to organize the cell pole. Super-resolution microscopy, such as Photo-Activated Localization Microscopy (PALM), provides the nanoscale localization of molecules and is crucial for better understanding of organization and dynamics in single-molecule. However, analytical tools are not fully available yet, in particular for bacterial cell biology. For example, quantitative and statistical analyses of subcellular localization with multiple cells from multiple fields of view are lacking. Furthermore, brightfield images are not sufficient to get accurate contours of small and low contrast bacterial cells, compared to subpixel presentation of target molecules. Here we describe a novel analytic tool for PALM which integrates precisely drawn cell outlines, of either inner membrane or periplasm, labelled by PALM-compatible fluorescent protein fusions, with molecule data for >10,000 molecules from >100 cells by fitting each cell into an oval arc. In the vibrioid bacterium Vibrio cholerae, the polar anchor HubP constitutes a big polar complex which includes multiple proteins involved in chemotaxis and the flagellum. With this pipeline, HubP is shown to be slightly skewed towards the inner curvature side of the cell, while its interaction partners showed rather loose polar localization.
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Affiliation(s)
- Ipek Altinoglu
- Department of Genome Biology, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Univ. Paris Sud, Gif sur Yvette, France.,Graduate School of Structure and Dynamics of Living Systems, Univ. Paris-Sud, Orsay, France
| | - Christien J Merrifield
- Department of Cell Biology, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Univ. Paris Sud, Gif sur Yvette, France
| | - Yoshiharu Yamaichi
- Department of Genome Biology, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Univ. Paris Sud, Gif sur Yvette, France.
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25
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Kolpe A, Arista-Romero M, Schepens B, Pujals S, Saelens X, Albertazzi L. Super-resolution microscopy reveals significant impact of M2e-specific monoclonal antibodies on influenza A virus filament formation at the host cell surface. Sci Rep 2019; 9:4450. [PMID: 30872764 PMCID: PMC6418112 DOI: 10.1038/s41598-019-41023-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/30/2019] [Indexed: 02/06/2023] Open
Abstract
Influenza A virions are highly pleomorphic, exhibiting either spherical or filamentous morphology. The influenza A virus strain A/Udorn/72 (H3N2) produces copious amounts of long filaments on the surface of infected cells where matrix protein 1 (M1) and 2 (M2) play a key role in virus filament formation. Previously, it was shown that an anti-M2 ectodomain (M2e) antibody could inhibit A/Udorn/72 virus filament formation. However, the study of these structures is limited by their small size and complex structure. Here, we show that M2e-specific IgG1 and IgG2a mouse monoclonal antibodies can reduce influenza A/Udorn/72 virus plaque growth and infectivity in vitro. Using Immuno-staining combined with super-resolution microscopy that allows us to study structures beyond the diffraction limit, we report that M2 is localized at the base of viral filaments that emerge from the membrane of infected cells. Filament formation was inhibited by treatment of A/Udorn/72 infected cells with M2e-specific IgG2a and IgG1 monoclonal antibodies and resulted in fragmentation of pre-existing filaments. We conclude that M2e-specific IgGs can reduce filamentous influenza A virus replication in vitro and suggest that in vitro inhibition of A/Udorn/72 virus replication by M2e-specific antibodies correlates with the inhibition of filament formation on the surface of infected cells.
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Affiliation(s)
- Annasaheb Kolpe
- VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
| | - Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), C\Baldiri Reixac 15-21, Helix Building, 08028, Barcelona, Spain
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), C\Baldiri Reixac 15-21, Helix Building, 08028, Barcelona, Spain
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, Ghent, B-9052, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium.
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), C\Baldiri Reixac 15-21, Helix Building, 08028, Barcelona, Spain. .,Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612AZ, Eindhoven, The Netherlands.
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26
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Callaghan NI, Hadipour-Lakmehsari S, Lee SH, Gramolini AO, Simmons CA. Modeling cardiac complexity: Advancements in myocardial models and analytical techniques for physiological investigation and therapeutic development in vitro. APL Bioeng 2019; 3:011501. [PMID: 31069331 PMCID: PMC6481739 DOI: 10.1063/1.5055873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/31/2018] [Indexed: 02/06/2023] Open
Abstract
Cardiomyopathies, heart failure, and arrhythmias or conduction blockages impact millions of patients worldwide and are associated with marked increases in sudden cardiac death, decline in the quality of life, and the induction of secondary pathologies. These pathologies stem from dysfunction in the contractile or conductive properties of the cardiomyocyte, which as a result is a focus of fundamental investigation, drug discovery and therapeutic development, and tissue engineering. All of these foci require in vitro myocardial models and experimental techniques to probe the physiological functions of the cardiomyocyte. In this review, we provide a detailed exploration of different cell models, disease modeling strategies, and tissue constructs used from basic to translational research. Furthermore, we highlight recent advancements in imaging, electrophysiology, metabolic measurements, and mechanical and contractile characterization modalities that are advancing our understanding of cardiomyocyte physiology. With this review, we aim to both provide a biological framework for engineers contributing to the field and demonstrate the technical basis and limitations underlying physiological measurement modalities for biologists attempting to take advantage of these state-of-the-art techniques.
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Affiliation(s)
| | | | | | | | - Craig A. Simmons
- Author to whom correspondence should be addressed: . Present address: Ted Rogers Centre for Heart
Research, 661 University Avenue, 14th Floor Toronto, Ontario M5G 1M1, Canada. Tel.:
416-946-0548. Fax: 416-978-7753
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27
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A Perspective on Data Processing in Super-resolution Fluorescence Microscopy Imaging. JOURNAL OF ANALYSIS AND TESTING 2018. [DOI: 10.1007/s41664-018-0076-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol 2018; 150:579-592. [PMID: 30238154 DOI: 10.1007/s00418-018-1726-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.
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29
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Halbeisen F, Hogg C, Alanin MC, Bukowy-Bieryllo Z, Dasi F, Duncan J, Friend A, Goutaki M, Jackson C, Keenan V, Harris A, Hirst RA, Latzin P, Marsh G, Nielsen K, Norris D, Pellicer D, Reula A, Rubbo B, Rumman N, Shoemark A, Walker WT, Kuehni CE, Lucas JS. Proceedings of the 2nd BEAT-PCD conference and 3rd PCD training school: part 1. BMC Proc 2018; 12:1. [PMID: 29630684 PMCID: PMC5841193 DOI: 10.1186/s12919-018-0098-9] [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] [Indexed: 01/30/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare heterogenous condition that causes progressive suppurative lung disease, chronic rhinosinusitis, chronic otitis media, infertility and abnormal situs. 'Better Experimental Approaches to Treat Primary Ciliary Dyskinesia' (BEAT-PCD) is a network of scientists and clinicians coordinating research from basic science through to clinical care with the intention of developing treatments and diagnostics that lead to improved long-term outcomes for patients. BEAT-PCD activities are supported by EU funded COST Action (BM1407). The second BEAT-PCD conference, and third PCD training school were held jointly in April 2017 in Valencia, Spain. Presentations and workshops focussed on advancing the knowledge and skills relating to PCD in: basic science, epidemiology, diagnostic testing, clinical management and clinical trials. The multidisciplinary conference provided an interactive platform for exchanging ideas through a program of lectures, poster presentations, breakout sessions and workshops. Three working groups met to plan consensus statements. Progress with BEAT-PCD projects was shared and new collaborations were fostered. In this report, we summarize the meeting, highlighting developments made during the meeting.
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Affiliation(s)
- Florian Halbeisen
- 1Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Claire Hogg
- 2Primary Ciliary Dyskinesia Centre, Departments of Paediatrics and Paediatric Respiratory Medicine, Imperial College and Royal Brompton Hospital, London, UK
| | - Mikkel C Alanin
- 3Department of Otolaryngology - Head and Neck Surgery and Audiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Zuzanna Bukowy-Bieryllo
- 4Department of Molecular and Clinical Genetics, Institute of Human Genetics Polish Academy of Sciences, Poznań, Poland
| | - Francisco Dasi
- 5Department of Physiology, Faculty of Medicine, Universitat de Valencia, Valencia, Spain.,UCIM Department, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Julie Duncan
- 7Primary Ciliary Dyskinesia Centre, Departments of Paediatrics and Paediatric Respiratory Medicine, Imperial College and Royal Brompton Hospital, London, UK
| | - Amanda Friend
- 8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Myrofora Goutaki
- 1Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Claire Jackson
- 8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Victoria Keenan
- 8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Amanda Harris
- 8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Philipp Latzin
- 10Paediatric Respiratory Medicine, University Children's Hospital of Bern, University of Bern, Bern, Switzerland
| | - Gemma Marsh
- 2Primary Ciliary Dyskinesia Centre, Departments of Paediatrics and Paediatric Respiratory Medicine, Imperial College and Royal Brompton Hospital, London, UK
| | - Kim Nielsen
- 11Danish PCD & chILD Centre, CF Centre Copenhagen Paediatric Pulmonary Service, ERN Accredited for PCD and CF Health Care, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Dominic Norris
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire, UK
| | - Daniel Pellicer
- 5Department of Physiology, Faculty of Medicine, Universitat de Valencia, Valencia, Spain.,UCIM Department, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Ana Reula
- 5Department of Physiology, Faculty of Medicine, Universitat de Valencia, Valencia, Spain.,UCIM Department, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Bruna Rubbo
- 8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Nisreen Rumman
- Pediatric Department, Makassed Hospital, East Jerusalem, Palestine
| | - Amelia Shoemark
- 2Primary Ciliary Dyskinesia Centre, Departments of Paediatrics and Paediatric Respiratory Medicine, Imperial College and Royal Brompton Hospital, London, UK.,14School of Medicine, University of Dundee, Dundee, UK
| | - Woolf T Walker
- 8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Claudia E Kuehni
- 1Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,10Paediatric Respiratory Medicine, University Children's Hospital of Bern, University of Bern, Bern, Switzerland
| | - Jane S Lucas
- 8Primary Ciliary Dyskinesia Centre, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
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Doi A, Oketani R, Nawa Y, Fujita K. High-resolution imaging in two-photon excitation microscopy using in situ estimations of the point spread function. BIOMEDICAL OPTICS EXPRESS 2018; 9:202-213. [PMID: 29359097 PMCID: PMC5772575 DOI: 10.1364/boe.9.000202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/06/2017] [Accepted: 12/10/2017] [Indexed: 05/06/2023]
Abstract
We present a technique for improving the spatial resolution of two-photon excitation microscopy; our technique combines annular illumination with an in situ estimation of the point spread function (PSF) used for deconvolution. For the in situ estimation of the PSF, we developed a technique called autocorrelation scanning, in which a sample is imaged by the scanning of two excitation foci that are overlapped over various distances. The image series obtained with the variation of the distance between the two foci provides the autocorrelation function of the PSF, which can be used to estimate the PSF at specific positions within a sample. We proved the principle and the effectiveness of this technique through observations of a fluorescent biological sample, and we confirmed that the improvement in the spatial resolution was ~1.7 times that of typical two-photon excitation microscopy by observing a mouse brain phantom at a depth of 200 µm.
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Affiliation(s)
- Atsushi Doi
- Olympus Corporation, 2-3 Kuboyama-cho, Hachioji-shi, Tokyo 192-8512, Japan
| | - Ryosuke Oketani
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasunori Nawa
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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31
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Hoess P, Mund M, Reitberger M, Ries J. Dual-Color and 3D Super-Resolution Microscopy of Multi-protein Assemblies. Methods Mol Biol 2018; 1764:237-251. [PMID: 29605918 DOI: 10.1007/978-1-4939-7759-8_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Breaking the resolution limit of conventional microscopy by super-resolution microscopy (SRM) led to many new biological insights into protein assemblies at the nanoscale. Here we provide detailed protocols for single-molecule localization microscopy (SMLM) to image the structure of a protein complex. As examples, we show how to acquire single- and dual-color super-resolution images of the nuclear pore complex (NPC) and dual-color 3D data on actin and paxillin in focal adhesions.
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Affiliation(s)
- Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Markus Mund
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Manuel Reitberger
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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32
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Gutiérrez-Arzaluz L, López-Arteaga R, Cortés-Guzmán F, Peon J. Nitrated Fluorophore Formation upon Two-Photon Excitation of an Azide with Extended Conjugation. J Phys Chem B 2017; 121:9910-9919. [PMID: 28981286 DOI: 10.1021/acs.jpcb.7b09446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The transformation of an aromatic azide into a highly fluorescent species through a nonlinear optical process was studied. The azide system was designed to undergo N2 release and nitrene to nitro conversion upon two-photon electronic excitation. The formation of the nitro form of the compound through reactions with O2 and its high radiative quantum yield implies that the azide can be used as a biphotonic activatable fluorogen. The electronic state in which the azide to nitrene transformation takes place can be accessed nonlinearly with near-infrared light which allows for photoactivation with commonly available lasers. Furthermore, the system was built with a sulfonate functionality which allows for the molecule to be adsorbed at surfaces like that of cadmium sulfide nanocrystals which further improves the nonlinear optical absorption properties in the composite, through an energy transfer mechanism. The yield of the process as a function of the excitation photon energy together with computational studies indicate that the N2 release in this azide is due to a reactive channel in the second singlet excited state of the molecule. This feature implies that the system is intrinsically photostable for excitation below and above a certain wavelength and that the system can be phototriggered selectively by the nonlinear optical process.
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Affiliation(s)
- Luis Gutiérrez-Arzaluz
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Rafael López-Arteaga
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Jorge Peon
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
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33
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Correcting for photodestruction in super-resolution optical fluctuation imaging. Sci Rep 2017; 7:10470. [PMID: 28874717 PMCID: PMC5585228 DOI: 10.1038/s41598-017-09666-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/24/2017] [Indexed: 12/03/2022] Open
Abstract
Super-resolution optical fluctuation imaging overcomes the diffraction limit by analyzing fluctuations in the fluorophore emission. A key assumption of the imaging is that the fluorophores are independent, though this is invalidated in the presence of photodestruction. In this work, we evaluate the effect of photodestruction on SOFI imaging using theoretical considerations and computer simulations. We find that photodestruction gives rise to an additional signal that does not present an easily interpretable view of the sample structure. This additional signal is strong and the resulting images typically exhibit less noise. Accordingly, these images may be mis-interpreted as being more visually pleasing or more informative. To address this uncertainty, we develop a procedure that can robustly estimate to what extent any particular experiment is affected by photodestruction. We also develop a detailed assessment methodology and use it to evaluate the performance of several correction algorithms. We identify two approaches that can correct for the presence of even strong photodestruction, one of which can be implemented directly in the SOFI calculation software.
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34
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Rodríguez-Romero J, Guarin CA, Arroyo-Pieck A, Gutiérrez-Arzaluz L, López-Arteaga R, Cortés-Guzmán F, Navarro P, Peon J. Fluorophore Release from a Polymethinic Photoremovable Protecting Group Through a Nonlinear Optical Process. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201700076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jesús Rodríguez-Romero
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Cesar A. Guarin
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Andres Arroyo-Pieck
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Luis Gutiérrez-Arzaluz
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Rafael López-Arteaga
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Fernando Cortés-Guzmán
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Pedro Navarro
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Jorge Peon
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
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35
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Abstract
Lysosomes and lysosomal proteases have been found to participate during several forms of cell death pathways including apoptosis. A critical step in the mediation of apoptotic signaling is the release of cathepsins to the cytosol, a process known as lysosomal membrane permeabilization (LMP). In this chapter, we describe immunofluorescence detection of LMP in cell cultures stained for cathepsin B and LAMP-2 using three confocal techniques namely laser scanning, spinning disk, and aperture correlation spinning disk confocal to obtain images. Image analysis is performed using Huygens software for deconvolution. LMP results in a decrease in the fraction of cathepsin B colocalizing with LAMP-2, which is quantified through Manders' colocalization coefficient. Analysis of the images obtained by the three techniques show the same trend but the magnitude of the decrease differs due to the axial resolution. The observations emphasize the use of highest possible resolution when determining colocalization.
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36
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Lee D, Huang TH, De La Cruz A, Callejas A, Lois C. Methods to investigate the structure and connectivity of the nervous system. Fly (Austin) 2017; 11:224-238. [PMID: 28277925 PMCID: PMC5552278 DOI: 10.1080/19336934.2017.1295189] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Understanding the computations that take place in neural circuits requires identifying how neurons in those circuits are connected to one another. In addition, recent research indicates that aberrant neuronal wiring may be the cause of several neurodevelopmental disorders, further emphasizing the importance of identifying the wiring diagrams of brain circuits. To address this issue, several new approaches have been recently developed. In this review, we describe several methods that are currently available to investigate the structure and connectivity of the brain, and discuss their strengths and limitations.
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Affiliation(s)
- Donghyung Lee
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA
| | - Ting-Hao Huang
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA
| | - Aubrie De La Cruz
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA
| | - Antuca Callejas
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA.,b Department of Cell Biology, School of Science , University of Extremadura , Badajoz , Spain
| | - Carlos Lois
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA
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Abstract
Myelination by oligodendrocytes in the central nervous system (CNS) and Schwann cells in the peripheral nervous system is essential for nervous system function and health. Despite its importance, we have a relatively poor understanding of the molecular and cellular mechanisms that regulate myelination in the living animal, particularly in the CNS. This is partly due to the fact that myelination commences around birth in mammals, by which time the CNS is complex and largely inaccessible, and thus very difficult to image live in its intact form. As a consequence, in recent years much effort has been invested in the use of smaller, simpler, transparent model organisms to investigate mechanisms of myelination in vivo. Although the majority of such studies have employed zebrafish, the Xenopus tadpole also represents an important complementary system with advantages for investigating myelin biology in vivo. Here we review how the natural features of zebrafish embryos and larvae and Xenopus tadpoles make them ideal systems for experimentally interrogating myelination by live imaging. We outline common transgenic technologies used to generate zebrafish and Xenopus that express fluorescent reporters, which can be used to image myelination. We also provide an extensive overview of the imaging modalities most commonly employed to date to image the nervous system in these transparent systems, and also emerging technologies that we anticipate will become widely used in studies of zebrafish and Xenopus myelination in the near future.
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Affiliation(s)
- Jenea M Bin
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
| | - David A Lyons
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
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38
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Byrne A, Burke CS, Keyes TE. Precision targeted ruthenium(ii) luminophores; highly effective probes for cell imaging by stimulated emission depletion (STED) microscopy. Chem Sci 2016; 7:6551-6562. [PMID: 28042459 PMCID: PMC5131359 DOI: 10.1039/c6sc02588a] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 06/29/2016] [Indexed: 12/18/2022] Open
Abstract
Fluorescence microscopy has undergone a dramatic evolution over the past two decades with development of super-resolution far-field microscopy methods that break the light diffraction limited resolution of conventional microscopy, offering unprecedented opportunity to interrogate cellular processes at the nanoscale. However, these methods make special demands of the luminescent agents used for contrast and development of probes suited to super-resolution fluorescent methods is still relatively in its infancy. In spite of their many photophysical advantages, metal complex luminophores have not yet been considered as probes in this regard, where to date, only organic fluorophores have been applied. Here, we report the first examples of metal complex luminophores applied as probes for use in stimulated emission depletion (STED) microscopy. Exemplified with endoplasmic reticulum and nuclear targeting complexes we demonstrate that luminescent Ru(ii) polypyridyl complexes can, through signal peptide targeting, be precisely and selectively delivered to key cell organelles without the need for membrane permeabilization, to give high quality STED images of these organelles. Detailed features of the tubular ER structure are revealed and in the case of the nuclear targeting probe we exploit the molecular light switch properties of a dipyrido[3,2-a:2',3'-c]phenazine containing complex which emits only on DNA/RNA binding to give outstanding STED contrast and resolution of the chromosomes within the nucleus. Comparing performance with a member of the AlexaFluor family commonly recommended for STED, we find that the performance of the ruthenium complexes is superior across both CW and gated STED microscopy methods in terms of image resolution and photostability. The large Stokes shifts of the Ru probes permit excellent matching of the stimulating depletion laser with their emission whilst avoiding anti-Stokes excitation. Their long lifetimes make them particularly amenable to gated STED, giving a much wider window for gating than traditional probes. Our findings indicate that ruthenium polypyridyl peptide targeted probes are a powerful new partner to STED microscopy, opening up new approaches to probe design for STED microscopy.
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Affiliation(s)
- Aisling Byrne
- School of Chemical Sciences , National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland . ; National Biophotonics and Imaging Platform , DCU , Ireland
| | - Christopher S Burke
- School of Chemical Sciences , National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland . ; National Biophotonics and Imaging Platform , DCU , Ireland
| | - Tia E Keyes
- School of Chemical Sciences , National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland . ; National Biophotonics and Imaging Platform , DCU , Ireland
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39
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STED imaging of tau filaments in Alzheimer's disease cortical grey matter. J Struct Biol 2016; 195:345-352. [PMID: 27402534 DOI: 10.1016/j.jsb.2016.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 11/20/2022]
Abstract
Alzheimer's disease (AD) involves the propagation of filaments of tau protein throughout the cerebral cortex. Imaging tau filaments and oligomers in human brain at high resolution would help contribute insight into the mechanism and progression of tauopathic diseases. STED microscopy is a nano-scale imaging technique and we aimed to test the abilities of this method for resolving tau structures within human brain. Using autopsied 50μm AD brain sections, we demonstrate that STED microscopy can resolve immunolabelled tau filaments at 77nm resolution. Ribbon-like tau filaments imaged by STED appeared smooth along their axis with limited axial undulations. STED also resolved 70-80nm wide tau puncta. Of the fluorophores tested, STAR635p was optimal for STED imaging in this tissue. This was in part due to brain tissue autofluorescence within the lower wavelength ranges (488-590nm). Further, the stability and minimal photobleaching of STAR635p allowed STED z-stacks of neurons packed with tau filaments (neurofibrillary tangles) to be collated. There was no loss of x-y image resolution of individual tau filaments through the 20μm z-stack. This demonstrates that STED can contribute to nano-scale analysis and characterisation of pathologies within banked human autopsied brain tissue. Resolving tau structures at this level of resolution provides promising avenues for understanding mechanisms of pathology propagation in the different tauopathies as well as illuminating what contributes to disease heterogeneity.
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40
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Beuzer P, La Clair JJ, Cang H. Color-Coded Super-Resolution Small-Molecule Imaging. Chembiochem 2016; 17:999-1003. [PMID: 26994590 PMCID: PMC5291120 DOI: 10.1002/cbic.201600013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 12/15/2022]
Abstract
Although the development of super-resolution microscopy dates back to 1994, its applications have been primarily focused on visualizing cellular structures and targets, including proteins, DNA and sugars. We now report on a system that allows both monitoring of the localization of exogenous small molecules in live cells at low resolution and subsequent super-resolution imaging by using stochastic optical reconstruction microscopy (STORM) on fixed cells. This represents a powerful new tool to understand the dynamics of subcellular trafficking associated with the mode and mechanism of action of exogenous small molecules.
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Affiliation(s)
- Paolo Beuzer
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - James J La Clair
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1052, USA.
| | - Hu Cang
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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41
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Gao J, Yang X, Djekidel MN, Wang Y, Xi P, Zhang MQ. Developing bioimaging and quantitative methods to study 3D genome. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0065-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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42
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Mattiazzi Usaj M, Styles EB, Verster AJ, Friesen H, Boone C, Andrews BJ. High-Content Screening for Quantitative Cell Biology. Trends Cell Biol 2016; 26:598-611. [PMID: 27118708 DOI: 10.1016/j.tcb.2016.03.008] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/25/2022]
Abstract
High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future.
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Affiliation(s)
| | - Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Adrian J Verster
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada.
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Abstract
PURPOSE OF REVIEW Throughout history, development of novel microscopy techniques has been of fundamental importance to advance the vascular biology field.This review offers a concise summary of the most recently developed imaging techniques and discusses how they can be applied to vascular biology. In addition, we reflect upon the most important fluorescent reporters for vascular research that are currently available. RECENT FINDINGS Recent advances in light sheet-based imaging techniques now offer the ability to live image the vascular system in whole organs or even in whole animals during development and in pathological conditions with a satisfactory spatial and temporal resolution. Conversely, super resolution microscopy now allows studying cellular processes at a near-molecular resolution. SUMMARY Major recent improvements in a number of imaging techniques now allow study of vascular biology in ways that could not be considered previously. Researchers now have well-developed tools to specifically examine the dynamic nature of vascular development during angiogenic sprouting, remodeling and regression as well as the vascular responses in disease situations in vivo. In addition, open questions in endothelial and lymphatic cell biology that require subcellular resolution such as actin dynamics, junctional complex formation and stability, vascular permeability and receptor trafficking can now be approached with high resolution.
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Affiliation(s)
- Bàrbara Laviña
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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44
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Turchin IV. Methods of biomedical optical imaging: from subcellular structures to tissues and organs. ACTA ACUST UNITED AC 2016. [DOI: 10.3367/ufnr.2015.12.037734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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45
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Abstract
Single-molecule localization microscopy (SMLM) is rapidly gaining popularity in the life sciences as an efficient approach to visualize molecular distribution with nanoscale precision. However, it has been challenging to obtain and analyze such data within a cellular context in tissue preparations. Here we describe a 5-d tissue processing and immunostaining procedure that is optimized for SMLM, and we provide example applications to fixed mouse brain, heart and kidney tissues. We then describe how to perform correlated confocal and 3D-superresolution imaging on these sections, which allows the visualization of nanoscale protein localization within labeled subcellular compartments of identified target cells in a few minutes. Finally, we describe the use of VividSTORM (http://katonalab.hu/index.php/vividstorm), an open-source software for correlated confocal and SMLM image analysis, which facilitates the measurement of molecular abundance, clustering, internalization, surface density and intermolecular distances in a cell-specific and subcellular compartment-restricted manner. The protocol requires only basic skills in tissue staining and microscopy.
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46
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Heller JP, Rusakov DA. Morphological plasticity of astroglia: Understanding synaptic microenvironment. Glia 2015; 63:2133-51. [PMID: 25782611 PMCID: PMC4737250 DOI: 10.1002/glia.22821] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 03/02/2015] [Indexed: 12/27/2022]
Abstract
Memory formation in the brain is thought to rely on the remodeling of synaptic connections which eventually results in neural network rewiring. This remodeling is likely to involve ultrathin astroglial protrusions which often occur in the immediate vicinity of excitatory synapses. The phenomenology, cellular mechanisms, and causal relationships of such astroglial restructuring remain, however, poorly understood. This is in large part because monitoring and probing of the underpinning molecular machinery on the scale of nanoscopic astroglial compartments remains a challenge. Here we briefly summarize the current knowledge regarding the cellular organisation of astroglia in the synaptic microenvironment and discuss molecular mechanisms potentially involved in use-dependent astroglial morphogenesis. We also discuss recent observations concerning morphological astroglial plasticity, the respective monitoring methods, and some of the newly emerging techniques that might help with conceptual advances in the area.
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Affiliation(s)
- Janosch P Heller
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, Queen Square, London, United Kingdom
| | - Dmitri A Rusakov
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, Queen Square, London, United Kingdom
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47
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Sydor AM, Czymmek KJ, Puchner EM, Mennella V. Super-Resolution Microscopy: From Single Molecules to Supramolecular Assemblies. Trends Cell Biol 2015; 25:730-748. [DOI: 10.1016/j.tcb.2015.10.004] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022]
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48
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Kupfer ME, Ogle BM. Advanced imaging approaches for regenerative medicine: Emerging technologies for monitoring stem cell fate in vitro and in vivo. Biotechnol J 2015; 10:1515-28. [DOI: 10.1002/biot.201400760] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/12/2015] [Accepted: 06/17/2015] [Indexed: 12/14/2022]
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49
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Kong D, Loncarek J. Correlative light and electron microscopy analysis of the centrosome: A step-by-step protocol. Methods Cell Biol 2015; 129:1-18. [PMID: 26175430 DOI: 10.1016/bs.mcb.2015.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Correlative light and electron microscopy harnesses the best from each of the two modalities of microscopy it utilizes; while light microscopy provides information about the dynamic properties of the cellular structure or fluorescently labeled protein, electron microscopy provides ultrastructural information in an unsurpassed resolution. However, tracing a particular cell and its rare and small structures such as centrosomes throughout numerous steps of the experiment is not a trivial task. In this chapter, we present the experimental workflow for combining live-cell fluorescence microscopy analysis with classical transmission electron microscopy, adapted for the studies of the centrosomes and basal bodies. We describe, in a step-by-step manner, an approach that can be affordably and successfully employed in any typical cell biology laboratory. The article details all key phases of the analysis starting from cell culture, live-cell microscopy, and sample fixation, through the steps of sample preparation for electron microscopy, to the identification of the target cell on the electron microscope.
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Affiliation(s)
- Dong Kong
- Laboratory of Protein Dynamics and Signaling, NIH/NCI/CCR-Frederick, Frederick, MD, USA
| | - Jadranka Loncarek
- Laboratory of Protein Dynamics and Signaling, NIH/NCI/CCR-Frederick, Frederick, MD, USA
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50
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Abstract
Light microscopy plays a key role in biological studies and medical diagnosis. The spatial resolution of conventional optical microscopes is limited to approximately half the wavelength of the illumination light as a result of the diffraction limit. Several approaches-including confocal microscopy, stimulated emission depletion microscopy, stochastic optical reconstruction microscopy, photoactivated localization microscopy, and structured illumination microscopy-have been established to achieve super-resolution imaging. However, none of these methods is suitable for the super-resolution ophthalmoscopy of retinal structures because of laser safety issues and inevitable eye movements. We recently experimentally validated virtually structured detection (VSD) as an alternative strategy to extend the diffraction limit. Without the complexity of structured illumination, VSD provides an easy, low-cost, and phase artifact-free strategy to achieve super-resolution in scanning laser microscopy. In this article we summarize the basic principles of the VSD method, review our demonstrated single-point and line-scan super-resolution systems, and discuss both technical challenges and the potential of VSD-based instrumentation for super-resolution ophthalmoscopy of the retina.
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Affiliation(s)
- Yanan Zhi
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
| | - Benquan Wang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
| | - Xincheng Yao
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL
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